=============================================================================== About this build: this rebuild has been done as part of reproduce.debian.net where we aim to reproduce Debian binary packages distributed via ftp.debian.org, by rebuilding using the exact same packages as the original build on the buildds, as described in the relevant .buildinfo file from buildinfos.debian.net. For more information please go to https://reproduce.debian.net or join #debian-reproducible on irc.debian.org =============================================================================== Preparing download of sources for /srv/rebuilderd/tmp/rebuilderdZaP6jO/inputs/moltemplate_2.22.5-1_all.buildinfo Source: moltemplate Version: 2.22.5-1 rebuilderd-worker node: ionos23-amd64 +------------------------------------------------------------------------------+ | Downloading sources Thu, 26 Feb 2026 05:28:29 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [57.6 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [54.0 kB] Get:6 https://deb.debian.org/debian forky InRelease [137 kB] Get:7 https://deb.debian.org/debian sid InRelease [187 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:10 https://deb.debian.org/debian trixie/non-free-firmware Sources [6552 B] Get:11 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:12 https://deb.debian.org/debian-security trixie-security/main Sources [136 kB] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [70.5 kB] Get:15 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [2468 B] Get:16 https://deb.debian.org/debian trixie-backports/main Sources [148 kB] Get:17 https://deb.debian.org/debian forky/main Sources [10.6 MB] Get:18 https://deb.debian.org/debian forky/non-free-firmware Sources [8304 B] Get:19 https://deb.debian.org/debian sid/main Sources [11.3 MB] Get:20 https://deb.debian.org/debian sid/non-free-firmware Sources [10.3 kB] Get:21 https://deb.debian.org/debian experimental/non-free-firmware Sources [2572 B] Get:22 https://deb.debian.org/debian experimental/main Sources [416 kB] Fetched 34.0 MB in 3s (10.2 MB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/m/moltemplate/moltemplate_2.22.5-1.dsc' moltemplate_2.22.5-1.dsc 2056 SHA256:a6d879a8308f9903d7b9efa5a740ec1c8ba67ff3241bfce8a718082d1d118734 'https://deb.debian.org/debian/pool/main/m/moltemplate/moltemplate_2.22.5.orig.tar.gz' moltemplate_2.22.5.orig.tar.gz 10342161 SHA256:fc1b7b738c256613bcb1d75971c2481cb9894724ce279210efe278d8d71e9aaf 'https://deb.debian.org/debian/pool/main/m/moltemplate/moltemplate_2.22.5-1.debian.tar.xz' moltemplate_2.22.5-1.debian.tar.xz 3964 SHA256:7f0e65bb5bc728262adcb7aa94ddf85cae04f7e6975106020872189731fcfcc2 fc1b7b738c256613bcb1d75971c2481cb9894724ce279210efe278d8d71e9aaf moltemplate_2.22.5.orig.tar.gz 7f0e65bb5bc728262adcb7aa94ddf85cae04f7e6975106020872189731fcfcc2 moltemplate_2.22.5-1.debian.tar.xz a6d879a8308f9903d7b9efa5a740ec1c8ba67ff3241bfce8a718082d1d118734 moltemplate_2.22.5-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Thu, 26 Feb 2026 05:28:33 +0000 | +------------------------------------------------------------------------------+ Rebuilding moltemplate=2.22.5-1 in /srv/rebuilderd/tmp/rebuilderdZaP6jO/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdZaP6jO/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdZaP6jO/inputs/moltemplate_2.22.5-1_all.buildinfo /srv/rebuilderd/tmp/rebuilderdZaP6jO/inputs/moltemplate_2.22.5-1_all.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/moltemplate-2.22.5 I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [187 kB] Get:2 http://snapshot.debian.org/archive/debian/20260224T144255Z forky InRelease [137 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages [10.2 MB] Get:4 http://snapshot.debian.org/archive/debian/20260224T144255Z forky/main amd64 Packages [9524 kB] Fetched 20.0 MB in 2s (9693 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260224T144255Z/dists/forky/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.5.2-4 [23.0 kB] Fetched 23.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpi8yqn8xo/libattr1_2.5.2-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Fetched 19.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0wlbpbem/libfile-stripnondeterminism-perl_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-3+b1 [308 kB] Fetched 308 kB in 0s (28.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn9tl9799/libzstd1_1.5.7+dfsg-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-files amd64 14 [72.9 kB] Fetched 72.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0rgo70cm/base-files_14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libubsan1 amd64 15.2.0-14 [1108 kB] Fetched 1108 kB in 0s (71.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpteiv21ha/libubsan1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.7-3 [3024 kB] Fetched 3024 kB in 0s (120 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfdvld3ce/coreutils_9.7-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b4 [56.6 kB] Fetched 56.6 kB in 0s (0 B/s) dpkg-name: info: moved 'libxpm4_1%3a3.5.17-1+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmpe0e06v50/libxpm4_3.5.17-1+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11 [710 kB] Fetched 710 kB in 0s (58.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_w3ox_5k/libdb5.3t64_5.3.28+dfsg2-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.46-2 [2635 kB] Fetched 2635 kB in 0s (110 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4aom3wlc/binutils-common_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Fetched 224 kB in 0s (22.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphuigweeh/python3-pkg-resources_78.1.1-0.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-3 [89.0 kB] Fetched 89.0 kB in 0s (8335 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpxq7bb0et/zlib1g_1.3.dfsg+really1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw_zyol75/autotools-dev_20240727.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.3+b1 [191 kB] Fetched 191 kB in 0s (0 B/s) dpkg-name: info: moved 'libxt6t64_1%3a1.2.1-1.3+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpxvihx9n2/libxt6t64_1.2.1-1.3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2025.20250727.75242+ds-5 [65.0 kB] Fetched 65.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppx31d46e/libsynctex2_2025.20250727.75242+ds-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive all 2025.20260124-1 [19.1 kB] Fetched 19.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmim8_sm5/texlive_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b3 [16.7 kB] Fetched 16.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr7_cwk7f/libpaper2_2.2.5-0.3+b3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b3 [25.5 kB] Fetched 25.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaz6l_tmg/libpotrace0_1.16-2+b3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xz-utils amd64 5.8.2-2 [706 kB] Fetched 706 kB in 0s (57.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwntcjq1p/xz-utils_5.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblzma5 amd64 5.8.2-2 [327 kB] Fetched 327 kB in 0s (31.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp196yoga7/liblzma5_5.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-5 [1200 B] Fetched 1200 B in 0s (61.2 kB/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp7wl9xyb1/g++-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.46-2 [282 kB] Fetched 282 kB in 0s (28.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph5dk6gju/binutils_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 15.2.0-14 [736 kB] Fetched 736 kB in 0s (56.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd75lboj2/libstdc++6_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [138 kB] Fetched 138 kB in 0s (0 B/s) dpkg-name: info: moved 'python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpugiindan/python3-numpy-dev_2.3.5+ds-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5+b1 [43.8 kB] Fetched 43.8 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpsvqnw41b/file_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1+b1 [66.8 kB] Fetched 66.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libice6_2%3a1.1.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpi_ipydgj/libice6_1.1.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-2 [8184 B] Fetched 8184 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ff36qzk/python3-jaraco.context_6.0.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Fetched 1469 kB in 0s (82.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgy3ncgsi/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-2 [1561 kB] Fetched 1561 kB in 0s (91.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl60812_j/bash_5.3-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7+b1 [2550 kB] Fetched 2550 kB in 0s (121 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmzbmrv5j/liblapack3_3.12.1-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc amd64 4:15.2.0-5 [5160 B] Fetched 5160 B in 0s (0 B/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpy5u21ihf/gcc_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.46-2 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptbko4v43/libctf-nobfd0_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-base amd64 5.40.1-7 [1679 kB] Fetched 1679 kB in 0s (96.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe6iobgfv/perl-base_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dash amd64 0.5.12-12 [98.5 kB] Fetched 98.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1uoiyvcm/dash_0.5.12-12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Fetched 39.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi5ym6ki8/init-system-helpers_1.69_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Fetched 71.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzhb8pbd8/python3-more-itertools_10.8.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260224T144255Z forky/main amd64 libudev1 amd64 259.1-1 [158 kB] Fetched 158 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyuxik_tw/libudev1_259.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Fetched 14.3 kB in 0s (1336 kB/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmpn1b6tale/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debianutils amd64 5.23.2 [92.4 kB] Fetched 92.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0etyq2fa/debianutils_5.23.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b2 [115 kB] Fetched 115 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbpln03c1/libxcb-render0_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15 amd64 15.2.0-14 [26.1 kB] Fetched 26.1 kB in 0s (1966 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplbghw6p7/g++-15_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpulzzuixh/hostname_3.25_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-13 [1123 kB] Fetched 1123 kB in 0s (74.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo74zs2s0/libc-gconv-modules-extra_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm6t64 amd64 1.26-1+b1 [78.9 kB] Fetched 78.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvuk25yd9/libgdbm6t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.9-3 [1048 B] Fetched 1048 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdg05pk5m/python3-all_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6+b1 [40.4 kB] Fetched 40.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbrlup8w4/libbz2-1.0_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap-ng0 amd64 0.9.1-1 [17.4 kB] Fetched 17.4 kB in 0s (1719 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnels2b1t/libcap-ng0_0.9.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Fetched 12.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0drulnpy/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.41.3-4 [1166 kB] Fetched 1166 kB in 0s (77.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2dp9rak2/util-linux_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.4-1 [116 kB] Fetched 116 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxyde2zid/libexpat1_2.7.4-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.41.3-4 [145 kB] Fetched 145 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdcy1hza2/libsmartcols1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.5 [1527 kB] Fetched 1527 kB in 0s (88.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8qbb1oa6/dpkg_1.23.5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-4 [181 kB] Fetched 181 kB in 0s (17.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplf5x1ti5/libreadline8t64_8.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9+b1 [66.1 kB] Fetched 66.1 kB in 0s (6483 kB/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-9+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpo46ihvl6/libproc2-0_4.0.4-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+26 [217 kB] Fetched 217 kB in 0s (16.3 MB/s) dpkg-name: info: moved 'x11-common_1%3a7.7+26_all.deb' to '/srv/rebuilderd/tmp/tmpx9wpyav7/x11-common_7.7+26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblsan0 amd64 15.2.0-14 [1249 kB] Fetched 1249 kB in 0s (58.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8tka2tvr/liblsan0_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.17.1-5 [132 kB] Fetched 132 kB in 0s (13.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4z3mgt2p/libfontconfig1_2.17.1-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.6+20251231-1 [445 kB] Fetched 445 kB in 0s (40.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptbjbceew/ncurses-bin_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-s1 amd64 15.2.0-14 [71.5 kB] Fetched 71.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbgvvukrc/libgcc-s1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.3.2-3 [32.7 kB] Fetched 32.7 kB in 0s (3244 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps_gra3q3/libacl1_2.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Fetched 840 kB in 0s (61.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf5nda71_/fonts-dejavu-core_2.37-8_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-5 [116 kB] Fetched 116 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4f7igm_y/libtexlua53-5_2025.20250727.75242+ds-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (32.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9vca91qd/sed_4.9-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.87.2-3 [1552 kB] Fetched 1552 kB in 0s (23.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbbndph00/libglib2.0-0t64_2.87.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.41.3-4 [212 kB] Fetched 212 kB in 0s (1856 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd6ngrhoz/libmount1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.9-3 [10.5 kB] Fetched 10.5 kB in 0s (41.2 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvowohbl_/libpython3-stdlib_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-4 [59.4 kB] Fetched 59.4 kB in 0s (460 kB/s) dpkg-name: info: moved 'libxmu6_2%3a1.1.3-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpuafeughm/libxmu6_1.1.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Fetched 11.0 kB in 0s (290 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphrvdlx2h/python3-zipp_3.23.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 15.2.0-14 [145 kB] Fetched 145 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsq55ibvg/libquadmath0_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1+b1 [215 kB] Fetched 215 kB in 0s (0 B/s) dpkg-name: info: moved 'libxaw7_2%3a1.0.16-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmplbtsa9s1/libxaw7_1.0.16-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-dev-bin amd64 2.42-13 [61.5 kB] Fetched 61.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa5y2i1c7/libc-dev-bin_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b2 [105 kB] Fetched 105 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqufyj1um/libxcb-shm0_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.9-3 [27.6 kB] Fetched 27.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmm0mvyh6/python3_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.41.3-4 [174 kB] Fetched 174 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy1hq0j3d/libblkid1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Fetched 1194 kB in 0s (87.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_z4w3fwp/groff-base_1.23.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Fetched 75.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0gfr4k1s/xdg-utils_1.2.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 make amd64 4.4.1-3 [463 kB] Fetched 463 kB in 0s (41.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps2n_b0z4/make_4.4.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-5+b1 [49.8 kB] Fetched 49.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk64v1t46/libpam-modules-bin_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b1 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpqswubrzi/libmagic1t64_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tar amd64 1.35+dfsg-4 [817 kB] Fetched 817 kB in 0s (46.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8xkcfdm5/tar_1.35+dfsg-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap2 amd64 1:2.75-10+b5 [28.8 kB] Fetched 28.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libcap2_1%3a2.75-10+b5_amd64.deb' to '/srv/rebuilderd/tmp/tmppdp7mqyp/libcap2_2.75-10+b5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (20.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4gt5d17o/po-debconf_1.0.22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcc1-0 amd64 15.2.0-14 [42.6 kB] Fetched 42.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6b2kl6wz/libcc1-0_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7+b1 [209 kB] Fetched 209 kB in 0s (1274 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpizuk_qtf/libblas3_3.12.1-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9+b1 [883 kB] Fetched 883 kB in 0s (10.8 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-9+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpj2b5s9z8/procps_4.0.4-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm-compat4t64 amd64 1.26-1+b1 [53.1 kB] Fetched 53.1 kB in 0s (4789 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_hpq1l15/libgdbm-compat4t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Fetched 489 kB in 0s (2923 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx4uxa6fj/fonts-dejavu-mono_2.37-8_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.46.4-1+b1 [259 kB] Fetched 259 kB in 0s (748 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpergq7eim/libpixman-1-0_0.46.4-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.46-2 [1058 kB] Fetched 1058 kB in 0s (9430 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprllxfz9e/binutils-x86-64-linux-gnu_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-python all 7.20260125 [119 kB] Fetched 119 kB in 0s (11.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvgz_dywk/dh-python_7.20260125_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Fetched 185 kB in 0s (17.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqfe8dovx/libelf1t64_0.194-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-2 [92.5 kB] Fetched 92.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3r5qs00b/python3-typing-extensions_4.15.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Fetched 27.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6jxiif71/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp95zvxsz3/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-5+b1 [179 kB] Fetched 179 kB in 0s (16.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpacjk8ms7/libpam-modules_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (52.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi7l02vr0/findutils_4.10.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 kB] Fetched 42.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe_61dfnb/libpipeline1_1.5.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcrypt1 amd64 1:4.5.1-1 [98.0 kB] Fetched 98.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpdcyistlp/libcrypt1_4.5.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4+b1 [36.7 kB] Fetched 36.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxy0fyeub/libmpfi0_1.5.4+ds-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Fetched 68.8 kB in 0s (6424 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi4o0yivj/libuchardet0_0.0.8-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.9-3 [27.6 kB] Fetched 27.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplu7p58fg/python3-minimal_3.13.9-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 15.2.0-14 [140 kB] Fetched 140 kB in 0s (13.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx1p6h0x5/libgomp1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Fetched 8808 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi2sikbks/libtext-wrapi18n-perl_0.06-10_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-14 [23.4 MB] Fetched 23.4 MB in 0s (82.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp991jm714/gcc-15-x86-64-linux-gnu_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b1 [561 kB] Fetched 561 kB in 0s (48.4 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp9rncx5l6/libgmp10_6.3.0+dfsg-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-14 [2718 kB] Fetched 2718 kB in 0s (121 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvvhe09nv/libgcc-15-dev_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Fetched 63.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw8eb9oka/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2025.20250727.75242+ds-5 [159 kB] Fetched 159 kB in 0s (15.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw3_cf8es/libkpathsea6_2025.20250727.75242+ds-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.20 [29.7 kB] Fetched 29.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpro6iy6sf/tex-common_6.20_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.31 [932 kB] Fetched 932 kB in 0s (66.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy0w7n9zp/debhelper_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b1 [338 kB] Fetched 338 kB in 0s (32.7 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpptkhrnzh/libmagic-mgc_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwasan0 amd64 15.2.0-14 [1538 kB] Fetched 1538 kB in 0s (90.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiwsny34v/libhwasan0_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libselinux1 amd64 3.9-4+b1 [86.1 kB] Fetched 86.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphw1mk1vr/libselinux1_3.9-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 patch amd64 2.8-2 [134 kB] Fetched 134 kB in 0s (13.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprsj3fyws/patch_2.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [7487 kB] Fetched 7487 kB in 0s (174 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a2.3.5+ds-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpm9okyglm/python3-numpy_2.3.5+ds-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssl3t64 amd64 3.5.5-1 [2449 kB] Fetched 2449 kB in 0s (121 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz3r0xin7/libssl3t64_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15 amd64 15.2.0-14 [1276 B] Fetched 1276 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgjxqu6uf/cpp-15_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libasan8 amd64 15.2.0-14 [2779 kB] Fetched 2779 kB in 0s (122 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxxmt_5_b/libasan8_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-9 [920 kB] Fetched 920 kB in 0s (65.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3wni2w8b/libsqlite3-0_3.46.1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260224T144255Z forky/main amd64 autoconf all 2.72-3.1 [494 kB] Fetched 494 kB in 0s (46.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_c4v0obx/autoconf_2.72-3.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b5 [9532 B] Fetched 9532 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe226hvqa/libtext-charwidth-perl_0.04-11+b5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6-dev amd64 2.42-13 [2016 kB] Fetched 2016 kB in 0s (96.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjejf0ijn/libc6-dev_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.3-1 [2263 kB] Fetched 2263 kB in 0s (113 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkj63_14g/libpython3.14-stdlib_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Fetched 11.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8msos4ju/python3-jaraco.text_4.0.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.12-1 [2267 kB] Fetched 2267 kB in 0s (110 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpceajh545/python3.13-minimal_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6 amd64 2.42-13 [1814 kB] Fetched 1814 kB in 0s (102 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_wz5oqzl/libc6_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.14.1+dfsg-2 [493 kB] Fetched 493 kB in 0s (46.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcxkvwko9/libfreetype6_2.14.1+dfsg-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-4 [74.8 kB] Fetched 74.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjle4yit_/readline-common_8.3-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.46-2 [92.2 kB] Fetched 92.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp370vqltm/libctf0_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mawk amd64 1.3.4.20260129-1 [143 kB] Fetched 143 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjle2vcmb/mawk_1.3.4.20260129-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Fetched 641 kB in 0s (51.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu7fcmqyk/libxml2-16_2.15.1+dfsg-2+b1_amd64.deb' Downloading dependency 1 of 233: libattr1:amd64=1:2.5.2-4 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libselinux1:amd64=3.9-4+b1 Downloading dependency 113 of 233: patch:amd64=2.8-2 Downloading dependency 114 of 233: python3-numpy:amd64=1:2.3.5+ds-3 Downloading dependency 115 of 233: libssl3t64:amd64=3.5.5-1 Downloading dependency 116 of 233: cpp-15:amd64=15.2.0-14 Downloading dependency 117 of 233: libasan8:amd64=15.2.0-14 Downloading dependency 118 of 233: libsqlite3-0:amd64=3.46.1-9 Downloading dependency 119 of 233: autoconf:amd64=2.72-3.1 Downloading dependency 120 of 233: libtext-charwidth-perl:amd64=0.04-11+b5 Downloading dependency 121 of 233: libc6-dev:amd64=2.42-13 Downloading dependency 122 of 233: libpython3.14-stdlib:amd64=3.14.3-1 Downloading dependency 123 of 233: python3-jaraco.text:amd64=4.0.0-1 Downloading dependency 124 of 233: python3.13-minimal:amd64=3.13.12-1 Downloading dependency 125 of 233: libc6:amd64=2.42-13 Downloading dependency 126 of 233: libfreetype6:amd64=2.14.1+dfsg-2 Downloading dependency 127 of 233: readline-common:amd64=8.3-4 Downloading dependency 128 of 233: libctf0:amd64=2.46-2 Downloading dependency 129 of 233: mawk:amd64=1.3.4.20260129-1 Downloading dependency 130 of 233: libxml2-16:amd64=2.15.1+dfsg-2+b1 Downloading dependency 131 of 233: libxext6:amd64=2:1.3.4-1+b4Get:1 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Fetched 50.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b4_amd64.deb' to '/srv/rebuilderd/tmp/tmpk8t7h3vw/libxext6_1.3.4-1+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.3-1 [836 kB] Fetched 836 kB in 0s (66.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpve7y2c27/python3.14_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libitm1 amd64 15.2.0-14 [26.5 kB] Fetched 26.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk9m_ft1r/libitm1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.41.3-4 [39.1 kB] Fetched 39.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ari7j7z/libuuid1_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.3-4 [98.9 kB] Fetched 98.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8_h67oxl/bsdextrautils_2.41.3-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b1 [20.8 kB] Fetched 20.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpci3i0rpb/libxau6_1.0.11-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2025.20260124-1 [8520 kB] Fetched 8520 kB in 0s (169 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk7g87gcn/texlive-latex-recommended_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-14 [12.1 MB] Fetched 12.1 MB in 0s (172 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj8934rwb/cpp-15-x86-64-linux-gnu_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 12.3.2-2 [514 kB] Fetched 514 kB in 0s (42.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpffqs6qcz/libharfbuzz0b_12.3.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libisl23 amd64 0.27-1+b1 [663 kB] Fetched 663 kB in 0s (50.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl272b4vr/libisl23_0.27-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Fetched 62.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpckg5wmzh/t1utils_1.41-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp amd64 4:15.2.0-5 [1564 B] Fetched 1564 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpaw_c1pqw/cpp_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjansson4 amd64 2.14-2+b4 [40.1 kB] Fetched 40.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptardzjux/libjansson4_2.14-2+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20251231-1 [354 kB] Fetched 354 kB in 0s (34.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7y83ucxg/libtinfo6_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpggthuuei/build-essential_12.12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-14 [862 kB] Fetched 862 kB in 0s (66.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp59shct6n/libgfortran5_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-4 [13.7 kB] Fetched 13.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp17laozf3/python3-autocommand_2.2.2-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdpkg-perl all 1.23.5 [668 kB] Fetched 668 kB in 0s (49.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp27jlaazv/libdpkg-perl_1.23.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-11+b1 [77.0 kB] Fetched 77.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4s8_m20o/libgraphite2-3_1.3.14-11+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-runtime all 1.7.0-5 [249 kB] Fetched 249 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_33h_npn/libpam-runtime_1.7.0-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Fetched 829 kB in 0s (65.8 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpdj2az05o/libx11-6_1.8.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr6iv4j79/libxcb1_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Fetched 346 kB in 0s (33.3 MB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.13-1_all.deb' to '/srv/rebuilderd/tmp/tmpgog98s23/libx11-data_1.8.13-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncursesw6 amd64 6.6+20251231-1 [137 kB] Fetched 137 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp68vlxbdf/libncursesw6_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libperl5.40 amd64 5.40.1-7 [4317 kB] Fetched 4317 kB in 0s (143 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpodqctluh/libperl5.40_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Fetched 12.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6vsvoz3g/netbase_6.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2+b1 [466 kB] Fetched 466 kB in 0s (41.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg11yf7_v/libunistring5_1.3-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-5 [5324 B] Fetched 5324 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpups_w_40/cpp-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++ amd64 4:15.2.0-5 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp0ugq5okm/g++_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Fetched 320 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ly5c5_a/libbrotli1_1.2.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b2 [36.2 kB] Fetched 36.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu0n6eq4r/libmd0_1.1.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtsan2 amd64 15.2.0-14 [2491 kB] Fetched 2491 kB in 0s (109 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc_lw_l8_/libtsan2_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0052 [43.3 kB] Fetched 43.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpifexo2a3/ucf_3.0052_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebconfclient0 amd64 0.282+b2 [11.2 kB] Fetched 11.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxk46u80e/libdebconfclient0_0.282+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl-provider-legacy amd64 3.5.5-1 [311 kB] Fetched 311 kB in 0s (29.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsfg7pwo7/openssl-provider-legacy_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (1714 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvxom7__s/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-1 [245 kB] Fetched 245 kB in 0s (21.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmk5g432e/gettext-base_0.23.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1+b1 [37.9 kB] Fetched 37.9 kB in 0s (0 B/s) dpkg-name: info: moved 'libsm6_2%3a1.2.6-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpb9_budoh/libsm6_1.2.6-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.13+ds-1 [369 kB] Fetched 369 kB in 0s (25.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsc524zla/libteckit0_2.5.13+ds-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2 [27.9 kB] Fetched 27.9 kB in 0s (0 B/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpc8gm2zo2/libxdmcp6_1.1.5-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Fetched 772 kB in 0s (64.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw7kr7kgs/autopoint_0.23.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-4+b1 [9752 kB] Fetched 9752 kB in 0s (168 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp40kvrukb/libicu76_76.1-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.2 [59.2 kB] Fetched 59.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj5kslqm4/libzzip-0-13t64_0.13.78+dfsg.1-0.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpfr6 amd64 4.2.2-2+b1 [729 kB] Fetched 729 kB in 0s (57.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptcnc0s86/libmpfr6_4.2.2-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Fetched 332 kB in 0s (29.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9b2ytv7f/m4_1.4.21-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp19nplr_6/dwz_0.16-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Fetched 30.8 kB in 0s (2868 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8hycuv4u/media-types_14.0.0_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsframe3 amd64 2.46-2 [84.6 kB] Fetched 84.6 kB in 0s (8318 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnvd4n8g1/libsframe3_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Fetched 54.6 kB in 0s (5222 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0wiua_hx/base-passwd_3.6.8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 linux-libc-dev all 6.18.12-1 [2574 kB] Fetched 2574 kB in 0s (123 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0eg8bl6v/linux-libc-dev_6.18.12-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debconf all 1.5.92 [123 kB] Fetched 123 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppz56blhe/debconf_1.5.92_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-2 [79.8 kB] Fetched 79.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libxi6_2%3a1.8.2-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpfwt4xk4p/libxi6_1.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bzip2 amd64 1.0.8-6+b1 [41.0 kB] Fetched 41.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_n2s4ei4/bzip2_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-5+b1 [70.4 kB] Fetched 70.4 kB in 0s (6633 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvhzfs6zp/libpam0g_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.55-1 [288 kB] Fetched 288 kB in 0s (26.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0_gcbef1/libpng16-16t64_1.6.55-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-2 [37.2 kB] Fetched 37.2 kB in 0s (3523 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp483kwxx0/python3-typeguard_4.4.4-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Fetched 4540 kB in 0s (145 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp02c2hpsr/fonts-lmodern_2.005-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15 amd64 15.2.0-14 [536 kB] Fetched 536 kB in 0s (42.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2v9nvdke/gcc-15_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-14 [13.2 MB] Fetched 13.2 MB in 0s (170 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2ajsq78i/g++-15-x86-64-linux-gnu_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.46-2 [548 kB] Fetched 548 kB in 0s (41.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5l2y0cc6/libbinutils_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.31 [75.7 kB] Fetched 75.7 kB in 0s (7406 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvp88ki9n/libdebhelper-perl_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libseccomp2 amd64 2.6.0-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcehbq5fs/libseccomp2_2.6.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Fetched 12.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxdu1s8q6/python3-jaraco.functools_4.1.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Fetched 738 kB in 0s (57.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm9yd5ve0/python3-setuptools_78.1.1-0.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-3+b1 [26.4 kB] Fetched 26.4 kB in 0s (2277 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp59p8dphm/libffi8_3.5.2-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-5 [1436 B] Fetched 1436 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp3958p_qr/gcc-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Fetched 8812 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmped34i91j/dh-strip-nondeterminism_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025c-3 [263 kB] Fetched 263 kB in 0s (26.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpynaijie9/tzdata_2025c-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-14 [2446 kB] Fetched 2446 kB in 0s (117 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7jztzme0/libstdc++-15-dev_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Fetched 33.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvkp6rai9/python3-inflect_7.5.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1+b1 [27.7 kB] Fetched 27.7 kB in 0s (0 B/s) dpkg-name: info: moved 'libxrender1_1%3a0.9.12-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpch8jml2x/libxrender1_0.9.12-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.46-2 [820 kB] Fetched 820 kB in 0s (61.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp0yx2_6f/libgprofng0_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.12-1 [866 kB] Fetched 866 kB in 0s (67.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp131b83f1/libpython3.13-minimal_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-bin amd64 2.42-13 [644 kB] Fetched 644 kB in 0s (52.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4q3y1j5l/libc-bin_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libatomic1 amd64 15.2.0-14 [9536 B] Fetched 9536 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_oi_qkwj/libatomic1_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpl5o_bgpk/libaudit1_4.1.2-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260224T144255Z forky/main amd64 libsystemd0 amd64 259.1-1 [471 kB] Fetched 471 kB in 0s (43.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk2idzxc5/libsystemd0_259.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-9 [540 kB] Fetched 540 kB in 0s (42.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpncnewzh4/libtool_2.5.4-9_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2025.20260124-1 [4992 kB] Fetched 4992 kB in 0s (140 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuu80ek9i/texlive-fonts-recommended_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sysvinit-utils amd64 3.15-6 [35.0 kB] Fetched 35.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwipr6l9t/sysvinit-utils_3.15-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-base all 6.6+20251231-1 [277 kB] Fetched 277 kB in 0s (24.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqotcaw42/ncurses-base_6.6+20251231-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2025.20260124-1 [23.1 MB] Fetched 23.1 MB in 0s (182 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa6_pdetx/texlive-base_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpc3 amd64 1.3.1-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp67qiav_r/libmpc3_1.3.1-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-3 [544 kB] Fetched 544 kB in 0s (46.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptwzod_mg/libcairo2_1.18.4-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl amd64 5.40.1-7 [267 kB] Fetched 267 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplpou2ez8/perl_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2025.20260124-1 [1340 kB] Fetched 1340 kB in 0s (80.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn30x3ran/texlive-latex-base_2025.20260124-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.12-1 [776 kB] Fetched 776 kB in 0s (58.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5ga80bik/python3.13_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 diffutils amd64 1:3.12-1 [405 kB] Fetched 405 kB in 0s (36.9 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp4rdjebni/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg-dev all 1.23.5 [1318 kB] Fetched 1318 kB in 0s (73.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpok0dwl_w/dpkg-dev_1.23.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-3 [878 kB] Fetched 878 kB in 0s (62.6 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-3_all.deb' to '/srv/rebuilderd/tmp/tmptpkwl_hp/automake_1.18.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2025.20250727.75242+ds-5 [8692 kB] Fetched 8692 kB in 0s (169 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpirbpkldo/texlive-binaries_2025.20250727.75242+ds-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpcre2-8-0 amd64 10.46-1+b1 [298 kB] Fetched 298 kB in 0s (27.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppp378yyh/libpcre2-8-0_10.46-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 kB] Fetched 1687 kB in 0s (102 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppwnwf3s7/gettext_0.23.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.17.1-5 [56.1 kB] Fetched 56.1 kB in 0s (5484 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpium511ma/fontconfig-config_2.17.1-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-14 [55.0 kB] Fetched 55.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptkntpi6v/gcc-15-base_15.2.0-14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.3-1 [2406 kB] Fetched 2406 kB in 0s (110 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkem9tgw8/python3.14-minimal_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.3-1 [897 kB] Fetched 897 kB in 0s (62.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfy2vqrbv/libpython3.14-minimal_3.14.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b3 [16.5 kB] Fetched 16.5 kB in 0s (1635 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu5agdcmd/libpaper-utils_2.2.5-0.3+b3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-modules-5.40 all 5.40.1-7 [3012 kB] Fetched 3012 kB in 0s (123 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo4_1m8gd/perl-modules-5.40_5.40.1-7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2025.20250727.75242+ds-5 [54.3 kB] Fetched 54.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwzwfvvjn/libptexenc1_2025.20250727.75242+ds-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.12-1 [1974 kB] Fetched 1974 kB in 0s (98.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo7eki_0x/libpython3.13-stdlib_3.13.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8aqcbfdm/gzip_1.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (36.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp72m0zpct/grep_3.12-1_amd64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-buildpackage: info: host architecture amd64 dpkg-source --before-build . debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmp8q2tdblw/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture amd64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.zvxCEfwMhC as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.zvxCEfwMhC 127.0.0.1 - - [26/Feb/2026 05:30:08] code 404, message File not found 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:41459 ./ InRelease 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:41459 ./ Release [462 B] 127.0.0.1 - - [26/Feb/2026 05:30:08] code 404, message File not found 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:41459 ./ Release.gpg 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:41459 ./ Packages [298 kB] Fetched 299 kB in 0s (10.6 MB/s) Reading package lists... usr-is-merged found but not real -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./gcc-15-base_15.2.0-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libc-gconv-modules-extra_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libc6_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libgcc-s1_15.2.0-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./mawk_1.3.4.20260129-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./base-files_14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libtinfo6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./debianutils_5.23.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./bash_5.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libacl1_2.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libattr1_2.5.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libcap2_2.75-10%2bb5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libgmp10_6.3.0%2bdfsg-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libpcre2-8-0_10.46-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libselinux1_3.9-4%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libzstd1_1.5.7%2bdfsg-3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./zlib1g_1.3.dfsg%2breally1.3.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:08] "GET /./libssl3t64_3.5.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./openssl-provider-legacy_3.5.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libsystemd0_259.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./coreutils_9.7-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./dash_0.5.12-12_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./diffutils_3.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libbz2-1.0_1.0.8-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./liblzma5_5.8.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libmd0_1.1.0-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./tar_1.35%2bdfsg-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./dpkg_1.23.5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./findutils_4.10.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./grep_3.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./gzip_1.13-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./hostname_3.25_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./ncurses-bin_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libcrypt1_4.5.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./perl-base_5.40.1-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./sed_4.9-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libaudit-common_4.1.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libcap-ng0_0.9.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libaudit1_4.1.2-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libdb5.3t64_5.3.28%2bdfsg2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./debconf_1.5.92_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libpam0g_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libpam-modules-bin_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libpam-modules_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libpam-runtime_1.7.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libblkid1_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libmount1_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libsmartcols1_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libudev1_259.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libuuid1_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./util-linux_2.41.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libdebconfclient0_0.282%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./base-passwd_3.6.8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./init-system-helpers_1.69_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./libc-bin_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./ncurses-base_6.6%2b20251231-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:09] "GET /./sysvinit-utils_3.15-6_amd64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.zvxCEfwMhC 127.0.0.1 - - [26/Feb/2026 05:30:10] code 404, message File not found 127.0.0.1 - - [26/Feb/2026 05:30:10] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:41459 ./ InRelease 127.0.0.1 - - [26/Feb/2026 05:30:10] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:41459 ./ Release 127.0.0.1 - - [26/Feb/2026 05:30:10] code 404, message File not found 127.0.0.1 - - [26/Feb/2026 05:30:10] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:41459 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... I: running --essential-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/essential00.sh /srv/rebuilderd/tmp/mmdebstrap.zvxCEfwMhC usr-is-merged was not installed in a previous hook -- not running merged-usr essential hook I: installing remaining packages inside the chroot... 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libexpat1_2.7.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libpython3.13-minimal_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./python3.13-minimal_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./python3-minimal_3.13.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./media-types_14.0.0_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./netbase_6.5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./tzdata_2025c-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libffi8_3.5.2-3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libncursesw6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./readline-common_8.3-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libreadline8t64_8.3-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libsqlite3-0_3.46.1-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libpython3.13-stdlib_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./python3.13_3.13.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libpython3-stdlib_3.13.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./python3_3.13.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./python3-numpy-dev_2.3.5%2bds-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libblas3_3.12.1-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libgfortran5_15.2.0-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./liblapack3_3.12.1-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libstdc%2b%2b6_15.2.0-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./python3-numpy_2.3.5%2bds-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libpython3.14-minimal_3.14.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./python3.14-minimal_3.14.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libtext-charwidth-perl_0.04-11%2bb5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libtext-wrapi18n-perl_0.06-10_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./sensible-utils_0.0.26_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./libuchardet0_0.0.8-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./groff-base_1.23.0-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:17] "GET /./bsdextrautils_2.41.3-4_amd64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [26/Feb/2026 05:30:19] "GET /./python3-jaraco.text_4.0.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:19] "GET /./python3-setuptools_78.1.1-0.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [26/Feb/2026 05:30:19] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmp8q2tdblw/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.zvxCEfwMhC Reading package lists... Building dependency tree... Reading state information... libattr1 is already the newest version (1:2.5.2-4). libfile-stripnondeterminism-perl is already the newest version (1.15.0-1). libfile-stripnondeterminism-perl set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-3+b1). base-files is already the newest version (14). libubsan1 is already the newest version (15.2.0-14). libubsan1 set to manually installed. coreutils is already the newest version (9.7-3). libxpm4 is already the newest version (1:3.5.17-1+b4). libxpm4 set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11). binutils-common is already the newest version (2.46-2). binutils-common set to manually installed. python3-pkg-resources is already the newest version (78.1.1-0.1). python3-pkg-resources set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-3). autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. libxt6t64 is already the newest version (1:1.2.1-1.3+b1). libxt6t64 set to manually installed. libsynctex2 is already the newest version (2025.20250727.75242+ds-5). libsynctex2 set to manually installed. texlive is already the newest version (2025.20260124-1). texlive set to manually installed. libpaper2 is already the newest version (2.2.5-0.3+b3). libpaper2 set to manually installed. libpotrace0 is already the newest version (1.16-2+b3). libpotrace0 set to manually installed. xz-utils is already the newest version (5.8.2-2). xz-utils set to manually installed. liblzma5 is already the newest version (5.8.2-2). g++-x86-64-linux-gnu is already the newest version (4:15.2.0-5). g++-x86-64-linux-gnu set to manually installed. binutils is already the newest version (2.46-2). binutils set to manually installed. libstdc++6 is already the newest version (15.2.0-14). libstdc++6 set to manually installed. python3-numpy-dev is already the newest version (1:2.3.5+ds-3). python3-numpy-dev set to manually installed. file is already the newest version (1:5.46-5+b1). file set to manually installed. libice6 is already the newest version (2:1.1.1-1+b1). libice6 set to manually installed. python3-jaraco.context is already the newest version (6.0.1-2). python3-jaraco.context set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. bash is already the newest version (5.3-2). liblapack3 is already the newest version (3.12.1-7+b1). liblapack3 set to manually installed. gcc is already the newest version (4:15.2.0-5). gcc set to manually installed. libctf-nobfd0 is already the newest version (2.46-2). libctf-nobfd0 set to manually installed. perl-base is already the newest version (5.40.1-7). dash is already the newest version (0.5.12-12). init-system-helpers is already the newest version (1.69). python3-more-itertools is already the newest version (10.8.0-1). python3-more-itertools set to manually installed. libudev1 is already the newest version (259.1-1). libaudit-common is already the newest version (1:4.1.2-1). debianutils is already the newest version (5.23.2). libxcb-render0 is already the newest version (1.17.0-2+b2). libxcb-render0 set to manually installed. g++-15 is already the newest version (15.2.0-14). g++-15 set to manually installed. hostname is already the newest version (3.25). libc-gconv-modules-extra is already the newest version (2.42-13). libgdbm6t64 is already the newest version (1.26-1+b1). libgdbm6t64 set to manually installed. python3-all is already the newest version (3.13.9-3). python3-all set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b1). libcap-ng0 is already the newest version (0.9.1-1). dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. util-linux is already the newest version (2.41.3-4). libexpat1 is already the newest version (2.7.4-1). libexpat1 set to manually installed. libsmartcols1 is already the newest version (2.41.3-4). dpkg is already the newest version (1.23.5). libreadline8t64 is already the newest version (8.3-4). libreadline8t64 set to manually installed. libproc2-0 is already the newest version (2:4.0.4-9+b1). libproc2-0 set to manually installed. x11-common is already the newest version (1:7.7+26). x11-common set to manually installed. liblsan0 is already the newest version (15.2.0-14). liblsan0 set to manually installed. libfontconfig1 is already the newest version (2.17.1-5). libfontconfig1 set to manually installed. ncurses-bin is already the newest version (6.6+20251231-1). libgcc-s1 is already the newest version (15.2.0-14). libacl1 is already the newest version (2.3.2-3). fonts-dejavu-core is already the newest version (2.37-8). fonts-dejavu-core set to manually installed. libtexlua53-5 is already the newest version (2025.20250727.75242+ds-5). libtexlua53-5 set to manually installed. sed is already the newest version (4.9-2). libglib2.0-0t64 is already the newest version (2.87.2-3). libglib2.0-0t64 set to manually installed. libmount1 is already the newest version (2.41.3-4). libpython3-stdlib is already the newest version (3.13.9-3). libpython3-stdlib set to manually installed. libxmu6 is already the newest version (2:1.1.3-4). libxmu6 set to manually installed. python3-zipp is already the newest version (3.23.0-1). python3-zipp set to manually installed. libquadmath0 is already the newest version (15.2.0-14). libquadmath0 set to manually installed. libxaw7 is already the newest version (2:1.0.16-1+b1). libxaw7 set to manually installed. libc-dev-bin is already the newest version (2.42-13). libc-dev-bin set to manually installed. libxcb-shm0 is already the newest version (1.17.0-2+b2). libxcb-shm0 set to manually installed. python3 is already the newest version (3.13.9-3). python3 set to manually installed. libblkid1 is already the newest version (2.41.3-4). groff-base is already the newest version (1.23.0-10). groff-base set to manually installed. xdg-utils is already the newest version (1.2.1-2). xdg-utils set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. libpam-modules-bin is already the newest version (1.7.0-5+b1). libmagic1t64 is already the newest version (1:5.46-5+b1). libmagic1t64 set to manually installed. tar is already the newest version (1.35+dfsg-4). libcap2 is already the newest version (1:2.75-10+b5). po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libcc1-0 is already the newest version (15.2.0-14). libcc1-0 set to manually installed. libblas3 is already the newest version (3.12.1-7+b1). libblas3 set to manually installed. procps is already the newest version (2:4.0.4-9+b1). procps set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b1). libgdbm-compat4t64 set to manually installed. fonts-dejavu-mono is already the newest version (2.37-8). fonts-dejavu-mono set to manually installed. libpixman-1-0 is already the newest version (0.46.4-1+b1). libpixman-1-0 set to manually installed. binutils-x86-64-linux-gnu is already the newest version (2.46-2). binutils-x86-64-linux-gnu set to manually installed. dh-python is already the newest version (7.20260125). dh-python set to manually installed. libelf1t64 is already the newest version (0.194-1). libelf1t64 set to manually installed. python3-typing-extensions is already the newest version (4.15.0-2). python3-typing-extensions set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libpam-modules is already the newest version (1.7.0-5+b1). findutils is already the newest version (4.10.0-3). libpipeline1 is already the newest version (1.5.8-2). libpipeline1 set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1). libmpfi0 is already the newest version (1.5.4+ds-4+b1). libmpfi0 set to manually installed. libuchardet0 is already the newest version (0.0.8-2+b1). libuchardet0 set to manually installed. python3-minimal is already the newest version (3.13.9-3). python3-minimal set to manually installed. libgomp1 is already the newest version (15.2.0-14). libgomp1 set to manually installed. libtext-wrapi18n-perl is already the newest version (0.06-10). libtext-wrapi18n-perl set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.2.0-14). gcc-15-x86-64-linux-gnu set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b1). libgcc-15-dev is already the newest version (15.2.0-14). libgcc-15-dev set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. libkpathsea6 is already the newest version (2025.20250727.75242+ds-5). libkpathsea6 set to manually installed. tex-common is already the newest version (6.20). tex-common set to manually installed. debhelper is already the newest version (13.31). debhelper set to manually installed. libmagic-mgc is already the newest version (1:5.46-5+b1). libmagic-mgc set to manually installed. libhwasan0 is already the newest version (15.2.0-14). libhwasan0 set to manually installed. libselinux1 is already the newest version (3.9-4+b1). patch is already the newest version (2.8-2). patch set to manually installed. python3-numpy is already the newest version (1:2.3.5+ds-3). python3-numpy set to manually installed. libssl3t64 is already the newest version (3.5.5-1). cpp-15 is already the newest version (15.2.0-14). cpp-15 set to manually installed. libasan8 is already the newest version (15.2.0-14). libasan8 set to manually installed. libsqlite3-0 is already the newest version (3.46.1-9). libsqlite3-0 set to manually installed. autoconf is already the newest version (2.72-3.1). autoconf set to manually installed. libtext-charwidth-perl is already the newest version (0.04-11+b5). libtext-charwidth-perl set to manually installed. libc6-dev is already the newest version (2.42-13). libc6-dev set to manually installed. libpython3.14-stdlib is already the newest version (3.14.3-1). libpython3.14-stdlib set to manually installed. python3-jaraco.text is already the newest version (4.0.0-1). python3-jaraco.text set to manually installed. python3.13-minimal is already the newest version (3.13.12-1). python3.13-minimal set to manually installed. libc6 is already the newest version (2.42-13). libfreetype6 is already the newest version (2.14.1+dfsg-2). libfreetype6 set to manually installed. readline-common is already the newest version (8.3-4). readline-common set to manually installed. libctf0 is already the newest version (2.46-2). libctf0 set to manually installed. mawk is already the newest version (1.3.4.20260129-1). libxml2-16 is already the newest version (2.15.1+dfsg-2+b1). libxml2-16 set to manually installed. libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. python3.14 is already the newest version (3.14.3-1). python3.14 set to manually installed. libitm1 is already the newest version (15.2.0-14). libitm1 set to manually installed. libuuid1 is already the newest version (2.41.3-4). bsdextrautils is already the newest version (2.41.3-4). bsdextrautils set to manually installed. libxau6 is already the newest version (1:1.0.11-1+b1). libxau6 set to manually installed. texlive-latex-recommended is already the newest version (2025.20260124-1). texlive-latex-recommended set to manually installed. cpp-15-x86-64-linux-gnu is already the newest version (15.2.0-14). cpp-15-x86-64-linux-gnu set to manually installed. libharfbuzz0b is already the newest version (12.3.2-2). libharfbuzz0b set to manually installed. libisl23 is already the newest version (0.27-1+b1). libisl23 set to manually installed. t1utils is already the newest version (1.41-4). t1utils set to manually installed. cpp is already the newest version (4:15.2.0-5). cpp set to manually installed. libjansson4 is already the newest version (2.14-2+b4). libjansson4 set to manually installed. libtinfo6 is already the newest version (6.6+20251231-1). build-essential is already the newest version (12.12). build-essential set to manually installed. libgfortran5 is already the newest version (15.2.0-14). libgfortran5 set to manually installed. python3-autocommand is already the newest version (2.2.2-4). python3-autocommand set to manually installed. libdpkg-perl is already the newest version (1.23.5). libdpkg-perl set to manually installed. libgraphite2-3 is already the newest version (1.3.14-11+b1). libgraphite2-3 set to manually installed. libpam-runtime is already the newest version (1.7.0-5). libx11-6 is already the newest version (2:1.8.13-1). libx11-6 set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. libncursesw6 is already the newest version (6.6+20251231-1). libncursesw6 set to manually installed. libperl5.40 is already the newest version (5.40.1-7). libperl5.40 set to manually installed. netbase is already the newest version (6.5). netbase set to manually installed. libunistring5 is already the newest version (1.3-2+b1). libunistring5 set to manually installed. cpp-x86-64-linux-gnu is already the newest version (4:15.2.0-5). cpp-x86-64-linux-gnu set to manually installed. g++ is already the newest version (4:15.2.0-5). g++ set to manually installed. libbrotli1 is already the newest version (1.2.0-3). libbrotli1 set to manually installed. libmd0 is already the newest version (1.1.0-2+b2). libtsan2 is already the newest version (15.2.0-14). libtsan2 set to manually installed. ucf is already the newest version (3.0052). ucf set to manually installed. libdebconfclient0 is already the newest version (0.282+b2). openssl-provider-legacy is already the newest version (3.5.5-1). intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. gettext-base is already the newest version (0.23.2-1). gettext-base set to manually installed. libsm6 is already the newest version (2:1.2.6-1+b1). libsm6 set to manually installed. libteckit0 is already the newest version (2.5.13+ds-1). libteckit0 set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2). libxdmcp6 set to manually installed. autopoint is already the newest version (0.23.2-1). autopoint set to manually installed. libicu76 is already the newest version (76.1-4+b1). libicu76 set to manually installed. libzzip-0-13t64 is already the newest version (0.13.78+dfsg.1-0.2). libzzip-0-13t64 set to manually installed. libmpfr6 is already the newest version (4.2.2-2+b1). libmpfr6 set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. dwz is already the newest version (0.16-2). dwz set to manually installed. media-types is already the newest version (14.0.0). media-types set to manually installed. libsframe3 is already the newest version (2.46-2). libsframe3 set to manually installed. base-passwd is already the newest version (3.6.8). linux-libc-dev is already the newest version (6.18.12-1). linux-libc-dev set to manually installed. debconf is already the newest version (1.5.92). libxi6 is already the newest version (2:1.8.2-2). libxi6 set to manually installed. bzip2 is already the newest version (1.0.8-6+b1). bzip2 set to manually installed. libpam0g is already the newest version (1.7.0-5+b1). libpng16-16t64 is already the newest version (1.6.55-1). libpng16-16t64 set to manually installed. python3-typeguard is already the newest version (4.4.4-2). python3-typeguard set to manually installed. fonts-lmodern is already the newest version (2.005-1). fonts-lmodern set to manually installed. gcc-15 is already the newest version (15.2.0-14). gcc-15 set to manually installed. g++-15-x86-64-linux-gnu is already the newest version (15.2.0-14). g++-15-x86-64-linux-gnu set to manually installed. libbinutils is already the newest version (2.46-2). libbinutils set to manually installed. libdebhelper-perl is already the newest version (13.31). libdebhelper-perl set to manually installed. libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. python3-jaraco.functools is already the newest version (4.1.0-1). python3-jaraco.functools set to manually installed. python3-setuptools is already the newest version (78.1.1-0.1). python3-setuptools set to manually installed. libffi8 is already the newest version (3.5.2-3+b1). libffi8 set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:15.2.0-5). gcc-x86-64-linux-gnu set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.0-1). dh-strip-nondeterminism set to manually installed. tzdata is already the newest version (2025c-3). tzdata set to manually installed. libstdc++-15-dev is already the newest version (15.2.0-14). libstdc++-15-dev set to manually installed. python3-inflect is already the newest version (7.5.0-1). python3-inflect set to manually installed. libxrender1 is already the newest version (1:0.9.12-1+b1). libxrender1 set to manually installed. libgprofng0 is already the newest version (2.46-2). libgprofng0 set to manually installed. libpython3.13-minimal is already the newest version (3.13.12-1). libpython3.13-minimal set to manually installed. libc-bin is already the newest version (2.42-13). libatomic1 is already the newest version (15.2.0-14). libatomic1 set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). libsystemd0 is already the newest version (259.1-1). libtool is already the newest version (2.5.4-9). libtool set to manually installed. texlive-fonts-recommended is already the newest version (2025.20260124-1). texlive-fonts-recommended set to manually installed. sysvinit-utils is already the newest version (3.15-6). ncurses-base is already the newest version (6.6+20251231-1). texlive-base is already the newest version (2025.20260124-1). texlive-base set to manually installed. libmpc3 is already the newest version (1.3.1-2+b1). libmpc3 set to manually installed. libcairo2 is already the newest version (1.18.4-3). libcairo2 set to manually installed. perl is already the newest version (5.40.1-7). perl set to manually installed. texlive-latex-base is already the newest version (2025.20260124-1). texlive-latex-base set to manually installed. python3.13 is already the newest version (3.13.12-1). python3.13 set to manually installed. diffutils is already the newest version (1:3.12-1). dpkg-dev is already the newest version (1.23.5). dpkg-dev set to manually installed. automake is already the newest version (1:1.18.1-3). automake set to manually installed. texlive-binaries is already the newest version (2025.20250727.75242+ds-5). texlive-binaries set to manually installed. libpcre2-8-0 is already the newest version (10.46-1+b1). gettext is already the newest version (0.23.2-1). gettext set to manually installed. fontconfig-config is already the newest version (2.17.1-5). fontconfig-config set to manually installed. gcc-15-base is already the newest version (15.2.0-14). python3.14-minimal is already the newest version (3.14.3-1). python3.14-minimal set to manually installed. libpython3.14-minimal is already the newest version (3.14.3-1). libpython3.14-minimal set to manually installed. libpaper-utils is already the newest version (2.2.5-0.3+b3). libpaper-utils set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-7). perl-modules-5.40 set to manually installed. libptexenc1 is already the newest version (2025.20250727.75242+ds-5). libptexenc1 set to manually installed. libpython3.13-stdlib is already the newest version (3.13.12-1). libpython3.13-stdlib set to manually installed. gzip is already the newest version (1.13-1). grep is already the newest version (3.12-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.zvxCEfwMhC (Reading database ... 28987 files and directories currently installed.) Removing debootsnap-dummy (1.0) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg-query --showformat '${binary:Package}=${Version}\n' --show > "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.zvxCEfwMhC I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.zvxCEfwMhC I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.zvxCEfwMhC... I: success in 94.3639 seconds Downloading dependency 132 of 233: python3.14:amd64=3.14.3-1 Downloading dependency 133 of 233: libitm1:amd64=15.2.0-14 Downloading dependency 134 of 233: libuuid1:amd64=2.41.3-4 Downloading dependency 135 of 233: bsdextrautils:amd64=2.41.3-4 Downloading dependency 136 of 233: libxau6:amd64=1:1.0.11-1+b1 Downloading dependency 137 of 233: texlive-latex-recommended:amd64=2025.20260124-1 Downloading dependency 138 of 233: cpp-15-x86-64-linux-gnu:amd64=15.2.0-14 Downloading dependency 139 of 233: libharfbuzz0b:amd64=12.3.2-2 Downloading dependency 140 of 233: libisl23:amd64=0.27-1+b1 Downloading dependency 141 of 233: t1utils:amd64=1.41-4 Downloading dependency 142 of 233: cpp:amd64=4:15.2.0-5 Downloading dependency 143 of 233: libjansson4:amd64=2.14-2+b4 Downloading dependency 144 of 233: libtinfo6:amd64=6.6+20251231-1 Downloading dependency 145 of 233: build-essential:amd64=12.12 Downloading dependency 146 of 233: libgfortran5:amd64=15.2.0-14 Downloading 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python3-setuptools:amd64=78.1.1-0.1 Downloading dependency 195 of 233: libffi8:amd64=3.5.2-3+b1 Downloading dependency 196 of 233: gcc-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 197 of 233: dh-strip-nondeterminism:amd64=1.15.0-1 Downloading dependency 198 of 233: tzdata:amd64=2025c-3 Downloading dependency 199 of 233: libstdc++-15-dev:amd64=15.2.0-14 Downloading dependency 200 of 233: python3-inflect:amd64=7.5.0-1 Downloading dependency 201 of 233: libxrender1:amd64=1:0.9.12-1+b1 Downloading dependency 202 of 233: libgprofng0:amd64=2.46-2 Downloading dependency 203 of 233: libpython3.13-minimal:amd64=3.13.12-1 Downloading dependency 204 of 233: libc-bin:amd64=2.42-13 Downloading dependency 205 of 233: libatomic1:amd64=15.2.0-14 Downloading dependency 206 of 233: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 207 of 233: libsystemd0:amd64=259.1-1 Downloading dependency 208 of 233: libtool:amd64=2.5.4-9 Downloading dependency 209 of 233: texlive-fonts-recommended:amd64=2025.20260124-1 Downloading dependency 210 of 233: sysvinit-utils:amd64=3.15-6 Downloading dependency 211 of 233: ncurses-base:amd64=6.6+20251231-1 Downloading dependency 212 of 233: texlive-base:amd64=2025.20260124-1 Downloading dependency 213 of 233: libmpc3:amd64=1.3.1-2+b1 Downloading dependency 214 of 233: libcairo2:amd64=1.18.4-3 Downloading dependency 215 of 233: perl:amd64=5.40.1-7 Downloading dependency 216 of 233: texlive-latex-base:amd64=2025.20260124-1 Downloading dependency 217 of 233: python3.13:amd64=3.13.12-1 Downloading dependency 218 of 233: diffutils:amd64=1:3.12-1 Downloading dependency 219 of 233: dpkg-dev:amd64=1.23.5 Downloading dependency 220 of 233: automake:amd64=1:1.18.1-3 Downloading dependency 221 of 233: texlive-binaries:amd64=2025.20250727.75242+ds-5 Downloading dependency 222 of 233: libpcre2-8-0:amd64=10.46-1+b1 Downloading dependency 223 of 233: gettext:amd64=0.23.2-1 Downloading dependency 224 of 233: fontconfig-config:amd64=2.17.1-5 Downloading dependency 225 of 233: gcc-15-base:amd64=15.2.0-14 Downloading dependency 226 of 233: python3.14-minimal:amd64=3.14.3-1 Downloading dependency 227 of 233: libpython3.14-minimal:amd64=3.14.3-1 Downloading dependency 228 of 233: libpaper-utils:amd64=2.2.5-0.3+b3 Downloading dependency 229 of 233: perl-modules-5.40:amd64=5.40.1-7 Downloading dependency 230 of 233: libptexenc1:amd64=2025.20250727.75242+ds-5 Downloading dependency 231 of 233: libpython3.13-stdlib:amd64=3.13.12-1 Downloading dependency 232 of 233: gzip:amd64=1.13-1 Downloading dependency 233 of 233: grep:amd64=3.12-1 env --chdir=/srv/rebuilderd/tmp/rebuilderdZaP6jO/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1772011094 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuild5fyHIU/debrebuild.sbuildrc.XWDefIYHN8tl sbuild --build=amd64 --host=amd64 --no-source --no-arch-any --arch-all --chroot=/srv/rebuilderd/tmp/debrebuild5fyHIU/debrebuild.tar.AmmN0OtK3kDE --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=moltemplate-2.22.5 /srv/rebuilderd/tmp/rebuilderdZaP6jO/inputs/moltemplate_2.22.5-1.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on ionos23-amd64.debian.net +==============================================================================+ | moltemplate 2.22.5-1 (amd64) Thu, 26 Feb 2026 05:31:43 +0000 | +==============================================================================+ Package: moltemplate Version: 2.22.5-1 Source Version: 2.22.5-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: all I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuild5fyHIU/debrebuild.tar.AmmN0OtK3kDE to /srv/rebuilderd/tmp/tmp.sbuild.Y4RrgVeR6i... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Thu, 26 Feb 2026 05:31:49 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdZaP6jO/inputs/moltemplate_2.22.5-1.dsc exists in /srv/rebuilderd/tmp/rebuilderdZaP6jO/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 26 Feb 2026 05:31:50 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-numpy, build-essential, texlive Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-numpy, build-essential, texlive dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-MKtt5C/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Thu, 26 Feb 2026 05:31:53 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment Thu, 26 Feb 2026 05:31:54 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.73+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.73-1 (2026-02-17) amd64 (x86_64) Toolchain package versions: binutils_2.46-2 dpkg-dev_1.23.5 g++-15_15.2.0-14 gcc-15_15.2.0-14 libc6-dev_2.42-13 libstdc++-15-dev_15.2.0-14 libstdc++6_15.2.0-14 linux-libc-dev_6.18.12-1 Package versions: autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-2 binutils_2.46-2 binutils-common_2.46-2 binutils-x86-64-linux-gnu_2.46-2 bsdextrautils_2.41.3-4 build-essential_12.12 bzip2_1.0.8-6+b1 coreutils_9.7-3 cpp_4:15.2.0-5 cpp-15_15.2.0-14 cpp-15-x86-64-linux-gnu_15.2.0-14 cpp-x86-64-linux-gnu_4:15.2.0-5 dash_0.5.12-12 debconf_1.5.92 debhelper_13.31 debianutils_5.23.2 dh-autoreconf_22 dh-python_7.20260125 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dpkg_1.23.5 dpkg-dev_1.23.5 dwz_0.16-2 file_1:5.46-5+b1 findutils_4.10.0-3 fontconfig-config_2.17.1-5 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lmodern_2.005-1 g++_4:15.2.0-5 g++-15_15.2.0-14 g++-15-x86-64-linux-gnu_15.2.0-14 g++-x86-64-linux-gnu_4:15.2.0-5 gcc_4:15.2.0-5 gcc-15_15.2.0-14 gcc-15-base_15.2.0-14 gcc-15-x86-64-linux-gnu_15.2.0-14 gcc-x86-64-linux-gnu_4:15.2.0-5 gettext_0.23.2-1 gettext-base_0.23.2-1 grep_3.12-1 groff-base_1.23.0-10 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libarchive-zip-perl_1.68-1 libasan8_15.2.0-14 libatomic1_15.2.0-14 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-2 libblas3_3.12.1-7+b1 libblkid1_2.41.3-4 libbrotli1_1.2.0-3 libbz2-1.0_1.0.8-6+b1 libc-bin_2.42-13 libc-dev-bin_2.42-13 libc-gconv-modules-extra_2.42-13 libc6_2.42-13 libc6-dev_2.42-13 libcairo2_1.18.4-3 libcap-ng0_0.9.1-1 libcap2_1:2.75-10+b5 libcc1-0_15.2.0-14 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.46-2 libctf0_2.46-2 libdb5.3t64_5.3.28+dfsg2-11 libdebconfclient0_0.282+b2 libdebhelper-perl_13.31 libdpkg-perl_1.23.5 libelf1t64_0.194-1 libexpat1_2.7.4-1 libffi8_3.5.2-3+b1 libfile-stripnondeterminism-perl_1.15.0-1 libfontconfig1_2.17.1-5 libfreetype6_2.14.1+dfsg-2 libgcc-15-dev_15.2.0-14 libgcc-s1_15.2.0-14 libgdbm-compat4t64_1.26-1+b1 libgdbm6t64_1.26-1+b1 libgfortran5_15.2.0-14 libglib2.0-0t64_2.87.2-3 libgmp10_2:6.3.0+dfsg-5+b1 libgomp1_15.2.0-14 libgprofng0_2.46-2 libgraphite2-3_1.3.14-11+b1 libharfbuzz0b_12.3.2-2 libhwasan0_15.2.0-14 libice6_2:1.1.1-1+b1 libicu76_76.1-4+b1 libisl23_0.27-1+b1 libitm1_15.2.0-14 libjansson4_2.14-2+b4 libkpathsea6_2025.20250727.75242+ds-5 liblapack3_3.12.1-7+b1 liblsan0_15.2.0-14 liblzma5_5.8.2-2 libmagic-mgc_1:5.46-5+b1 libmagic1t64_1:5.46-5+b1 libmd0_1.1.0-2+b2 libmount1_2.41.3-4 libmpc3_1.3.1-2+b1 libmpfi0_1.5.4+ds-4+b1 libmpfr6_4.2.2-2+b1 libncursesw6_6.6+20251231-1 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpaper-utils_2.2.5-0.3+b3 libpaper2_2.2.5-0.3+b3 libpcre2-8-0_10.46-1+b1 libperl5.40_5.40.1-7 libpipeline1_1.5.8-2 libpixman-1-0_0.46.4-1+b1 libpng16-16t64_1.6.55-1 libpotrace0_1.16-2+b3 libproc2-0_2:4.0.4-9+b1 libptexenc1_2025.20250727.75242+ds-5 libpython3-stdlib_3.13.9-3 libpython3.13-minimal_3.13.12-1 libpython3.13-stdlib_3.13.12-1 libpython3.14-minimal_3.14.3-1 libpython3.14-stdlib_3.14.3-1 libquadmath0_15.2.0-14 libreadline8t64_8.3-4 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+b1 libsframe3_2.46-2 libsm6_2:1.2.6-1+b1 libsmartcols1_2.41.3-4 libsqlite3-0_3.46.1-9 libssl3t64_3.5.5-1 libstdc++-15-dev_15.2.0-14 libstdc++6_15.2.0-14 libsynctex2_2025.20250727.75242+ds-5 libsystemd0_259.1-1 libteckit0_2.5.13+ds-1 libtexlua53-5_2025.20250727.75242+ds-5 libtext-charwidth-perl_0.04-11+b5 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.6+20251231-1 libtool_2.5.4-9 libtsan2_15.2.0-14 libubsan1_15.2.0-14 libuchardet0_0.0.8-2+b1 libudev1_259.1-1 libunistring5_1.3-2+b1 libuuid1_2.41.3-4 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxau6_1:1.0.11-1+b1 libxaw7_2:1.0.16-1+b1 libxcb-render0_1.17.0-2+b2 libxcb-shm0_1.17.0-2+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2 libxext6_2:1.3.4-1+b4 libxi6_2:1.8.2-2 libxml2-16_2.15.1+dfsg-2+b1 libxmu6_2:1.1.3-4 libxpm4_1:3.5.17-1+b4 libxrender1_1:0.9.12-1+b1 libxt6t64_1:1.2.1-1.3+b1 libzstd1_1.5.7+dfsg-3+b1 libzzip-0-13t64_0.13.78+dfsg.1-0.2 linux-libc-dev_6.18.12-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260129-1 media-types_14.0.0 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 netbase_6.5 openssl-provider-legacy_3.5.5-1 patch_2.8-2 perl_5.40.1-7 perl-base_5.40.1-7 perl-modules-5.40_5.40.1-7 po-debconf_1.0.22 procps_2:4.0.4-9+b1 python3_3.13.9-3 python3-all_3.13.9-3 python3-autocommand_2.2.2-4 python3-inflect_7.5.0-1 python3-jaraco.context_6.0.1-2 python3-jaraco.functools_4.1.0-1 python3-jaraco.text_4.0.0-1 python3-minimal_3.13.9-3 python3-more-itertools_10.8.0-1 python3-numpy_1:2.3.5+ds-3 python3-numpy-dev_1:2.3.5+ds-3 python3-pkg-resources_78.1.1-0.1 python3-setuptools_78.1.1-0.1 python3-typeguard_4.4.4-2 python3-typing-extensions_4.15.0-2 python3-zipp_3.23.0-1 python3.13_3.13.12-1 python3.13-minimal_3.13.12-1 python3.14_3.14.3-1 python3.14-minimal_3.14.3-1 readline-common_8.3-4 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.26 sysvinit-utils_3.15-6 t1utils_1.41-4 tar_1.35+dfsg-4 tex-common_6.20 texlive_2025.20260124-1 texlive-base_2025.20260124-1 texlive-binaries_2025.20250727.75242+ds-5 texlive-fonts-recommended_2025.20260124-1 texlive-latex-base_2025.20260124-1 texlive-latex-recommended_2025.20260124-1 tzdata_2025c-3 ucf_3.0052 util-linux_2.41.3-4 x11-common_1:7.7+26 xdg-utils_1.2.1-2 xz-utils_5.8.2-2 zlib1g_1:1.3.dfsg+really1.3.1-3 +------------------------------------------------------------------------------+ | Build Thu, 26 Feb 2026 05:31:54 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: moltemplate Binary: python3-moltemplate, moltemplate-doc Architecture: all Version: 2.22.5-1 Maintainer: Drew Parsons Homepage: https://moltemplate.org/ Standards-Version: 4.7.3 Vcs-Browser: https://salsa.debian.org/science-team/moltemplate Vcs-Git: https://salsa.debian.org/science-team/moltemplate.git Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-numpy Build-Depends-Indep: texlive Package-List: moltemplate-doc deb doc optional arch=all python3-moltemplate deb science optional arch=all Checksums-Sha1: 1afb2560061874e9d331f0455b860837f85fe273 10342161 moltemplate_2.22.5.orig.tar.gz 5b6b275ec558704f56753c8beff619468e307b3d 3964 moltemplate_2.22.5-1.debian.tar.xz Checksums-Sha256: fc1b7b738c256613bcb1d75971c2481cb9894724ce279210efe278d8d71e9aaf 10342161 moltemplate_2.22.5.orig.tar.gz 7f0e65bb5bc728262adcb7aa94ddf85cae04f7e6975106020872189731fcfcc2 3964 moltemplate_2.22.5-1.debian.tar.xz Files: c7e6e661423fae57358a39cec17f4c7a 10342161 moltemplate_2.22.5.orig.tar.gz f20d8964966836a10e502dfb08f3d189 3964 moltemplate_2.22.5-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmmevzcACgkQVz7x5L1a AfraNhAAmIUSJT/WnUa4imVj8YyNfnUREVEUB7C745KstbOczemfumNua4+wSk7S RD3+4XNMLNXwpINBWnHuEl93u6ktxj4Y4AC9UA3o+RnexugBe8QqZ2hVUvje0Mws i3zdh/bGxYzBapDexvp9oaGV+nkPPG9JCUYyCx3O1TSkVPskSSsSpxDTUGG30pPQ 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keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting moltemplate in /build/reproducible-path/moltemplate-2.22.5 dpkg-source: info: unpacking moltemplate_2.22.5.orig.tar.gz dpkg-source: info: unpacking moltemplate_2.22.5-1.debian.tar.xz Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=6 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1772011094 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -A dpkg-buildpackage: info: source package moltemplate dpkg-buildpackage: info: source version 2.22.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-source: info: using options from moltemplate-2.22.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:384: python3.14 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.14' does not exist -- can't clean it I: pybuild base:384: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-indep dh binary-indep --buildsystem=pybuild dh_update_autotools_config -i -O--buildsystem=pybuild dh_autoreconf -i -O--buildsystem=pybuild dh_auto_configure -i -O--buildsystem=pybuild I: pybuild base:384: python3.14 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config I: pybuild base:384: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config dh_auto_build -i -O--buildsystem=pybuild I: pybuild base:384: /usr/bin/python3.14 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/lttree_check.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/ttree_render.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/genpoly_lt.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/ordereddict.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/recenter_coords.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/extract_espresso_atom_types.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/ettree_styles.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/ltemplify.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/nbody_by_type_lib.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/postprocess_input_script.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/postprocess_transitions.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/nbody_Dihedrals.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/interpolate_curve.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/bonds_by_type.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/renumber_DATA_first_column.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/lttree_styles.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/raw2data.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/nbody_fix_ttree_assignments.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/ttree_matrix_stack.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/nbody_Bonds.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/remove_duplicates_nbody.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/genpoly_modify_lt.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/lttree_postprocess.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/ettree.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/__init__.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/mol22lt.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/postprocess_coeffs.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/extract_lammps_data.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/ttree_lex.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/remove_duplicate_atoms.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/amber2lt.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/charge_by_bond.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/nbody_Angles.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/pdbsort.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/nbody_Impropers.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/dump2data.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/ttree.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/lttree.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/nbody_reorder_atoms.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/nbody_by_type.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate copying moltemplate/nbody_graph_search.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenJswapIL.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenKswapIL.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/bonds_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/gaff_imp.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/__init__.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenIsortJKL.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenIswapJK.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/dihedrals_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/angles_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/impropers_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenJsortIKL.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry running egg_info creating moltemplate.egg-info writing moltemplate.egg-info/PKG-INFO writing dependency_links to moltemplate.egg-info/dependency_links.txt writing entry points to moltemplate.egg-info/entry_points.txt writing requirements to moltemplate.egg-info/requires.txt writing top-level names to moltemplate.egg-info/top_level.txt writing manifest file 'moltemplate.egg-info/SOURCES.txt' reading manifest file 'moltemplate.egg-info/SOURCES.txt' adding license file 'LICENSE.md' writing manifest file 'moltemplate.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'moltemplate.force_fields' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'moltemplate.force_fields' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'moltemplate.force_fields' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'moltemplate.force_fields' to be distributed and are already explicitly excluding 'moltemplate.force_fields' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'moltemplate.scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'moltemplate.scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'moltemplate.scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'moltemplate.scripts' to be distributed and are already explicitly excluding 'moltemplate.scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/compass_published.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/cooke_deserno_lipid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/dreiding.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/drymartini.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/gaff.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/gaff2.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/graphene.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/graphene_rectangular.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/graphite.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/loplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/loplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/loplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/martini.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/sdk.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spc_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spc_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spc_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_amber.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_dreiding.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_ice_rect16.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_ice_rect32.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_ice_rect8.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_more_comments.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_charmm.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_charmm_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_2004.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_2004_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_2004_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_2004_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip5p_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip5p_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip5p_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/trappe1998.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/watmw.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields creating /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/cleanup_moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/emoltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/molc.sh -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/pdb2crds.awk -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts running build_scripts creating build/scripts-3.14 copying moltemplate/scripts/moltemplate.sh -> build/scripts-3.14 copying moltemplate/scripts/cleanup_moltemplate.sh -> build/scripts-3.14 copying moltemplate/scripts/molc.sh -> build/scripts-3.14 copying moltemplate/scripts/pdb2crds.awk -> build/scripts-3.14 copying moltemplate/scripts/emoltemplate.sh -> build/scripts-3.14 I: pybuild base:384: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/lttree_check.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/ttree_render.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/genpoly_lt.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/ordereddict.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/recenter_coords.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/extract_espresso_atom_types.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/ettree_styles.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/ltemplify.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/nbody_by_type_lib.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/postprocess_input_script.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/postprocess_transitions.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/nbody_Dihedrals.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/interpolate_curve.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/bonds_by_type.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/renumber_DATA_first_column.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/lttree_styles.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/raw2data.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/nbody_fix_ttree_assignments.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/ttree_matrix_stack.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/nbody_Bonds.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/remove_duplicates_nbody.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/genpoly_modify_lt.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/lttree_postprocess.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/ettree.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/__init__.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/mol22lt.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/postprocess_coeffs.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/extract_lammps_data.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/ttree_lex.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/remove_duplicate_atoms.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/amber2lt.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/charge_by_bond.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/nbody_Angles.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/pdbsort.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/nbody_Impropers.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/dump2data.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/ttree.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/lttree.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/nbody_reorder_atoms.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/nbody_by_type.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate copying moltemplate/nbody_graph_search.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenJswapIL.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenKswapIL.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/bonds_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/gaff_imp.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/__init__.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenIsortJKL.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenIswapJK.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/dihedrals_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/angles_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/impropers_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry copying moltemplate/nbody_alt_symmetry/cenJsortIKL.py -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry running egg_info writing moltemplate.egg-info/PKG-INFO writing dependency_links to moltemplate.egg-info/dependency_links.txt writing entry points to moltemplate.egg-info/entry_points.txt writing requirements to moltemplate.egg-info/requires.txt writing top-level names to moltemplate.egg-info/top_level.txt reading manifest file 'moltemplate.egg-info/SOURCES.txt' adding license file 'LICENSE.md' writing manifest file 'moltemplate.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'moltemplate.force_fields' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'moltemplate.force_fields' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'moltemplate.force_fields' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'moltemplate.force_fields' to be distributed and are already explicitly excluding 'moltemplate.force_fields' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'moltemplate.scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'moltemplate.scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'moltemplate.scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'moltemplate.scripts' to be distributed and are already explicitly excluding 'moltemplate.scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/compass_published.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/cooke_deserno_lipid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/dreiding.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/drymartini.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/gaff.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/gaff2.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/graphene.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/graphene_rectangular.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/graphite.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/loplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/loplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/loplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/martini.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/sdk.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spc_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spc_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spc_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_amber.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_dreiding.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_ice_rect16.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_ice_rect32.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_ice_rect8.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_more_comments.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/spce_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_charmm.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_charmm_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_1983_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_2004.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_2004_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_2004_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip3p_2004_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip5p_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip5p_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/tip5p_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/trappe1998.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields copying moltemplate/force_fields/watmw.lt -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields creating /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/cleanup_moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/emoltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/molc.sh -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts copying moltemplate/scripts/pdb2crds.awk -> /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts running build_scripts creating build/scripts-3.13 copying moltemplate/scripts/moltemplate.sh -> build/scripts-3.13 copying moltemplate/scripts/cleanup_moltemplate.sh -> build/scripts-3.13 copying moltemplate/scripts/molc.sh -> build/scripts-3.13 copying moltemplate/scripts/pdb2crds.awk -> build/scripts-3.13 copying moltemplate/scripts/emoltemplate.sh -> build/scripts-3.13 debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/moltemplate-2.22.5' cp -r doc/moltemplate_manual_src .pybuild cd .pybuild/moltemplate_manual_src; \ pdflatex moltemplate_manual; \ pdflatex moltemplate_manual; \ bibtex moltemplate_manual; \ bibtex moltemplate_manual; \ pdflatex moltemplate_manual; \ pdflatex moltemplate_manual This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./moltemplate_manual.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2025/01/22 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) 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(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) No file moltemplate_manual.toc. LaTeX Warning: Reference `sec:installation' on page 1 undefined on input line 6 6. LaTeX Warning: Citation `MOLTEMPLATE' on page 1 undefined on input line 72. Overfull \hbox (12.60272pt too wide) in paragraph at lines 91--111 \OT1/cmr/m/n/10.95 which can be con-verted into moltem-plate for-mat (LT for-ma t) us-ing []\OT1/cmtt/m/n/10.95 mol22lt.py[] [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map} <./author_email.png>] LaTeX Warning: Reference `sec:limitations' on page 2 undefined on input line 14 1. Overfull \hbox (2.16733pt too wide) in paragraph at lines 197--197 []\OT1/cmtt/m/n/10.95 moltemplate.sh -xyz coords.xyz -atomstyle "full" -vmd sys tem.lt LaTeX Warning: Reference `sec:ltemplify' on page 2 undefined on input line 217. LaTeX Warning: Citation `ATB' on page 2 undefined on input line 299. Overfull \hbox (1.51479pt too wide) in paragraph at lines 299--306 \OT1/cmr/m/n/10.95 The \OT1/cmr/bx/n/10.95 ATB \OT1/cmr/m/n/10.95 ser-vice [[]] men-tioned ear-lier ([]$\OT1/cmtt/m/n/10.95 https : / / atb . uq . edu . au$[] \OT1/cmr/m/n/10.95 ) is a repos- LaTeX Warning: Citation `topotools' on page 2 undefined on input line 308. LaTeX Warning: Citation `OpenBABEL' on page 2 undefined on input line 309. LaTeX Warning: Citation `VMD' on page 2 undefined on input line 312. LaTeX Warning: Citation `topotools' on page 2 undefined on input line 312. LaTeX Warning: Citation `OVITO' on page 2 undefined on input line 312. 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[3] Overfull \hbox (19.41339pt too wide) in paragraph at lines 471--471 []\OT1/cmtt/m/n/10.95 python -m venv ~/venv #(or "virtualenv venv" if using python2) Overfull \hbox (7.91602pt too wide) in paragraph at lines 496--496 []\OT1/cmtt/m/n/10.95 git clone https://github.com/jewettaij/moltemplate ~/molt emplate Overfull \hbox (30.91077pt too wide) in paragraph at lines 517--517 []\OT1/cmtt/m/n/10.95 pip3 install . # (or "pip3 install --user", or "pip" if that fails)[] Overfull \hbox (0.52628pt too wide) in paragraph at lines 520--526 []\OT1/cmr/m/n/10.95 As men-tioned ear-lier, if you are hav-ing dif-fi-culty, t ry to in-stalling moltem- [4] Overfull \hbox (25.16208pt too wide) in paragraph at lines 593--609 \OT1/cmtt/m/n/10.95 bashonubuntuonwindows / comments / 6bu1d1 / since _ we _ sh ouldnt _ edit _ files _ [5] [6] Overfull \hbox (0.32121pt too wide) in paragraph at lines 612--612 []\OT1/cmr/bx/n/14.4 Quick ref-er-ence \OT1/cmr/bx/it/14.4 (SKIP ON FIRST READ- ING) LaTeX Warning: Reference `sec:tutorial' on page 7 undefined on input line 616. (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) LaTeX Warning: Reference `sec:spce_example' on page 7 undefined on input line 6 47. LaTeX Warning: Reference `sec:2bead' on page 7 undefined on input line 647. LaTeX Warning: Reference `sec:inheritance' on page 7 undefined on input line 64 8. LaTeX Warning: Reference `sec:trappe' on page 7 undefined on input line 648. LaTeX Warning: Reference `sec:spce_example' on page 7 undefined on input line 6 54. LaTeX Warning: Reference `sec:coords_intro' on page 7 undefined on input line 6 60. LaTeX Warning: Reference `sec:xforms_table' on page 7 undefined on input line 6 60. LaTeX Warning: Reference `sec:coords_intro' on page 7 undefined on input line 6 70. LaTeX Warning: Reference `sec:arrays+xform' on page 7 undefined on input line 6 70. LaTeX Warning: Reference `sec:xforms_table' on page 7 undefined on input line 6 71. LaTeX Warning: Reference `sec:multidimensional_arrays' on page 7 undefined on i nput line 673. LaTeX Warning: Reference `sec:xform+arrays+xform' on page 7 undefined on input line 686. LaTeX Warning: Reference `sec:xform_order' on page 7 undefined on input line 68 6. Underfull \hbox (badness 7064) in paragraph at lines 683--688 []|\OT1/cmr/m/n/10.95 Apply co-or-di-nate trans-for-ma-tions ([] to LaTeX Warning: Reference `sec:random_arrays' on page 7 undefined on input line 715. LaTeX Warning: Reference `sec:random_advanced' on page 7 undefined on input lin e 715. LaTeX Warning: Reference `sec:molecule_customization' on page 7 undefined on in put line 722. LaTeX Warning: Reference `sec:molecule_customization' on page 7 undefined on in put line 729. LaTeX Warning: Reference `sec:inheritance_intro' on page 7 undefined on input l ine 750. LaTeX Warning: Reference `sec:inheritance' on page 7 undefined on input line 75 1. LaTeX Warning: Reference `sec:multiple_inheritance' on page 7 undefined on inpu t line 751. LaTeX Warning: Reference `sec:molecule_customization' on page 7 undefined on in put line 758. LaTeX Warning: Reference `sec:custom_xform' on page 7 undefined on input line 7 67. LaTeX Warning: Reference `sec:coords_intro' on page 7 undefined on input line 7 67. LaTeX Warning: Reference `sec:array_wildcards_intro' on page 7 undefined on inp ut line 776. LaTeX Warning: Reference `sec:custom_xform' on page 7 undefined on input line 7 76. LaTeX Warning: Reference `sec:delete' on page 7 undefined on input line 787. LaTeX Warning: Reference `sec:delete' on page 7 undefined on input line 795. LaTeX Warning: Reference `sec:delete_holes' on page 7 undefined on input line 7 95. Underfull \hbox (badness 10000) in paragraph at lines 792--797 []|\OT1/cmr/m/n/10.95 Delete a range of molecules spec-i-fied by Underfull \hbox (badness 1616) in paragraph at lines 792--797 []\OT1/cmr/m/n/10.95 . (This also works for mul-ti-di- LaTeX Warning: Reference `sec:write' on page 7 undefined on input line 807. LaTeX Warning: Reference `sec:variables' on page 7 undefined on input line 807. LaTeX Warning: Reference `sec:write' on page 7 undefined on input line 822. LaTeX Warning: Reference `sec:variables' on page 7 undefined on input line 822. LaTeX Warning: Reference `sec:DataIn' on page 7 undefined on input line 830. LaTeX Warning: Reference `sec:custom_categories' on page 7 undefined on input l ine 868. LaTeX Warning: Reference `sec:2beadPolymer' on page 7 undefined on input line 8 84. LaTeX Warning: Reference `sec:replace_command' on page 7 undefined on input lin e 890. Overfull \hbox (121.47046pt too wide) in alignment at lines 623--895 [] [] ignored error: Infinite glue shrinkage found in box being split [7] ignored error: Infinite glue shrinkage found in box being split [8] [9] LaTeX Warning: Reference `sec:variables' on page 10 undefined on input line 907 . Underfull \hbox (badness 10000) in paragraph at lines 907--909 LaTeX Warning: Reference `sec:2beadPolymer' on page 10 undefined on input line 982. LaTeX Warning: Reference `sec:ellipsis_mol' on page 10 undefined on input line 983. LaTeX Warning: Reference `sec:adv_variable_syntax' on page 10 undefined on inpu t line 985. LaTeX Warning: Reference `sec:vardetails' on page 10 undefined on input line 10 32. Overfull \hbox (131.64603pt too wide) in alignment at lines 909--1047 [] [] ignored error: Infinite glue shrinkage found in box being split [10] [11] LaTeX Warning: Reference `sec:coords_intro' on page 12 undefined on input line 1058. LaTeX Warning: Reference `sec:arrays+xform' on page 12 undefined on input line 1058. Underfull \hbox (badness 10000) in paragraph at lines 1058--1061 Underfull \hbox (badness 10000) in paragraph at lines 1058--1061 LaTeX Warning: Reference `sec:arrays+xform' on page 12 undefined on input line 1168. 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Underfull \hbox (badness 1418) in paragraph at lines 1387--1391 \OT1/cmr/m/n/10.95 ``bond[]coeff'', ``an-gle[]coeff'', ``di-he-dral[]coeff'', a nd ``im- Overfull \hbox (123.88596pt too wide) in alignment at lines 1203--1417 [] [] ignored error: Infinite glue shrinkage found in box being split [13] ignored error: Infinite glue shrinkage found in box being split [14] [15] Overfull \hbox (13.54758pt too wide) in paragraph at lines 1432--1454 \OT1/cmr/m/n/10.95 tackle the same steep learning-curve (and oc-ca-sional bugs) that other LAMMPS Overfull \hbox (16.26949pt too wide) in paragraph at lines 1459--1459 []\OT1/cmr/bx/n/12 Simulating a box of wa-ter us-ing moltem-plate and LAMMPS LaTeX Warning: Citation `Berendsen++StraatsmaJPhysChem1987' on page 16 undefine d on input line 1475. Overfull \hbox (53.90552pt too wide) in paragraph at lines 1494--1494 [] \OT1/cmtt/m/n/10.95 ## Atom properties and bond topology go in various "Dat a ..." sections[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1496--1496 [] \OT1/cmtt/m/n/10.95 # We selected "atom_style full". That means we use this column format:[] [16 <./single_water_LR.jpg>] Overfull \hbox (19.41339pt too wide) in paragraph at lines 1497--1497 [] \OT1/cmtt/m/n/10.95 # atomID molID atomType charge coordX coordY coordZ[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1500--1500 [] \OT1/cmtt/m/n/10.95 $atom:o $mol:w @atom:O -0.8476 0.0000000 0.00000 0 0.00000[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1501--1501 [] \OT1/cmtt/m/n/10.95 $atom:h1 $mol:w @atom:H 0.4238 0.8164904 0.57735 90 0.00000[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 1502--1502 [] \OT1/cmtt/m/n/10.95 $atom:h2 $mol:w @atom:H 0.4238 -0.8164904 0.5773 590 0.00000[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 1505--1505 [] \OT1/cmtt/m/n/10.95 # Variables beginning with $ or @ will be replaced by n umbers LAMMPS will[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 1506--1506 [] \OT1/cmtt/m/n/10.95 # eventually read. Each of the three atoms" will be as signed unique[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1507--1507 [] \OT1/cmtt/m/n/10.95 # atomIDs (denoted here by "$atom:o", "$atom:h1", "$ato m:h2"), even if[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 1508--1508 [] \OT1/cmtt/m/n/10.95 # they belong to different molecules. However, the ato m types[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 1509--1509 [] \OT1/cmtt/m/n/10.95 # (denoted "@atom:O", "@atom:H") are shared for atoms i n all molecules.[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1510--1510 [] \OT1/cmtt/m/n/10.95 # All 3 atoms share same molID number (represeted here by "$mol:w")[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1511--1511 [] \OT1/cmtt/m/n/10.95 # however that number is different for different water molecules.[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1530--1530 [] \OT1/cmtt/m/n/10.95 # --- Force-field parameters go in the "In Settings" se ction: ---[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1534--1534 [] \OT1/cmtt/m/n/10.95 # atomType1 atomType2 parameter-list (epsil on, sigma)[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 1537--1537 [] \OT1/cmtt/m/n/10.95 # (mixing rules determine interactions between types @atom:O and @atom:H)[] [17] Overfull \hbox (99.89502pt too wide) in paragraph at lines 1545--1545 [] \OT1/cmtt/m/n/10.95 # Group definitions and constraints can also go in th e "In Settings" section[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 1547--1547 [] \OT1/cmtt/m/n/10.95 fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @ang le:HOH[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1548--1548 [] \OT1/cmtt/m/n/10.95 # (lammps quirk: Remember to "unfix fSHAKE" during mi nimization.)[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1551--1551 [] \OT1/cmtt/m/n/10.95 # LAMMPS supports a large number of force-field styles. We must select[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 1552--1552 [] \OT1/cmtt/m/n/10.95 # which ones we need. This information belongs in the " In Init" section.[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 1555--1555 [] \OT1/cmtt/m/n/10.95 units real # angstroms, kCal/m ole, Daltons, Kelvin[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 1556--1556 [] \OT1/cmtt/m/n/10.95 atom_style full # select column for mat for Atoms section[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 1557--1557 [] \OT1/cmtt/m/n/10.95 pair_style lj/charmm/coul/long 9.0 10.0 10 # param s needed: epsilon sigma[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1558--1558 [] \OT1/cmtt/m/n/10.95 bond_style harmonic # parameters needed : k_bond, r0[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 1559--1559 [] \OT1/cmtt/m/n/10.95 angle_style harmonic # parameters needed : k_theta, theta0[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 1560--1560 [] \OT1/cmtt/m/n/10.95 kspace_style pppm 0.0001 # long-range electr ostatics sum method[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 1561--1561 [] \OT1/cmtt/m/n/10.95 pair_modify mix arithmetic # using Lorenz-Bert helot mixing rules[] LaTeX Warning: Reference `sec:variables' on page 18 undefined on input line 156 8. Overfull \hbox (14.12546pt too wide) in paragraph at lines 1575--1576 \OT1/cmr/m/n/10.95 You can now use ``moltem-plate.sh'' to cre-ate sim-u-la-tion in-put files for LAMMPS LaTeX Warning: Reference `sec:pbc' on page 18 undefined on input line 1598. LaTeX Warning: Reference `sec:coordinates' on page 18 undefined on input line 1 609. [18] LaTeX Warning: Reference `sec:coordinates' on page 19 undefined on input line 1 637. LaTeX Warning: Reference `sec:coordinates' on page 19 undefined on input line 1 648. LaTeX Warning: Reference `sec:xforms_table' on page 19 undefined on input line 1651. Overfull \hbox (10.06793pt too wide) in paragraph at lines 1656--1659 \OT1/cmr/m/n/10.95 spec-ify the di-men-sions of the sim-u-la-tion bound-ary us- ing the ``write[]once(``Data [19] LaTeX Warning: Reference `fig:spce_x_1000' on page 20 undefined on input line 1 676. LaTeX Warning: Reference `sec:vmd_topotools' on page 20 undefined on input line 1700. LaTeX Warning: Reference `sec:vmd_advanced' on page 20 undefined on input line 1700. LaTeX Warning: Reference `sec:vmd_topotools' on page 20 undefined on input line 1700. LaTeX Warning: Reference `sec:vmd_advanced' on page 20 undefined on input line 1700. [20 <./waterSPCEx1000_LR.jpg> <./waterSPCEx1000_t=25_LR.jpg>] LaTeX Warning: Reference `sec:vmd_trajectory' on page 21 undefined on input lin e 1767. LaTeX Warning: Reference `sec:vmd_advanced' on page 21 undefined on input line 1774. LaTeX Warning: Citation `OVITO' on page 21 undefined on input line 1783. Overfull \hbox (33.74133pt too wide) in paragraph at lines 1799--1809 []\OT1/cmr/m/n/10.95 Moltemplate will cre-ate the fol-low-ing files: ``sys-tem. data'', ``run.in.EXAMPLE'', [21] LaTeX Warning: Citation `VMD' on page 22 undefined on input line 2007. Overfull \hbox (5.23363pt too wide) in paragraph at lines 2004--2011 \OT1/cmr/m/n/10.95 which can vi-su-al-ize the sys-tem. If you have saved your t ra-jec-tory in LAMMPS [22] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2012--2012 []\OT1/cmtt/m/n/10.95 dump 1 all custom 1000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz Overfull \hbox (29.2559pt too wide) in paragraph at lines 2019--2022 []\OT1/cmr/m/n/10.95 a) Start VMD From the menu in the upper-left, se-lect \OT1 /cmr/bx/n/10.95 File$\OMS/cmsy/m/n/10.95 !$[] LaTeX Warning: Reference `sec:vmd_advanced' on page 23 undefined on input line 2033. LaTeX Warning: Reference `sec:instance_variables' on page 23 undefined on input line 2075. LaTeX Warning: Reference `sec:DataIn' on page 23 undefined on input line 2091. [23] LaTeX Warning: Reference `sec:manual_assignment' on page 24 undefined on input line 2117. LaTeX Warning: Reference `sec:custom_categories' on page 24 undefined on input line 2117. Overfull \hbox (24.8004pt too wide) in paragraph at lines 2168--2175 \OT1/cmr/m/n/10.95 In the ex-am-ple above, the \TS1/cmr/m/n/10.95 $ \OT1/cmr/m/ n/10.95 vari-ables have full-names like ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.9 5 atom:wat[8][3][7]/h1'', [24] LaTeX Warning: Reference `sec:2bead' on page 25 undefined on input line 2214. LaTeX Warning: Reference `sec:paths' on page 25 undefined on input line 2237. LaTeX Warning: Reference `sec:adv_variable_syntax' on page 25 undefined on inpu t line 2237. LaTeX Warning: Reference `sec:spce_example' on page 25 undefined on input line 2257. LaTeX Warning: Reference `sec:custom_data' on page 25 undefined on input line 2 271. [25] LaTeX Warning: Reference `sec:aux_files' on page 26 undefined on input line 228 4. [26] Overfull \hbox (0.77374pt too wide) in paragraph at lines 2342--2342 []\OT1/cmr/bx/it/12 (Advanced) \OT1/cmr/bx/n/12 Us-ing moltem-plate to gen-er-a te aux-il-iary files Overfull \hbox (36.65945pt too wide) in paragraph at lines 2353--2353 [] \OT1/cmtt/m/n/10.95 mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.33333 7.04956 0. 602224 4 0 0[] LaTeX Warning: Reference `sec:wildcard_bug' on page 27 undefined on input line 2400. [27] [28] LaTeX Warning: Reference `sec:2bead' on page 29 undefined on input line 2451. LaTeX Warning: Reference `sec:multidimensional_arrays' on page 29 undefined on input line 2451. LaTeX Warning: Reference `sec:vmd_topotools' on page 29 undefined on input line 2451. LaTeX Warning: Reference `sec:vmd_advanced' on page 29 undefined on input line 2451. LaTeX Warning: Reference `sec:2bead' on page 29 undefined on input line 2451. LaTeX Warning: Reference `sec:multidimensional_arrays' on page 29 undefined on input line 2451. LaTeX Warning: Reference `sec:vmd_topotools' on page 29 undefined on input line 2451. LaTeX Warning: Reference `sec:vmd_advanced' on page 29 undefined on input line 2451. [29 <./2bead_monomer.jpg> <./2bead_polymer.jpg> <./2bead_polymers_nopbc_t=0_LR. jpg> <./2bead_polymers_t=100ps_LR.jpg>] Overfull \hbox (0.3771pt too wide) in paragraph at lines 2460--2461 \OT1/cmr/m/n/10.95 Consider the fol-low-ing sim-ple 2-atom dumbell-shaped molel ule (``Monomer'') Overfull \hbox (7.91602pt too wide) in paragraph at lines 2470--2470 [] \OT1/cmtt/m/n/10.95 $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0. 0000000[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 2471--2471 [] \OT1/cmtt/m/n/10.95 $atom:r $mol:... @atom:R 0.0 0.000 4.4000 0. 0000000[] LaTeX Warning: Reference `sec:ellipsis_mol' on page 30 undefined on input line 2488. LaTeX Warning: Reference `sec:nbody_by_type_intro' on page 30 undefined on inpu t line 2488. Overfull \hbox (53.90552pt too wide) in paragraph at lines 2505--2505 [] \OT1/cmtt/m/n/10.95 create_var {$mol} #(force all Monomers to share the sa me molecule-ID)[] [30] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2519--2519 [] \OT1/cmtt/m/n/10.95 $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom :mon2/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2520--2520 [] \OT1/cmtt/m/n/10.95 $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom :mon3/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2521--2521 [] \OT1/cmtt/m/n/10.95 $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom :mon4/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2522--2522 [] \OT1/cmtt/m/n/10.95 $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom :mon5/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2523--2523 [] \OT1/cmtt/m/n/10.95 $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom :mon6/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2524--2524 [] \OT1/cmtt/m/n/10.95 $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom :mon7/ca[] LaTeX Warning: Reference `sec:xforms_table' on page 31 undefined on input line 2539. LaTeX Warning: Reference `sec:arrays' on page 31 undefined on input line 2543. LaTeX Warning: Reference `sec:random_arrays' on page 31 undefined on input line 2543. [31] Overfull \hbox (42.40814pt too wide) in paragraph at lines 2631--2631 [] \OT1/cmtt/m/n/10.95 # Force-field parameters ("coeffs") go in the "In Setti ngs" section:[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 2638--2638 [] \OT1/cmtt/m/n/10.95 # (Interactions between different atoms are determine d by mixing rules.)[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2651--2651 [] \OT1/cmtt/m/n/10.95 # Although the simple "Monomer" object we defined above has only[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2652--2652 [] \OT1/cmtt/m/n/10.95 # two atoms, later on, we will create molecules with ma ny bonds.[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 2653--2653 [] \OT1/cmtt/m/n/10.95 # By convention, in this file we keep track of all of t he possible[] [32] Overfull \hbox (76.90027pt too wide) in paragraph at lines 2656--2656 [] \OT1/cmtt/m/n/10.95 # Rules for determining 3-body (angle) interactions by atom and bond type:[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2657--2657 [] \OT1/cmtt/m/n/10.95 # angle-type atomType1 atomType2 atomType3 bondTyp e1 bondType2[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2660--2660 [] \OT1/cmtt/m/n/10.95 @angle:Backbone @atom:CA @atom:CA @atom:CA @bond :* @bond:*[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2661--2661 [] \OT1/cmtt/m/n/10.95 @angle:Sidechain @atom:CA @atom:CA @atom:R @bond :* @bond:*[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 2674--2674 [] \OT1/cmtt/m/n/10.95 # 4-body interactions in this example are listed by ato m type and (optionally)[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2675--2675 [] \OT1/cmtt/m/n/10.95 # by bond type. (You can use wildcards * to accept all bond types.)[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 2677--2677 [] \OT1/cmtt/m/n/10.95 # dihedralType atmType1 atmType2 atmType3 atmType4 bo ndType1 bType2 bType3[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 2679--2679 [] \OT1/cmtt/m/n/10.95 @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @ bond:* @bond:* @bond:*[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 2680--2680 [] \OT1/cmtt/m/n/10.95 @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @ bond:* @bond:* @bond:*[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2699--2699 [] \OT1/cmtt/m/n/10.95 # -- (Changing these styles will change the formulas above) --[] [33] LaTeX Warning: Reference `sec:nbody_by_type_custom' on page 34 undefined on inp ut line 2720. LaTeX Warning: Reference `sec:regex' on page 34 undefined on input line 2759. [34] Overfull \hbox (9.77596pt too wide) in paragraph at lines 2782--2789 \OT1/cmr/m/n/10.95 Notice that we did not spec-ify the ``@bond:SideChain'' and ``@bond:Backbone'' Overfull \hbox (76.60141pt too wide) in paragraph at lines 2795--2808 \OT1/cmr/m/n/10.95 names can be quite long and dif-fi-cult to type (such as ``@ atom:h1h[]ph1h[]bh1h[]ah1[]dh1[]ih1''). [35] Overfull \hbox (14.1924pt too wide) in paragraph at lines 2873--2874 \OT1/cmr/m/n/10.95 For de-tails, see the ``cen-JswapIL.py'' file (lo-cated in t he ``nbody[]alt[]symmetry/'' [36] [37] Overfull \hbox (19.81343pt too wide) in paragraph at lines 2963--2973 \OT1/cmr/m/n/10.95 The first line tells moltem-plate that any bond be-tween ato ms of type ``@atom:h1'' [38] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3058--3058 [] \OT1/cmtt/m/n/10.95 # Note: This will not overwrite the preexisting "ForceF ield" object.[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3059--3059 [] \OT1/cmtt/m/n/10.95 # (Instead, it augments the "ForceField" object d efined earlier.)[] Overfull \hbox (2.11093pt too wide) in paragraph at lines 3074--3079 \OT1/cmr/m/n/10.95 ``@atom:R'', and ``@atom:CB'', since they all be-long to the same ``[]'' Overfull \hbox (59.6542pt too wide) in paragraph at lines 3084--3084 [] \OT1/cmtt/m/n/10.95 # Here you can refer to @atoms, @bonds, etc... defined in either file:[] [39] LaTeX Warning: Reference `sec:full_names' on page 40 undefined on input line 31 11. LaTeX Warning: Reference `sec:coords_intro' on page 40 undefined on input line 3122. LaTeX Warning: Reference `sec:multidimensional_arrays' on page 40 undefined on input line 3122. LaTeX Warning: Reference `sec:2beadPolymer' on page 40 undefined on input line 3125. Overfull \hbox (94.14633pt too wide) in paragraph at lines 3139--3139 [] \OT1/cmtt/m/n/10.95 $bond:backbone1 @bond:Backbone $atom:monomers[0]/ca $atom:monomers[1]/ca[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3140--3140 [] \OT1/cmtt/m/n/10.95 $bond:backbone2 @bond:Backbone $atom:monomers[1]/ca $atom:monomers[2]/ca[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3141--3141 [] \OT1/cmtt/m/n/10.95 $bond:backbone3 @bond:Backbone $atom:monomers[2]/ca $atom:monomers[3]/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 3142--3142 [] \OT1/cmtt/m/n/10.95 : : : :[] LaTeX Warning: Reference `sec:2beadPolymer' on page 40 undefined on input line 3154. Overfull \hbox (9.44891pt too wide) in paragraph at lines 3159--3163 \OT1/cmr/m/n/10.95 This will cre-ate 7 molecules. The co-or-di-nates of the fir st molecule \OT1/cmr/m/it/10.95 monomers[0] [40] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3169--3169 [] \OT1/cmtt/m/n/10.95 monomers = new Monomer.scale(1.5) [7].rot(180, 1,0,0).m ove(3.2,0,0) Overfull \hbox (25.16208pt too wide) in paragraph at lines 3185--3185 [] \OT1/cmtt/m/n/10.95 # "monomers[0]", "monomers[1]", "monomers[2]", ... "mon omers[6]".[] LaTeX Warning: Reference `sec:random_exact' on page 41 undefined on input line 3244. LaTeX Warning: Reference `sec:random_exact' on page 41 undefined on input line 3244. LaTeX Warning: Reference `fig:random_heteropolymer' on page 41 undefined on inp ut line 3250. [41] Overfull \hbox (7.91602pt too wide) in paragraph at lines 3255--3255 [] \OT1/cmtt/m/n/10.95 monomers = new random([Monomer, Monomer3], [0.6, 0.4], 123456)[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3260--3260 [] \OT1/cmtt/m/n/10.95 $bond:bb1 @bond:Backbone $atom:monomers[0]/ca $atom:m onomers[1]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3261--3261 [] \OT1/cmtt/m/n/10.95 $bond:bb2 @bond:Backbone $atom:monomers[1]/ca $atom:m onomers[2]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3262--3262 [] \OT1/cmtt/m/n/10.95 $bond:bb3 @bond:Backbone $atom:monomers[2]/ca $atom:m onomers[3]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3263--3263 [] \OT1/cmtt/m/n/10.95 $bond:bb4 @bond:Backbone $atom:monomers[3]/ca $atom:m onomers[4]/ca[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3268--3268 [] \OT1/cmtt/m/n/10.95 $bond:bb50 @bond:Backbone $atom:monomers[48]/ca $atom :monomers[49]/ca Overfull \hbox (19.41339pt too wide) in paragraph at lines 3270--3270 [] \OT1/cmtt/m/n/10.95 #(Note: Both the "Monomer" and "Monomer3" subunits cont ain atoms[] LaTeX Warning: Reference `sec:random_advanced' on page 42 undefined on input li ne 3276. LaTeX Warning: Reference `fig:random_heteropolymer' on page 42 undefined on inp ut line 3296. [42 <./random_2bead.jpg> <./random_3bead.jpg> <./random_heteropolymer.jpg>] LaTeX Warning: Reference `sec:random_multidim_exact' on page 43 undefined on in put line 3311. Overfull \hbox (21.21399pt too wide) in paragraph at lines 3324--3328 []\OT1/cmr/m/it/10.95 Note: \OT1/cmr/m/n/10.95 Al-though this ex-am-ple, there are only two monomer types (``Monomer'' LaTeX Warning: Reference `sec:random_vacancies' on page 43 undefined on input l ine 3337. Overfull \hbox (31.28319pt too wide) in paragraph at lines 3339--3343 []\OT1/cmr/m/it/10.95 Note: \OT1/cmr/m/n/10.95 Once a molecule con-tain-ing ran -dom monomers is de-fined, ([] [43] Overfull \hbox (30.91077pt too wide) in paragraph at lines 3409--3409 [] \OT1/cmtt/m/n/10.95 monomers[1-48] = new random([Monomer, Monomer3], [30, 1 8], 123456)[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3412--3412 [] \OT1/cmtt/m/n/10.95 # It's a good idea to move these monomers to keep them from overlapping[] [44] LaTeX Warning: Reference `fig:2bead_polymer' on page 45 undefined on input line 3452. Overfull \hbox (53.90552pt too wide) in paragraph at lines 3460--3460 []\OT1/cmtt/m/n/10.95 delete molecules[0-1][1][1-2] # (shorthand for delete mol ecules[0][1][1] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3461--3461 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[0][1][2][] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3462--3462 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[1][1][1][] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3463--3463 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[1][1][2])[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 3469--3469 []\OT1/cmtt/m/n/10.95 # ...and move them back to the location of the vacancies we created[] LaTeX Warning: Reference `fig:random_bilayer' on page 45 undefined on input lin e 3480. Overfull \hbox (4.88002pt too wide) in paragraph at lines 3478--3484 \OT1/cmr/m/n/10.95 You can use [] to fill space with a ran-dom mix-ture of mole cules. Overfull \hbox (53.90552pt too wide) in paragraph at lines 3485--3485 []\OT1/cmtt/m/n/10.95 import "lipids" # def ine DPPC & DLPC Overfull \hbox (48.15683pt too wide) in paragraph at lines 3486--3486 []\OT1/cmtt/m/n/10.95 lipids = new random([DPPC,DLPC], [0.5,0.5], 123) # "12 3"=random_seed[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3487--3487 [] \OT1/cmtt/m/n/10.95 [19].move(7.5, 0, 0) # lat tice spacing 7.5[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 3488--3488 [] \OT1/cmtt/m/n/10.95 [22].move(3.75, 6.49519, 0) # hex agonal lattice[] [45] Overfull \hbox (19.41339pt too wide) in paragraph at lines 3489--3489 [] \OT1/cmtt/m/n/10.95 [2].rot(180, 1, 0, 0) # 2 m onolayers[] LaTeX Warning: Reference `sec:random_advanced' on page 46 undefined on input li ne 3509. LaTeX Warning: Reference `sec:random_vacancies' on page 46 undefined on input l ine 3509. LaTeX Warning: Reference `sec:random_advanced' on page 46 undefined on input li ne 3509. LaTeX Warning: Reference `sec:random_vacancies' on page 46 undefined on input l ine 3509. Overfull \hbox (94.14633pt too wide) in paragraph at lines 3516--3516 []\OT1/cmtt/m/n/10.95 lipids = new random([DPPC, ,DLPC], [0.35,0.3,0.35], 123) # 2nd element is blank LaTeX Warning: Reference `fig:random_bilayer' on page 46 undefined on input lin e 3521. LaTeX Warning: Reference `fig:delete_holes' on page 46 undefined on input line 3554. [46 <./lipid_bilayer_mixture.jpg> <./lipid_bilayer_vacancies.jpg>] LaTeX Warning: Reference `fig:delete_holes' on page 47 undefined on input line 3570. LaTeX Warning: Reference `sec:xform_after_instance' on page 47 undefined on inp ut line 3597. LaTeX Warning: Reference `sec:delete_atoms_bonds' on page 47 undefined on input line 3603. LaTeX Warning: Reference `sec:custom_atom' on page 47 undefined on input line 3 604. LaTeX Warning: Reference `sec:custom_bond' on page 47 undefined on input line 3 605. LaTeX Warning: Reference `sec:adding_atoms_bonds' on page 47 undefined on input line 3606. [47 <./delete_holes1.jpg>] LaTeX Warning: Reference `fig:mol_complex' on page 48 undefined on input line 3 625. LaTeX Warning: Reference `sec:2bead' on page 48 undefined on input line 3637. Overfull \hbox (33.65005pt too wide) in paragraph at lines 3640--3642 []\OT1/cmr/m/n/10.95 We can sub-squently cus-tomize the po-si-tion of the 3rd m onomer (``monomers[2]'') LaTeX Warning: Reference `sec:array_wildcards_intro' on page 48 undefined on in put line 3661. LaTeX Warning: Reference `sec:molecule_customization' on page 48 undefined on i nput line 3665. Overfull \hbox (128.63846pt too wide) in paragraph at lines 3678--3678 [] \OT1/cmtt/m/n/10.95 $atom:mol_complex/polymers[0]/monomers[2]/ca $mol:mol_c omplex @atom:R 0 6.4 8.2 0.6[] Overfull \hbox (190.20093pt too wide) in paragraph at lines 3681--3691 \OT1/cmr/m/n/10.95 This is a sit-u-a-tion where we must use the \OT1/cmr/m/it/1 0.95 full \OT1/cmr/m/n/10.95 name of the atom (``\TS1/cmr/m/n/10.95 $\OT1/cmr/m /n/10.95 atom:mol[]complex/polymers[0]/monomers[2]/ca'') [48] Overfull \hbox (25.16208pt too wide) in paragraph at lines 3695--3695 [] \OT1/cmtt/m/n/10.95 $atom:polymers[0]/monomers[2]/ca $mol:... @atom:R 0 6 .4 8.2 0.6[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3714--3714 [] \OT1/cmtt/m/n/10.95 $bond:mol_complex/polymers[0]/backbone3 @bond:ForceFiel d/LongBond &[] LaTeX Warning: Reference `sec:delete' on page 49 undefined on input line 3727. Overfull \hbox (30.91077pt too wide) in paragraph at lines 3736--3736 []\OT1/cmtt/m/n/10.95 # Note: This will augment the "ForceField" object, not ov erwrite it: LaTeX Warning: Reference `sec:2beadPolymer' on page 49 undefined on input line 3752. LaTeX Warning: Reference `sec:delete' on page 49 undefined on input line 3755. [49] Overfull \hbox (65.4029pt too wide) in paragraph at lines 3774--3774 []\OT1/cmtt/m/n/10.95 delete mol_complex/polymers[1]/monomers[3]/ca #<-- dele tes the "ca" atom Overfull \hbox (65.4029pt too wide) in paragraph at lines 3775--3775 []\OT1/cmtt/m/n/10.95 delete mol_complex/polymers[1]/monomers[4]/cr #<-- dele tes the "cr" bond[] LaTeX Warning: Reference `sec:array_wildcards_intro' on page 50 undefined on in put line 3799. LaTeX Warning: Reference `sec:vmd_topotools' on page 50 undefined on input line 3818. LaTeX Warning: Reference `sec:vmd_advanced' on page 50 undefined on input line 3818. [50] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3865--3865 []\OT1/cmtt/m/n/10.95 MolecularComplex0 = MolecularComplex.move(-9.6,-6.2, 0).s cale(0.3125) Overfull \hbox (25.16208pt too wide) in paragraph at lines 3882--3882 []\OT1/cmtt/m/n/10.95 # Add some new atoms connecting the two polymers in the m ol_complex[] LaTeX Warning: Reference `fig:mol_complex' on page 51 undefined on input line 3 905. LaTeX Warning: Reference `sec:2beadPolymer' on page 51 undefined on input line 3924. LaTeX Warning: Reference `sec:2beadPolymer' on page 51 undefined on input line 3924. Overfull \hbox (2.00154pt too wide) in paragraph at lines 3936--3937 []\OT1/cmr/m/it/10.95 Note: These co-or-di-nate trans-for-ma-tions will be ap-p lied \OT1/cmr/bx/it/10.95 af-ter \OT1/cmr/m/it/10.95 the molecule [51] LaTeX Warning: Reference `sec:inheritance' on page 52 undefined on input line 3 947. LaTeX Warning: Reference `sec:inheritance' on page 52 undefined on input line 3 954. LaTeX Warning: Reference `sec:inheritance_vs_object_composition' on page 52 und efined on input line 3955. LaTeX Warning: Reference `sec:inheritance' on page 52 undefined on input line 3 976. LaTeX Warning: Reference `sec:force_fields' on page 52 undefined on input line 3976. LaTeX Warning: Reference `sec:spce_example' on page 52 undefined on input line 3991. [52 <./mol_complex_LR.jpg> <./mol_complex+mol_complex0_transparent_LR.jpg>] Overfull \hbox (2.16733pt too wide) in paragraph at lines 4031--4031 [] \OT1/cmtt/m/n/10.95 $atom:o $mol:w @atom:O -0.8476 0.0000000 0.00000 0. 000000[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4032--4032 [] \OT1/cmtt/m/n/10.95 $atom:h1 $mol:w @atom:H 0.4238 0.8164904 0.00000 0 .5773590[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4033--4033 [] \OT1/cmtt/m/n/10.95 $atom:h2 $mol:w @atom:H 0.4238 -0.8164904 0.00000 0 .5773590[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4044--4044 [] \OT1/cmtt/m/n/10.95 # atomTypeI atomTypeJ pair-style-name p arameter-list[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4046--4046 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:O @atom:O lj/charmm/coul/long 0 .1553 3.166[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4047--4047 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:H @atom:H lj/charmm/coul/long 0 .0 2.058[] [53] Overfull \hbox (2.16733pt too wide) in paragraph at lines 4076--4076 [] \OT1/cmtt/m/n/10.95 fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @ang le:HOH[] LaTeX Warning: Reference `sec:spce_example' on page 54 undefined on input line 4084. Overfull \hbox (25.39783pt too wide) in paragraph at lines 4082--4085 \OT1/cmr/m/n/10.95 There are two dif-fer-ences be-tween this molecule def-i-ni- tion and the ``spce[]simple.lt'' LaTeX Warning: Reference `sec:overriding_styles' on page 54 undefined on input line 4109. [54] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4172--4172 [] \OT1/cmtt/m/n/10.95 pair_style hybrid lj/charmm/coul/long 9 10 10 table spl ine 1000[] Overfull \hbox (11.69077pt too wide) in paragraph at lines 4187--4187 [][]\OT1/cmr/bx/n/10.95 Warning: Force-field pa-ram-e-ters be-long in ``In Set- tings'', not ``Data'' [55] LaTeX Warning: Reference `sec:butane' on page 56 undefined on input line 4241. Overfull \hbox (30.91077pt too wide) in paragraph at lines 4261--4261 [] \OT1/cmtt/m/n/10.95 # AtomID MolID('.'=this) AtomType charge coordX coor dY coordZ[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4263--4263 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.000000 000 1.0000000[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4264--4264 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.951056 516 0.3090170[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4265--4265 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.587785 252 -0.809017[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 4266--4266 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 -0.58778 5252 -0.809017[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 4267--4267 [] \OT1/cmtt/m/n/10.95 $atom:c5 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 -0.95105 6516 0.3090170[] LaTeX Warning: Reference `sec:inheritance' on page 56 undefined on input line 4 283. Overfull \hbox (36.65945pt too wide) in paragraph at lines 4287--4287 []\OT1/cmtt/m/n/10.95 # A cubic lattice of 125 cyclopentane molecules (12-angst rom spacing) [56] Overfull \hbox (65.4029pt too wide) in paragraph at lines 4288--4288 []\OT1/cmtt/m/n/10.95 mols = new Cyclopentane [5].move(0,0,12) [5].move(0,12,0) [5].move(12,0,0)[] LaTeX Warning: Citation `TraPPE' on page 57 undefined on input line 4295. LaTeX Warning: Reference `sec:butane' on page 57 undefined on input line 4304. Overfull \hbox (42.40814pt too wide) in paragraph at lines 4319--4319 [] \OT1/cmtt/m/n/10.95 dihedral_coeff @dihedral:CCCC opls 1.411036 -0.271016 3.145034 0.0[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 4320--4320 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 4321--4321 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4322--4322 [] \OT1/cmtt/m/n/10.95 # (Interactions between different atom types use mixi ng rules.)[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 4329--4329 [] \OT1/cmtt/m/n/10.95 @dihedral:CCCC @atom:C* @atom:C* @atom:C* @atom:C* @bo nd:CC @bond:CC @bond:CC[] [57] LaTeX Warning: Reference `sec:butane' on page 58 undefined on input line 4375. LaTeX Warning: Reference `sec:trappe' on page 58 undefined on input line 4383. Overfull \hbox (30.91077pt too wide) in paragraph at lines 4395--4395 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:bt @atom:TraPPE/CH3 0.0 0.419372 0.00 0 -1.937329[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4396--4396 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:bt @atom:TraPPE/CH2 0.0 -0.419372 0.0 00 -0.645776[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4397--4397 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:bt @atom:TraPPE/CH2 0.0 0.419372 0.00 0 0.645776[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4398--4398 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:bt @atom:TraPPE/CH3 0.0 -0.419372 0.0 000 1.937329[] LaTeX Warning: Reference `sec:inheritance' on page 58 undefined on input line 4 419. [58] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4433--4433 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:bt @atom:../CH3 0.0 0.419372 0.000 -1.937329[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4434--4434 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:bt @atom:../CH2 0.0 -0.419372 0.000 -0.645776[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4435--4435 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:bt @atom:../CH2 0.0 0.419372 0.000 0.645776[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4436--4436 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:bt @atom:../CH3 0.0 -0.419372 0.000 0 1.937329[] LaTeX Warning: Reference `sec:inheritance' on page 59 undefined on input line 4 448. Overfull \hbox (6.15454pt too wide) in paragraph at lines 4448--4449 \OT1/cmr/bx/it/10.95 NOTE: Again, al-though the ``nest-ing'' method ex-plained here works, LaTeX Warning: Reference `sec:variable_scope' on page 59 undefined on input lin e 4459. LaTeX Warning: Reference `sec:inheritance' on page 59 undefined on input line 4 483. LaTeX Warning: Reference `sec:multiple_inheritance' on page 59 undefined on inp ut line 4483. [59] LaTeX Warning: Reference `sec:spce_example' on page 60 undefined on input line 4522. LaTeX Warning: Reference `sec:2bead' on page 60 undefined on input line 4536. LaTeX Warning: Reference `sec:paths' on page 60 undefined on input line 4537. LaTeX Warning: Reference `sec:adv_variable_syntax' on page 60 undefined on inpu t line 4538. [60] Overfull \hbox (19.81343pt too wide) in paragraph at lines 4615--4625 \OT1/cmr/m/n/10.95 atom type ``@atom:CH3'' in-stead of ``@atom:TraPPE/CH3'', or ``@atom:../CH3'' LaTeX Warning: Reference `sec:extending_a_force_field' on page 61 undefined on input line 4650. Overfull \hbox (23.57642pt too wide) in paragraph at lines 4655--4662 \OT1/cmr/m/n/10.95 If two molecules are re-lated to each other this way: [], [61] [62] [63] LaTeX Warning: Reference `sec:nbody_by_type_utility' on page 64 undefined on in put line 4948. Overfull \hbox (40.92256pt too wide) in paragraph at lines 4955--4962 []\OT1/cmr/m/n/10.95 , [], or [] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4967--4967 [] \OT1/cmtt/m/n/10.95 @angle:CCCsaturated @atom:C @atom:C @atom:C @bond:SAT @bond:SAT[] Overfull \hbox (54.72884pt too wide) in paragraph at lines 4973--4978 []\OT1/cmr/m/n/10.95 The first line will gen-er-ate a 3-body an-gle in-ter-ac-t ion (of type []) Overfull \hbox (31.27754pt too wide) in paragraph at lines 4980--4988 []\OT1/cmr/m/n/10.95 The sec-ond line will gen-er-ate a 3-body in-ter-ac-tion o f type [] Overfull \hbox (34.34967pt too wide) in paragraph at lines 4990--4995 []\OT1/cmr/m/n/10.95 The third line will gen-er-ate a 3-body in-ter-ac-tion of type [] [64] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5089--5089 []\OT1/cmtt/m/n/10.95 ltemplify.py -name MoleculeName -mol MolID INPUT_SCRIPT D ATA_FILE > FILE.lt LaTeX Warning: Reference `sec:ltemplify_args_table' on page 65 undefined on inp ut line 5098. LaTeX Warning: Reference `sec:ltemplify_examples' on page 65 undefined on input line 5102. Overfull \hbox (8.73274pt too wide) in paragraph at lines 5102--5102 [][]\OT1/cmr/bx/n/10.95 First time read-ers should prob-a-bly skip to the ex-am -ples in section[]. [65] [66] Overfull \hbox (69.51059pt too wide) in paragraph at lines 5127--5232 [] LaTeX Warning: Reference `sec:ltemplify_examples' on page 67 undefined on input line 5235. [67] LaTeX Warning: Reference `sec:ltemplify_limitations' on page 68 undefined on in put line 5262. Overfull \hbox (6.57567pt too wide) in paragraph at lines 5291--5295 \OT1/cmr/m/it/10.95 However, \OT1/cmr/m/n/10.95 ltem-plify.py uses com-ments in the ``Masses'' sec-tion of the LAMMPS [68] Overfull \hbox (26.77591pt too wide) in paragraph at lines 5344--5353 []\OT1/cmr/m/n/10.95 In this ex-am-ple, bonds of type 1 and 2 will be re-ferred to as ``@bond:CCethane'' [69] Overfull \hbox (1.40111pt too wide) in paragraph at lines 5370--5378 \OT1/cmr/m/n/10.95 PASS''), con-tain rules for gen-er-at-ing these in-ter-ac-ti ons au-to-mat-i-cally. Hence, [70] LaTeX Warning: Reference `sec:ltemplify_examples_force_fields' on page 71 undef ined on input line 5449. LaTeX Warning: Reference `sec:ltemplify_fix_group' on page 71 undefined on inpu t line 5479. Overfull \hbox (19.41339pt too wide) in paragraph at lines 5496--5496 []\OT1/cmtt/m/n/10.95 ltemplify.py -name Ethane -molid "1" FILE.in FILE.data > ethane.lt [71] Overfull \hbox (30.91077pt too wide) in paragraph at lines 5566--5566 []\OT1/cmtt/m/n/10.95 ltemplify.py -name EntireSystem FILE.in FILE.data > entir e_system.lt [72] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5593--5593 []\OT1/cmtt/m/n/10.95 # This example creates a new file, "ethane.lt", which wil l contain the Overfull \hbox (30.91077pt too wide) in paragraph at lines 5594--5594 []\OT1/cmtt/m/n/10.95 # instructions for building a "Ethane" molecule using "GA FF2". First[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5595--5595 []\OT1/cmtt/m/n/10.95 # specify which file contains the definition of the "GAFF 2" force field:[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5599--5599 []\OT1/cmtt/m/n/10.95 # Then use ltemplify.py to extract information from FILE. in, FILE.data[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 5603--5603 [] \OT1/cmtt/m/n/10.95 -ignore-angles -ignore-bond-types -ignore-co effs \[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 5606--5606 []\OT1/cmtt/m/n/10.95 # Note: if you want to build a simulation containing thes e molecules,[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5607--5607 []\OT1/cmtt/m/n/10.95 # you will have to create a "system.lt" file which refers to "ethane.lt"[] LaTeX Warning: Reference `sec:manual_assignment' on page 73 undefined on input line 5696. [73] LaTeX Warning: Reference `sec:limitations' on page 74 undefined on input line 5 705. [74] LaTeX Warning: Reference `sec:variables' on page 75 undefined on input line 581 0. LaTeX Warning: Reference `sec:ttree_assignments' on page 75 undefined on input line 5815. [75] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5893--5893 []\OT1/cmtt/m/n/10.95 -atomstyle style By default, moltemplate.sh assumes you are using the "full"[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 5894--5894 [] \OT1/cmtt/m/n/10.95 atom style in LAMMPS. You can change the atom style to "dipole"[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5895--5895 [] \OT1/cmtt/m/n/10.95 using -atomstyle dipole. If you are usin g a hybrid style,[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5896--5896 [] \OT1/cmtt/m/n/10.95 you must enclose the list of styles in qu otes. For example:[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 5898--5898 [] \OT1/cmtt/m/n/10.95 For custom atom styles, you can also spec ify the[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5899--5899 [] \OT1/cmtt/m/n/10.95 list of column names manually (enclosed i n quotes):[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 5900--5900 [] \OT1/cmtt/m/n/10.95 -atomstyle "molid x y z atomid atomtype m ux muy muz"[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5901--5901 [] \OT1/cmtt/m/n/10.95 Be careful to enclose the entire list in quotes(").[] Overfull \hbox (134.38715pt too wide) in paragraph at lines 5903--5903 []\OT1/cmtt/m/n/10.95 -raw raw_file The raw_file file should contain the atom ic coordinates in RAW format.[] Overfull \hbox (117.14108pt too wide) in paragraph at lines 5904--5904 [] \OT1/cmtt/m/n/10.95 RAW files are simple 3-column ASCII files containin the coordinates[] Overfull \hbox (122.88977pt too wide) in paragraph at lines 5905--5905 [] \OT1/cmtt/m/n/10.95 for the atoms in the system. (One line pe r atom, 3 numbers per line.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5906--5906 [] \OT1/cmtt/m/n/10.95 The atoms must appear in the same order i n the data file.)[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5907--5907 []\OT1/cmtt/m/n/10.95 -xyz xyz_file An xyz_file argument should be supplied a s an argument[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 5909--5909 [] \OT1/cmtt/m/n/10.95 This file should contain the atomic coord inates in xyz format.[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5910--5910 [] \OT1/cmtt/m/n/10.95 (The atoms must appear in the same order in the data file.)[] Overfull \hbox (134.38715pt too wide) in paragraph at lines 5912--5912 []\OT1/cmtt/m/n/10.95 -pdb pdb_file The pdb_file file should contain the atom ic coordinates in PDB format.[] Overfull \hbox (117.14108pt too wide) in paragraph at lines 5914--5914 [] \OT1/cmtt/m/n/10.95 This file should contain one ATOM or HETA TM record per atom. Atoms[] [76] Overfull \hbox (105.6437pt too wide) in paragraph at lines 5916--5916 [] \OT1/cmtt/m/n/10.95 are sorted by chainID, resID, insertCode, atomID (in that order).[] Overfull \hbox (111.3924pt too wide) in paragraph at lines 5917--5917 [] \OT1/cmtt/m/n/10.95 This order must match the order the atoms appear in the data file.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5919--5919 [] \OT1/cmtt/m/n/10.95 If the PDB file contains periodic boundar y box information[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5920--5920 [] \OT1/cmtt/m/n/10.95 (IE., a "CRYST1" record), this informatio n is also copied[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5922--5922 [] \OT1/cmtt/m/n/10.95 (Support for triclinic cells is experimen tal as of 2019-9-03.[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5923--5923 [] \OT1/cmtt/m/n/10.95 Other molecular structure formats may be supported later.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5926--5926 [] \OT1/cmtt/m/n/10.95 The user can customize the numbers assign ed to atom, bond,[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5927--5927 [] \OT1/cmtt/m/n/10.95 angle, dihedral, and improper types or id numbers by using[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5929--5929 [] \OT1/cmtt/m/n/10.95 for each variable you want to modify. If there are many[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5930--5930 [] \OT1/cmtt/m/n/10.95 variables you want to modify, you can sav e them in a file[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5931--5931 [] \OT1/cmtt/m/n/10.95 (one variable per line). For an example of the file format[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5932--5932 [] \OT1/cmtt/m/n/10.95 run moltemplate.sh once and search for a file named[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5933--5933 [] \OT1/cmtt/m/n/10.95 "ttree_assignments.txt". (This file is o ften located in[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5934--5934 [] \OT1/cmtt/m/n/10.95 the "output_ttree/" directory.) Once assi gned, the remaining[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5935--5935 [] \OT1/cmtt/m/n/10.95 variables in the same category will be au tomatically assigned[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 5936--5936 [] \OT1/cmtt/m/n/10.95 to values which do not overlap with your chosen values.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5938--5938 [] \OT1/cmtt/m/n/10.95 "-b" is similar to "-a". However, in this case, no attempt[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5939--5939 [] \OT1/cmtt/m/n/10.95 is made to assign exclusive (unique) valu es to each variable.[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5941--5941 [] \OT1/cmtt/m/n/10.95 Normally moltemplate.sh checks for common errors and typos and[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 5942--5942 [] \OT1/cmtt/m/n/10.95 halts if it thinks it has found one. This forces the variables[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5943--5943 [] \OT1/cmtt/m/n/10.95 and categories as well as write(file) and write_once(file)[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5944--5944 [] \OT1/cmtt/m/n/10.95 commands to obey standard naming conventio ns. The "-nocheck"[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 5945--5945 [] \OT1/cmtt/m/n/10.95 argument bypasses these checks and elimina tes these restrictions.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5947--5947 [] \OT1/cmtt/m/n/10.95 This cause moltemplate.sh to check to mak e sure that there[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5948--5948 [] \OT1/cmtt/m/n/10.95 are valid angle and dihedral interactions defined for every[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 5949--5949 [] \OT1/cmtt/m/n/10.95 3 or 4 consecutively bonded atoms in the system[] [77] Overfull \hbox (13.6647pt too wide) in paragraph at lines 6010--6010 []\OT1/cmtt/m/n/10.95 moltemplate.sh -a '@atom:SPCE/O 2' -a '@atom:SPCE/H 1' s ystem.lt LaTeX Warning: Reference `sec:nbody_by_type_utility' on page 78 undefined on in put line 6049. [78] Overfull \hbox (43.572pt too wide) in paragraph at lines 6093--6095 []\OT1/cmr/m/n/10.95 The ``ttree[]assignments.txt'' file has the same for-mat a s the ``new[]assignments.txt'' LaTeX Warning: Reference `sec:custom_categories' on page 79 undefined on input line 6103. Overfull \hbox (0.80295pt too wide) in paragraph at lines 6115--6118 \OT1/cmr/m/n/10.95 If for some rea-son, you are us-ing ``lt-tree.py'' or ``ttre e.py'' in-stead of ``moltem- [79] [80] [81] LaTeX Warning: Reference `sec:nbody_by_type' on page 82 undefined on input line 6381. [82] [83] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6502--6502 [] \OT1/cmtt/m/n/10.95 natom++; print "set atom "natom" x "$1" y "$2" z "$ 3" "}}' \[] [84] Overfull \hbox (8.35524pt too wide) in paragraph at lines 6562--6563 \OT1/cmr/m/it/10.95 file with the ap-pro-pri-ate in-te-ger be-fore you copy the con-tents into the LAMMPS Overfull \hbox (59.6542pt too wide) in paragraph at lines 6594--6594 [] \OT1/cmtt/m/n/10.95 nbody_by_type.py reads a LAMMPS data file (or an exce rpt of a LAMMPS) Overfull \hbox (25.16208pt too wide) in paragraph at lines 6595--6595 [] \OT1/cmtt/m/n/10.95 data file containing bonded many-body interactions by atom type[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6596--6596 [] \OT1/cmtt/m/n/10.95 (and bond type), and generates a list of additional i nteractions[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 6597--6597 [] \OT1/cmtt/m/n/10.95 in LAMMPS format consistent with those type (to the s tandard out).[] [85] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6615--6615 [] \OT1/cmtt/m/n/10.95 Support for other interaction types can be added by t he user. See below.[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6617--6617 [] \OT1/cmtt/m/n/10.95 Note: The optional "-subgraph" argument allows you to customize the[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6618--6618 [] \OT1/cmtt/m/n/10.95 rules used to match and generate interactions o f that type.[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6619--6619 [] \OT1/cmtt/m/n/10.95 It is optional, and is only useful for forcefie lds which[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6620--6620 [] \OT1/cmtt/m/n/10.95 use non-standard dihedral or improper atom-orde r convetions.)[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 6628--6628 [] \OT1/cmtt/m/n/10.95 "Dihedrals", or "Impropers"). It also looks a sectio n named "X By Type",[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6629--6629 [] \OT1/cmtt/m/n/10.95 (eg. "Angles By type", "Impropers By type", "Impro pers By type")[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6630--6630 [] \OT1/cmtt/m/n/10.95 which contains a list of criteria for automatically d efining additional[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6631--6631 [] \OT1/cmtt/m/n/10.95 interactions of that type. For example, this file mi ght contain:[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 6642--6642 [] \OT1/cmtt/m/n/10.95 The * is a wildcard symbol indicating there is no pre ference for bond types[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6643--6643 [] \OT1/cmtt/m/n/10.95 in this example. (Optionally, regular expressions ca n also be used to[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6644--6644 [] \OT1/cmtt/m/n/10.95 define a type match, by enclosing the atom or bond ty pe in / slashes.)[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6646--6646 [] \OT1/cmtt/m/n/10.95 The first line tells us to that there should be a 3-body "Angle"[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6647--6647 [] \OT1/cmtt/m/n/10.95 interaction of type "7" whenever an atom of type 1 is bonded to an atom[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6648--6648 [] \OT1/cmtt/m/n/10.95 of type "2", which is bonded to another atom of type "1" again.[] [86] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6649--6649 [] \OT1/cmtt/m/n/10.95 The second line tells us that an angle is defined whe never three atoms[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 6654--6654 [] \OT1/cmtt/m/n/10.95 atoms which match these criteria if they are bonded t ogether[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6655--6655 [] \OT1/cmtt/m/n/10.95 in the relevant way for that interaction type (as det ermined by[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6656--6656 [] \OT1/cmtt/m/n/10.95 nbody_X.py), and printed to the standard output. For example,[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 6657--6657 [] \OT1/cmtt/m/n/10.95 suppose you are automatically generating 3-body "Angl e" interactions using:[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6661--6661 [] \OT1/cmtt/m/n/10.95 The file "new.data" will be identical to "old.data", however the[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6662--6662 [] \OT1/cmtt/m/n/10.95 "Angles By Type" section will be deleted, and the fol lowing lines of[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6671--6671 [] \OT1/cmtt/m/n/10.95 The numbers in the first column are counters which as sign a ID to[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 6672--6672 [] \OT1/cmtt/m/n/10.95 every interaction of that type, and start where the o riginal "Angles"[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6673--6673 [] \OT1/cmtt/m/n/10.95 data left off (New angle ID numbers do not overlap wi th old ID numbers).[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6674--6674 [] \OT1/cmtt/m/n/10.95 The text in the second column ("7", "9", ...) matches the text from the[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6675--6675 [] \OT1/cmtt/m/n/10.95 first column of the "Angle By Type" section of the in put file.[] [87] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6697--6697 [] \OT1/cmtt/m/n/10.95 When run this way, nbody_by_type.py behaves exactly t he same way[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6698--6698 [] \OT1/cmtt/m/n/10.95 as in Example 1, however only the lines of text corre sponding to[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6699--6699 [] \OT1/cmtt/m/n/10.95 the new generated interactions are printed, (not the entire data file).[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 6700--6700 [] \OT1/cmtt/m/n/10.95 Also note, that when run this way, nbody_by_type.py d oes not read the[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6701--6701 [] \OT1/cmtt/m/n/10.95 LAMMPS data from the standard input. Instead, it rea ds each section of[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6702--6702 [] \OT1/cmtt/m/n/10.95 the data file from a different file indicated by the arguments following[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 6703--6703 [] \OT1/cmtt/m/n/10.95 the "-atoms", "-bonds", "-nbody", and "-nbodybytype" flags.[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6705--6705 [] \OT1/cmtt/m/n/10.95 "Angles" is a 3-body interaction style. So when run this way,[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6706--6706 [] \OT1/cmtt/m/n/10.95 nbody_by_type.py will create a 5 (=3+2) column file ( new_Angles.data).[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 6708--6708 []\OT1/cmtt/m/n/10.95 Note: the atom, bond and other IDs/types in need not be i ntegers.[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 6710--6710 []\OT1/cmtt/m/n/10.95 Note: This program must be distributed with several pytho n modules, including:[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6711--6711 [] \OT1/cmtt/m/n/10.95 nbody_Angles.py, nbody_Dihedrals.py, and nbody_Im propers.py. These[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 6712--6712 [] \OT1/cmtt/m/n/10.95 contain bond definitions for angular, dihedral, and improper interactions.[] Overfull \hbox (1.14366pt too wide) in paragraph at lines 6717--6732 \OT1/cmr/m/n/10.95 im-ports ex-ter-nal mod-ules named ``nbody[]Angles.py'', ``n body[]Dihedrals.py'', LaTeX Warning: Reference `sec:adv_variable_syntax' on page 88 undefined on inpu t line 6742. Overfull \hbox (4.07088pt too wide) in paragraph at lines 6741--6743 \OT1/cmr/m/n/10.95 Moltemplate.sh is a script which in-vokes a python pro-gram pro-gram (\OT1/cmr/m/it/10.95 ttree.py\OT1/cmr/m/n/10.95 ) [88] Overfull \hbox (82.64896pt too wide) in paragraph at lines 6766--6766 []\OT1/cmtt/m/n/10.95 String ::= InstanceName | ObjectTypeName | FileName | Cat egoryName | OtherStr LaTeX Warning: Reference `sec:custom_categories' on page 89 undefined on input line 6774. LaTeX Warning: Reference `sec:adv_variable_syntax' on page 89 undefined on inpu t line 6781. Overfull \hbox (76.90027pt too wide) in paragraph at lines 6796--6796 []\OT1/cmtt/m/n/10.95 Command ::= ObjectDef | InstanceCommand | DeleteCommand | WriteC | WriteOC | Overfull \hbox (48.15683pt too wide) in paragraph at lines 6797--6797 [] \OT1/cmtt/m/n/10.95 ImportCommand | CategoryDef | InstanceMod | O bjectTypeMod |[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6798--6798 [] \OT1/cmtt/m/n/10.95 ObjectDefMod | ReplaceCommand | UsingCommand | PushXform[] [89] Overfull \hbox (7.91602pt too wide) in paragraph at lines 6813--6813 []\OT1/cmtt/m/n/10.95 RotXform ::= ".rot(" Number "," Number "," Number "," Num ber ")"[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6833--6833 []\OT1/cmtt/m/n/10.95 TemplText ::= "" | String TemplText | StatVar TemplText | InstVar TemplText[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 6837--6837 []\OT1/cmtt/m/n/10.95 WriteOC ::= "write_once(" FileName ")" "{" TemplateTextSt at "}"[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6838--6838 []\OT1/cmtt/m/n/10.95 TemplTextStat ::= "" | String TemplTextStat | StatVar Tem plTextStat[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6849--6849 []\OT1/cmtt/m/n/10.95 CatCommandStat ::= "category" "@"CategoryName"(" Integer "," Integer ")"[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6850--6850 []\OT1/cmtt/m/n/10.95 CatCommandInst ::= "category" "$"CategoryName"(" Integer "," Integer ")"[] [90] LaTeX Warning: Reference `sec:cpath_simple' on page 91 undefined on input line 6906. LaTeX Warning: Reference `sec:cpath_simple' on page 91 undefined on input line 6911. LaTeX Warning: Reference `sec:variables_shorthand' on page 91 undefined on inpu t line 6918. [91] LaTeX Warning: Reference `sec:cpath_simple' on page 92 undefined on input line 6947. Overfull \hbox (5.00008pt too wide) in paragraph at lines 6955--6959 []\OT1/cmr/m/n/10.95 Find the cat-e-gory name and ob-ject cor-re-spond-ing to ` `\TS1/cmr/m/n/10.95 $\OT1/cmr/bx/it/10.95 cpath\OT1/cmr/m/n/10.95 /\OT1/cmr/bx/ it/10.95 catname\OT1/cmr/m/n/10.95 :'' [92] Overfull \hbox (43.72781pt too wide) in paragraph at lines 6972--6973 \OT1/cmr/m/n/10.95 file (al-though you can use it any-where else in an ``.LT'' file). In ``ttree[]assignments.txt'' No file moltemplate_manual.bbl. [93] (./moltemplate_manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcbi1200 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcbi1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcbi1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcbi.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txitlod.mf Ok [48] [49] [53] [54] [56] [57] [50] [51] [52] [55]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txisuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txifract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tcbi1200.tfm. Output written on tcbi1200.600gf (128 characters, 27688 bytes). Transcript written on tcbi1200.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcbi1200.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `moltemplate_manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcbx1095 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcbx1095 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcbx1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tcbx1095.tfm. Output written on tcbx1095.600gf (128 characters, 25176 bytes). Transcript written on tcbx1095.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcbx1095.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcbx1200 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcbx1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcbx1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tcbx1200.tfm. Output written on tcbx1200.600gf (128 characters, 27420 bytes). Transcript written on tcbx1200.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcbx1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcti1095 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcti1095 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcti1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcti.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txitlod.mf Ok [48] [49] [53] [54] [56] [57] [50] [51] [52] [55]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txisuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txifract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tcti1095.tfm. Output written on tcti1095.600gf (128 characters, 25768 bytes). Transcript written on tcti1095.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcti1095.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1095 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1095 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06952pt) Font metrics written on tcrm1095.tfm. Output written on tcrm1095.600gf (128 characters, 25592 bytes). Transcript written on tcrm1095.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1095.600pk: successfully generated. Output written on moltemplate_manual.pdf (93 pages, 810639 bytes). Transcript written on moltemplate_manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./moltemplate_manual.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2025/01/22 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./moltemplate_manual.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./moltemplate_manual.out) (./moltemplate_manual.out) (./moltemplate_manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map} <./author_email.png>] [2]) LaTeX Warning: Citation `MOLTEMPLATE' on page 3 undefined on input line 72. [3] Overfull \hbox (12.60272pt too wide) in paragraph at lines 91--111 \OT1/cmr/m/n/10.95 which can be con-verted into moltem-plate for-mat (LT for-ma t) us-ing []\OT1/cmtt/m/n/10.95 mol22lt.py[] [4] Overfull \hbox (2.16733pt too wide) in paragraph at lines 197--197 []\OT1/cmtt/m/n/10.95 moltemplate.sh -xyz coords.xyz -atomstyle "full" -vmd sys tem.lt LaTeX Warning: Citation `ATB' on page 5 undefined on input line 299. Overfull \hbox (1.51479pt too wide) in paragraph at lines 299--306 \OT1/cmr/m/n/10.95 The \OT1/cmr/bx/n/10.95 ATB \OT1/cmr/m/n/10.95 ser-vice [[]] men-tioned ear-lier ([]$\OT1/cmtt/m/n/10.95 https : / / atb . uq . edu . au$[] \OT1/cmr/m/n/10.95 ) is a repos- LaTeX Warning: Citation `topotools' on page 5 undefined on input line 308. LaTeX Warning: Citation `OpenBABEL' on page 5 undefined on input line 309. LaTeX Warning: Citation `VMD' on page 5 undefined on input line 312. LaTeX Warning: Citation `topotools' on page 5 undefined on input line 312. LaTeX Warning: Citation `OVITO' on page 5 undefined on input line 312. LaTeX Warning: Citation `packmol' on page 5 undefined on input line 321. [5] Overfull \hbox (19.41339pt too wide) in paragraph at lines 471--471 []\OT1/cmtt/m/n/10.95 python -m venv ~/venv #(or "virtualenv venv" if using python2) [6] Overfull \hbox (7.91602pt too wide) in paragraph at lines 496--496 []\OT1/cmtt/m/n/10.95 git clone https://github.com/jewettaij/moltemplate ~/molt emplate Overfull \hbox (30.91077pt too wide) in paragraph at lines 517--517 []\OT1/cmtt/m/n/10.95 pip3 install . # (or "pip3 install --user", or "pip" if that fails)[] Overfull \hbox (0.52628pt too wide) in paragraph at lines 520--526 []\OT1/cmr/m/n/10.95 As men-tioned ear-lier, if you are hav-ing dif-fi-culty, t ry to in-stalling moltem- [7] Overfull \hbox (25.16208pt too wide) in paragraph at lines 593--609 \OT1/cmtt/m/n/10.95 bashonubuntuonwindows / comments / 6bu1d1 / since _ we _ sh ouldnt _ edit _ files _ [8] Overfull \hbox (0.32121pt too wide) in paragraph at lines 612--612 []\OT1/cmr/bx/n/14.4 Quick ref-er-ence \OT1/cmr/bx/it/14.4 (SKIP ON FIRST READ- ING) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Underfull \hbox (badness 7064) in paragraph at lines 683--688 []|\OT1/cmr/m/n/10.95 Apply co-or-di-nate trans-for-ma-tions ([] to Underfull \hbox (badness 10000) in paragraph at lines 792--797 []|\OT1/cmr/m/n/10.95 Delete a range of molecules spec-i-fied by Underfull \hbox (badness 1616) in paragraph at lines 792--797 []\OT1/cmr/m/n/10.95 . (This also works for mul-ti-di- Overfull \hbox (121.47046pt too wide) in alignment at lines 623--895 [] [] ignored error: Infinite glue shrinkage found in box being split [9] ignored error: Infinite glue shrinkage found in box being split [10] [11] Underfull \hbox (badness 10000) in paragraph at lines 907--909 Overfull \hbox (131.64603pt too wide) in alignment at lines 909--1047 [] [] ignored error: Infinite glue shrinkage found in box being split [12] [13] Underfull \hbox (badness 10000) in paragraph at lines 1058--1061 Underfull \hbox (badness 10000) in paragraph at lines 1058--1061 Overfull \hbox (124.34627pt too wide) in alignment at lines 1061--1190 [] [] [14] Underfull \hbox (badness 1418) in paragraph at lines 1387--1391 \OT1/cmr/m/n/10.95 ``bond[]coeff'', ``an-gle[]coeff'', ``di-he-dral[]coeff'', a nd ``im- Overfull \hbox (123.88596pt too wide) in alignment at lines 1203--1417 [] [] ignored error: Infinite glue shrinkage found in box being split [15] ignored error: Infinite glue shrinkage found in box being split [16] [17] Overfull \hbox (13.54758pt too wide) in paragraph at lines 1432--1454 \OT1/cmr/m/n/10.95 tackle the same steep learning-curve (and oc-ca-sional bugs) that other LAMMPS Overfull \hbox (16.26949pt too wide) in paragraph at lines 1459--1459 []\OT1/cmr/bx/n/12 Simulating a box of wa-ter us-ing moltem-plate and LAMMPS LaTeX Warning: Citation `Berendsen++StraatsmaJPhysChem1987' on page 18 undefine d on input line 1475. Overfull \hbox (53.90552pt too wide) in paragraph at lines 1494--1494 [] \OT1/cmtt/m/n/10.95 ## Atom properties and bond topology go in various "Dat a ..." sections[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1496--1496 [] \OT1/cmtt/m/n/10.95 # We selected "atom_style full". That means we use this column format:[] [18 <./single_water_LR.jpg>] Overfull \hbox (19.41339pt too wide) in paragraph at lines 1497--1497 [] \OT1/cmtt/m/n/10.95 # atomID molID atomType charge coordX coordY coordZ[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1500--1500 [] \OT1/cmtt/m/n/10.95 $atom:o $mol:w @atom:O -0.8476 0.0000000 0.00000 0 0.00000[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1501--1501 [] \OT1/cmtt/m/n/10.95 $atom:h1 $mol:w @atom:H 0.4238 0.8164904 0.57735 90 0.00000[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 1502--1502 [] \OT1/cmtt/m/n/10.95 $atom:h2 $mol:w @atom:H 0.4238 -0.8164904 0.5773 590 0.00000[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 1505--1505 [] \OT1/cmtt/m/n/10.95 # Variables beginning with $ or @ will be replaced by n umbers LAMMPS will[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 1506--1506 [] \OT1/cmtt/m/n/10.95 # eventually read. Each of the three atoms" will be as signed unique[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1507--1507 [] \OT1/cmtt/m/n/10.95 # atomIDs (denoted here by "$atom:o", "$atom:h1", "$ato m:h2"), even if[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 1508--1508 [] \OT1/cmtt/m/n/10.95 # they belong to different molecules. However, the ato m types[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 1509--1509 [] \OT1/cmtt/m/n/10.95 # (denoted "@atom:O", "@atom:H") are shared for atoms i n all molecules.[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1510--1510 [] \OT1/cmtt/m/n/10.95 # All 3 atoms share same molID number (represeted here by "$mol:w")[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1511--1511 [] \OT1/cmtt/m/n/10.95 # however that number is different for different water molecules.[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1530--1530 [] \OT1/cmtt/m/n/10.95 # --- Force-field parameters go in the "In Settings" se ction: ---[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1534--1534 [] \OT1/cmtt/m/n/10.95 # atomType1 atomType2 parameter-list (epsil on, sigma)[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 1537--1537 [] \OT1/cmtt/m/n/10.95 # (mixing rules determine interactions between types @atom:O and @atom:H)[] [19] Overfull \hbox (99.89502pt too wide) in paragraph at lines 1545--1545 [] \OT1/cmtt/m/n/10.95 # Group definitions and constraints can also go in th e "In Settings" section[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 1547--1547 [] \OT1/cmtt/m/n/10.95 fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @ang le:HOH[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1548--1548 [] \OT1/cmtt/m/n/10.95 # (lammps quirk: Remember to "unfix fSHAKE" during mi nimization.)[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1551--1551 [] \OT1/cmtt/m/n/10.95 # LAMMPS supports a large number of force-field styles. We must select[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 1552--1552 [] \OT1/cmtt/m/n/10.95 # which ones we need. This information belongs in the " In Init" section.[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 1555--1555 [] \OT1/cmtt/m/n/10.95 units real # angstroms, kCal/m ole, Daltons, Kelvin[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 1556--1556 [] \OT1/cmtt/m/n/10.95 atom_style full # select column for mat for Atoms section[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 1557--1557 [] \OT1/cmtt/m/n/10.95 pair_style lj/charmm/coul/long 9.0 10.0 10 # param s needed: epsilon sigma[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1558--1558 [] \OT1/cmtt/m/n/10.95 bond_style harmonic # parameters needed : k_bond, r0[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 1559--1559 [] \OT1/cmtt/m/n/10.95 angle_style harmonic # parameters needed : k_theta, theta0[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 1560--1560 [] \OT1/cmtt/m/n/10.95 kspace_style pppm 0.0001 # long-range electr ostatics sum method[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 1561--1561 [] \OT1/cmtt/m/n/10.95 pair_modify mix arithmetic # using Lorenz-Bert helot mixing rules[] Overfull \hbox (14.12546pt too wide) in paragraph at lines 1575--1576 \OT1/cmr/m/n/10.95 You can now use ``moltem-plate.sh'' to cre-ate sim-u-la-tion in-put files for LAMMPS [20] Overfull \hbox (0.73196pt too wide) in paragraph at lines 1637--1649 \OT1/cmr/m/n/10.95 (See sec-tion []6[] for more de-tails and ex-am-ples.) This will cre-ate 1000 molecules Overfull \hbox (40.6773pt too wide) in paragraph at lines 1637--1649 \OT1/cmr/m/n/10.95 ta-tion: ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.95 atom:wat[2 ][3][4]/h1'', ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.95 bond:wat[0][5][1]/oh1'', ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.95 an-gle:wat[2][8][3]/hoh'', Overfull \hbox (10.06793pt too wide) in paragraph at lines 1656--1659 \OT1/cmr/m/n/10.95 spec-ify the di-men-sions of the sim-u-la-tion bound-ary us- ing the ``write[]once(``Data [21] [22 <./waterSPCEx1000_LR.jpg> <./waterSPCEx1000_t=25_LR.jpg>] LaTeX Warning: Citation `OVITO' on page 23 undefined on input line 1783. Overfull \hbox (33.74133pt too wide) in paragraph at lines 1799--1809 []\OT1/cmr/m/n/10.95 Moltemplate will cre-ate the fol-low-ing files: ``sys-tem. data'', ``run.in.EXAMPLE'', [23] LaTeX Warning: Citation `VMD' on page 24 undefined on input line 2007. Overfull \hbox (5.23363pt too wide) in paragraph at lines 2004--2011 \OT1/cmr/m/n/10.95 which can vi-su-al-ize the sys-tem. If you have saved your t ra-jec-tory in LAMMPS [24] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2012--2012 []\OT1/cmtt/m/n/10.95 dump 1 all custom 1000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz Overfull \hbox (29.2559pt too wide) in paragraph at lines 2019--2022 []\OT1/cmr/m/n/10.95 a) Start VMD From the menu in the upper-left, se-lect \OT1 /cmr/bx/n/10.95 File$\OMS/cmsy/m/n/10.95 !$[] [25] Overfull \hbox (24.8004pt too wide) in paragraph at lines 2168--2175 \OT1/cmr/m/n/10.95 In the ex-am-ple above, the \TS1/cmr/m/n/10.95 $ \OT1/cmr/m/ n/10.95 vari-ables have full-names like ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.9 5 atom:wat[8][3][7]/h1'', [26] [27] [28] Overfull \hbox (0.77374pt too wide) in paragraph at lines 2342--2342 []\OT1/cmr/bx/it/12 (Advanced) \OT1/cmr/bx/n/12 Us-ing moltem-plate to gen-er-a te aux-il-iary files Overfull \hbox (36.65945pt too wide) in paragraph at lines 2353--2353 [] \OT1/cmtt/m/n/10.95 mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.33333 7.04956 0. 602224 4 0 0[] [29] [30] [31 <./2bead_monomer.jpg> <./2bead_polymer.jpg> <./2bead_polymers_nop bc_t=0_LR.jpg> <./2bead_polymers_t=100ps_LR.jpg>] Overfull \hbox (0.3771pt too wide) in paragraph at lines 2460--2461 \OT1/cmr/m/n/10.95 Consider the fol-low-ing sim-ple 2-atom dumbell-shaped molel ule (``Monomer'') Overfull \hbox (7.91602pt too wide) in paragraph at lines 2470--2470 [] \OT1/cmtt/m/n/10.95 $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0. 0000000[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 2471--2471 [] \OT1/cmtt/m/n/10.95 $atom:r $mol:... @atom:R 0.0 0.000 4.4000 0. 0000000[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 2505--2505 [] \OT1/cmtt/m/n/10.95 create_var {$mol} #(force all Monomers to share the sa me molecule-ID)[] [32] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2519--2519 [] \OT1/cmtt/m/n/10.95 $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom :mon2/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2520--2520 [] \OT1/cmtt/m/n/10.95 $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom :mon3/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2521--2521 [] \OT1/cmtt/m/n/10.95 $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom :mon4/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2522--2522 [] \OT1/cmtt/m/n/10.95 $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom :mon5/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2523--2523 [] \OT1/cmtt/m/n/10.95 $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom :mon6/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2524--2524 [] \OT1/cmtt/m/n/10.95 $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom :mon7/ca[] [33] Overfull \hbox (42.40814pt too wide) in paragraph at lines 2631--2631 [] \OT1/cmtt/m/n/10.95 # Force-field parameters ("coeffs") go in the "In Setti ngs" section:[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 2638--2638 [] \OT1/cmtt/m/n/10.95 # (Interactions between different atoms are determine d by mixing rules.)[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2651--2651 [] \OT1/cmtt/m/n/10.95 # Although the simple "Monomer" object we defined above has only[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2652--2652 [] \OT1/cmtt/m/n/10.95 # two atoms, later on, we will create molecules with ma ny bonds.[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 2653--2653 [] \OT1/cmtt/m/n/10.95 # By convention, in this file we keep track of all of t he possible[] [34] Overfull \hbox (76.90027pt too wide) in paragraph at lines 2656--2656 [] \OT1/cmtt/m/n/10.95 # Rules for determining 3-body (angle) interactions by atom and bond type:[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2657--2657 [] \OT1/cmtt/m/n/10.95 # angle-type atomType1 atomType2 atomType3 bondTyp e1 bondType2[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2660--2660 [] \OT1/cmtt/m/n/10.95 @angle:Backbone @atom:CA @atom:CA @atom:CA @bond :* @bond:*[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2661--2661 [] \OT1/cmtt/m/n/10.95 @angle:Sidechain @atom:CA @atom:CA @atom:R @bond :* @bond:*[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 2674--2674 [] \OT1/cmtt/m/n/10.95 # 4-body interactions in this example are listed by ato m type and (optionally)[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2675--2675 [] \OT1/cmtt/m/n/10.95 # by bond type. (You can use wildcards * to accept all bond types.)[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 2677--2677 [] \OT1/cmtt/m/n/10.95 # dihedralType atmType1 atmType2 atmType3 atmType4 bo ndType1 bType2 bType3[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 2679--2679 [] \OT1/cmtt/m/n/10.95 @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @ bond:* @bond:* @bond:*[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 2680--2680 [] \OT1/cmtt/m/n/10.95 @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @ bond:* @bond:* @bond:*[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2699--2699 [] \OT1/cmtt/m/n/10.95 # -- (Changing these styles will change the formulas above) --[] [35] [36] Overfull \hbox (9.77596pt too wide) in paragraph at lines 2782--2789 \OT1/cmr/m/n/10.95 Notice that we did not spec-ify the ``@bond:SideChain'' and ``@bond:Backbone'' Overfull \hbox (76.60141pt too wide) in paragraph at lines 2795--2808 \OT1/cmr/m/n/10.95 names can be quite long and dif-fi-cult to type (such as ``@ atom:h1h[]ph1h[]bh1h[]ah1[]dh1[]ih1''). [37] Overfull \hbox (14.1924pt too wide) in paragraph at lines 2873--2874 \OT1/cmr/m/n/10.95 For de-tails, see the ``cen-JswapIL.py'' file (lo-cated in t he ``nbody[]alt[]symmetry/'' [38] [39] Overfull \hbox (19.81343pt too wide) in paragraph at lines 2963--2973 \OT1/cmr/m/n/10.95 The first line tells moltem-plate that any bond be-tween ato ms of type ``@atom:h1'' [40] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3058--3058 [] \OT1/cmtt/m/n/10.95 # Note: This will not overwrite the preexisting "ForceF ield" object.[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3059--3059 [] \OT1/cmtt/m/n/10.95 # (Instead, it augments the "ForceField" object d efined earlier.)[] Overfull \hbox (2.11093pt too wide) in paragraph at lines 3074--3079 \OT1/cmr/m/n/10.95 ``@atom:R'', and ``@atom:CB'', since they all be-long to the same ``[]'' Overfull \hbox (59.6542pt too wide) in paragraph at lines 3084--3084 [] \OT1/cmtt/m/n/10.95 # Here you can refer to @atoms, @bonds, etc... defined in either file:[] [41] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3139--3139 [] \OT1/cmtt/m/n/10.95 $bond:backbone1 @bond:Backbone $atom:monomers[0]/ca $atom:monomers[1]/ca[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3140--3140 [] \OT1/cmtt/m/n/10.95 $bond:backbone2 @bond:Backbone $atom:monomers[1]/ca $atom:monomers[2]/ca[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3141--3141 [] \OT1/cmtt/m/n/10.95 $bond:backbone3 @bond:Backbone $atom:monomers[2]/ca $atom:monomers[3]/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 3142--3142 [] \OT1/cmtt/m/n/10.95 : : : :[] Overfull \hbox (9.44891pt too wide) in paragraph at lines 3159--3163 \OT1/cmr/m/n/10.95 This will cre-ate 7 molecules. The co-or-di-nates of the fir st molecule \OT1/cmr/m/it/10.95 monomers[0] [42] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3169--3169 [] \OT1/cmtt/m/n/10.95 monomers = new Monomer.scale(1.5) [7].rot(180, 1,0,0).m ove(3.2,0,0) Overfull \hbox (25.16208pt too wide) in paragraph at lines 3185--3185 [] \OT1/cmtt/m/n/10.95 # "monomers[0]", "monomers[1]", "monomers[2]", ... "mon omers[6]".[] [43] Overfull \hbox (7.91602pt too wide) in paragraph at lines 3255--3255 [] \OT1/cmtt/m/n/10.95 monomers = new random([Monomer, Monomer3], [0.6, 0.4], 123456)[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3260--3260 [] \OT1/cmtt/m/n/10.95 $bond:bb1 @bond:Backbone $atom:monomers[0]/ca $atom:m onomers[1]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3261--3261 [] \OT1/cmtt/m/n/10.95 $bond:bb2 @bond:Backbone $atom:monomers[1]/ca $atom:m onomers[2]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3262--3262 [] \OT1/cmtt/m/n/10.95 $bond:bb3 @bond:Backbone $atom:monomers[2]/ca $atom:m onomers[3]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3263--3263 [] \OT1/cmtt/m/n/10.95 $bond:bb4 @bond:Backbone $atom:monomers[3]/ca $atom:m onomers[4]/ca[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3268--3268 [] \OT1/cmtt/m/n/10.95 $bond:bb50 @bond:Backbone $atom:monomers[48]/ca $atom :monomers[49]/ca Overfull \hbox (19.41339pt too wide) in paragraph at lines 3270--3270 [] \OT1/cmtt/m/n/10.95 #(Note: Both the "Monomer" and "Monomer3" subunits cont ain atoms[] [44 <./random_2bead.jpg> <./random_3bead.jpg> <./random_heteropolymer.jpg>] Overfull \hbox (21.21399pt too wide) in paragraph at lines 3324--3328 []\OT1/cmr/m/it/10.95 Note: \OT1/cmr/m/n/10.95 Al-though this ex-am-ple, there are only two monomer types (``Monomer'' Overfull \hbox (31.28319pt too wide) in paragraph at lines 3339--3343 []\OT1/cmr/m/it/10.95 Note: \OT1/cmr/m/n/10.95 Once a molecule con-tain-ing ran -dom monomers is de-fined, ([] [45] Overfull \hbox (30.91077pt too wide) in paragraph at lines 3409--3409 [] \OT1/cmtt/m/n/10.95 monomers[1-48] = new random([Monomer, Monomer3], [30, 1 8], 123456)[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3412--3412 [] \OT1/cmtt/m/n/10.95 # It's a good idea to move these monomers to keep them from overlapping[] [46] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3460--3460 []\OT1/cmtt/m/n/10.95 delete molecules[0-1][1][1-2] # (shorthand for delete mol ecules[0][1][1] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3461--3461 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[0][1][2][] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3462--3462 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[1][1][1][] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3463--3463 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[1][1][2])[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 3469--3469 []\OT1/cmtt/m/n/10.95 # ...and move them back to the location of the vacancies we created[] Overfull \hbox (4.88002pt too wide) in paragraph at lines 3478--3484 \OT1/cmr/m/n/10.95 You can use [] to fill space with a ran-dom mix-ture of mole cules. Overfull \hbox (53.90552pt too wide) in paragraph at lines 3485--3485 []\OT1/cmtt/m/n/10.95 import "lipids" # def ine DPPC & DLPC Overfull \hbox (48.15683pt too wide) in paragraph at lines 3486--3486 []\OT1/cmtt/m/n/10.95 lipids = new random([DPPC,DLPC], [0.5,0.5], 123) # "12 3"=random_seed[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3487--3487 [] \OT1/cmtt/m/n/10.95 [19].move(7.5, 0, 0) # lat tice spacing 7.5[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 3488--3488 [] \OT1/cmtt/m/n/10.95 [22].move(3.75, 6.49519, 0) # hex agonal lattice[] [47] Overfull \hbox (19.41339pt too wide) in paragraph at lines 3489--3489 [] \OT1/cmtt/m/n/10.95 [2].rot(180, 1, 0, 0) # 2 m onolayers[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3516--3516 []\OT1/cmtt/m/n/10.95 lipids = new random([DPPC, ,DLPC], [0.35,0.3,0.35], 123) # 2nd element is blank [48 <./lipid_bilayer_mixture.jpg> <./lipid_bilayer_vacancies.jpg>] [49 <./delet e_holes1.jpg>] Overfull \hbox (33.65005pt too wide) in paragraph at lines 3640--3642 []\OT1/cmr/m/n/10.95 We can sub-squently cus-tomize the po-si-tion of the 3rd m onomer (``monomers[2]'') Overfull \hbox (128.63846pt too wide) in paragraph at lines 3678--3678 [] \OT1/cmtt/m/n/10.95 $atom:mol_complex/polymers[0]/monomers[2]/ca $mol:mol_c omplex @atom:R 0 6.4 8.2 0.6[] Overfull \hbox (190.20093pt too wide) in paragraph at lines 3681--3691 \OT1/cmr/m/n/10.95 This is a sit-u-a-tion where we must use the \OT1/cmr/m/it/1 0.95 full \OT1/cmr/m/n/10.95 name of the atom (``\TS1/cmr/m/n/10.95 $\OT1/cmr/m /n/10.95 atom:mol[]complex/polymers[0]/monomers[2]/ca'') [50] Overfull \hbox (25.16208pt too wide) in paragraph at lines 3695--3695 [] \OT1/cmtt/m/n/10.95 $atom:polymers[0]/monomers[2]/ca $mol:... @atom:R 0 6 .4 8.2 0.6[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3714--3714 [] \OT1/cmtt/m/n/10.95 $bond:mol_complex/polymers[0]/backbone3 @bond:ForceFiel d/LongBond &[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 3736--3736 []\OT1/cmtt/m/n/10.95 # Note: This will augment the "ForceField" object, not ov erwrite it: [51] Overfull \hbox (65.4029pt too wide) in paragraph at lines 3774--3774 []\OT1/cmtt/m/n/10.95 delete mol_complex/polymers[1]/monomers[3]/ca #<-- dele tes the "ca" atom Overfull \hbox (65.4029pt too wide) in paragraph at lines 3775--3775 []\OT1/cmtt/m/n/10.95 delete mol_complex/polymers[1]/monomers[4]/cr #<-- dele tes the "cr" bond[] [52] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3865--3865 []\OT1/cmtt/m/n/10.95 MolecularComplex0 = MolecularComplex.move(-9.6,-6.2, 0).s cale(0.3125) Overfull \hbox (25.16208pt too wide) in paragraph at lines 3882--3882 []\OT1/cmtt/m/n/10.95 # Add some new atoms connecting the two polymers in the m ol_complex[] Overfull \hbox (2.00154pt too wide) in paragraph at lines 3936--3937 []\OT1/cmr/m/it/10.95 Note: These co-or-di-nate trans-for-ma-tions will be ap-p lied \OT1/cmr/bx/it/10.95 af-ter \OT1/cmr/m/it/10.95 the molecule [53] [54 <./mol_complex_LR.jpg> <./mol_complex+mol_complex0_transparent_LR.jpg> ] Overfull \hbox (2.16733pt too wide) in paragraph at lines 4031--4031 [] \OT1/cmtt/m/n/10.95 $atom:o $mol:w @atom:O -0.8476 0.0000000 0.00000 0. 000000[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4032--4032 [] \OT1/cmtt/m/n/10.95 $atom:h1 $mol:w @atom:H 0.4238 0.8164904 0.00000 0 .5773590[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4033--4033 [] \OT1/cmtt/m/n/10.95 $atom:h2 $mol:w @atom:H 0.4238 -0.8164904 0.00000 0 .5773590[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4044--4044 [] \OT1/cmtt/m/n/10.95 # atomTypeI atomTypeJ pair-style-name p arameter-list[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4046--4046 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:O @atom:O lj/charmm/coul/long 0 .1553 3.166[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4047--4047 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:H @atom:H lj/charmm/coul/long 0 .0 2.058[] [55] Overfull \hbox (2.16733pt too wide) in paragraph at lines 4076--4076 [] \OT1/cmtt/m/n/10.95 fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @ang le:HOH[] Overfull \hbox (25.39783pt too wide) in paragraph at lines 4082--4085 \OT1/cmr/m/n/10.95 There are two dif-fer-ences be-tween this molecule def-i-ni- tion and the ``spce[]simple.lt'' [56] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4172--4172 [] \OT1/cmtt/m/n/10.95 pair_style hybrid lj/charmm/coul/long 9 10 10 table spl ine 1000[] Overfull \hbox (11.69077pt too wide) in paragraph at lines 4187--4187 [][]\OT1/cmr/bx/n/10.95 Warning: Force-field pa-ram-e-ters be-long in ``In Set- tings'', not ``Data'' [57] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4261--4261 [] \OT1/cmtt/m/n/10.95 # AtomID MolID('.'=this) AtomType charge coordX coor dY coordZ[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4263--4263 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.000000 000 1.0000000[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4264--4264 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.951056 516 0.3090170[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4265--4265 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.587785 252 -0.809017[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 4266--4266 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 -0.58778 5252 -0.809017[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 4267--4267 [] \OT1/cmtt/m/n/10.95 $atom:c5 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 -0.95105 6516 0.3090170[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4287--4287 []\OT1/cmtt/m/n/10.95 # A cubic lattice of 125 cyclopentane molecules (12-angst rom spacing) [58] Overfull \hbox (65.4029pt too wide) in paragraph at lines 4288--4288 []\OT1/cmtt/m/n/10.95 mols = new Cyclopentane [5].move(0,0,12) [5].move(0,12,0) [5].move(12,0,0)[] LaTeX Warning: Citation `TraPPE' on page 59 undefined on input line 4295. Overfull \hbox (42.40814pt too wide) in paragraph at lines 4319--4319 [] \OT1/cmtt/m/n/10.95 dihedral_coeff @dihedral:CCCC opls 1.411036 -0.271016 3.145034 0.0[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 4320--4320 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 4321--4321 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4322--4322 [] \OT1/cmtt/m/n/10.95 # (Interactions between different atom types use mixi ng rules.)[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 4329--4329 [] \OT1/cmtt/m/n/10.95 @dihedral:CCCC @atom:C* @atom:C* @atom:C* @atom:C* @bo nd:CC @bond:CC @bond:CC[] [59] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4395--4395 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:bt @atom:TraPPE/CH3 0.0 0.419372 0.00 0 -1.937329[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4396--4396 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:bt @atom:TraPPE/CH2 0.0 -0.419372 0.0 00 -0.645776[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4397--4397 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:bt @atom:TraPPE/CH2 0.0 0.419372 0.00 0 0.645776[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4398--4398 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:bt @atom:TraPPE/CH3 0.0 -0.419372 0.0 000 1.937329[] [60] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4433--4433 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:bt @atom:../CH3 0.0 0.419372 0.000 -1.937329[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4434--4434 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:bt @atom:../CH2 0.0 -0.419372 0.000 -0.645776[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4435--4435 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:bt @atom:../CH2 0.0 0.419372 0.000 0.645776[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4436--4436 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:bt @atom:../CH3 0.0 -0.419372 0.000 0 1.937329[] Overfull \hbox (6.15454pt too wide) in paragraph at lines 4448--4449 \OT1/cmr/bx/it/10.95 NOTE: Again, al-though the ``nest-ing'' method ex-plained here works, [61] [62] Overfull \hbox (19.81343pt too wide) in paragraph at lines 4615--4625 \OT1/cmr/m/n/10.95 atom type ``@atom:CH3'' in-stead of ``@atom:TraPPE/CH3'', or ``@atom:../CH3'' Overfull \hbox (23.57642pt too wide) in paragraph at lines 4655--4662 \OT1/cmr/m/n/10.95 If two molecules are re-lated to each other this way: [], [63] [64] [65] Overfull \hbox (40.92256pt too wide) in paragraph at lines 4955--4962 []\OT1/cmr/m/n/10.95 , [], or [] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4967--4967 [] \OT1/cmtt/m/n/10.95 @angle:CCCsaturated @atom:C @atom:C @atom:C @bond:SAT @bond:SAT[] Overfull \hbox (54.72884pt too wide) in paragraph at lines 4973--4978 []\OT1/cmr/m/n/10.95 The first line will gen-er-ate a 3-body an-gle in-ter-ac-t ion (of type []) Overfull \hbox (31.27754pt too wide) in paragraph at lines 4980--4988 []\OT1/cmr/m/n/10.95 The sec-ond line will gen-er-ate a 3-body in-ter-ac-tion o f type [] Overfull \hbox (34.34967pt too wide) in paragraph at lines 4990--4995 []\OT1/cmr/m/n/10.95 The third line will gen-er-ate a 3-body in-ter-ac-tion of type [] [66] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5089--5089 []\OT1/cmtt/m/n/10.95 ltemplify.py -name MoleculeName -mol MolID INPUT_SCRIPT D ATA_FILE > FILE.lt [67] [68] Overfull \hbox (69.51059pt too wide) in paragraph at lines 5127--5232 [] [69] Overfull \hbox (6.57567pt too wide) in paragraph at lines 5291--5295 \OT1/cmr/m/it/10.95 However, \OT1/cmr/m/n/10.95 ltem-plify.py uses com-ments in the ``Masses'' sec-tion of the LAMMPS [70] Overfull \hbox (26.77591pt too wide) in paragraph at lines 5344--5353 []\OT1/cmr/m/n/10.95 In this ex-am-ple, bonds of type 1 and 2 will be re-ferred to as ``@bond:CCethane'' [71] Overfull \hbox (1.40111pt too wide) in paragraph at lines 5370--5378 \OT1/cmr/m/n/10.95 PASS''), con-tain rules for gen-er-at-ing these in-ter-ac-ti ons au-to-mat-i-cally. Hence, [72] Overfull \hbox (19.41339pt too wide) in paragraph at lines 5496--5496 []\OT1/cmtt/m/n/10.95 ltemplify.py -name Ethane -molid "1" FILE.in FILE.data > ethane.lt [73] Overfull \hbox (30.91077pt too wide) in paragraph at lines 5566--5566 []\OT1/cmtt/m/n/10.95 ltemplify.py -name EntireSystem FILE.in FILE.data > entir e_system.lt [74] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5593--5593 []\OT1/cmtt/m/n/10.95 # This example creates a new file, "ethane.lt", which wil l contain the Overfull \hbox (30.91077pt too wide) in paragraph at lines 5594--5594 []\OT1/cmtt/m/n/10.95 # instructions for building a "Ethane" molecule using "GA FF2". First[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5595--5595 []\OT1/cmtt/m/n/10.95 # specify which file contains the definition of the "GAFF 2" force field:[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5599--5599 []\OT1/cmtt/m/n/10.95 # Then use ltemplify.py to extract information from FILE. in, FILE.data[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 5603--5603 [] \OT1/cmtt/m/n/10.95 -ignore-angles -ignore-bond-types -ignore-co effs \[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 5606--5606 []\OT1/cmtt/m/n/10.95 # Note: if you want to build a simulation containing thes e molecules,[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5607--5607 []\OT1/cmtt/m/n/10.95 # you will have to create a "system.lt" file which refers to "ethane.lt"[] [75] [76] [77] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5893--5893 []\OT1/cmtt/m/n/10.95 -atomstyle style By default, moltemplate.sh assumes you are using the "full"[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 5894--5894 [] \OT1/cmtt/m/n/10.95 atom style in LAMMPS. You can change the atom style to "dipole"[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5895--5895 [] \OT1/cmtt/m/n/10.95 using -atomstyle dipole. If you are usin g a hybrid style,[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5896--5896 [] \OT1/cmtt/m/n/10.95 you must enclose the list of styles in qu otes. For example:[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 5898--5898 [] \OT1/cmtt/m/n/10.95 For custom atom styles, you can also spec ify the[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5899--5899 [] \OT1/cmtt/m/n/10.95 list of column names manually (enclosed i n quotes):[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 5900--5900 [] \OT1/cmtt/m/n/10.95 -atomstyle "molid x y z atomid atomtype m ux muy muz"[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5901--5901 [] \OT1/cmtt/m/n/10.95 Be careful to enclose the entire list in quotes(").[] Overfull \hbox (134.38715pt too wide) in paragraph at lines 5903--5903 []\OT1/cmtt/m/n/10.95 -raw raw_file The raw_file file should contain the atom ic coordinates in RAW format.[] Overfull \hbox (117.14108pt too wide) in paragraph at lines 5904--5904 [] \OT1/cmtt/m/n/10.95 RAW files are simple 3-column ASCII files containin the coordinates[] Overfull \hbox (122.88977pt too wide) in paragraph at lines 5905--5905 [] \OT1/cmtt/m/n/10.95 for the atoms in the system. (One line pe r atom, 3 numbers per line.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5906--5906 [] \OT1/cmtt/m/n/10.95 The atoms must appear in the same order i n the data file.)[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5907--5907 []\OT1/cmtt/m/n/10.95 -xyz xyz_file An xyz_file argument should be supplied a s an argument[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 5909--5909 [] \OT1/cmtt/m/n/10.95 This file should contain the atomic coord inates in xyz format.[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5910--5910 [] \OT1/cmtt/m/n/10.95 (The atoms must appear in the same order in the data file.)[] Overfull \hbox (134.38715pt too wide) in paragraph at lines 5912--5912 []\OT1/cmtt/m/n/10.95 -pdb pdb_file The pdb_file file should contain the atom ic coordinates in PDB format.[] [78] Overfull \hbox (117.14108pt too wide) in paragraph at lines 5914--5914 [] \OT1/cmtt/m/n/10.95 This file should contain one ATOM or HETA TM record per atom. Atoms[] Overfull \hbox (105.6437pt too wide) in paragraph at lines 5916--5916 [] \OT1/cmtt/m/n/10.95 are sorted by chainID, resID, insertCode, atomID (in that order).[] Overfull \hbox (111.3924pt too wide) in paragraph at lines 5917--5917 [] \OT1/cmtt/m/n/10.95 This order must match the order the atoms appear in the data file.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5919--5919 [] \OT1/cmtt/m/n/10.95 If the PDB file contains periodic boundar y box information[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5920--5920 [] \OT1/cmtt/m/n/10.95 (IE., a "CRYST1" record), this informatio n is also copied[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5922--5922 [] \OT1/cmtt/m/n/10.95 (Support for triclinic cells is experimen tal as of 2019-9-03.[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5923--5923 [] \OT1/cmtt/m/n/10.95 Other molecular structure formats may be supported later.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5926--5926 [] \OT1/cmtt/m/n/10.95 The user can customize the numbers assign ed to atom, bond,[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5927--5927 [] \OT1/cmtt/m/n/10.95 angle, dihedral, and improper types or id numbers by using[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5929--5929 [] \OT1/cmtt/m/n/10.95 for each variable you want to modify. If there are many[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5930--5930 [] \OT1/cmtt/m/n/10.95 variables you want to modify, you can sav e them in a file[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5931--5931 [] \OT1/cmtt/m/n/10.95 (one variable per line). For an example of the file format[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5932--5932 [] \OT1/cmtt/m/n/10.95 run moltemplate.sh once and search for a file named[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5933--5933 [] \OT1/cmtt/m/n/10.95 "ttree_assignments.txt". (This file is o ften located in[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5934--5934 [] \OT1/cmtt/m/n/10.95 the "output_ttree/" directory.) Once assi gned, the remaining[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5935--5935 [] \OT1/cmtt/m/n/10.95 variables in the same category will be au tomatically assigned[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 5936--5936 [] \OT1/cmtt/m/n/10.95 to values which do not overlap with your chosen values.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5938--5938 [] \OT1/cmtt/m/n/10.95 "-b" is similar to "-a". However, in this case, no attempt[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5939--5939 [] \OT1/cmtt/m/n/10.95 is made to assign exclusive (unique) valu es to each variable.[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5941--5941 [] \OT1/cmtt/m/n/10.95 Normally moltemplate.sh checks for common errors and typos and[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 5942--5942 [] \OT1/cmtt/m/n/10.95 halts if it thinks it has found one. This forces the variables[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5943--5943 [] \OT1/cmtt/m/n/10.95 and categories as well as write(file) and write_once(file)[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5944--5944 [] \OT1/cmtt/m/n/10.95 commands to obey standard naming conventio ns. The "-nocheck"[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 5945--5945 [] \OT1/cmtt/m/n/10.95 argument bypasses these checks and elimina tes these restrictions.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5947--5947 [] \OT1/cmtt/m/n/10.95 This cause moltemplate.sh to check to mak e sure that there[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5948--5948 [] \OT1/cmtt/m/n/10.95 are valid angle and dihedral interactions defined for every[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 5949--5949 [] \OT1/cmtt/m/n/10.95 3 or 4 consecutively bonded atoms in the system[] [79] Overfull \hbox (13.6647pt too wide) in paragraph at lines 6010--6010 []\OT1/cmtt/m/n/10.95 moltemplate.sh -a '@atom:SPCE/O 2' -a '@atom:SPCE/H 1' s ystem.lt [80] Overfull \hbox (43.572pt too wide) in paragraph at lines 6093--6095 []\OT1/cmr/m/n/10.95 The ``ttree[]assignments.txt'' file has the same for-mat a s the ``new[]assignments.txt'' Overfull \hbox (0.80295pt too wide) in paragraph at lines 6115--6118 \OT1/cmr/m/n/10.95 If for some rea-son, you are us-ing ``lt-tree.py'' or ``ttre e.py'' in-stead of ``moltem- [81] [82] [83] [84] [85] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6502--6502 [] \OT1/cmtt/m/n/10.95 natom++; print "set atom "natom" x "$1" y "$2" z "$ 3" "}}' \[] [86] Overfull \hbox (8.35524pt too wide) in paragraph at lines 6562--6563 \OT1/cmr/m/it/10.95 file with the ap-pro-pri-ate in-te-ger be-fore you copy the con-tents into the LAMMPS Overfull \hbox (59.6542pt too wide) in paragraph at lines 6594--6594 [] \OT1/cmtt/m/n/10.95 nbody_by_type.py reads a LAMMPS data file (or an exce rpt of a LAMMPS) Overfull \hbox (25.16208pt too wide) in paragraph at lines 6595--6595 [] \OT1/cmtt/m/n/10.95 data file containing bonded many-body interactions by atom type[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6596--6596 [] \OT1/cmtt/m/n/10.95 (and bond type), and generates a list of additional i nteractions[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 6597--6597 [] \OT1/cmtt/m/n/10.95 in LAMMPS format consistent with those type (to the s tandard out).[] [87] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6615--6615 [] \OT1/cmtt/m/n/10.95 Support for other interaction types can be added by t he user. See below.[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6617--6617 [] \OT1/cmtt/m/n/10.95 Note: The optional "-subgraph" argument allows you to customize the[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6618--6618 [] \OT1/cmtt/m/n/10.95 rules used to match and generate interactions o f that type.[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6619--6619 [] \OT1/cmtt/m/n/10.95 It is optional, and is only useful for forcefie lds which[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6620--6620 [] \OT1/cmtt/m/n/10.95 use non-standard dihedral or improper atom-orde r convetions.)[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 6628--6628 [] \OT1/cmtt/m/n/10.95 "Dihedrals", or "Impropers"). It also looks a sectio n named "X By Type",[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6629--6629 [] \OT1/cmtt/m/n/10.95 (eg. "Angles By type", "Impropers By type", "Impro pers By type")[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6630--6630 [] \OT1/cmtt/m/n/10.95 which contains a list of criteria for automatically d efining additional[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6631--6631 [] \OT1/cmtt/m/n/10.95 interactions of that type. For example, this file mi ght contain:[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 6642--6642 [] \OT1/cmtt/m/n/10.95 The * is a wildcard symbol indicating there is no pre ference for bond types[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6643--6643 [] \OT1/cmtt/m/n/10.95 in this example. (Optionally, regular expressions ca n also be used to[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6644--6644 [] \OT1/cmtt/m/n/10.95 define a type match, by enclosing the atom or bond ty pe in / slashes.)[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6646--6646 [] \OT1/cmtt/m/n/10.95 The first line tells us to that there should be a 3-body "Angle"[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6647--6647 [] \OT1/cmtt/m/n/10.95 interaction of type "7" whenever an atom of type 1 is bonded to an atom[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6648--6648 [] \OT1/cmtt/m/n/10.95 of type "2", which is bonded to another atom of type "1" again.[] [88] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6649--6649 [] \OT1/cmtt/m/n/10.95 The second line tells us that an angle is defined whe never three atoms[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 6654--6654 [] \OT1/cmtt/m/n/10.95 atoms which match these criteria if they are bonded t ogether[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6655--6655 [] \OT1/cmtt/m/n/10.95 in the relevant way for that interaction type (as det ermined by[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6656--6656 [] \OT1/cmtt/m/n/10.95 nbody_X.py), and printed to the standard output. For example,[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 6657--6657 [] \OT1/cmtt/m/n/10.95 suppose you are automatically generating 3-body "Angl e" interactions using:[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6661--6661 [] \OT1/cmtt/m/n/10.95 The file "new.data" will be identical to "old.data", however the[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6662--6662 [] \OT1/cmtt/m/n/10.95 "Angles By Type" section will be deleted, and the fol lowing lines of[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6671--6671 [] \OT1/cmtt/m/n/10.95 The numbers in the first column are counters which as sign a ID to[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 6672--6672 [] \OT1/cmtt/m/n/10.95 every interaction of that type, and start where the o riginal "Angles"[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6673--6673 [] \OT1/cmtt/m/n/10.95 data left off (New angle ID numbers do not overlap wi th old ID numbers).[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6674--6674 [] \OT1/cmtt/m/n/10.95 The text in the second column ("7", "9", ...) matches the text from the[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6675--6675 [] \OT1/cmtt/m/n/10.95 first column of the "Angle By Type" section of the in put file.[] [89] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6697--6697 [] \OT1/cmtt/m/n/10.95 When run this way, nbody_by_type.py behaves exactly t he same way[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6698--6698 [] \OT1/cmtt/m/n/10.95 as in Example 1, however only the lines of text corre sponding to[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6699--6699 [] \OT1/cmtt/m/n/10.95 the new generated interactions are printed, (not the entire data file).[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 6700--6700 [] \OT1/cmtt/m/n/10.95 Also note, that when run this way, nbody_by_type.py d oes not read the[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6701--6701 [] \OT1/cmtt/m/n/10.95 LAMMPS data from the standard input. Instead, it rea ds each section of[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6702--6702 [] \OT1/cmtt/m/n/10.95 the data file from a different file indicated by the arguments following[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 6703--6703 [] \OT1/cmtt/m/n/10.95 the "-atoms", "-bonds", "-nbody", and "-nbodybytype" flags.[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6705--6705 [] \OT1/cmtt/m/n/10.95 "Angles" is a 3-body interaction style. So when run this way,[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6706--6706 [] \OT1/cmtt/m/n/10.95 nbody_by_type.py will create a 5 (=3+2) column file ( new_Angles.data).[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 6708--6708 []\OT1/cmtt/m/n/10.95 Note: the atom, bond and other IDs/types in need not be i ntegers.[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 6710--6710 []\OT1/cmtt/m/n/10.95 Note: This program must be distributed with several pytho n modules, including:[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6711--6711 [] \OT1/cmtt/m/n/10.95 nbody_Angles.py, nbody_Dihedrals.py, and nbody_Im propers.py. These[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 6712--6712 [] \OT1/cmtt/m/n/10.95 contain bond definitions for angular, dihedral, and improper interactions.[] Overfull \hbox (1.14366pt too wide) in paragraph at lines 6717--6732 \OT1/cmr/m/n/10.95 im-ports ex-ter-nal mod-ules named ``nbody[]Angles.py'', ``n body[]Dihedrals.py'', Overfull \hbox (4.07088pt too wide) in paragraph at lines 6741--6743 \OT1/cmr/m/n/10.95 Moltemplate.sh is a script which in-vokes a python pro-gram pro-gram (\OT1/cmr/m/it/10.95 ttree.py\OT1/cmr/m/n/10.95 ) [90] Overfull \hbox (82.64896pt too wide) in paragraph at lines 6766--6766 []\OT1/cmtt/m/n/10.95 String ::= InstanceName | ObjectTypeName | FileName | Cat egoryName | OtherStr Overfull \hbox (76.90027pt too wide) in paragraph at lines 6796--6796 []\OT1/cmtt/m/n/10.95 Command ::= ObjectDef | InstanceCommand | DeleteCommand | WriteC | WriteOC | Overfull \hbox (48.15683pt too wide) in paragraph at lines 6797--6797 [] \OT1/cmtt/m/n/10.95 ImportCommand | CategoryDef | InstanceMod | O bjectTypeMod |[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6798--6798 [] \OT1/cmtt/m/n/10.95 ObjectDefMod | ReplaceCommand | UsingCommand | PushXform[] [91] Overfull \hbox (7.91602pt too wide) in paragraph at lines 6813--6813 []\OT1/cmtt/m/n/10.95 RotXform ::= ".rot(" Number "," Number "," Number "," Num ber ")"[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6833--6833 []\OT1/cmtt/m/n/10.95 TemplText ::= "" | String TemplText | StatVar TemplText | InstVar TemplText[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 6837--6837 []\OT1/cmtt/m/n/10.95 WriteOC ::= "write_once(" FileName ")" "{" TemplateTextSt at "}"[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6838--6838 []\OT1/cmtt/m/n/10.95 TemplTextStat ::= "" | String TemplTextStat | StatVar Tem plTextStat[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6849--6849 []\OT1/cmtt/m/n/10.95 CatCommandStat ::= "category" "@"CategoryName"(" Integer "," Integer ")"[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6850--6850 []\OT1/cmtt/m/n/10.95 CatCommandInst ::= "category" "$"CategoryName"(" Integer "," Integer ")"[] [92] [93] Overfull \hbox (5.00008pt too wide) in paragraph at lines 6955--6959 []\OT1/cmr/m/n/10.95 Find the cat-e-gory name and ob-ject cor-re-spond-ing to ` `\TS1/cmr/m/n/10.95 $\OT1/cmr/bx/it/10.95 cpath\OT1/cmr/m/n/10.95 /\OT1/cmr/bx/ it/10.95 catname\OT1/cmr/m/n/10.95 :'' [94] Overfull \hbox (43.72781pt too wide) in paragraph at lines 6972--6973 \OT1/cmr/m/n/10.95 file (al-though you can use it any-where else in an ``.LT'' file). In ``ttree[]assignments.txt'' No file moltemplate_manual.bbl. [95] (./moltemplate_manual.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on moltemplate_manual.pdf (95 pages, 833954 bytes). Transcript written on moltemplate_manual.log. This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: moltemplate_manual.aux The style file: unsrt.bst Database file #1: refs.bib This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: moltemplate_manual.aux The style file: unsrt.bst Database file #1: refs.bib This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./moltemplate_manual.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2025/01/22 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./moltemplate_manual.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./moltemplate_manual.out) (./moltemplate_manual.out) (./moltemplate_manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map} <./author_email.png>] [2]) LaTeX Warning: Citation `MOLTEMPLATE' on page 3 undefined on input line 72. [3] Overfull \hbox (12.60272pt too wide) in paragraph at lines 91--111 \OT1/cmr/m/n/10.95 which can be con-verted into moltem-plate for-mat (LT for-ma t) us-ing []\OT1/cmtt/m/n/10.95 mol22lt.py[] [4] Overfull \hbox (2.16733pt too wide) in paragraph at lines 197--197 []\OT1/cmtt/m/n/10.95 moltemplate.sh -xyz coords.xyz -atomstyle "full" -vmd sys tem.lt LaTeX Warning: Citation `ATB' on page 5 undefined on input line 299. Overfull \hbox (1.51479pt too wide) in paragraph at lines 299--306 \OT1/cmr/m/n/10.95 The \OT1/cmr/bx/n/10.95 ATB \OT1/cmr/m/n/10.95 ser-vice [[]] men-tioned ear-lier ([]$\OT1/cmtt/m/n/10.95 https : / / atb . uq . edu . au$[] \OT1/cmr/m/n/10.95 ) is a repos- LaTeX Warning: Citation `topotools' on page 5 undefined on input line 308. LaTeX Warning: Citation `OpenBABEL' on page 5 undefined on input line 309. LaTeX Warning: Citation `VMD' on page 5 undefined on input line 312. LaTeX Warning: Citation `topotools' on page 5 undefined on input line 312. LaTeX Warning: Citation `OVITO' on page 5 undefined on input line 312. LaTeX Warning: Citation `packmol' on page 5 undefined on input line 321. [5] Overfull \hbox (19.41339pt too wide) in paragraph at lines 471--471 []\OT1/cmtt/m/n/10.95 python -m venv ~/venv #(or "virtualenv venv" if using python2) [6] Overfull \hbox (7.91602pt too wide) in paragraph at lines 496--496 []\OT1/cmtt/m/n/10.95 git clone https://github.com/jewettaij/moltemplate ~/molt emplate Overfull \hbox (30.91077pt too wide) in paragraph at lines 517--517 []\OT1/cmtt/m/n/10.95 pip3 install . # (or "pip3 install --user", or "pip" if that fails)[] Overfull \hbox (0.52628pt too wide) in paragraph at lines 520--526 []\OT1/cmr/m/n/10.95 As men-tioned ear-lier, if you are hav-ing dif-fi-culty, t ry to in-stalling moltem- [7] Overfull \hbox (25.16208pt too wide) in paragraph at lines 593--609 \OT1/cmtt/m/n/10.95 bashonubuntuonwindows / comments / 6bu1d1 / since _ we _ sh ouldnt _ edit _ files _ [8] Overfull \hbox (0.32121pt too wide) in paragraph at lines 612--612 []\OT1/cmr/bx/n/14.4 Quick ref-er-ence \OT1/cmr/bx/it/14.4 (SKIP ON FIRST READ- ING) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Underfull \hbox (badness 7064) in paragraph at lines 683--688 []|\OT1/cmr/m/n/10.95 Apply co-or-di-nate trans-for-ma-tions ([] to Underfull \hbox (badness 10000) in paragraph at lines 792--797 []|\OT1/cmr/m/n/10.95 Delete a range of molecules spec-i-fied by Underfull \hbox (badness 1616) in paragraph at lines 792--797 []\OT1/cmr/m/n/10.95 . (This also works for mul-ti-di- Overfull \hbox (121.47046pt too wide) in alignment at lines 623--895 [] [] ignored error: Infinite glue shrinkage found in box being split [9] ignored error: Infinite glue shrinkage found in box being split [10] [11] Underfull \hbox (badness 10000) in paragraph at lines 907--909 Overfull \hbox (131.64603pt too wide) in alignment at lines 909--1047 [] [] ignored error: Infinite glue shrinkage found in box being split [12] [13] Underfull \hbox (badness 10000) in paragraph at lines 1058--1061 Underfull \hbox (badness 10000) in paragraph at lines 1058--1061 Overfull \hbox (124.34627pt too wide) in alignment at lines 1061--1190 [] [] [14] Underfull \hbox (badness 1418) in paragraph at lines 1387--1391 \OT1/cmr/m/n/10.95 ``bond[]coeff'', ``an-gle[]coeff'', ``di-he-dral[]coeff'', a nd ``im- Overfull \hbox (123.88596pt too wide) in alignment at lines 1203--1417 [] [] ignored error: Infinite glue shrinkage found in box being split [15] ignored error: Infinite glue shrinkage found in box being split [16] [17] Overfull \hbox (13.54758pt too wide) in paragraph at lines 1432--1454 \OT1/cmr/m/n/10.95 tackle the same steep learning-curve (and oc-ca-sional bugs) that other LAMMPS Overfull \hbox (16.26949pt too wide) in paragraph at lines 1459--1459 []\OT1/cmr/bx/n/12 Simulating a box of wa-ter us-ing moltem-plate and LAMMPS LaTeX Warning: Citation `Berendsen++StraatsmaJPhysChem1987' on page 18 undefine d on input line 1475. Overfull \hbox (53.90552pt too wide) in paragraph at lines 1494--1494 [] \OT1/cmtt/m/n/10.95 ## Atom properties and bond topology go in various "Dat a ..." sections[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1496--1496 [] \OT1/cmtt/m/n/10.95 # We selected "atom_style full". That means we use this column format:[] [18 <./single_water_LR.jpg>] Overfull \hbox (19.41339pt too wide) in paragraph at lines 1497--1497 [] \OT1/cmtt/m/n/10.95 # atomID molID atomType charge coordX coordY coordZ[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1500--1500 [] \OT1/cmtt/m/n/10.95 $atom:o $mol:w @atom:O -0.8476 0.0000000 0.00000 0 0.00000[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1501--1501 [] \OT1/cmtt/m/n/10.95 $atom:h1 $mol:w @atom:H 0.4238 0.8164904 0.57735 90 0.00000[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 1502--1502 [] \OT1/cmtt/m/n/10.95 $atom:h2 $mol:w @atom:H 0.4238 -0.8164904 0.5773 590 0.00000[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 1505--1505 [] \OT1/cmtt/m/n/10.95 # Variables beginning with $ or @ will be replaced by n umbers LAMMPS will[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 1506--1506 [] \OT1/cmtt/m/n/10.95 # eventually read. Each of the three atoms" will be as signed unique[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1507--1507 [] \OT1/cmtt/m/n/10.95 # atomIDs (denoted here by "$atom:o", "$atom:h1", "$ato m:h2"), even if[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 1508--1508 [] \OT1/cmtt/m/n/10.95 # they belong to different molecules. However, the ato m types[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 1509--1509 [] \OT1/cmtt/m/n/10.95 # (denoted "@atom:O", "@atom:H") are shared for atoms i n all molecules.[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1510--1510 [] \OT1/cmtt/m/n/10.95 # All 3 atoms share same molID number (represeted here by "$mol:w")[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1511--1511 [] \OT1/cmtt/m/n/10.95 # however that number is different for different water molecules.[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1530--1530 [] \OT1/cmtt/m/n/10.95 # --- Force-field parameters go in the "In Settings" se ction: ---[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1534--1534 [] \OT1/cmtt/m/n/10.95 # atomType1 atomType2 parameter-list (epsil on, sigma)[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 1537--1537 [] \OT1/cmtt/m/n/10.95 # (mixing rules determine interactions between types @atom:O and @atom:H)[] [19] Overfull \hbox (99.89502pt too wide) in paragraph at lines 1545--1545 [] \OT1/cmtt/m/n/10.95 # Group definitions and constraints can also go in th e "In Settings" section[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 1547--1547 [] \OT1/cmtt/m/n/10.95 fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @ang le:HOH[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1548--1548 [] \OT1/cmtt/m/n/10.95 # (lammps quirk: Remember to "unfix fSHAKE" during mi nimization.)[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1551--1551 [] \OT1/cmtt/m/n/10.95 # LAMMPS supports a large number of force-field styles. We must select[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 1552--1552 [] \OT1/cmtt/m/n/10.95 # which ones we need. This information belongs in the " In Init" section.[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 1555--1555 [] \OT1/cmtt/m/n/10.95 units real # angstroms, kCal/m ole, Daltons, Kelvin[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 1556--1556 [] \OT1/cmtt/m/n/10.95 atom_style full # select column for mat for Atoms section[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 1557--1557 [] \OT1/cmtt/m/n/10.95 pair_style lj/charmm/coul/long 9.0 10.0 10 # param s needed: epsilon sigma[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1558--1558 [] \OT1/cmtt/m/n/10.95 bond_style harmonic # parameters needed : k_bond, r0[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 1559--1559 [] \OT1/cmtt/m/n/10.95 angle_style harmonic # parameters needed : k_theta, theta0[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 1560--1560 [] \OT1/cmtt/m/n/10.95 kspace_style pppm 0.0001 # long-range electr ostatics sum method[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 1561--1561 [] \OT1/cmtt/m/n/10.95 pair_modify mix arithmetic # using Lorenz-Bert helot mixing rules[] Overfull \hbox (14.12546pt too wide) in paragraph at lines 1575--1576 \OT1/cmr/m/n/10.95 You can now use ``moltem-plate.sh'' to cre-ate sim-u-la-tion in-put files for LAMMPS [20] Overfull \hbox (0.73196pt too wide) in paragraph at lines 1637--1649 \OT1/cmr/m/n/10.95 (See sec-tion []6[] for more de-tails and ex-am-ples.) This will cre-ate 1000 molecules Overfull \hbox (40.6773pt too wide) in paragraph at lines 1637--1649 \OT1/cmr/m/n/10.95 ta-tion: ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.95 atom:wat[2 ][3][4]/h1'', ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.95 bond:wat[0][5][1]/oh1'', ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.95 an-gle:wat[2][8][3]/hoh'', Overfull \hbox (10.06793pt too wide) in paragraph at lines 1656--1659 \OT1/cmr/m/n/10.95 spec-ify the di-men-sions of the sim-u-la-tion bound-ary us- ing the ``write[]once(``Data [21] [22 <./waterSPCEx1000_LR.jpg> <./waterSPCEx1000_t=25_LR.jpg>] LaTeX Warning: Citation `OVITO' on page 23 undefined on input line 1783. Overfull \hbox (33.74133pt too wide) in paragraph at lines 1799--1809 []\OT1/cmr/m/n/10.95 Moltemplate will cre-ate the fol-low-ing files: ``sys-tem. data'', ``run.in.EXAMPLE'', [23] LaTeX Warning: Citation `VMD' on page 24 undefined on input line 2007. Overfull \hbox (5.23363pt too wide) in paragraph at lines 2004--2011 \OT1/cmr/m/n/10.95 which can vi-su-al-ize the sys-tem. If you have saved your t ra-jec-tory in LAMMPS [24] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2012--2012 []\OT1/cmtt/m/n/10.95 dump 1 all custom 1000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz Overfull \hbox (29.2559pt too wide) in paragraph at lines 2019--2022 []\OT1/cmr/m/n/10.95 a) Start VMD From the menu in the upper-left, se-lect \OT1 /cmr/bx/n/10.95 File$\OMS/cmsy/m/n/10.95 !$[] [25] Overfull \hbox (24.8004pt too wide) in paragraph at lines 2168--2175 \OT1/cmr/m/n/10.95 In the ex-am-ple above, the \TS1/cmr/m/n/10.95 $ \OT1/cmr/m/ n/10.95 vari-ables have full-names like ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.9 5 atom:wat[8][3][7]/h1'', [26] [27] [28] Overfull \hbox (0.77374pt too wide) in paragraph at lines 2342--2342 []\OT1/cmr/bx/it/12 (Advanced) \OT1/cmr/bx/n/12 Us-ing moltem-plate to gen-er-a te aux-il-iary files Overfull \hbox (36.65945pt too wide) in paragraph at lines 2353--2353 [] \OT1/cmtt/m/n/10.95 mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.33333 7.04956 0. 602224 4 0 0[] [29] [30] [31 <./2bead_monomer.jpg> <./2bead_polymer.jpg> <./2bead_polymers_nop bc_t=0_LR.jpg> <./2bead_polymers_t=100ps_LR.jpg>] Overfull \hbox (0.3771pt too wide) in paragraph at lines 2460--2461 \OT1/cmr/m/n/10.95 Consider the fol-low-ing sim-ple 2-atom dumbell-shaped molel ule (``Monomer'') Overfull \hbox (7.91602pt too wide) in paragraph at lines 2470--2470 [] \OT1/cmtt/m/n/10.95 $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0. 0000000[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 2471--2471 [] \OT1/cmtt/m/n/10.95 $atom:r $mol:... @atom:R 0.0 0.000 4.4000 0. 0000000[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 2505--2505 [] \OT1/cmtt/m/n/10.95 create_var {$mol} #(force all Monomers to share the sa me molecule-ID)[] [32] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2519--2519 [] \OT1/cmtt/m/n/10.95 $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom :mon2/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2520--2520 [] \OT1/cmtt/m/n/10.95 $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom :mon3/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2521--2521 [] \OT1/cmtt/m/n/10.95 $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom :mon4/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2522--2522 [] \OT1/cmtt/m/n/10.95 $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom :mon5/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2523--2523 [] \OT1/cmtt/m/n/10.95 $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom :mon6/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2524--2524 [] \OT1/cmtt/m/n/10.95 $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom :mon7/ca[] [33] Overfull \hbox (42.40814pt too wide) in paragraph at lines 2631--2631 [] \OT1/cmtt/m/n/10.95 # Force-field parameters ("coeffs") go in the "In Setti ngs" section:[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 2638--2638 [] \OT1/cmtt/m/n/10.95 # (Interactions between different atoms are determine d by mixing rules.)[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2651--2651 [] \OT1/cmtt/m/n/10.95 # Although the simple "Monomer" object we defined above has only[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2652--2652 [] \OT1/cmtt/m/n/10.95 # two atoms, later on, we will create molecules with ma ny bonds.[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 2653--2653 [] \OT1/cmtt/m/n/10.95 # By convention, in this file we keep track of all of t he possible[] [34] Overfull \hbox (76.90027pt too wide) in paragraph at lines 2656--2656 [] \OT1/cmtt/m/n/10.95 # Rules for determining 3-body (angle) interactions by atom and bond type:[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2657--2657 [] \OT1/cmtt/m/n/10.95 # angle-type atomType1 atomType2 atomType3 bondTyp e1 bondType2[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2660--2660 [] \OT1/cmtt/m/n/10.95 @angle:Backbone @atom:CA @atom:CA @atom:CA @bond :* @bond:*[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2661--2661 [] \OT1/cmtt/m/n/10.95 @angle:Sidechain @atom:CA @atom:CA @atom:R @bond :* @bond:*[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 2674--2674 [] \OT1/cmtt/m/n/10.95 # 4-body interactions in this example are listed by ato m type and (optionally)[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2675--2675 [] \OT1/cmtt/m/n/10.95 # by bond type. (You can use wildcards * to accept all bond types.)[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 2677--2677 [] \OT1/cmtt/m/n/10.95 # dihedralType atmType1 atmType2 atmType3 atmType4 bo ndType1 bType2 bType3[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 2679--2679 [] \OT1/cmtt/m/n/10.95 @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @ bond:* @bond:* @bond:*[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 2680--2680 [] \OT1/cmtt/m/n/10.95 @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @ bond:* @bond:* @bond:*[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2699--2699 [] \OT1/cmtt/m/n/10.95 # -- (Changing these styles will change the formulas above) --[] [35] [36] Overfull \hbox (9.77596pt too wide) in paragraph at lines 2782--2789 \OT1/cmr/m/n/10.95 Notice that we did not spec-ify the ``@bond:SideChain'' and ``@bond:Backbone'' Overfull \hbox (76.60141pt too wide) in paragraph at lines 2795--2808 \OT1/cmr/m/n/10.95 names can be quite long and dif-fi-cult to type (such as ``@ atom:h1h[]ph1h[]bh1h[]ah1[]dh1[]ih1''). [37] Overfull \hbox (14.1924pt too wide) in paragraph at lines 2873--2874 \OT1/cmr/m/n/10.95 For de-tails, see the ``cen-JswapIL.py'' file (lo-cated in t he ``nbody[]alt[]symmetry/'' [38] [39] Overfull \hbox (19.81343pt too wide) in paragraph at lines 2963--2973 \OT1/cmr/m/n/10.95 The first line tells moltem-plate that any bond be-tween ato ms of type ``@atom:h1'' [40] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3058--3058 [] \OT1/cmtt/m/n/10.95 # Note: This will not overwrite the preexisting "ForceF ield" object.[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3059--3059 [] \OT1/cmtt/m/n/10.95 # (Instead, it augments the "ForceField" object d efined earlier.)[] Overfull \hbox (2.11093pt too wide) in paragraph at lines 3074--3079 \OT1/cmr/m/n/10.95 ``@atom:R'', and ``@atom:CB'', since they all be-long to the same ``[]'' Overfull \hbox (59.6542pt too wide) in paragraph at lines 3084--3084 [] \OT1/cmtt/m/n/10.95 # Here you can refer to @atoms, @bonds, etc... defined in either file:[] [41] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3139--3139 [] \OT1/cmtt/m/n/10.95 $bond:backbone1 @bond:Backbone $atom:monomers[0]/ca $atom:monomers[1]/ca[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3140--3140 [] \OT1/cmtt/m/n/10.95 $bond:backbone2 @bond:Backbone $atom:monomers[1]/ca $atom:monomers[2]/ca[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3141--3141 [] \OT1/cmtt/m/n/10.95 $bond:backbone3 @bond:Backbone $atom:monomers[2]/ca $atom:monomers[3]/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 3142--3142 [] \OT1/cmtt/m/n/10.95 : : : :[] Overfull \hbox (9.44891pt too wide) in paragraph at lines 3159--3163 \OT1/cmr/m/n/10.95 This will cre-ate 7 molecules. The co-or-di-nates of the fir st molecule \OT1/cmr/m/it/10.95 monomers[0] [42] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3169--3169 [] \OT1/cmtt/m/n/10.95 monomers = new Monomer.scale(1.5) [7].rot(180, 1,0,0).m ove(3.2,0,0) Overfull \hbox (25.16208pt too wide) in paragraph at lines 3185--3185 [] \OT1/cmtt/m/n/10.95 # "monomers[0]", "monomers[1]", "monomers[2]", ... "mon omers[6]".[] [43] Overfull \hbox (7.91602pt too wide) in paragraph at lines 3255--3255 [] \OT1/cmtt/m/n/10.95 monomers = new random([Monomer, Monomer3], [0.6, 0.4], 123456)[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3260--3260 [] \OT1/cmtt/m/n/10.95 $bond:bb1 @bond:Backbone $atom:monomers[0]/ca $atom:m onomers[1]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3261--3261 [] \OT1/cmtt/m/n/10.95 $bond:bb2 @bond:Backbone $atom:monomers[1]/ca $atom:m onomers[2]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3262--3262 [] \OT1/cmtt/m/n/10.95 $bond:bb3 @bond:Backbone $atom:monomers[2]/ca $atom:m onomers[3]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3263--3263 [] \OT1/cmtt/m/n/10.95 $bond:bb4 @bond:Backbone $atom:monomers[3]/ca $atom:m onomers[4]/ca[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3268--3268 [] \OT1/cmtt/m/n/10.95 $bond:bb50 @bond:Backbone $atom:monomers[48]/ca $atom :monomers[49]/ca Overfull \hbox (19.41339pt too wide) in paragraph at lines 3270--3270 [] \OT1/cmtt/m/n/10.95 #(Note: Both the "Monomer" and "Monomer3" subunits cont ain atoms[] [44 <./random_2bead.jpg> <./random_3bead.jpg> <./random_heteropolymer.jpg>] Overfull \hbox (21.21399pt too wide) in paragraph at lines 3324--3328 []\OT1/cmr/m/it/10.95 Note: \OT1/cmr/m/n/10.95 Al-though this ex-am-ple, there are only two monomer types (``Monomer'' Overfull \hbox (31.28319pt too wide) in paragraph at lines 3339--3343 []\OT1/cmr/m/it/10.95 Note: \OT1/cmr/m/n/10.95 Once a molecule con-tain-ing ran -dom monomers is de-fined, ([] [45] Overfull \hbox (30.91077pt too wide) in paragraph at lines 3409--3409 [] \OT1/cmtt/m/n/10.95 monomers[1-48] = new random([Monomer, Monomer3], [30, 1 8], 123456)[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3412--3412 [] \OT1/cmtt/m/n/10.95 # It's a good idea to move these monomers to keep them from overlapping[] [46] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3460--3460 []\OT1/cmtt/m/n/10.95 delete molecules[0-1][1][1-2] # (shorthand for delete mol ecules[0][1][1] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3461--3461 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[0][1][2][] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3462--3462 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[1][1][1][] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3463--3463 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[1][1][2])[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 3469--3469 []\OT1/cmtt/m/n/10.95 # ...and move them back to the location of the vacancies we created[] Overfull \hbox (4.88002pt too wide) in paragraph at lines 3478--3484 \OT1/cmr/m/n/10.95 You can use [] to fill space with a ran-dom mix-ture of mole cules. Overfull \hbox (53.90552pt too wide) in paragraph at lines 3485--3485 []\OT1/cmtt/m/n/10.95 import "lipids" # def ine DPPC & DLPC Overfull \hbox (48.15683pt too wide) in paragraph at lines 3486--3486 []\OT1/cmtt/m/n/10.95 lipids = new random([DPPC,DLPC], [0.5,0.5], 123) # "12 3"=random_seed[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3487--3487 [] \OT1/cmtt/m/n/10.95 [19].move(7.5, 0, 0) # lat tice spacing 7.5[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 3488--3488 [] \OT1/cmtt/m/n/10.95 [22].move(3.75, 6.49519, 0) # hex agonal lattice[] [47] Overfull \hbox (19.41339pt too wide) in paragraph at lines 3489--3489 [] \OT1/cmtt/m/n/10.95 [2].rot(180, 1, 0, 0) # 2 m onolayers[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3516--3516 []\OT1/cmtt/m/n/10.95 lipids = new random([DPPC, ,DLPC], [0.35,0.3,0.35], 123) # 2nd element is blank [48 <./lipid_bilayer_mixture.jpg> <./lipid_bilayer_vacancies.jpg>] [49 <./delet e_holes1.jpg>] Overfull \hbox (33.65005pt too wide) in paragraph at lines 3640--3642 []\OT1/cmr/m/n/10.95 We can sub-squently cus-tomize the po-si-tion of the 3rd m onomer (``monomers[2]'') Overfull \hbox (128.63846pt too wide) in paragraph at lines 3678--3678 [] \OT1/cmtt/m/n/10.95 $atom:mol_complex/polymers[0]/monomers[2]/ca $mol:mol_c omplex @atom:R 0 6.4 8.2 0.6[] Overfull \hbox (190.20093pt too wide) in paragraph at lines 3681--3691 \OT1/cmr/m/n/10.95 This is a sit-u-a-tion where we must use the \OT1/cmr/m/it/1 0.95 full \OT1/cmr/m/n/10.95 name of the atom (``\TS1/cmr/m/n/10.95 $\OT1/cmr/m /n/10.95 atom:mol[]complex/polymers[0]/monomers[2]/ca'') [50] Overfull \hbox (25.16208pt too wide) in paragraph at lines 3695--3695 [] \OT1/cmtt/m/n/10.95 $atom:polymers[0]/monomers[2]/ca $mol:... @atom:R 0 6 .4 8.2 0.6[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3714--3714 [] \OT1/cmtt/m/n/10.95 $bond:mol_complex/polymers[0]/backbone3 @bond:ForceFiel d/LongBond &[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 3736--3736 []\OT1/cmtt/m/n/10.95 # Note: This will augment the "ForceField" object, not ov erwrite it: [51] Overfull \hbox (65.4029pt too wide) in paragraph at lines 3774--3774 []\OT1/cmtt/m/n/10.95 delete mol_complex/polymers[1]/monomers[3]/ca #<-- dele tes the "ca" atom Overfull \hbox (65.4029pt too wide) in paragraph at lines 3775--3775 []\OT1/cmtt/m/n/10.95 delete mol_complex/polymers[1]/monomers[4]/cr #<-- dele tes the "cr" bond[] [52] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3865--3865 []\OT1/cmtt/m/n/10.95 MolecularComplex0 = MolecularComplex.move(-9.6,-6.2, 0).s cale(0.3125) Overfull \hbox (25.16208pt too wide) in paragraph at lines 3882--3882 []\OT1/cmtt/m/n/10.95 # Add some new atoms connecting the two polymers in the m ol_complex[] Overfull \hbox (2.00154pt too wide) in paragraph at lines 3936--3937 []\OT1/cmr/m/it/10.95 Note: These co-or-di-nate trans-for-ma-tions will be ap-p lied \OT1/cmr/bx/it/10.95 af-ter \OT1/cmr/m/it/10.95 the molecule [53] [54 <./mol_complex_LR.jpg> <./mol_complex+mol_complex0_transparent_LR.jpg> ] Overfull \hbox (2.16733pt too wide) in paragraph at lines 4031--4031 [] \OT1/cmtt/m/n/10.95 $atom:o $mol:w @atom:O -0.8476 0.0000000 0.00000 0. 000000[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4032--4032 [] \OT1/cmtt/m/n/10.95 $atom:h1 $mol:w @atom:H 0.4238 0.8164904 0.00000 0 .5773590[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4033--4033 [] \OT1/cmtt/m/n/10.95 $atom:h2 $mol:w @atom:H 0.4238 -0.8164904 0.00000 0 .5773590[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4044--4044 [] \OT1/cmtt/m/n/10.95 # atomTypeI atomTypeJ pair-style-name p arameter-list[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4046--4046 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:O @atom:O lj/charmm/coul/long 0 .1553 3.166[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4047--4047 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:H @atom:H lj/charmm/coul/long 0 .0 2.058[] [55] Overfull \hbox (2.16733pt too wide) in paragraph at lines 4076--4076 [] \OT1/cmtt/m/n/10.95 fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @ang le:HOH[] Overfull \hbox (25.39783pt too wide) in paragraph at lines 4082--4085 \OT1/cmr/m/n/10.95 There are two dif-fer-ences be-tween this molecule def-i-ni- tion and the ``spce[]simple.lt'' [56] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4172--4172 [] \OT1/cmtt/m/n/10.95 pair_style hybrid lj/charmm/coul/long 9 10 10 table spl ine 1000[] Overfull \hbox (11.69077pt too wide) in paragraph at lines 4187--4187 [][]\OT1/cmr/bx/n/10.95 Warning: Force-field pa-ram-e-ters be-long in ``In Set- tings'', not ``Data'' [57] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4261--4261 [] \OT1/cmtt/m/n/10.95 # AtomID MolID('.'=this) AtomType charge coordX coor dY coordZ[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4263--4263 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.000000 000 1.0000000[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4264--4264 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.951056 516 0.3090170[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4265--4265 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.587785 252 -0.809017[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 4266--4266 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 -0.58778 5252 -0.809017[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 4267--4267 [] \OT1/cmtt/m/n/10.95 $atom:c5 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 -0.95105 6516 0.3090170[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4287--4287 []\OT1/cmtt/m/n/10.95 # A cubic lattice of 125 cyclopentane molecules (12-angst rom spacing) [58] Overfull \hbox (65.4029pt too wide) in paragraph at lines 4288--4288 []\OT1/cmtt/m/n/10.95 mols = new Cyclopentane [5].move(0,0,12) [5].move(0,12,0) [5].move(12,0,0)[] LaTeX Warning: Citation `TraPPE' on page 59 undefined on input line 4295. Overfull \hbox (42.40814pt too wide) in paragraph at lines 4319--4319 [] \OT1/cmtt/m/n/10.95 dihedral_coeff @dihedral:CCCC opls 1.411036 -0.271016 3.145034 0.0[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 4320--4320 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 4321--4321 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4322--4322 [] \OT1/cmtt/m/n/10.95 # (Interactions between different atom types use mixi ng rules.)[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 4329--4329 [] \OT1/cmtt/m/n/10.95 @dihedral:CCCC @atom:C* @atom:C* @atom:C* @atom:C* @bo nd:CC @bond:CC @bond:CC[] [59] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4395--4395 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:bt @atom:TraPPE/CH3 0.0 0.419372 0.00 0 -1.937329[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4396--4396 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:bt @atom:TraPPE/CH2 0.0 -0.419372 0.0 00 -0.645776[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4397--4397 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:bt @atom:TraPPE/CH2 0.0 0.419372 0.00 0 0.645776[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4398--4398 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:bt @atom:TraPPE/CH3 0.0 -0.419372 0.0 000 1.937329[] [60] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4433--4433 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:bt @atom:../CH3 0.0 0.419372 0.000 -1.937329[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4434--4434 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:bt @atom:../CH2 0.0 -0.419372 0.000 -0.645776[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4435--4435 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:bt @atom:../CH2 0.0 0.419372 0.000 0.645776[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4436--4436 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:bt @atom:../CH3 0.0 -0.419372 0.000 0 1.937329[] Overfull \hbox (6.15454pt too wide) in paragraph at lines 4448--4449 \OT1/cmr/bx/it/10.95 NOTE: Again, al-though the ``nest-ing'' method ex-plained here works, [61] [62] Overfull \hbox (19.81343pt too wide) in paragraph at lines 4615--4625 \OT1/cmr/m/n/10.95 atom type ``@atom:CH3'' in-stead of ``@atom:TraPPE/CH3'', or ``@atom:../CH3'' Overfull \hbox (23.57642pt too wide) in paragraph at lines 4655--4662 \OT1/cmr/m/n/10.95 If two molecules are re-lated to each other this way: [], [63] [64] [65] Overfull \hbox (40.92256pt too wide) in paragraph at lines 4955--4962 []\OT1/cmr/m/n/10.95 , [], or [] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4967--4967 [] \OT1/cmtt/m/n/10.95 @angle:CCCsaturated @atom:C @atom:C @atom:C @bond:SAT @bond:SAT[] Overfull \hbox (54.72884pt too wide) in paragraph at lines 4973--4978 []\OT1/cmr/m/n/10.95 The first line will gen-er-ate a 3-body an-gle in-ter-ac-t ion (of type []) Overfull \hbox (31.27754pt too wide) in paragraph at lines 4980--4988 []\OT1/cmr/m/n/10.95 The sec-ond line will gen-er-ate a 3-body in-ter-ac-tion o f type [] Overfull \hbox (34.34967pt too wide) in paragraph at lines 4990--4995 []\OT1/cmr/m/n/10.95 The third line will gen-er-ate a 3-body in-ter-ac-tion of type [] [66] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5089--5089 []\OT1/cmtt/m/n/10.95 ltemplify.py -name MoleculeName -mol MolID INPUT_SCRIPT D ATA_FILE > FILE.lt [67] [68] Overfull \hbox (69.51059pt too wide) in paragraph at lines 5127--5232 [] [69] Overfull \hbox (6.57567pt too wide) in paragraph at lines 5291--5295 \OT1/cmr/m/it/10.95 However, \OT1/cmr/m/n/10.95 ltem-plify.py uses com-ments in the ``Masses'' sec-tion of the LAMMPS [70] Overfull \hbox (26.77591pt too wide) in paragraph at lines 5344--5353 []\OT1/cmr/m/n/10.95 In this ex-am-ple, bonds of type 1 and 2 will be re-ferred to as ``@bond:CCethane'' [71] Overfull \hbox (1.40111pt too wide) in paragraph at lines 5370--5378 \OT1/cmr/m/n/10.95 PASS''), con-tain rules for gen-er-at-ing these in-ter-ac-ti ons au-to-mat-i-cally. Hence, [72] Overfull \hbox (19.41339pt too wide) in paragraph at lines 5496--5496 []\OT1/cmtt/m/n/10.95 ltemplify.py -name Ethane -molid "1" FILE.in FILE.data > ethane.lt [73] Overfull \hbox (30.91077pt too wide) in paragraph at lines 5566--5566 []\OT1/cmtt/m/n/10.95 ltemplify.py -name EntireSystem FILE.in FILE.data > entir e_system.lt [74] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5593--5593 []\OT1/cmtt/m/n/10.95 # This example creates a new file, "ethane.lt", which wil l contain the Overfull \hbox (30.91077pt too wide) in paragraph at lines 5594--5594 []\OT1/cmtt/m/n/10.95 # instructions for building a "Ethane" molecule using "GA FF2". First[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5595--5595 []\OT1/cmtt/m/n/10.95 # specify which file contains the definition of the "GAFF 2" force field:[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5599--5599 []\OT1/cmtt/m/n/10.95 # Then use ltemplify.py to extract information from FILE. in, FILE.data[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 5603--5603 [] \OT1/cmtt/m/n/10.95 -ignore-angles -ignore-bond-types -ignore-co effs \[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 5606--5606 []\OT1/cmtt/m/n/10.95 # Note: if you want to build a simulation containing thes e molecules,[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5607--5607 []\OT1/cmtt/m/n/10.95 # you will have to create a "system.lt" file which refers to "ethane.lt"[] [75] [76] [77] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5893--5893 []\OT1/cmtt/m/n/10.95 -atomstyle style By default, moltemplate.sh assumes you are using the "full"[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 5894--5894 [] \OT1/cmtt/m/n/10.95 atom style in LAMMPS. You can change the atom style to "dipole"[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5895--5895 [] \OT1/cmtt/m/n/10.95 using -atomstyle dipole. If you are usin g a hybrid style,[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5896--5896 [] \OT1/cmtt/m/n/10.95 you must enclose the list of styles in qu otes. For example:[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 5898--5898 [] \OT1/cmtt/m/n/10.95 For custom atom styles, you can also spec ify the[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5899--5899 [] \OT1/cmtt/m/n/10.95 list of column names manually (enclosed i n quotes):[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 5900--5900 [] \OT1/cmtt/m/n/10.95 -atomstyle "molid x y z atomid atomtype m ux muy muz"[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5901--5901 [] \OT1/cmtt/m/n/10.95 Be careful to enclose the entire list in quotes(").[] Overfull \hbox (134.38715pt too wide) in paragraph at lines 5903--5903 []\OT1/cmtt/m/n/10.95 -raw raw_file The raw_file file should contain the atom ic coordinates in RAW format.[] Overfull \hbox (117.14108pt too wide) in paragraph at lines 5904--5904 [] \OT1/cmtt/m/n/10.95 RAW files are simple 3-column ASCII files containin the coordinates[] Overfull \hbox (122.88977pt too wide) in paragraph at lines 5905--5905 [] \OT1/cmtt/m/n/10.95 for the atoms in the system. (One line pe r atom, 3 numbers per line.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5906--5906 [] \OT1/cmtt/m/n/10.95 The atoms must appear in the same order i n the data file.)[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5907--5907 []\OT1/cmtt/m/n/10.95 -xyz xyz_file An xyz_file argument should be supplied a s an argument[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 5909--5909 [] \OT1/cmtt/m/n/10.95 This file should contain the atomic coord inates in xyz format.[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5910--5910 [] \OT1/cmtt/m/n/10.95 (The atoms must appear in the same order in the data file.)[] Overfull \hbox (134.38715pt too wide) in paragraph at lines 5912--5912 []\OT1/cmtt/m/n/10.95 -pdb pdb_file The pdb_file file should contain the atom ic coordinates in PDB format.[] [78] Overfull \hbox (117.14108pt too wide) in paragraph at lines 5914--5914 [] \OT1/cmtt/m/n/10.95 This file should contain one ATOM or HETA TM record per atom. Atoms[] Overfull \hbox (105.6437pt too wide) in paragraph at lines 5916--5916 [] \OT1/cmtt/m/n/10.95 are sorted by chainID, resID, insertCode, atomID (in that order).[] Overfull \hbox (111.3924pt too wide) in paragraph at lines 5917--5917 [] \OT1/cmtt/m/n/10.95 This order must match the order the atoms appear in the data file.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5919--5919 [] \OT1/cmtt/m/n/10.95 If the PDB file contains periodic boundar y box information[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5920--5920 [] \OT1/cmtt/m/n/10.95 (IE., a "CRYST1" record), this informatio n is also copied[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5922--5922 [] \OT1/cmtt/m/n/10.95 (Support for triclinic cells is experimen tal as of 2019-9-03.[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5923--5923 [] \OT1/cmtt/m/n/10.95 Other molecular structure formats may be supported later.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5926--5926 [] \OT1/cmtt/m/n/10.95 The user can customize the numbers assign ed to atom, bond,[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5927--5927 [] \OT1/cmtt/m/n/10.95 angle, dihedral, and improper types or id numbers by using[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5929--5929 [] \OT1/cmtt/m/n/10.95 for each variable you want to modify. If there are many[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5930--5930 [] \OT1/cmtt/m/n/10.95 variables you want to modify, you can sav e them in a file[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5931--5931 [] \OT1/cmtt/m/n/10.95 (one variable per line). For an example of the file format[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5932--5932 [] \OT1/cmtt/m/n/10.95 run moltemplate.sh once and search for a file named[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5933--5933 [] \OT1/cmtt/m/n/10.95 "ttree_assignments.txt". (This file is o ften located in[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5934--5934 [] \OT1/cmtt/m/n/10.95 the "output_ttree/" directory.) Once assi gned, the remaining[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5935--5935 [] \OT1/cmtt/m/n/10.95 variables in the same category will be au tomatically assigned[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 5936--5936 [] \OT1/cmtt/m/n/10.95 to values which do not overlap with your chosen values.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5938--5938 [] \OT1/cmtt/m/n/10.95 "-b" is similar to "-a". However, in this case, no attempt[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5939--5939 [] \OT1/cmtt/m/n/10.95 is made to assign exclusive (unique) valu es to each variable.[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5941--5941 [] \OT1/cmtt/m/n/10.95 Normally moltemplate.sh checks for common errors and typos and[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 5942--5942 [] \OT1/cmtt/m/n/10.95 halts if it thinks it has found one. This forces the variables[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5943--5943 [] \OT1/cmtt/m/n/10.95 and categories as well as write(file) and write_once(file)[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5944--5944 [] \OT1/cmtt/m/n/10.95 commands to obey standard naming conventio ns. The "-nocheck"[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 5945--5945 [] \OT1/cmtt/m/n/10.95 argument bypasses these checks and elimina tes these restrictions.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5947--5947 [] \OT1/cmtt/m/n/10.95 This cause moltemplate.sh to check to mak e sure that there[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5948--5948 [] \OT1/cmtt/m/n/10.95 are valid angle and dihedral interactions defined for every[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 5949--5949 [] \OT1/cmtt/m/n/10.95 3 or 4 consecutively bonded atoms in the system[] [79] Overfull \hbox (13.6647pt too wide) in paragraph at lines 6010--6010 []\OT1/cmtt/m/n/10.95 moltemplate.sh -a '@atom:SPCE/O 2' -a '@atom:SPCE/H 1' s ystem.lt [80] Overfull \hbox (43.572pt too wide) in paragraph at lines 6093--6095 []\OT1/cmr/m/n/10.95 The ``ttree[]assignments.txt'' file has the same for-mat a s the ``new[]assignments.txt'' Overfull \hbox (0.80295pt too wide) in paragraph at lines 6115--6118 \OT1/cmr/m/n/10.95 If for some rea-son, you are us-ing ``lt-tree.py'' or ``ttre e.py'' in-stead of ``moltem- [81] [82] [83] [84] [85] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6502--6502 [] \OT1/cmtt/m/n/10.95 natom++; print "set atom "natom" x "$1" y "$2" z "$ 3" "}}' \[] [86] Overfull \hbox (8.35524pt too wide) in paragraph at lines 6562--6563 \OT1/cmr/m/it/10.95 file with the ap-pro-pri-ate in-te-ger be-fore you copy the con-tents into the LAMMPS Overfull \hbox (59.6542pt too wide) in paragraph at lines 6594--6594 [] \OT1/cmtt/m/n/10.95 nbody_by_type.py reads a LAMMPS data file (or an exce rpt of a LAMMPS) Overfull \hbox (25.16208pt too wide) in paragraph at lines 6595--6595 [] \OT1/cmtt/m/n/10.95 data file containing bonded many-body interactions by atom type[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6596--6596 [] \OT1/cmtt/m/n/10.95 (and bond type), and generates a list of additional i nteractions[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 6597--6597 [] \OT1/cmtt/m/n/10.95 in LAMMPS format consistent with those type (to the s tandard out).[] [87] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6615--6615 [] \OT1/cmtt/m/n/10.95 Support for other interaction types can be added by t he user. See below.[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6617--6617 [] \OT1/cmtt/m/n/10.95 Note: The optional "-subgraph" argument allows you to customize the[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6618--6618 [] \OT1/cmtt/m/n/10.95 rules used to match and generate interactions o f that type.[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6619--6619 [] \OT1/cmtt/m/n/10.95 It is optional, and is only useful for forcefie lds which[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6620--6620 [] \OT1/cmtt/m/n/10.95 use non-standard dihedral or improper atom-orde r convetions.)[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 6628--6628 [] \OT1/cmtt/m/n/10.95 "Dihedrals", or "Impropers"). It also looks a sectio n named "X By Type",[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6629--6629 [] \OT1/cmtt/m/n/10.95 (eg. "Angles By type", "Impropers By type", "Impro pers By type")[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6630--6630 [] \OT1/cmtt/m/n/10.95 which contains a list of criteria for automatically d efining additional[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6631--6631 [] \OT1/cmtt/m/n/10.95 interactions of that type. For example, this file mi ght contain:[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 6642--6642 [] \OT1/cmtt/m/n/10.95 The * is a wildcard symbol indicating there is no pre ference for bond types[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6643--6643 [] \OT1/cmtt/m/n/10.95 in this example. (Optionally, regular expressions ca n also be used to[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6644--6644 [] \OT1/cmtt/m/n/10.95 define a type match, by enclosing the atom or bond ty pe in / slashes.)[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6646--6646 [] \OT1/cmtt/m/n/10.95 The first line tells us to that there should be a 3-body "Angle"[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6647--6647 [] \OT1/cmtt/m/n/10.95 interaction of type "7" whenever an atom of type 1 is bonded to an atom[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6648--6648 [] \OT1/cmtt/m/n/10.95 of type "2", which is bonded to another atom of type "1" again.[] [88] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6649--6649 [] \OT1/cmtt/m/n/10.95 The second line tells us that an angle is defined whe never three atoms[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 6654--6654 [] \OT1/cmtt/m/n/10.95 atoms which match these criteria if they are bonded t ogether[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6655--6655 [] \OT1/cmtt/m/n/10.95 in the relevant way for that interaction type (as det ermined by[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6656--6656 [] \OT1/cmtt/m/n/10.95 nbody_X.py), and printed to the standard output. For example,[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 6657--6657 [] \OT1/cmtt/m/n/10.95 suppose you are automatically generating 3-body "Angl e" interactions using:[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6661--6661 [] \OT1/cmtt/m/n/10.95 The file "new.data" will be identical to "old.data", however the[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6662--6662 [] \OT1/cmtt/m/n/10.95 "Angles By Type" section will be deleted, and the fol lowing lines of[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6671--6671 [] \OT1/cmtt/m/n/10.95 The numbers in the first column are counters which as sign a ID to[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 6672--6672 [] \OT1/cmtt/m/n/10.95 every interaction of that type, and start where the o riginal "Angles"[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6673--6673 [] \OT1/cmtt/m/n/10.95 data left off (New angle ID numbers do not overlap wi th old ID numbers).[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6674--6674 [] \OT1/cmtt/m/n/10.95 The text in the second column ("7", "9", ...) matches the text from the[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6675--6675 [] \OT1/cmtt/m/n/10.95 first column of the "Angle By Type" section of the in put file.[] [89] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6697--6697 [] \OT1/cmtt/m/n/10.95 When run this way, nbody_by_type.py behaves exactly t he same way[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6698--6698 [] \OT1/cmtt/m/n/10.95 as in Example 1, however only the lines of text corre sponding to[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6699--6699 [] \OT1/cmtt/m/n/10.95 the new generated interactions are printed, (not the entire data file).[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 6700--6700 [] \OT1/cmtt/m/n/10.95 Also note, that when run this way, nbody_by_type.py d oes not read the[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6701--6701 [] \OT1/cmtt/m/n/10.95 LAMMPS data from the standard input. Instead, it rea ds each section of[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6702--6702 [] \OT1/cmtt/m/n/10.95 the data file from a different file indicated by the arguments following[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 6703--6703 [] \OT1/cmtt/m/n/10.95 the "-atoms", "-bonds", "-nbody", and "-nbodybytype" flags.[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6705--6705 [] \OT1/cmtt/m/n/10.95 "Angles" is a 3-body interaction style. So when run this way,[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6706--6706 [] \OT1/cmtt/m/n/10.95 nbody_by_type.py will create a 5 (=3+2) column file ( new_Angles.data).[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 6708--6708 []\OT1/cmtt/m/n/10.95 Note: the atom, bond and other IDs/types in need not be i ntegers.[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 6710--6710 []\OT1/cmtt/m/n/10.95 Note: This program must be distributed with several pytho n modules, including:[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6711--6711 [] \OT1/cmtt/m/n/10.95 nbody_Angles.py, nbody_Dihedrals.py, and nbody_Im propers.py. These[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 6712--6712 [] \OT1/cmtt/m/n/10.95 contain bond definitions for angular, dihedral, and improper interactions.[] Overfull \hbox (1.14366pt too wide) in paragraph at lines 6717--6732 \OT1/cmr/m/n/10.95 im-ports ex-ter-nal mod-ules named ``nbody[]Angles.py'', ``n body[]Dihedrals.py'', Overfull \hbox (4.07088pt too wide) in paragraph at lines 6741--6743 \OT1/cmr/m/n/10.95 Moltemplate.sh is a script which in-vokes a python pro-gram pro-gram (\OT1/cmr/m/it/10.95 ttree.py\OT1/cmr/m/n/10.95 ) [90] Overfull \hbox (82.64896pt too wide) in paragraph at lines 6766--6766 []\OT1/cmtt/m/n/10.95 String ::= InstanceName | ObjectTypeName | FileName | Cat egoryName | OtherStr Overfull \hbox (76.90027pt too wide) in paragraph at lines 6796--6796 []\OT1/cmtt/m/n/10.95 Command ::= ObjectDef | InstanceCommand | DeleteCommand | WriteC | WriteOC | Overfull \hbox (48.15683pt too wide) in paragraph at lines 6797--6797 [] \OT1/cmtt/m/n/10.95 ImportCommand | CategoryDef | InstanceMod | O bjectTypeMod |[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6798--6798 [] \OT1/cmtt/m/n/10.95 ObjectDefMod | ReplaceCommand | UsingCommand | PushXform[] [91] Overfull \hbox (7.91602pt too wide) in paragraph at lines 6813--6813 []\OT1/cmtt/m/n/10.95 RotXform ::= ".rot(" Number "," Number "," Number "," Num ber ")"[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6833--6833 []\OT1/cmtt/m/n/10.95 TemplText ::= "" | String TemplText | StatVar TemplText | InstVar TemplText[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 6837--6837 []\OT1/cmtt/m/n/10.95 WriteOC ::= "write_once(" FileName ")" "{" TemplateTextSt at "}"[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6838--6838 []\OT1/cmtt/m/n/10.95 TemplTextStat ::= "" | String TemplTextStat | StatVar Tem plTextStat[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6849--6849 []\OT1/cmtt/m/n/10.95 CatCommandStat ::= "category" "@"CategoryName"(" Integer "," Integer ")"[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6850--6850 []\OT1/cmtt/m/n/10.95 CatCommandInst ::= "category" "$"CategoryName"(" Integer "," Integer ")"[] [92] [93] Overfull \hbox (5.00008pt too wide) in paragraph at lines 6955--6959 []\OT1/cmr/m/n/10.95 Find the cat-e-gory name and ob-ject cor-re-spond-ing to ` `\TS1/cmr/m/n/10.95 $\OT1/cmr/bx/it/10.95 cpath\OT1/cmr/m/n/10.95 /\OT1/cmr/bx/ it/10.95 catname\OT1/cmr/m/n/10.95 :'' [94] Overfull \hbox (43.72781pt too wide) in paragraph at lines 6972--6973 \OT1/cmr/m/n/10.95 file (al-though you can use it any-where else in an ``.LT'' file). In ``ttree[]assignments.txt'' (./moltemplate_manual.bbl [95]) [96] (./moltemplate_manual.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on moltemplate_manual.pdf (96 pages, 836971 bytes). Transcript written on moltemplate_manual.log. This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./moltemplate_manual.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2025/01/22 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./moltemplate_manual.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./moltemplate_manual.out) (./moltemplate_manual.out) (./moltemplate_manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map} <./author_email.png>] [2]) [3] Overfull \hbox (12.60272pt too wide) in paragraph at lines 91--111 \OT1/cmr/m/n/10.95 which can be con-verted into moltem-plate for-mat (LT for-ma t) us-ing []\OT1/cmtt/m/n/10.95 mol22lt.py[] [4] Overfull \hbox (2.16733pt too wide) in paragraph at lines 197--197 []\OT1/cmtt/m/n/10.95 moltemplate.sh -xyz coords.xyz -atomstyle "full" -vmd sys tem.lt Overfull \hbox (1.04338pt too wide) in paragraph at lines 299--306 \OT1/cmr/m/n/10.95 The \OT1/cmr/bx/n/10.95 ATB \OT1/cmr/m/n/10.95 ser-vice [[]] men-tioned ear-lier ([]$\OT1/cmtt/m/n/10.95 https : / / atb . uq . edu . au$[] \OT1/cmr/m/n/10.95 ) is a repos- [5] Overfull \hbox (19.41339pt too wide) in paragraph at lines 471--471 []\OT1/cmtt/m/n/10.95 python -m venv ~/venv #(or "virtualenv venv" if using python2) [6] Overfull \hbox (7.91602pt too wide) in paragraph at lines 496--496 []\OT1/cmtt/m/n/10.95 git clone https://github.com/jewettaij/moltemplate ~/molt emplate Overfull \hbox (30.91077pt too wide) in paragraph at lines 517--517 []\OT1/cmtt/m/n/10.95 pip3 install . # (or "pip3 install --user", or "pip" if that fails)[] Overfull \hbox (0.52628pt too wide) in paragraph at lines 520--526 []\OT1/cmr/m/n/10.95 As men-tioned ear-lier, if you are hav-ing dif-fi-culty, t ry to in-stalling moltem- [7] Overfull \hbox (25.16208pt too wide) in paragraph at lines 593--609 \OT1/cmtt/m/n/10.95 bashonubuntuonwindows / comments / 6bu1d1 / since _ we _ sh ouldnt _ edit _ files _ [8] Overfull \hbox (0.32121pt too wide) in paragraph at lines 612--612 []\OT1/cmr/bx/n/14.4 Quick ref-er-ence \OT1/cmr/bx/it/14.4 (SKIP ON FIRST READ- ING) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Underfull \hbox (badness 7064) in paragraph at lines 683--688 []|\OT1/cmr/m/n/10.95 Apply co-or-di-nate trans-for-ma-tions ([] to Underfull \hbox (badness 10000) in paragraph at lines 792--797 []|\OT1/cmr/m/n/10.95 Delete a range of molecules spec-i-fied by Underfull \hbox (badness 1616) in paragraph at lines 792--797 []\OT1/cmr/m/n/10.95 . (This also works for mul-ti-di- Overfull \hbox (121.47046pt too wide) in alignment at lines 623--895 [] [] ignored error: Infinite glue shrinkage found in box being split [9] ignored error: Infinite glue shrinkage found in box being split [10] [11] Underfull \hbox (badness 10000) in paragraph at lines 907--909 Overfull \hbox (131.64603pt too wide) in alignment at lines 909--1047 [] [] ignored error: Infinite glue shrinkage found in box being split [12] [13] Underfull \hbox (badness 10000) in paragraph at lines 1058--1061 Underfull \hbox (badness 10000) in paragraph at lines 1058--1061 Overfull \hbox (124.34627pt too wide) in alignment at lines 1061--1190 [] [] [14] Underfull \hbox (badness 1418) in paragraph at lines 1387--1391 \OT1/cmr/m/n/10.95 ``bond[]coeff'', ``an-gle[]coeff'', ``di-he-dral[]coeff'', a nd ``im- Overfull \hbox (123.88596pt too wide) in alignment at lines 1203--1417 [] [] ignored error: Infinite glue shrinkage found in box being split [15] ignored error: Infinite glue shrinkage found in box being split [16] [17] Overfull \hbox (13.54758pt too wide) in paragraph at lines 1432--1454 \OT1/cmr/m/n/10.95 tackle the same steep learning-curve (and oc-ca-sional bugs) that other LAMMPS Overfull \hbox (16.26949pt too wide) in paragraph at lines 1459--1459 []\OT1/cmr/bx/n/12 Simulating a box of wa-ter us-ing moltem-plate and LAMMPS Overfull \hbox (53.90552pt too wide) in paragraph at lines 1494--1494 [] \OT1/cmtt/m/n/10.95 ## Atom properties and bond topology go in various "Dat a ..." sections[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1496--1496 [] \OT1/cmtt/m/n/10.95 # We selected "atom_style full". That means we use this column format:[] [18 <./single_water_LR.jpg>] Overfull \hbox (19.41339pt too wide) in paragraph at lines 1497--1497 [] \OT1/cmtt/m/n/10.95 # atomID molID atomType charge coordX coordY coordZ[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1500--1500 [] \OT1/cmtt/m/n/10.95 $atom:o $mol:w @atom:O -0.8476 0.0000000 0.00000 0 0.00000[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1501--1501 [] \OT1/cmtt/m/n/10.95 $atom:h1 $mol:w @atom:H 0.4238 0.8164904 0.57735 90 0.00000[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 1502--1502 [] \OT1/cmtt/m/n/10.95 $atom:h2 $mol:w @atom:H 0.4238 -0.8164904 0.5773 590 0.00000[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 1505--1505 [] \OT1/cmtt/m/n/10.95 # Variables beginning with $ or @ will be replaced by n umbers LAMMPS will[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 1506--1506 [] \OT1/cmtt/m/n/10.95 # eventually read. Each of the three atoms" will be as signed unique[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1507--1507 [] \OT1/cmtt/m/n/10.95 # atomIDs (denoted here by "$atom:o", "$atom:h1", "$ato m:h2"), even if[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 1508--1508 [] \OT1/cmtt/m/n/10.95 # they belong to different molecules. However, the ato m types[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 1509--1509 [] \OT1/cmtt/m/n/10.95 # (denoted "@atom:O", "@atom:H") are shared for atoms i n all molecules.[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1510--1510 [] \OT1/cmtt/m/n/10.95 # All 3 atoms share same molID number (represeted here by "$mol:w")[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1511--1511 [] \OT1/cmtt/m/n/10.95 # however that number is different for different water molecules.[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1530--1530 [] \OT1/cmtt/m/n/10.95 # --- Force-field parameters go in the "In Settings" se ction: ---[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 1534--1534 [] \OT1/cmtt/m/n/10.95 # atomType1 atomType2 parameter-list (epsil on, sigma)[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 1537--1537 [] \OT1/cmtt/m/n/10.95 # (mixing rules determine interactions between types @atom:O and @atom:H)[] [19] Overfull \hbox (99.89502pt too wide) in paragraph at lines 1545--1545 [] \OT1/cmtt/m/n/10.95 # Group definitions and constraints can also go in th e "In Settings" section[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 1547--1547 [] \OT1/cmtt/m/n/10.95 fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @ang le:HOH[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1548--1548 [] \OT1/cmtt/m/n/10.95 # (lammps quirk: Remember to "unfix fSHAKE" during mi nimization.)[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 1551--1551 [] \OT1/cmtt/m/n/10.95 # LAMMPS supports a large number of force-field styles. We must select[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 1552--1552 [] \OT1/cmtt/m/n/10.95 # which ones we need. This information belongs in the " In Init" section.[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 1555--1555 [] \OT1/cmtt/m/n/10.95 units real # angstroms, kCal/m ole, Daltons, Kelvin[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 1556--1556 [] \OT1/cmtt/m/n/10.95 atom_style full # select column for mat for Atoms section[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 1557--1557 [] \OT1/cmtt/m/n/10.95 pair_style lj/charmm/coul/long 9.0 10.0 10 # param s needed: epsilon sigma[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 1558--1558 [] \OT1/cmtt/m/n/10.95 bond_style harmonic # parameters needed : k_bond, r0[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 1559--1559 [] \OT1/cmtt/m/n/10.95 angle_style harmonic # parameters needed : k_theta, theta0[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 1560--1560 [] \OT1/cmtt/m/n/10.95 kspace_style pppm 0.0001 # long-range electr ostatics sum method[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 1561--1561 [] \OT1/cmtt/m/n/10.95 pair_modify mix arithmetic # using Lorenz-Bert helot mixing rules[] Overfull \hbox (14.12546pt too wide) in paragraph at lines 1575--1576 \OT1/cmr/m/n/10.95 You can now use ``moltem-plate.sh'' to cre-ate sim-u-la-tion in-put files for LAMMPS [20] Overfull \hbox (0.73196pt too wide) in paragraph at lines 1637--1649 \OT1/cmr/m/n/10.95 (See sec-tion []6[] for more de-tails and ex-am-ples.) This will cre-ate 1000 molecules Overfull \hbox (40.6773pt too wide) in paragraph at lines 1637--1649 \OT1/cmr/m/n/10.95 ta-tion: ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.95 atom:wat[2 ][3][4]/h1'', ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.95 bond:wat[0][5][1]/oh1'', ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.95 an-gle:wat[2][8][3]/hoh'', Overfull \hbox (10.06793pt too wide) in paragraph at lines 1656--1659 \OT1/cmr/m/n/10.95 spec-ify the di-men-sions of the sim-u-la-tion bound-ary us- ing the ``write[]once(``Data [21] [22 <./waterSPCEx1000_LR.jpg> <./waterSPCEx1000_t=25_LR.jpg>] Overfull \hbox (33.74133pt too wide) in paragraph at lines 1799--1809 []\OT1/cmr/m/n/10.95 Moltemplate will cre-ate the fol-low-ing files: ``sys-tem. data'', ``run.in.EXAMPLE'', [23] Overfull \hbox (5.23363pt too wide) in paragraph at lines 2004--2011 \OT1/cmr/m/n/10.95 which can vi-su-al-ize the sys-tem. If you have saved your t ra-jec-tory in LAMMPS [24] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2012--2012 []\OT1/cmtt/m/n/10.95 dump 1 all custom 1000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz Overfull \hbox (29.2559pt too wide) in paragraph at lines 2019--2022 []\OT1/cmr/m/n/10.95 a) Start VMD From the menu in the upper-left, se-lect \OT1 /cmr/bx/n/10.95 File$\OMS/cmsy/m/n/10.95 !$[] [25] Overfull \hbox (24.8004pt too wide) in paragraph at lines 2168--2175 \OT1/cmr/m/n/10.95 In the ex-am-ple above, the \TS1/cmr/m/n/10.95 $ \OT1/cmr/m/ n/10.95 vari-ables have full-names like ``\TS1/cmr/m/n/10.95 $\OT1/cmr/m/n/10.9 5 atom:wat[8][3][7]/h1'', [26] [27] [28] Overfull \hbox (0.77374pt too wide) in paragraph at lines 2342--2342 []\OT1/cmr/bx/it/12 (Advanced) \OT1/cmr/bx/n/12 Us-ing moltem-plate to gen-er-a te aux-il-iary files Overfull \hbox (36.65945pt too wide) in paragraph at lines 2353--2353 [] \OT1/cmtt/m/n/10.95 mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.33333 7.04956 0. 602224 4 0 0[] [29] [30] [31 <./2bead_monomer.jpg> <./2bead_polymer.jpg> <./2bead_polymers_nop bc_t=0_LR.jpg> <./2bead_polymers_t=100ps_LR.jpg>] Overfull \hbox (0.3771pt too wide) in paragraph at lines 2460--2461 \OT1/cmr/m/n/10.95 Consider the fol-low-ing sim-ple 2-atom dumbell-shaped molel ule (``Monomer'') Overfull \hbox (7.91602pt too wide) in paragraph at lines 2470--2470 [] \OT1/cmtt/m/n/10.95 $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0. 0000000[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 2471--2471 [] \OT1/cmtt/m/n/10.95 $atom:r $mol:... @atom:R 0.0 0.000 4.4000 0. 0000000[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 2505--2505 [] \OT1/cmtt/m/n/10.95 create_var {$mol} #(force all Monomers to share the sa me molecule-ID)[] [32] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2519--2519 [] \OT1/cmtt/m/n/10.95 $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom :mon2/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2520--2520 [] \OT1/cmtt/m/n/10.95 $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom :mon3/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2521--2521 [] \OT1/cmtt/m/n/10.95 $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom :mon4/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2522--2522 [] \OT1/cmtt/m/n/10.95 $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom :mon5/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2523--2523 [] \OT1/cmtt/m/n/10.95 $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom :mon6/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 2524--2524 [] \OT1/cmtt/m/n/10.95 $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom :mon7/ca[] [33] Overfull \hbox (42.40814pt too wide) in paragraph at lines 2631--2631 [] \OT1/cmtt/m/n/10.95 # Force-field parameters ("coeffs") go in the "In Setti ngs" section:[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 2638--2638 [] \OT1/cmtt/m/n/10.95 # (Interactions between different atoms are determine d by mixing rules.)[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2651--2651 [] \OT1/cmtt/m/n/10.95 # Although the simple "Monomer" object we defined above has only[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2652--2652 [] \OT1/cmtt/m/n/10.95 # two atoms, later on, we will create molecules with ma ny bonds.[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 2653--2653 [] \OT1/cmtt/m/n/10.95 # By convention, in this file we keep track of all of t he possible[] [34] Overfull \hbox (76.90027pt too wide) in paragraph at lines 2656--2656 [] \OT1/cmtt/m/n/10.95 # Rules for determining 3-body (angle) interactions by atom and bond type:[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2657--2657 [] \OT1/cmtt/m/n/10.95 # angle-type atomType1 atomType2 atomType3 bondTyp e1 bondType2[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2660--2660 [] \OT1/cmtt/m/n/10.95 @angle:Backbone @atom:CA @atom:CA @atom:CA @bond :* @bond:*[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2661--2661 [] \OT1/cmtt/m/n/10.95 @angle:Sidechain @atom:CA @atom:CA @atom:R @bond :* @bond:*[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 2674--2674 [] \OT1/cmtt/m/n/10.95 # 4-body interactions in this example are listed by ato m type and (optionally)[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 2675--2675 [] \OT1/cmtt/m/n/10.95 # by bond type. (You can use wildcards * to accept all bond types.)[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 2677--2677 [] \OT1/cmtt/m/n/10.95 # dihedralType atmType1 atmType2 atmType3 atmType4 bo ndType1 bType2 bType3[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 2679--2679 [] \OT1/cmtt/m/n/10.95 @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @ bond:* @bond:* @bond:*[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 2680--2680 [] \OT1/cmtt/m/n/10.95 @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @ bond:* @bond:* @bond:*[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 2699--2699 [] \OT1/cmtt/m/n/10.95 # -- (Changing these styles will change the formulas above) --[] [35] [36] Overfull \hbox (9.77596pt too wide) in paragraph at lines 2782--2789 \OT1/cmr/m/n/10.95 Notice that we did not spec-ify the ``@bond:SideChain'' and ``@bond:Backbone'' Overfull \hbox (76.60141pt too wide) in paragraph at lines 2795--2808 \OT1/cmr/m/n/10.95 names can be quite long and dif-fi-cult to type (such as ``@ atom:h1h[]ph1h[]bh1h[]ah1[]dh1[]ih1''). [37] Overfull \hbox (14.1924pt too wide) in paragraph at lines 2873--2874 \OT1/cmr/m/n/10.95 For de-tails, see the ``cen-JswapIL.py'' file (lo-cated in t he ``nbody[]alt[]symmetry/'' [38] [39] Overfull \hbox (19.81343pt too wide) in paragraph at lines 2963--2973 \OT1/cmr/m/n/10.95 The first line tells moltem-plate that any bond be-tween ato ms of type ``@atom:h1'' [40] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3058--3058 [] \OT1/cmtt/m/n/10.95 # Note: This will not overwrite the preexisting "ForceF ield" object.[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3059--3059 [] \OT1/cmtt/m/n/10.95 # (Instead, it augments the "ForceField" object d efined earlier.)[] Overfull \hbox (2.11093pt too wide) in paragraph at lines 3074--3079 \OT1/cmr/m/n/10.95 ``@atom:R'', and ``@atom:CB'', since they all be-long to the same ``[]'' Overfull \hbox (59.6542pt too wide) in paragraph at lines 3084--3084 [] \OT1/cmtt/m/n/10.95 # Here you can refer to @atoms, @bonds, etc... defined in either file:[] [41] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3139--3139 [] \OT1/cmtt/m/n/10.95 $bond:backbone1 @bond:Backbone $atom:monomers[0]/ca $atom:monomers[1]/ca[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3140--3140 [] \OT1/cmtt/m/n/10.95 $bond:backbone2 @bond:Backbone $atom:monomers[1]/ca $atom:monomers[2]/ca[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3141--3141 [] \OT1/cmtt/m/n/10.95 $bond:backbone3 @bond:Backbone $atom:monomers[2]/ca $atom:monomers[3]/ca[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 3142--3142 [] \OT1/cmtt/m/n/10.95 : : : :[] Overfull \hbox (9.44891pt too wide) in paragraph at lines 3159--3163 \OT1/cmr/m/n/10.95 This will cre-ate 7 molecules. The co-or-di-nates of the fir st molecule \OT1/cmr/m/it/10.95 monomers[0] [42] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3169--3169 [] \OT1/cmtt/m/n/10.95 monomers = new Monomer.scale(1.5) [7].rot(180, 1,0,0).m ove(3.2,0,0) Overfull \hbox (25.16208pt too wide) in paragraph at lines 3185--3185 [] \OT1/cmtt/m/n/10.95 # "monomers[0]", "monomers[1]", "monomers[2]", ... "mon omers[6]".[] [43] Overfull \hbox (7.91602pt too wide) in paragraph at lines 3255--3255 [] \OT1/cmtt/m/n/10.95 monomers = new random([Monomer, Monomer3], [0.6, 0.4], 123456)[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3260--3260 [] \OT1/cmtt/m/n/10.95 $bond:bb1 @bond:Backbone $atom:monomers[0]/ca $atom:m onomers[1]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3261--3261 [] \OT1/cmtt/m/n/10.95 $bond:bb2 @bond:Backbone $atom:monomers[1]/ca $atom:m onomers[2]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3262--3262 [] \OT1/cmtt/m/n/10.95 $bond:bb3 @bond:Backbone $atom:monomers[2]/ca $atom:m onomers[3]/ca[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 3263--3263 [] \OT1/cmtt/m/n/10.95 $bond:bb4 @bond:Backbone $atom:monomers[3]/ca $atom:m onomers[4]/ca[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3268--3268 [] \OT1/cmtt/m/n/10.95 $bond:bb50 @bond:Backbone $atom:monomers[48]/ca $atom :monomers[49]/ca Overfull \hbox (19.41339pt too wide) in paragraph at lines 3270--3270 [] \OT1/cmtt/m/n/10.95 #(Note: Both the "Monomer" and "Monomer3" subunits cont ain atoms[] [44 <./random_2bead.jpg> <./random_3bead.jpg> <./random_heteropolymer.jpg>] Overfull \hbox (21.21399pt too wide) in paragraph at lines 3324--3328 []\OT1/cmr/m/it/10.95 Note: \OT1/cmr/m/n/10.95 Al-though this ex-am-ple, there are only two monomer types (``Monomer'' Overfull \hbox (31.28319pt too wide) in paragraph at lines 3339--3343 []\OT1/cmr/m/it/10.95 Note: \OT1/cmr/m/n/10.95 Once a molecule con-tain-ing ran -dom monomers is de-fined, ([] [45] Overfull \hbox (30.91077pt too wide) in paragraph at lines 3409--3409 [] \OT1/cmtt/m/n/10.95 monomers[1-48] = new random([Monomer, Monomer3], [30, 1 8], 123456)[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3412--3412 [] \OT1/cmtt/m/n/10.95 # It's a good idea to move these monomers to keep them from overlapping[] [46] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3460--3460 []\OT1/cmtt/m/n/10.95 delete molecules[0-1][1][1-2] # (shorthand for delete mol ecules[0][1][1] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3461--3461 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[0][1][2][] Overfull \hbox (53.90552pt too wide) in paragraph at lines 3462--3462 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[1][1][1][] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3463--3463 [] \OT1/cmtt/m/n/10.95 # delete mol ecules[1][1][2])[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 3469--3469 []\OT1/cmtt/m/n/10.95 # ...and move them back to the location of the vacancies we created[] Overfull \hbox (4.88002pt too wide) in paragraph at lines 3478--3484 \OT1/cmr/m/n/10.95 You can use [] to fill space with a ran-dom mix-ture of mole cules. Overfull \hbox (53.90552pt too wide) in paragraph at lines 3485--3485 []\OT1/cmtt/m/n/10.95 import "lipids" # def ine DPPC & DLPC Overfull \hbox (48.15683pt too wide) in paragraph at lines 3486--3486 []\OT1/cmtt/m/n/10.95 lipids = new random([DPPC,DLPC], [0.5,0.5], 123) # "12 3"=random_seed[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 3487--3487 [] \OT1/cmtt/m/n/10.95 [19].move(7.5, 0, 0) # lat tice spacing 7.5[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 3488--3488 [] \OT1/cmtt/m/n/10.95 [22].move(3.75, 6.49519, 0) # hex agonal lattice[] [47] Overfull \hbox (19.41339pt too wide) in paragraph at lines 3489--3489 [] \OT1/cmtt/m/n/10.95 [2].rot(180, 1, 0, 0) # 2 m onolayers[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 3516--3516 []\OT1/cmtt/m/n/10.95 lipids = new random([DPPC, ,DLPC], [0.35,0.3,0.35], 123) # 2nd element is blank [48 <./lipid_bilayer_mixture.jpg> <./lipid_bilayer_vacancies.jpg>] [49 <./delet e_holes1.jpg>] Overfull \hbox (33.65005pt too wide) in paragraph at lines 3640--3642 []\OT1/cmr/m/n/10.95 We can sub-squently cus-tomize the po-si-tion of the 3rd m onomer (``monomers[2]'') Overfull \hbox (128.63846pt too wide) in paragraph at lines 3678--3678 [] \OT1/cmtt/m/n/10.95 $atom:mol_complex/polymers[0]/monomers[2]/ca $mol:mol_c omplex @atom:R 0 6.4 8.2 0.6[] Overfull \hbox (190.20093pt too wide) in paragraph at lines 3681--3691 \OT1/cmr/m/n/10.95 This is a sit-u-a-tion where we must use the \OT1/cmr/m/it/1 0.95 full \OT1/cmr/m/n/10.95 name of the atom (``\TS1/cmr/m/n/10.95 $\OT1/cmr/m /n/10.95 atom:mol[]complex/polymers[0]/monomers[2]/ca'') [50] Overfull \hbox (25.16208pt too wide) in paragraph at lines 3695--3695 [] \OT1/cmtt/m/n/10.95 $atom:polymers[0]/monomers[2]/ca $mol:... @atom:R 0 6 .4 8.2 0.6[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3714--3714 [] \OT1/cmtt/m/n/10.95 $bond:mol_complex/polymers[0]/backbone3 @bond:ForceFiel d/LongBond &[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 3736--3736 []\OT1/cmtt/m/n/10.95 # Note: This will augment the "ForceField" object, not ov erwrite it: [51] Overfull \hbox (65.4029pt too wide) in paragraph at lines 3774--3774 []\OT1/cmtt/m/n/10.95 delete mol_complex/polymers[1]/monomers[3]/ca #<-- dele tes the "ca" atom Overfull \hbox (65.4029pt too wide) in paragraph at lines 3775--3775 []\OT1/cmtt/m/n/10.95 delete mol_complex/polymers[1]/monomers[4]/cr #<-- dele tes the "cr" bond[] [52] Overfull \hbox (36.65945pt too wide) in paragraph at lines 3865--3865 []\OT1/cmtt/m/n/10.95 MolecularComplex0 = MolecularComplex.move(-9.6,-6.2, 0).s cale(0.3125) Overfull \hbox (25.16208pt too wide) in paragraph at lines 3882--3882 []\OT1/cmtt/m/n/10.95 # Add some new atoms connecting the two polymers in the m ol_complex[] Overfull \hbox (2.00154pt too wide) in paragraph at lines 3936--3937 []\OT1/cmr/m/it/10.95 Note: These co-or-di-nate trans-for-ma-tions will be ap-p lied \OT1/cmr/bx/it/10.95 af-ter \OT1/cmr/m/it/10.95 the molecule [53] [54 <./mol_complex_LR.jpg> <./mol_complex+mol_complex0_transparent_LR.jpg> ] Overfull \hbox (2.16733pt too wide) in paragraph at lines 4031--4031 [] \OT1/cmtt/m/n/10.95 $atom:o $mol:w @atom:O -0.8476 0.0000000 0.00000 0. 000000[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4032--4032 [] \OT1/cmtt/m/n/10.95 $atom:h1 $mol:w @atom:H 0.4238 0.8164904 0.00000 0 .5773590[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4033--4033 [] \OT1/cmtt/m/n/10.95 $atom:h2 $mol:w @atom:H 0.4238 -0.8164904 0.00000 0 .5773590[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4044--4044 [] \OT1/cmtt/m/n/10.95 # atomTypeI atomTypeJ pair-style-name p arameter-list[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4046--4046 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:O @atom:O lj/charmm/coul/long 0 .1553 3.166[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4047--4047 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:H @atom:H lj/charmm/coul/long 0 .0 2.058[] [55] Overfull \hbox (2.16733pt too wide) in paragraph at lines 4076--4076 [] \OT1/cmtt/m/n/10.95 fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @ang le:HOH[] Overfull \hbox (25.39783pt too wide) in paragraph at lines 4082--4085 \OT1/cmr/m/n/10.95 There are two dif-fer-ences be-tween this molecule def-i-ni- tion and the ``spce[]simple.lt'' [56] Overfull \hbox (13.6647pt too wide) in paragraph at lines 4172--4172 [] \OT1/cmtt/m/n/10.95 pair_style hybrid lj/charmm/coul/long 9 10 10 table spl ine 1000[] Overfull \hbox (11.69077pt too wide) in paragraph at lines 4187--4187 [][]\OT1/cmr/bx/n/10.95 Warning: Force-field pa-ram-e-ters be-long in ``In Set- tings'', not ``Data'' [57] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4261--4261 [] \OT1/cmtt/m/n/10.95 # AtomID MolID('.'=this) AtomType charge coordX coor dY coordZ[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4263--4263 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.000000 000 1.0000000[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4264--4264 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.951056 516 0.3090170[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4265--4265 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 0.587785 252 -0.809017[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 4266--4266 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 -0.58778 5252 -0.809017[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 4267--4267 [] \OT1/cmtt/m/n/10.95 $atom:c5 $mol:cp @atom:TraPPE/CH2 0.0 0.0000 -0.95105 6516 0.3090170[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4287--4287 []\OT1/cmtt/m/n/10.95 # A cubic lattice of 125 cyclopentane molecules (12-angst rom spacing) [58] Overfull \hbox (65.4029pt too wide) in paragraph at lines 4288--4288 []\OT1/cmtt/m/n/10.95 mols = new Cyclopentane [5].move(0,0,12) [5].move(0,12,0) [5].move(12,0,0)[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 4319--4319 [] \OT1/cmtt/m/n/10.95 dihedral_coeff @dihedral:CCCC opls 1.411036 -0.271016 3.145034 0.0[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 4320--4320 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 4321--4321 [] \OT1/cmtt/m/n/10.95 pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4322--4322 [] \OT1/cmtt/m/n/10.95 # (Interactions between different atom types use mixi ng rules.)[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 4329--4329 [] \OT1/cmtt/m/n/10.95 @dihedral:CCCC @atom:C* @atom:C* @atom:C* @atom:C* @bo nd:CC @bond:CC @bond:CC[] [59] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4395--4395 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:bt @atom:TraPPE/CH3 0.0 0.419372 0.00 0 -1.937329[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4396--4396 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:bt @atom:TraPPE/CH2 0.0 -0.419372 0.0 00 -0.645776[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 4397--4397 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:bt @atom:TraPPE/CH2 0.0 0.419372 0.00 0 0.645776[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 4398--4398 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:bt @atom:TraPPE/CH3 0.0 -0.419372 0.0 000 1.937329[] [60] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4433--4433 [] \OT1/cmtt/m/n/10.95 $atom:c1 $mol:bt @atom:../CH3 0.0 0.419372 0.000 -1.937329[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4434--4434 [] \OT1/cmtt/m/n/10.95 $atom:c2 $mol:bt @atom:../CH2 0.0 -0.419372 0.000 -0.645776[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4435--4435 [] \OT1/cmtt/m/n/10.95 $atom:c3 $mol:bt @atom:../CH2 0.0 0.419372 0.000 0.645776[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 4436--4436 [] \OT1/cmtt/m/n/10.95 $atom:c4 $mol:bt @atom:../CH3 0.0 -0.419372 0.000 0 1.937329[] Overfull \hbox (6.15454pt too wide) in paragraph at lines 4448--4449 \OT1/cmr/bx/it/10.95 NOTE: Again, al-though the ``nest-ing'' method ex-plained here works, [61] [62] Overfull \hbox (19.81343pt too wide) in paragraph at lines 4615--4625 \OT1/cmr/m/n/10.95 atom type ``@atom:CH3'' in-stead of ``@atom:TraPPE/CH3'', or ``@atom:../CH3'' Overfull \hbox (23.57642pt too wide) in paragraph at lines 4655--4662 \OT1/cmr/m/n/10.95 If two molecules are re-lated to each other this way: [], [63] [64] [65] Overfull \hbox (40.92256pt too wide) in paragraph at lines 4955--4962 []\OT1/cmr/m/n/10.95 , [], or [] Overfull \hbox (19.41339pt too wide) in paragraph at lines 4967--4967 [] \OT1/cmtt/m/n/10.95 @angle:CCCsaturated @atom:C @atom:C @atom:C @bond:SAT @bond:SAT[] Overfull \hbox (54.72884pt too wide) in paragraph at lines 4973--4978 []\OT1/cmr/m/n/10.95 The first line will gen-er-ate a 3-body an-gle in-ter-ac-t ion (of type []) Overfull \hbox (31.27754pt too wide) in paragraph at lines 4980--4988 []\OT1/cmr/m/n/10.95 The sec-ond line will gen-er-ate a 3-body in-ter-ac-tion o f type [] Overfull \hbox (34.34967pt too wide) in paragraph at lines 4990--4995 []\OT1/cmr/m/n/10.95 The third line will gen-er-ate a 3-body in-ter-ac-tion of type [] [66] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5089--5089 []\OT1/cmtt/m/n/10.95 ltemplify.py -name MoleculeName -mol MolID INPUT_SCRIPT D ATA_FILE > FILE.lt [67] [68] Overfull \hbox (69.51059pt too wide) in paragraph at lines 5127--5232 [] [69] Overfull \hbox (6.57567pt too wide) in paragraph at lines 5291--5295 \OT1/cmr/m/it/10.95 However, \OT1/cmr/m/n/10.95 ltem-plify.py uses com-ments in the ``Masses'' sec-tion of the LAMMPS [70] Overfull \hbox (26.77591pt too wide) in paragraph at lines 5344--5353 []\OT1/cmr/m/n/10.95 In this ex-am-ple, bonds of type 1 and 2 will be re-ferred to as ``@bond:CCethane'' [71] Overfull \hbox (1.40111pt too wide) in paragraph at lines 5370--5378 \OT1/cmr/m/n/10.95 PASS''), con-tain rules for gen-er-at-ing these in-ter-ac-ti ons au-to-mat-i-cally. Hence, [72] Overfull \hbox (19.41339pt too wide) in paragraph at lines 5496--5496 []\OT1/cmtt/m/n/10.95 ltemplify.py -name Ethane -molid "1" FILE.in FILE.data > ethane.lt [73] Overfull \hbox (30.91077pt too wide) in paragraph at lines 5566--5566 []\OT1/cmtt/m/n/10.95 ltemplify.py -name EntireSystem FILE.in FILE.data > entir e_system.lt [74] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5593--5593 []\OT1/cmtt/m/n/10.95 # This example creates a new file, "ethane.lt", which wil l contain the Overfull \hbox (30.91077pt too wide) in paragraph at lines 5594--5594 []\OT1/cmtt/m/n/10.95 # instructions for building a "Ethane" molecule using "GA FF2". First[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5595--5595 []\OT1/cmtt/m/n/10.95 # specify which file contains the definition of the "GAFF 2" force field:[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5599--5599 []\OT1/cmtt/m/n/10.95 # Then use ltemplify.py to extract information from FILE. in, FILE.data[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 5603--5603 [] \OT1/cmtt/m/n/10.95 -ignore-angles -ignore-bond-types -ignore-co effs \[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 5606--5606 []\OT1/cmtt/m/n/10.95 # Note: if you want to build a simulation containing thes e molecules,[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5607--5607 []\OT1/cmtt/m/n/10.95 # you will have to create a "system.lt" file which refers to "ethane.lt"[] [75] [76] [77] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5893--5893 []\OT1/cmtt/m/n/10.95 -atomstyle style By default, moltemplate.sh assumes you are using the "full"[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 5894--5894 [] \OT1/cmtt/m/n/10.95 atom style in LAMMPS. You can change the atom style to "dipole"[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5895--5895 [] \OT1/cmtt/m/n/10.95 using -atomstyle dipole. If you are usin g a hybrid style,[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5896--5896 [] \OT1/cmtt/m/n/10.95 you must enclose the list of styles in qu otes. For example:[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 5898--5898 [] \OT1/cmtt/m/n/10.95 For custom atom styles, you can also spec ify the[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5899--5899 [] \OT1/cmtt/m/n/10.95 list of column names manually (enclosed i n quotes):[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 5900--5900 [] \OT1/cmtt/m/n/10.95 -atomstyle "molid x y z atomid atomtype m ux muy muz"[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5901--5901 [] \OT1/cmtt/m/n/10.95 Be careful to enclose the entire list in quotes(").[] Overfull \hbox (134.38715pt too wide) in paragraph at lines 5903--5903 []\OT1/cmtt/m/n/10.95 -raw raw_file The raw_file file should contain the atom ic coordinates in RAW format.[] Overfull \hbox (117.14108pt too wide) in paragraph at lines 5904--5904 [] \OT1/cmtt/m/n/10.95 RAW files are simple 3-column ASCII files containin the coordinates[] Overfull \hbox (122.88977pt too wide) in paragraph at lines 5905--5905 [] \OT1/cmtt/m/n/10.95 for the atoms in the system. (One line pe r atom, 3 numbers per line.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5906--5906 [] \OT1/cmtt/m/n/10.95 The atoms must appear in the same order i n the data file.)[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 5907--5907 []\OT1/cmtt/m/n/10.95 -xyz xyz_file An xyz_file argument should be supplied a s an argument[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 5909--5909 [] \OT1/cmtt/m/n/10.95 This file should contain the atomic coord inates in xyz format.[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5910--5910 [] \OT1/cmtt/m/n/10.95 (The atoms must appear in the same order in the data file.)[] Overfull \hbox (134.38715pt too wide) in paragraph at lines 5912--5912 []\OT1/cmtt/m/n/10.95 -pdb pdb_file The pdb_file file should contain the atom ic coordinates in PDB format.[] [78] Overfull \hbox (117.14108pt too wide) in paragraph at lines 5914--5914 [] \OT1/cmtt/m/n/10.95 This file should contain one ATOM or HETA TM record per atom. Atoms[] Overfull \hbox (105.6437pt too wide) in paragraph at lines 5916--5916 [] \OT1/cmtt/m/n/10.95 are sorted by chainID, resID, insertCode, atomID (in that order).[] Overfull \hbox (111.3924pt too wide) in paragraph at lines 5917--5917 [] \OT1/cmtt/m/n/10.95 This order must match the order the atoms appear in the data file.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5919--5919 [] \OT1/cmtt/m/n/10.95 If the PDB file contains periodic boundar y box information[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5920--5920 [] \OT1/cmtt/m/n/10.95 (IE., a "CRYST1" record), this informatio n is also copied[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5922--5922 [] \OT1/cmtt/m/n/10.95 (Support for triclinic cells is experimen tal as of 2019-9-03.[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5923--5923 [] \OT1/cmtt/m/n/10.95 Other molecular structure formats may be supported later.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5926--5926 [] \OT1/cmtt/m/n/10.95 The user can customize the numbers assign ed to atom, bond,[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5927--5927 [] \OT1/cmtt/m/n/10.95 angle, dihedral, and improper types or id numbers by using[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5929--5929 [] \OT1/cmtt/m/n/10.95 for each variable you want to modify. If there are many[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5930--5930 [] \OT1/cmtt/m/n/10.95 variables you want to modify, you can sav e them in a file[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5931--5931 [] \OT1/cmtt/m/n/10.95 (one variable per line). For an example of the file format[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 5932--5932 [] \OT1/cmtt/m/n/10.95 run moltemplate.sh once and search for a file named[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 5933--5933 [] \OT1/cmtt/m/n/10.95 "ttree_assignments.txt". (This file is o ften located in[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5934--5934 [] \OT1/cmtt/m/n/10.95 the "output_ttree/" directory.) Once assi gned, the remaining[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5935--5935 [] \OT1/cmtt/m/n/10.95 variables in the same category will be au tomatically assigned[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 5936--5936 [] \OT1/cmtt/m/n/10.95 to values which do not overlap with your chosen values.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5938--5938 [] \OT1/cmtt/m/n/10.95 "-b" is similar to "-a". However, in this case, no attempt[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5939--5939 [] \OT1/cmtt/m/n/10.95 is made to assign exclusive (unique) valu es to each variable.[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 5941--5941 [] \OT1/cmtt/m/n/10.95 Normally moltemplate.sh checks for common errors and typos and[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 5942--5942 [] \OT1/cmtt/m/n/10.95 halts if it thinks it has found one. This forces the variables[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 5943--5943 [] \OT1/cmtt/m/n/10.95 and categories as well as write(file) and write_once(file)[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 5944--5944 [] \OT1/cmtt/m/n/10.95 commands to obey standard naming conventio ns. The "-nocheck"[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 5945--5945 [] \OT1/cmtt/m/n/10.95 argument bypasses these checks and elimina tes these restrictions.[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 5947--5947 [] \OT1/cmtt/m/n/10.95 This cause moltemplate.sh to check to mak e sure that there[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 5948--5948 [] \OT1/cmtt/m/n/10.95 are valid angle and dihedral interactions defined for every[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 5949--5949 [] \OT1/cmtt/m/n/10.95 3 or 4 consecutively bonded atoms in the system[] [79] Overfull \hbox (13.6647pt too wide) in paragraph at lines 6010--6010 []\OT1/cmtt/m/n/10.95 moltemplate.sh -a '@atom:SPCE/O 2' -a '@atom:SPCE/H 1' s ystem.lt [80] Overfull \hbox (43.572pt too wide) in paragraph at lines 6093--6095 []\OT1/cmr/m/n/10.95 The ``ttree[]assignments.txt'' file has the same for-mat a s the ``new[]assignments.txt'' Overfull \hbox (0.80295pt too wide) in paragraph at lines 6115--6118 \OT1/cmr/m/n/10.95 If for some rea-son, you are us-ing ``lt-tree.py'' or ``ttre e.py'' in-stead of ``moltem- [81] [82] [83] [84] [85] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6502--6502 [] \OT1/cmtt/m/n/10.95 natom++; print "set atom "natom" x "$1" y "$2" z "$ 3" "}}' \[] [86] Overfull \hbox (8.35524pt too wide) in paragraph at lines 6562--6563 \OT1/cmr/m/it/10.95 file with the ap-pro-pri-ate in-te-ger be-fore you copy the con-tents into the LAMMPS Overfull \hbox (59.6542pt too wide) in paragraph at lines 6594--6594 [] \OT1/cmtt/m/n/10.95 nbody_by_type.py reads a LAMMPS data file (or an exce rpt of a LAMMPS) Overfull \hbox (25.16208pt too wide) in paragraph at lines 6595--6595 [] \OT1/cmtt/m/n/10.95 data file containing bonded many-body interactions by atom type[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6596--6596 [] \OT1/cmtt/m/n/10.95 (and bond type), and generates a list of additional i nteractions[] Overfull \hbox (42.40814pt too wide) in paragraph at lines 6597--6597 [] \OT1/cmtt/m/n/10.95 in LAMMPS format consistent with those type (to the s tandard out).[] [87] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6615--6615 [] \OT1/cmtt/m/n/10.95 Support for other interaction types can be added by t he user. See below.[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6617--6617 [] \OT1/cmtt/m/n/10.95 Note: The optional "-subgraph" argument allows you to customize the[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6618--6618 [] \OT1/cmtt/m/n/10.95 rules used to match and generate interactions o f that type.[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6619--6619 [] \OT1/cmtt/m/n/10.95 It is optional, and is only useful for forcefie lds which[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6620--6620 [] \OT1/cmtt/m/n/10.95 use non-standard dihedral or improper atom-orde r convetions.)[] Overfull \hbox (82.64896pt too wide) in paragraph at lines 6628--6628 [] \OT1/cmtt/m/n/10.95 "Dihedrals", or "Impropers"). It also looks a sectio n named "X By Type",[] Overfull \hbox (48.15683pt too wide) in paragraph at lines 6629--6629 [] \OT1/cmtt/m/n/10.95 (eg. "Angles By type", "Impropers By type", "Impro pers By type")[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6630--6630 [] \OT1/cmtt/m/n/10.95 which contains a list of criteria for automatically d efining additional[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6631--6631 [] \OT1/cmtt/m/n/10.95 interactions of that type. For example, this file mi ght contain:[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 6642--6642 [] \OT1/cmtt/m/n/10.95 The * is a wildcard symbol indicating there is no pre ference for bond types[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6643--6643 [] \OT1/cmtt/m/n/10.95 in this example. (Optionally, regular expressions ca n also be used to[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6644--6644 [] \OT1/cmtt/m/n/10.95 define a type match, by enclosing the atom or bond ty pe in / slashes.)[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6646--6646 [] \OT1/cmtt/m/n/10.95 The first line tells us to that there should be a 3-body "Angle"[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6647--6647 [] \OT1/cmtt/m/n/10.95 interaction of type "7" whenever an atom of type 1 is bonded to an atom[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6648--6648 [] \OT1/cmtt/m/n/10.95 of type "2", which is bonded to another atom of type "1" again.[] [88] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6649--6649 [] \OT1/cmtt/m/n/10.95 The second line tells us that an angle is defined whe never three atoms[] Overfull \hbox (7.91602pt too wide) in paragraph at lines 6654--6654 [] \OT1/cmtt/m/n/10.95 atoms which match these criteria if they are bonded t ogether[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6655--6655 [] \OT1/cmtt/m/n/10.95 in the relevant way for that interaction type (as det ermined by[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6656--6656 [] \OT1/cmtt/m/n/10.95 nbody_X.py), and printed to the standard output. For example,[] Overfull \hbox (94.14633pt too wide) in paragraph at lines 6657--6657 [] \OT1/cmtt/m/n/10.95 suppose you are automatically generating 3-body "Angl e" interactions using:[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6661--6661 [] \OT1/cmtt/m/n/10.95 The file "new.data" will be identical to "old.data", however the[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6662--6662 [] \OT1/cmtt/m/n/10.95 "Angles By Type" section will be deleted, and the fol lowing lines of[] Overfull \hbox (36.65945pt too wide) in paragraph at lines 6671--6671 [] \OT1/cmtt/m/n/10.95 The numbers in the first column are counters which as sign a ID to[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 6672--6672 [] \OT1/cmtt/m/n/10.95 every interaction of that type, and start where the o riginal "Angles"[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6673--6673 [] \OT1/cmtt/m/n/10.95 data left off (New angle ID numbers do not overlap wi th old ID numbers).[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6674--6674 [] \OT1/cmtt/m/n/10.95 The text in the second column ("7", "9", ...) matches the text from the[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6675--6675 [] \OT1/cmtt/m/n/10.95 first column of the "Angle By Type" section of the in put file.[] [89] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6697--6697 [] \OT1/cmtt/m/n/10.95 When run this way, nbody_by_type.py behaves exactly t he same way[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6698--6698 [] \OT1/cmtt/m/n/10.95 as in Example 1, however only the lines of text corre sponding to[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6699--6699 [] \OT1/cmtt/m/n/10.95 the new generated interactions are printed, (not the entire data file).[] Overfull \hbox (59.6542pt too wide) in paragraph at lines 6700--6700 [] \OT1/cmtt/m/n/10.95 Also note, that when run this way, nbody_by_type.py d oes not read the[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6701--6701 [] \OT1/cmtt/m/n/10.95 LAMMPS data from the standard input. Instead, it rea ds each section of[] Overfull \hbox (76.90027pt too wide) in paragraph at lines 6702--6702 [] \OT1/cmtt/m/n/10.95 the data file from a different file indicated by the arguments following[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 6703--6703 [] \OT1/cmtt/m/n/10.95 the "-atoms", "-bonds", "-nbody", and "-nbodybytype" flags.[] Overfull \hbox (19.41339pt too wide) in paragraph at lines 6705--6705 [] \OT1/cmtt/m/n/10.95 "Angles" is a 3-body interaction style. So when run this way,[] Overfull \hbox (65.4029pt too wide) in paragraph at lines 6706--6706 [] \OT1/cmtt/m/n/10.95 nbody_by_type.py will create a 5 (=3+2) column file ( new_Angles.data).[] Overfull \hbox (13.6647pt too wide) in paragraph at lines 6708--6708 []\OT1/cmtt/m/n/10.95 Note: the atom, bond and other IDs/types in need not be i ntegers.[] Overfull \hbox (88.39764pt too wide) in paragraph at lines 6710--6710 []\OT1/cmtt/m/n/10.95 Note: This program must be distributed with several pytho n modules, including:[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6711--6711 [] \OT1/cmtt/m/n/10.95 nbody_Angles.py, nbody_Dihedrals.py, and nbody_Im propers.py. These[] Overfull \hbox (99.89502pt too wide) in paragraph at lines 6712--6712 [] \OT1/cmtt/m/n/10.95 contain bond definitions for angular, dihedral, and improper interactions.[] Overfull \hbox (1.14366pt too wide) in paragraph at lines 6717--6732 \OT1/cmr/m/n/10.95 im-ports ex-ter-nal mod-ules named ``nbody[]Angles.py'', ``n body[]Dihedrals.py'', Overfull \hbox (4.07088pt too wide) in paragraph at lines 6741--6743 \OT1/cmr/m/n/10.95 Moltemplate.sh is a script which in-vokes a python pro-gram pro-gram (\OT1/cmr/m/it/10.95 ttree.py\OT1/cmr/m/n/10.95 ) [90] Overfull \hbox (82.64896pt too wide) in paragraph at lines 6766--6766 []\OT1/cmtt/m/n/10.95 String ::= InstanceName | ObjectTypeName | FileName | Cat egoryName | OtherStr Overfull \hbox (76.90027pt too wide) in paragraph at lines 6796--6796 []\OT1/cmtt/m/n/10.95 Command ::= ObjectDef | InstanceCommand | DeleteCommand | WriteC | WriteOC | Overfull \hbox (48.15683pt too wide) in paragraph at lines 6797--6797 [] \OT1/cmtt/m/n/10.95 ImportCommand | CategoryDef | InstanceMod | O bjectTypeMod |[] Overfull \hbox (30.91077pt too wide) in paragraph at lines 6798--6798 [] \OT1/cmtt/m/n/10.95 ObjectDefMod | ReplaceCommand | UsingCommand | PushXform[] [91] Overfull \hbox (7.91602pt too wide) in paragraph at lines 6813--6813 []\OT1/cmtt/m/n/10.95 RotXform ::= ".rot(" Number "," Number "," Number "," Num ber ")"[] Overfull \hbox (71.15158pt too wide) in paragraph at lines 6833--6833 []\OT1/cmtt/m/n/10.95 TemplText ::= "" | String TemplText | StatVar TemplText | InstVar TemplText[] Overfull \hbox (2.16733pt too wide) in paragraph at lines 6837--6837 []\OT1/cmtt/m/n/10.95 WriteOC ::= "write_once(" FileName ")" "{" TemplateTextSt at "}"[] Overfull \hbox (25.16208pt too wide) in paragraph at lines 6838--6838 []\OT1/cmtt/m/n/10.95 TemplTextStat ::= "" | String TemplTextStat | StatVar Tem plTextStat[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6849--6849 []\OT1/cmtt/m/n/10.95 CatCommandStat ::= "category" "@"CategoryName"(" Integer "," Integer ")"[] Overfull \hbox (53.90552pt too wide) in paragraph at lines 6850--6850 []\OT1/cmtt/m/n/10.95 CatCommandInst ::= "category" "$"CategoryName"(" Integer "," Integer ")"[] [92] [93] Overfull \hbox (5.00008pt too wide) in paragraph at lines 6955--6959 []\OT1/cmr/m/n/10.95 Find the cat-e-gory name and ob-ject cor-re-spond-ing to ` `\TS1/cmr/m/n/10.95 $\OT1/cmr/bx/it/10.95 cpath\OT1/cmr/m/n/10.95 /\OT1/cmr/bx/ it/10.95 catname\OT1/cmr/m/n/10.95 :'' [94] Overfull \hbox (43.72781pt too wide) in paragraph at lines 6972--6973 \OT1/cmr/m/n/10.95 file (al-though you can use it any-where else in an ``.LT'' file). In ``ttree[]assignments.txt'' (./moltemplate_manual.bbl [95]) [96] (./moltemplate_manual.aux) ) (see the transcript file for additional information) Output written on moltemplate_manual.pdf (96 pages, 837379 bytes). Transcript written on moltemplate_manual.log. make[1]: Leaving directory '/build/reproducible-path/moltemplate-2.22.5' dh_auto_test -i -O--buildsystem=pybuild W: pybuild base:327: No test runner selected, defaulting to unittest, ignoring test discovery problems. Use --test-unittest to explicitly select the unittest runner. I: pybuild base:384: cd /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build; python3.14 -m unittest discover -v /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ttree.py:4981: SyntaxWarning: "\$" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\$"? A raw string is also an option. ' For example, use: \'$atom:wat[2]/H1 20\' or "\$atom:wat[2]/H1 to 20"\n' /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ttree_lex.py:1817: SyntaxWarning: "\}" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\}"? A raw string is also an option. (for example, '}' in "\}" does not cause terminate parsing). /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ltemplify.py:2197: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option. ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ltemplify.py:2250: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option. ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN W: pybuild base:327: No test runner selected, defaulting to unittest, ignoring test discovery problems. Use --test-unittest to explicitly select the unittest runner. I: pybuild base:384: cd /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build; python3.13 -m unittest discover -v /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ttree.py:4981: SyntaxWarning: invalid escape sequence '\$' ' For example, use: \'$atom:wat[2]/H1 20\' or "\$atom:wat[2]/H1 to 20"\n' /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ttree_lex.py:1817: SyntaxWarning: invalid escape sequence '\}' (for example, '}' in "\}" does not cause terminate parsing). /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ltemplify.py:2197: SyntaxWarning: invalid escape sequence '\*' ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ltemplify.py:2250: SyntaxWarning: invalid escape sequence '\*' ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=pybuild dh_prep -i -O--buildsystem=pybuild dh_auto_install -i -O--buildsystem=pybuild I: pybuild base:384: /usr/bin/python3.14 setup.py install --root /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing moltemplate.egg-info/PKG-INFO writing dependency_links to moltemplate.egg-info/dependency_links.txt writing entry points to moltemplate.egg-info/entry_points.txt writing requirements to moltemplate.egg-info/requires.txt writing top-level names to moltemplate.egg-info/top_level.txt reading manifest file 'moltemplate.egg-info/SOURCES.txt' adding license file 'LICENSE.md' writing manifest file 'moltemplate.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'moltemplate.force_fields' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'moltemplate.force_fields' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'moltemplate.force_fields' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'moltemplate.force_fields' to be distributed and are already explicitly excluding 'moltemplate.force_fields' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'moltemplate.scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'moltemplate.scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'moltemplate.scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'moltemplate.scripts' to be distributed and are already explicitly excluding 'moltemplate.scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_scripts running install_lib creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/lttree_check.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ttree_render.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/genpoly_lt.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ordereddict.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/recenter_coords.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/extract_espresso_atom_types.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ettree_styles.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ltemplify.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_by_type_lib.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/postprocess_input_script.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/postprocess_transitions.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_Dihedrals.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/interpolate_curve.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_2004.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/loplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_1983_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce_ice_rect32.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spc_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_1983_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce_dreiding.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip5p_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/cooke_deserno_lipid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce_more_comments.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce_ice_rect8.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_2004_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/martini.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/watmw.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_2004_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/compass_published.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/gaff2.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/sdk.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_1983_charmm_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spc_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/trappe1998.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip5p_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/dreiding.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_1983_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/loplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce_amber.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip5p_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce_ice_rect16.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spc_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/loplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_2004_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/graphite.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/graphene.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_1983_charmm.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/spce_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/gaff.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_1983.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/drymartini.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/graphene_rectangular.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/force_fields/tip3p_1983_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/bonds_by_type.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/renumber_DATA_first_column.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/lttree_styles.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/raw2data.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_fix_ttree_assignments.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ttree_matrix_stack.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts/molc.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts/moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts/emoltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts/cleanup_moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/scripts/pdb2crds.awk -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_Bonds.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/remove_duplicates_nbody.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/genpoly_modify_lt.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/lttree_postprocess.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ettree.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__init__.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/mol22lt.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/postprocess_coeffs.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/extract_lammps_data.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ttree_lex.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/remove_duplicate_atoms.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/amber2lt.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/cenJswapIL.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/cenKswapIL.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/bonds_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/gaff_imp.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/__init__.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/cenIsortJKL.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/cenIswapJK.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/dihedrals_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/__pycache__/__init__.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/angles_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/impropers_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_alt_symmetry/cenJsortIKL.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/charge_by_bond.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_Angles.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/pdbsort.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_Impropers.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/dump2data.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/ettree.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/ltemplify.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/dump2data.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/ttree_render.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/interpolate_curve.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/ttree_lex.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/genpoly_modify_lt.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/nbody_by_type.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/__init__.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/ttree.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/genpoly_lt.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/ttree_matrix_stack.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/mol22lt.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/raw2data.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/nbody_graph_search.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/ettree_styles.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/nbody_by_type_lib.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/lttree.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/amber2lt.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/lttree_styles.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/__pycache__/extract_lammps_data.cpython-314.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/ttree.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/lttree.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_reorder_atoms.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_by_type.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.14_moltemplate/build/moltemplate/nbody_graph_search.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/lttree_check.py to lttree_check.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/ttree_render.py to ttree_render.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/genpoly_lt.py to genpoly_lt.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/ordereddict.py to ordereddict.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/recenter_coords.py to recenter_coords.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/extract_espresso_atom_types.py to extract_espresso_atom_types.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/ettree_styles.py to ettree_styles.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/ltemplify.py to ltemplify.cpython-314.pyc /usr/lib/python3.14/dist-packages/moltemplate/ltemplify.py:2197: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option. /usr/lib/python3.14/dist-packages/moltemplate/ltemplify.py:2250: SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\*"? A raw string is also an option. byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_by_type_lib.py to nbody_by_type_lib.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/postprocess_input_script.py to postprocess_input_script.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/postprocess_transitions.py to postprocess_transitions.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_Dihedrals.py to nbody_Dihedrals.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/interpolate_curve.py to interpolate_curve.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/bonds_by_type.py to bonds_by_type.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/renumber_DATA_first_column.py to renumber_DATA_first_column.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/lttree_styles.py to lttree_styles.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/raw2data.py to raw2data.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_fix_ttree_assignments.py to nbody_fix_ttree_assignments.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/ttree_matrix_stack.py to ttree_matrix_stack.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_Bonds.py to nbody_Bonds.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/remove_duplicates_nbody.py to remove_duplicates_nbody.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/genpoly_modify_lt.py to genpoly_modify_lt.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/lttree_postprocess.py to lttree_postprocess.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/ettree.py to ettree.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/__init__.py to __init__.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/mol22lt.py to mol22lt.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/postprocess_coeffs.py to postprocess_coeffs.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/extract_lammps_data.py to extract_lammps_data.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/ttree_lex.py to ttree_lex.cpython-314.pyc /usr/lib/python3.14/dist-packages/moltemplate/ttree_lex.py:1817: SyntaxWarning: "\}" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\}"? A raw string is also an option. byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/remove_duplicate_atoms.py to remove_duplicate_atoms.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/amber2lt.py to amber2lt.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/cenJswapIL.py to cenJswapIL.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/cenKswapIL.py to cenKswapIL.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/bonds_nosym.py to bonds_nosym.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/gaff_imp.py to gaff_imp.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/__init__.py to __init__.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/cenIsortJKL.py to cenIsortJKL.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/cenIswapJK.py to cenIswapJK.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/dihedrals_nosym.py to dihedrals_nosym.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/angles_nosym.py to angles_nosym.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/impropers_nosym.py to impropers_nosym.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_alt_symmetry/cenJsortIKL.py to cenJsortIKL.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/charge_by_bond.py to charge_by_bond.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_Angles.py to nbody_Angles.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/pdbsort.py to pdbsort.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_Impropers.py to nbody_Impropers.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/dump2data.py to dump2data.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/ttree.py to ttree.cpython-314.pyc /usr/lib/python3.14/dist-packages/moltemplate/ttree.py:4981: SyntaxWarning: "\$" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\$"? A raw string is also an option. byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/lttree.py to lttree.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_reorder_atoms.py to nbody_reorder_atoms.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_by_type.py to nbody_by_type.cpython-314.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate/nbody_graph_search.py to nbody_graph_search.cpython-314.pyc running install_egg_info Copying moltemplate.egg-info to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.14/dist-packages/moltemplate-2.22.5.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin copying build/scripts-3.14/molc.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin copying build/scripts-3.14/moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin copying build/scripts-3.14/emoltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin copying build/scripts-3.14/cleanup_moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin copying build/scripts-3.14/pdb2crds.awk -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/molc.sh to 755 changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/moltemplate.sh to 755 changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/emoltemplate.sh to 755 changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/cleanup_moltemplate.sh to 755 changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/pdb2crds.awk to 755 Installing bonds_by_type.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing charge_by_bond.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing dump2data.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing ettree.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing extract_espresso_atom_types.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing extract_lammps_data.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing genpoly_lt.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing genpoly_modify_lt.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing interpolate_curve.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing ltemplify.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing lttree.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing lttree_check.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing lttree_postprocess.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing mol22lt.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing nbody_by_type.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing nbody_fix_ttree_assignments.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing nbody_reorder_atoms.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing pdbsort.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing postprocess_coeffs.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing postprocess_input_script.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing raw2data.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing recenter_coords.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing remove_duplicate_atoms.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing remove_duplicates_nbody.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing renumber_DATA_first_column.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing ttree.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing ttree_render.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin I: pybuild base:384: /usr/bin/python3 setup.py install --root /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing moltemplate.egg-info/PKG-INFO writing dependency_links to moltemplate.egg-info/dependency_links.txt writing entry points to moltemplate.egg-info/entry_points.txt writing requirements to moltemplate.egg-info/requires.txt writing top-level names to moltemplate.egg-info/top_level.txt reading manifest file 'moltemplate.egg-info/SOURCES.txt' adding license file 'LICENSE.md' writing manifest file 'moltemplate.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'moltemplate.force_fields' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'moltemplate.force_fields' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'moltemplate.force_fields' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'moltemplate.force_fields' to be distributed and are already explicitly excluding 'moltemplate.force_fields' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'moltemplate.scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'moltemplate.scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'moltemplate.scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'moltemplate.scripts' to be distributed and are already explicitly excluding 'moltemplate.scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_scripts running install_lib creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/lttree_check.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ttree_render.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/genpoly_lt.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ordereddict.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/recenter_coords.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/extract_espresso_atom_types.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ettree_styles.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ltemplify.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_by_type_lib.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/postprocess_input_script.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/postprocess_transitions.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_Dihedrals.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/interpolate_curve.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_2004.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/loplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_1983_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce_ice_rect32.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spc_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_1983_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce_dreiding.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip5p_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/cooke_deserno_lipid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce_more_comments.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce_ice_rect8.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_2004_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/martini.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/watmw.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_2004_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/compass_published.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/gaff2.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/sdk.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_1983_charmm_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spc_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/trappe1998.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip5p_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/dreiding.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_1983_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/loplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce_amber.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip5p_oplsaa.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce_ice_rect16.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spc_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/loplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_2004_oplsaa2024.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/graphite.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/graphene.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_1983_charmm.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/spce_hybrid.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/gaff.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_1983.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/drymartini.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/graphene_rectangular.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/force_fields/tip3p_1983_oplsaa2008.lt -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/force_fields copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/bonds_by_type.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/renumber_DATA_first_column.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/lttree_styles.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/raw2data.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_fix_ttree_assignments.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ttree_matrix_stack.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts/molc.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts/moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts/emoltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts/cleanup_moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/scripts/pdb2crds.awk -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/scripts copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_Bonds.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/remove_duplicates_nbody.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/genpoly_modify_lt.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/lttree_postprocess.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ettree.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__init__.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/mol22lt.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/postprocess_coeffs.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/extract_lammps_data.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ttree_lex.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/remove_duplicate_atoms.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/amber2lt.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/cenJswapIL.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/cenKswapIL.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/bonds_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/gaff_imp.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/__init__.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/cenIsortJKL.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/cenIswapJK.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/dihedrals_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/angles_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/impropers_nosym.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_alt_symmetry/cenJsortIKL.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/charge_by_bond.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_Angles.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/pdbsort.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_Impropers.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/dump2data.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate creating /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/ettree.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/dump2data.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/nbody_by_type_lib.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/ttree.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/lttree_styles.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/nbody_graph_search.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/ltemplify.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/interpolate_curve.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/lttree.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/ettree_styles.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/nbody_by_type.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/ttree_render.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/ttree_lex.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/genpoly_lt.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/amber2lt.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/mol22lt.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/raw2data.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/extract_lammps_data.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/ttree_matrix_stack.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/__pycache__/genpoly_modify_lt.cpython-313.pyc -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__pycache__ copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/ttree.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/lttree.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_reorder_atoms.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_by_type.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate copying /build/reproducible-path/moltemplate-2.22.5/.pybuild/cpython3_3.13_moltemplate/build/moltemplate/nbody_graph_search.py -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/lttree_check.py to lttree_check.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/ttree_render.py to ttree_render.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/genpoly_lt.py to genpoly_lt.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/ordereddict.py to ordereddict.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/recenter_coords.py to recenter_coords.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/extract_espresso_atom_types.py to extract_espresso_atom_types.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/ettree_styles.py to ettree_styles.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/ltemplify.py to ltemplify.cpython-313.pyc /usr/lib/python3.13/dist-packages/moltemplate/ltemplify.py:2197: SyntaxWarning: invalid escape sequence '\*' /usr/lib/python3.13/dist-packages/moltemplate/ltemplify.py:2250: SyntaxWarning: invalid escape sequence '\*' byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_by_type_lib.py to nbody_by_type_lib.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/postprocess_input_script.py to postprocess_input_script.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/postprocess_transitions.py to postprocess_transitions.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_Dihedrals.py to nbody_Dihedrals.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/interpolate_curve.py to interpolate_curve.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/bonds_by_type.py to bonds_by_type.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/renumber_DATA_first_column.py to renumber_DATA_first_column.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/lttree_styles.py to lttree_styles.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/raw2data.py to raw2data.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_fix_ttree_assignments.py to nbody_fix_ttree_assignments.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/ttree_matrix_stack.py to ttree_matrix_stack.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_Bonds.py to nbody_Bonds.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/remove_duplicates_nbody.py to remove_duplicates_nbody.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/genpoly_modify_lt.py to genpoly_modify_lt.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/lttree_postprocess.py to lttree_postprocess.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/ettree.py to ettree.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/mol22lt.py to mol22lt.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/postprocess_coeffs.py to postprocess_coeffs.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/extract_lammps_data.py to extract_lammps_data.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/ttree_lex.py to ttree_lex.cpython-313.pyc /usr/lib/python3.13/dist-packages/moltemplate/ttree_lex.py:1817: SyntaxWarning: invalid escape sequence '\}' byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/remove_duplicate_atoms.py to remove_duplicate_atoms.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/amber2lt.py to amber2lt.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/cenJswapIL.py to cenJswapIL.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/cenKswapIL.py to cenKswapIL.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/bonds_nosym.py to bonds_nosym.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/gaff_imp.py to gaff_imp.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/cenIsortJKL.py to cenIsortJKL.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/cenIswapJK.py to cenIswapJK.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/dihedrals_nosym.py to dihedrals_nosym.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/angles_nosym.py to angles_nosym.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/impropers_nosym.py to impropers_nosym.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_alt_symmetry/cenJsortIKL.py to cenJsortIKL.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/charge_by_bond.py to charge_by_bond.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_Angles.py to nbody_Angles.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/pdbsort.py to pdbsort.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_Impropers.py to nbody_Impropers.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/dump2data.py to dump2data.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/ttree.py to ttree.cpython-313.pyc /usr/lib/python3.13/dist-packages/moltemplate/ttree.py:4981: SyntaxWarning: invalid escape sequence '\$' byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/lttree.py to lttree.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_reorder_atoms.py to nbody_reorder_atoms.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_by_type.py to nbody_by_type.cpython-313.pyc byte-compiling /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate/nbody_graph_search.py to nbody_graph_search.cpython-313.pyc running install_egg_info Copying moltemplate.egg-info to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/lib/python3.13/dist-packages/moltemplate-2.22.5.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.13/molc.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin copying build/scripts-3.13/moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin copying build/scripts-3.13/emoltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin copying build/scripts-3.13/cleanup_moltemplate.sh -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin copying build/scripts-3.13/pdb2crds.awk -> /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/molc.sh to 755 changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/moltemplate.sh to 755 changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/emoltemplate.sh to 755 changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/cleanup_moltemplate.sh to 755 changing mode of /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin/pdb2crds.awk to 755 Installing bonds_by_type.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing charge_by_bond.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing dump2data.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing ettree.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing extract_espresso_atom_types.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing extract_lammps_data.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing genpoly_lt.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing genpoly_modify_lt.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing interpolate_curve.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing ltemplify.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing lttree.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing lttree_check.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing lttree_postprocess.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing mol22lt.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing nbody_by_type.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing nbody_fix_ttree_assignments.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing nbody_reorder_atoms.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing pdbsort.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing postprocess_coeffs.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing postprocess_input_script.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing raw2data.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing recenter_coords.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing remove_duplicate_atoms.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing remove_duplicates_nbody.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing renumber_DATA_first_column.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing ttree.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin Installing ttree_render.py script to /build/reproducible-path/moltemplate-2.22.5/debian/python3-moltemplate/usr/bin dh_installdocs -i -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for moltemplate-doc. If the default is wrong, please use --doc-main-package or the X-Doc-Main-Package field dh_installchangelogs -i -O--buildsystem=pybuild dh_python3 -i -O--buildsystem=pybuild I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/lttree_check.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/ttree_render.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/genpoly_lt.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/recenter_coords.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/extract_espresso_atom_types.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/ltemplify.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/postprocess_input_script.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/interpolate_curve.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/bonds_by_type.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/renumber_DATA_first_column.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/raw2data.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/nbody_fix_ttree_assignments.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/remove_duplicates_nbody.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/genpoly_modify_lt.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/lttree_postprocess.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/ettree.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/mol22lt.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/postprocess_coeffs.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/extract_lammps_data.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/remove_duplicate_atoms.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/charge_by_bond.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/pdbsort.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/dump2data.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/ttree.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/lttree.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/nbody_reorder_atoms.py I: dh_python3 tools:128: replacing shebang in debian/python3-moltemplate/usr/bin/nbody_by_type.py dh_installsystemduser -i -O--buildsystem=pybuild dh_lintian -i -O--buildsystem=pybuild dh_perl -i -O--buildsystem=pybuild dh_link -i -O--buildsystem=pybuild dh_strip_nondeterminism -i -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/moltemplate-2.22.5' dh_compress --exclude=moltemplate_manual.pdf make[1]: Leaving directory '/build/reproducible-path/moltemplate-2.22.5' dh_fixperms -i -O--buildsystem=pybuild dh_missing -i -O--buildsystem=pybuild dh_installdeb -i -O--buildsystem=pybuild dh_gencontrol -i -O--buildsystem=pybuild dh_md5sums -i -O--buildsystem=pybuild dh_builddeb -i -O--buildsystem=pybuild dpkg-deb: building package 'python3-moltemplate' in '../python3-moltemplate_2.22.5-1_all.deb'. dpkg-deb: building package 'moltemplate-doc' in '../moltemplate-doc_2.22.5-1_all.deb'. dpkg-genbuildinfo --build=all -O../moltemplate_2.22.5-1_all.buildinfo dpkg-genchanges --build=all -O../moltemplate_2.22.5-1_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-source: info: using options from moltemplate-2.22.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2026-02-26T05:32:11Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Thu, 26 Feb 2026 05:32:13 +0000 | +------------------------------------------------------------------------------+ moltemplate_2.22.5-1_all.changes: --------------------------------- Format: 1.8 Date: Wed, 25 Feb 2026 10:18:14 +0100 Source: moltemplate Binary: moltemplate-doc python3-moltemplate Architecture: all Version: 2.22.5-1 Distribution: unstable Urgency: medium Maintainer: Drew Parsons Changed-By: Drew Parsons Description: moltemplate-doc - text-based molecule builder for LAMMPS (documentation) python3-moltemplate - text-based molecule builder for LAMMPS Changes: moltemplate (2.22.5-1) unstable; urgency=medium . * New upstream release * Standards-Version: 4.7.3 Checksums-Sha1: b0a41f22fbfb4d3c2e8c0e3750d7133357b44f7f 824176 moltemplate-doc_2.22.5-1_all.deb f62f9fbbbb4c613b801c9d81499945e758ea0ecf 7695 moltemplate_2.22.5-1_all.buildinfo 6e82af2c062e1305d54d4a27048b7e3126481386 583404 python3-moltemplate_2.22.5-1_all.deb Checksums-Sha256: 7ebcd43207a611b901d0a54f48ad3e3c751b59fb1bcd18a20b319c196c30a6a5 824176 moltemplate-doc_2.22.5-1_all.deb 745290004e4c7dd87fbfb5f4b4cbf00936b064331d1295358d38e18210b52945 7695 moltemplate_2.22.5-1_all.buildinfo c4cff36e3ff956aec504eaad9e2d67de2c06a1698ade6bc25c94b37852d3917a 583404 python3-moltemplate_2.22.5-1_all.deb Files: 9a3ea52e5091f64798b6371a1aa586a9 824176 doc optional moltemplate-doc_2.22.5-1_all.deb f2ec6f3b49b4bd88bde70eb95d70ae6b 7695 science optional moltemplate_2.22.5-1_all.buildinfo 2af6dc4dfde614b9ecb51057b7a1bba7 583404 science optional python3-moltemplate_2.22.5-1_all.deb +------------------------------------------------------------------------------+ | Buildinfo Thu, 26 Feb 2026 05:32:13 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: moltemplate Binary: moltemplate-doc python3-moltemplate Architecture: all Version: 2.22.5-1 Checksums-Md5: 9a3ea52e5091f64798b6371a1aa586a9 824176 moltemplate-doc_2.22.5-1_all.deb 2af6dc4dfde614b9ecb51057b7a1bba7 583404 python3-moltemplate_2.22.5-1_all.deb Checksums-Sha1: b0a41f22fbfb4d3c2e8c0e3750d7133357b44f7f 824176 moltemplate-doc_2.22.5-1_all.deb 6e82af2c062e1305d54d4a27048b7e3126481386 583404 python3-moltemplate_2.22.5-1_all.deb Checksums-Sha256: 7ebcd43207a611b901d0a54f48ad3e3c751b59fb1bcd18a20b319c196c30a6a5 824176 moltemplate-doc_2.22.5-1_all.deb c4cff36e3ff956aec504eaad9e2d67de2c06a1698ade6bc25c94b37852d3917a 583404 python3-moltemplate_2.22.5-1_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 26 Feb 2026 05:32:11 +0000 Build-Path: /build/reproducible-path/moltemplate-2.22.5 Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-3), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-2), binutils (= 2.46-2), binutils-common (= 2.46-2), binutils-x86-64-linux-gnu (= 2.46-2), bsdextrautils (= 2.41.3-4), build-essential (= 12.12), bzip2 (= 1.0.8-6+b1), coreutils (= 9.7-3), cpp (= 4:15.2.0-5), cpp-15 (= 15.2.0-14), cpp-15-x86-64-linux-gnu (= 15.2.0-14), cpp-x86-64-linux-gnu (= 4:15.2.0-5), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.31), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-python (= 7.20260125), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.23.5), dpkg-dev (= 1.23.5), dwz (= 0.16-2), file (= 1:5.46-5+b1), findutils (= 4.10.0-3), fontconfig-config (= 2.17.1-5), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-lmodern (= 2.005-1), g++ (= 4:15.2.0-5), g++-15 (= 15.2.0-14), g++-15-x86-64-linux-gnu (= 15.2.0-14), g++-x86-64-linux-gnu (= 4:15.2.0-5), gcc (= 4:15.2.0-5), gcc-15 (= 15.2.0-14), gcc-15-base (= 15.2.0-14), gcc-15-x86-64-linux-gnu (= 15.2.0-14), gcc-x86-64-linux-gnu (= 4:15.2.0-5), gettext (= 0.23.2-1), gettext-base (= 0.23.2-1), grep (= 3.12-1), groff-base (= 1.23.0-10), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-14), libatomic1 (= 15.2.0-14), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46-2), libblas3 (= 3.12.1-7+b1), libblkid1 (= 2.41.3-4), libbrotli1 (= 1.2.0-3), libbz2-1.0 (= 1.0.8-6+b1), libc-bin (= 2.42-13), libc-dev-bin (= 2.42-13), libc-gconv-modules-extra (= 2.42-13), libc6 (= 2.42-13), libc6-dev (= 2.42-13), libcairo2 (= 1.18.4-3), libcap-ng0 (= 0.9.1-1), libcap2 (= 1:2.75-10+b5), libcc1-0 (= 15.2.0-14), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.46-2), libctf0 (= 2.46-2), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.31), libdpkg-perl (= 1.23.5), libelf1t64 (= 0.194-1), libexpat1 (= 2.7.4-1), libffi8 (= 3.5.2-3+b1), libfile-stripnondeterminism-perl (= 1.15.0-1), libfontconfig1 (= 2.17.1-5), libfreetype6 (= 2.14.1+dfsg-2), libgcc-15-dev (= 15.2.0-14), libgcc-s1 (= 15.2.0-14), libgdbm-compat4t64 (= 1.26-1+b1), libgdbm6t64 (= 1.26-1+b1), libgfortran5 (= 15.2.0-14), libglib2.0-0t64 (= 2.87.2-3), libgmp10 (= 2:6.3.0+dfsg-5+b1), libgomp1 (= 15.2.0-14), libgprofng0 (= 2.46-2), libgraphite2-3 (= 1.3.14-11+b1), libharfbuzz0b (= 12.3.2-2), libhwasan0 (= 15.2.0-14), libice6 (= 2:1.1.1-1+b1), libicu76 (= 76.1-4+b1), libisl23 (= 0.27-1+b1), libitm1 (= 15.2.0-14), libjansson4 (= 2.14-2+b4), libkpathsea6 (= 2025.20250727.75242+ds-5), liblapack3 (= 3.12.1-7+b1), liblsan0 (= 15.2.0-14), liblzma5 (= 5.8.2-2), libmagic-mgc (= 1:5.46-5+b1), libmagic1t64 (= 1:5.46-5+b1), libmd0 (= 1.1.0-2+b2), libmount1 (= 2.41.3-4), libmpc3 (= 1.3.1-2+b1), libmpfi0 (= 1.5.4+ds-4+b1), libmpfr6 (= 4.2.2-2+b1), libncursesw6 (= 6.6+20251231-1), libpam-modules (= 1.7.0-5+b1), libpam-modules-bin (= 1.7.0-5+b1), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b1), libpaper-utils (= 2.2.5-0.3+b3), libpaper2 (= 2.2.5-0.3+b3), libpcre2-8-0 (= 10.46-1+b1), libperl5.40 (= 5.40.1-7), libpipeline1 (= 1.5.8-2), libpixman-1-0 (= 0.46.4-1+b1), libpng16-16t64 (= 1.6.55-1), libpotrace0 (= 1.16-2+b3), libproc2-0 (= 2:4.0.4-9+b1), libptexenc1 (= 2025.20250727.75242+ds-5), libpython3-stdlib (= 3.13.9-3), libpython3.13-minimal (= 3.13.12-1), libpython3.13-stdlib (= 3.13.12-1), libpython3.14-minimal (= 3.14.3-1), libpython3.14-stdlib (= 3.14.3-1), libquadmath0 (= 15.2.0-14), libreadline8t64 (= 8.3-4), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.9-4+b1), libsframe3 (= 2.46-2), libsm6 (= 2:1.2.6-1+b1), libsmartcols1 (= 2.41.3-4), libsqlite3-0 (= 3.46.1-9), libssl3t64 (= 3.5.5-1), libstdc++-15-dev (= 15.2.0-14), libstdc++6 (= 15.2.0-14), libsynctex2 (= 2025.20250727.75242+ds-5), libsystemd0 (= 259.1-1), libteckit0 (= 2.5.13+ds-1), libtexlua53-5 (= 2025.20250727.75242+ds-5), libtext-charwidth-perl (= 0.04-11+b5), libtext-wrapi18n-perl (= 0.06-10), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-9), libtsan2 (= 15.2.0-14), libubsan1 (= 15.2.0-14), libuchardet0 (= 0.0.8-2+b1), libudev1 (= 259.1-1), libunistring5 (= 1.3-2+b1), libuuid1 (= 2.41.3-4), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b1), libxaw7 (= 2:1.0.16-1+b1), libxcb-render0 (= 1.17.0-2+b2), libxcb-shm0 (= 1.17.0-2+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2), libxext6 (= 2:1.3.4-1+b4), libxi6 (= 2:1.8.2-2), libxml2-16 (= 2.15.1+dfsg-2+b1), libxmu6 (= 2:1.1.3-4), libxpm4 (= 1:3.5.17-1+b4), libxrender1 (= 1:0.9.12-1+b1), libxt6t64 (= 1:1.2.1-1.3+b1), libzstd1 (= 1.5.7+dfsg-3+b1), libzzip-0-13t64 (= 0.13.78+dfsg.1-0.2), linux-libc-dev (= 6.18.12-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260129-1), media-types (= 14.0.0), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), netbase (= 6.5), openssl-provider-legacy (= 3.5.5-1), patch (= 2.8-2), perl (= 5.40.1-7), perl-base (= 5.40.1-7), perl-modules-5.40 (= 5.40.1-7), po-debconf (= 1.0.22), procps (= 2:4.0.4-9+b1), python3 (= 3.13.9-3), python3-all (= 3.13.9-3), python3-autocommand (= 2.2.2-4), python3-inflect (= 7.5.0-1), python3-jaraco.context (= 6.0.1-2), python3-jaraco.functools (= 4.1.0-1), python3-jaraco.text (= 4.0.0-1), python3-minimal (= 3.13.9-3), python3-more-itertools (= 10.8.0-1), python3-numpy (= 1:2.3.5+ds-3), python3-numpy-dev (= 1:2.3.5+ds-3), python3-pkg-resources (= 78.1.1-0.1), python3-setuptools (= 78.1.1-0.1), python3-typeguard (= 4.4.4-2), python3-typing-extensions (= 4.15.0-2), python3-zipp (= 3.23.0-1), python3.13 (= 3.13.12-1), python3.13-minimal (= 3.13.12-1), python3.14 (= 3.14.3-1), python3.14-minimal (= 3.14.3-1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), sysvinit-utils (= 3.15-6), t1utils (= 1.41-4), tar (= 1.35+dfsg-4), tex-common (= 6.20), texlive (= 2025.20260124-1), texlive-base (= 2025.20260124-1), texlive-binaries (= 2025.20250727.75242+ds-5), texlive-fonts-recommended (= 2025.20260124-1), texlive-latex-base (= 2025.20260124-1), texlive-latex-recommended (= 2025.20260124-1), tzdata (= 2025c-3), ucf (= 3.0052), util-linux (= 2.41.3-4), x11-common (= 1:7.7+26), xdg-utils (= 1.2.1-2), xz-utils (= 5.8.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-3) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1772011094" +------------------------------------------------------------------------------+ | Package contents Thu, 26 Feb 2026 05:32:13 +0000 | +------------------------------------------------------------------------------+ moltemplate-doc_2.22.5-1_all.deb -------------------------------- new Debian package, version 2.0. size 824176 bytes: control archive=1376 bytes. 1723 bytes, 35 lines control 326 bytes, 4 lines md5sums Package: moltemplate-doc Source: moltemplate Version: 2.22.5-1 Architecture: all Maintainer: Drew Parsons Installed-Size: 831 Section: doc Priority: optional Homepage: https://moltemplate.org/ Description: text-based molecule builder for LAMMPS (documentation) Moltemplate is a general cross-platform text-based molecule builder for LAMMPS. Moltemplate was intended for building custom coarse-grained molecular models, but it can be used to prepare realistic all-atom simulations as well. It supports the ATB molecule database, as well as a wide variety of existing force fields and models including: OPLSAA (2023) , OPLSUA (2008) , LOPLS (2015) , AMBER (GAFF,GAFF2) , DREIDING , COMPASS , MOLC , TraPPE (1998) , EFF , mW , ELBA (water) , and oxDNA2 . But it can also be used to build molecules using any of the exotic force fields (and atom styles) available in LAMMPS, including new force fields created by modifying the LAMMPS source code. (Note: Careful selection of atom types is necessary. Moltemplate does not support atom typing, and is not suitable for all-atom protein simulations.) Molecules can be copied, combined, and linked together as building-blocks to define new molecules (hierarchically). Once built, individual molecules and subunits can be customized (atoms, bonds, and subunits can be moved and deleted). . Moltemplate is inter-operable with ATB, LigParGen, AmberTools, OpenBabel, RED-server, VMD, topotools, PACKMOL, EMC, CellPACK, Vipster, struc2lammpsdf, and any other program that generates MOL2 or LAMMPS DATA (.lmpdat) files (by using the mol22lt.py and ltemplify.py file converters). . This is the documentation package providing the pdf manual. drwxr-xr-x root/root 0 2026-02-25 09:18 ./ drwxr-xr-x root/root 0 2026-02-25 09:18 ./usr/ drwxr-xr-x root/root 0 2026-02-25 09:18 ./usr/share/ drwxr-xr-x root/root 0 2026-02-25 09:18 ./usr/share/doc-base/ -rw-r--r-- root/root 248 2026-02-25 09:18 ./usr/share/doc-base/moltemplate-doc.moltemplate drwxr-xr-x root/root 0 2026-02-25 09:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-02-25 09:18 ./usr/share/doc/moltemplate-doc/ -rw-r--r-- root/root 463 2026-02-25 09:18 ./usr/share/doc/moltemplate-doc/changelog.Debian.gz -rw-r--r-- root/root 3094 2026-02-25 09:18 ./usr/share/doc/moltemplate-doc/copyright -rw-r--r-- root/root 837379 2026-02-25 09:18 ./usr/share/doc/moltemplate-doc/moltemplate_manual.pdf python3-moltemplate_2.22.5-1_all.deb ------------------------------------ new Debian package, version 2.0. size 583404 bytes: control archive=5228 bytes. 1789 bytes, 37 lines control 13249 bytes, 144 lines md5sums 281 bytes, 12 lines * postinst #!/bin/sh 419 bytes, 12 lines * prerm #!/bin/sh Package: python3-moltemplate Source: moltemplate Version: 2.22.5-1 Architecture: all Maintainer: Drew Parsons Installed-Size: 9079 Depends: python3-numpy, python3:any Suggests: moltemplate-doc Section: science Priority: optional Homepage: https://moltemplate.org/ Description: text-based molecule builder for LAMMPS Moltemplate is a general cross-platform text-based molecule builder for LAMMPS. Moltemplate was intended for building custom coarse-grained molecular models, but it can be used to prepare realistic all-atom simulations as well. It supports the ATB molecule database, as well as a wide variety of existing force fields and models including: OPLSAA (2023) , OPLSUA (2008) , LOPLS (2015) , AMBER (GAFF,GAFF2) , DREIDING , COMPASS , MOLC , TraPPE (1998) , EFF , mW , ELBA (water) , and oxDNA2 . But it can also be used to build molecules using any of the exotic force fields (and atom styles) available in LAMMPS, including new force fields created by modifying the LAMMPS source code. (Note: Careful selection of atom types is necessary. Moltemplate does not support atom typing, and is not suitable for all-atom protein simulations.) Molecules can be copied, combined, and linked together as building-blocks to define new molecules (hierarchically). Once built, individual molecules and subunits can be customized (atoms, bonds, and subunits can be moved and deleted). . Moltemplate is inter-operable with ATB, LigParGen, AmberTools, OpenBabel, RED-server, VMD, topotools, PACKMOL, EMC, CellPACK, Vipster, struc2lammpsdf, and any other program that generates MOL2 or LAMMPS DATA (.lmpdat) files (by using the mol22lt.py and ltemplify.py file converters). . 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2026-02-25 09:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-02-25 09:18 ./usr/share/doc/python3-moltemplate/ -rw-r--r-- root/root 463 2026-02-25 09:18 ./usr/share/doc/python3-moltemplate/changelog.Debian.gz -rw-r--r-- root/root 3094 2026-02-25 09:18 ./usr/share/doc/python3-moltemplate/copyright drwxr-xr-x root/root 0 2026-02-25 09:18 ./usr/share/lintian/ drwxr-xr-x root/root 0 2026-02-25 09:18 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 212 2026-02-25 09:18 ./usr/share/lintian/overrides/python3-moltemplate +------------------------------------------------------------------------------+ | Post Build Thu, 26 Feb 2026 05:32:14 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Thu, 26 Feb 2026 05:32:14 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Thu, 26 Feb 2026 05:32:17 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: all Build-Space: 60532 Build-Time: 15 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderdZaP6jO/inputs/moltemplate_2.22.5-1.dsc Machine Architecture: amd64 Package: moltemplate Package-Time: 28 Source-Version: 2.22.5-1 Space: 60532 Status: successful Version: 2.22.5-1 -------------------------------------------------------------------------------- Finished at 2026-02-26T05:32:11Z Build needed 00:00:28, 60532k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdZaP6jO/out size differs for moltemplate-doc_2.22.5-1_all.deb checking moltemplate-doc_2.22.5-1_all.deb: