--- /srv/rebuilderd/tmp/rebuilderdmoe8Hp/inputs/gromacs-data_2025.4-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdmoe8Hp/out/gromacs-data_2025.4-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2025-11-22 16:49:29.000000 debian-binary │ --rw-r--r-- 0 0 0 461276 2025-11-22 16:49:29.000000 control.tar.xz │ --rw-r--r-- 0 0 0 45517432 2025-11-22 16:49:29.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 461408 2025-11-22 16:49:29.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 45516772 2025-11-22 16:49:29.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -4909,15 +4909,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 57841 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/domdechelper_8h__incl.svg │ │ │ -rw-r--r-- 0 root (0) root (0) 4939 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/dot_inline_dotgraph_1.svg │ │ │ -rw-r--r-- 0 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root (0) 45631 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/doxygen.css │ │ │ -rw-r--r-- 0 root (0) root (0) 15461 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/doxygen.svg │ │ │ -rw-r--r-- 0 root (0) root (0) 6490 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/dssp_8h.xhtml │ │ │ -rw-r--r-- 0 root (0) root (0) 3968 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/dssp_8h__dep__incl.svg │ │ │ -rw-r--r-- 0 root (0) root (0) 22066 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/dssp_8h__incl.svg │ │ │ -rw-r--r-- 0 root (0) root (0) 7704 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/dynsections.js │ │ │ -rw-r--r-- 0 root (0) root (0) 21946 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/edsam_8h.xhtml │ │ │ @@ -8975,39 +8975,39 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 11855 2025-11-22 16:49:29.000000 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./usr/share/doc/gromacs/html/doxygen/html-full/search/all_10.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 115218 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_10.js │ │ │ -rw-r--r-- 0 root (0) root (0) 110497 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_11.js │ │ │ --rw-r--r-- 0 root (0) root (0) 101169 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_12.js │ │ │ --rw-r--r-- 0 root (0) root (0) 181835 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_13.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 101175 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_12.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 181894 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_13.js │ │ │ -rw-r--r-- 0 root (0) root (0) 7829 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_14.js │ │ │ --rw-r--r-- 0 root (0) root (0) 119300 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_15.js │ │ │ --rw-r--r-- 0 root (0) root (0) 293446 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_16.js │ │ │ --rw-r--r-- 0 root (0) root (0) 103186 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_17.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 119157 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_15.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 293611 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_16.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 103425 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_17.js │ │ │ -rw-r--r-- 0 root (0) root (0) 32889 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_18.js │ │ │ -rw-r--r-- 0 root (0) root (0) 30659 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_19.js │ │ │ -rw-r--r-- 0 root (0) root (0) 29292 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_1a.js │ │ │ -rw-r--r-- 0 root (0) root (0) 18491 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_1b.js │ │ │ -rw-r--r-- 0 root (0) root (0) 1912 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_1c.js │ │ │ -rw-r--r-- 0 root (0) root (0) 1847 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_1d.js │ │ │ -rw-r--r-- 0 root (0) root (0) 11233 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_1e.js │ │ │ -rw-r--r-- 0 root (0) root (0) 209 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_2.js │ │ │ -rw-r--r-- 0 root (0) root (0) 40617 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_3.js │ │ │ -rw-r--r-- 0 root (0) root (0) 148476 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_4.js │ │ │ --rw-r--r-- 0 root (0) root (0) 74932 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_5.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 74852 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_5.js │ │ │ -rw-r--r-- 0 root (0) root (0) 276577 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_6.js │ │ │ -rw-r--r-- 0 root (0) root (0) 139162 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_7.js │ │ │ -rw-r--r-- 0 root (0) root (0) 138222 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_8.js │ │ │ --rw-r--r-- 0 root (0) root (0) 128841 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_9.js │ │ │ --rw-r--r-- 0 root (0) root (0) 272321 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_a.js │ │ │ --rw-r--r-- 0 root (0) root (0) 43175 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_b.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 128882 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_9.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 272459 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_a.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 43102 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_b.js │ │ │ -rw-r--r-- 0 root (0) root (0) 153214 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_c.js │ │ │ -rw-r--r-- 0 root (0) root (0) 2423 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_d.js │ │ │ -rw-r--r-- 0 root (0) root (0) 11123 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_e.js │ │ │ -rw-r--r-- 0 root (0) root (0) 58582 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_f.js │ │ │ -rw-r--r-- 0 root (0) root (0) 14886 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/classes_0.js │ │ │ -rw-r--r-- 0 root (0) root (0) 8152 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/classes_1.js │ │ │ -rw-r--r-- 0 root (0) root (0) 1421 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-full/search/classes_10.js │ │ │ @@ -13221,15 +13221,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 46761 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_10.js │ │ │ -rw-r--r-- 0 root (0) root (0) 73359 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_11.js │ │ │ -rw-r--r-- 0 root (0) root (0) 69228 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_12.js │ │ │ -rw-r--r-- 0 root (0) root (0) 1412 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_13.js │ │ │ -rw-r--r-- 0 root (0) root (0) 54955 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_14.js │ │ │ -rw-r--r-- 0 root (0) root (0) 132295 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_15.js │ │ │ -rw-r--r-- 0 root (0) root (0) 47529 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_16.js │ │ │ --rw-r--r-- 0 root (0) root (0) 17542 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_17.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 17519 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_17.js │ │ │ -rw-r--r-- 0 root (0) root (0) 14423 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_18.js │ │ │ -rw-r--r-- 0 root (0) root (0) 11042 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_19.js │ │ │ -rw-r--r-- 0 root (0) root (0) 11783 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1a.js │ │ │ -rw-r--r-- 0 root (0) root (0) 1554 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1b.js │ │ │ -rw-r--r-- 0 root (0) root (0) 402 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1c.js │ │ │ -rw-r--r-- 0 root (0) root (0) 5778 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1d.js │ │ │ -rw-r--r-- 0 root (0) root (0) 1392 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_2.js │ │ │ @@ -14661,15 +14661,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 28008 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_10.js │ │ │ -rw-r--r-- 0 root (0) root (0) 35056 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_11.js │ │ │ -rw-r--r-- 0 root (0) root (0) 36704 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_12.js │ │ │ -rw-r--r-- 0 root (0) root (0) 351 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_13.js │ │ │ -rw-r--r-- 0 root (0) root (0) 30036 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_14.js │ │ │ -rw-r--r-- 0 root (0) root (0) 74024 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_15.js │ │ │ -rw-r--r-- 0 root (0) root (0) 21176 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_16.js │ │ │ --rw-r--r-- 0 root (0) root (0) 7128 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_17.js │ │ │ +-rw-r--r-- 0 root (0) root (0) 7088 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_17.js │ │ │ -rw-r--r-- 0 root (0) root (0) 8573 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_18.js │ │ │ -rw-r--r-- 0 root (0) root (0) 5070 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_19.js │ │ │ -rw-r--r-- 0 root (0) root (0) 2337 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_1a.js │ │ │ -rw-r--r-- 0 root (0) root (0) 954 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_1b.js │ │ │ -rw-r--r-- 0 root (0) root (0) 2677 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_1d.js │ │ │ -rw-r--r-- 0 root (0) root (0) 1269 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_2.js │ │ │ -rw-r--r-- 0 root (0) root (0) 47150 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_3.js │ │ │ @@ -17313,15 +17313,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 1697 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/xml/impl__reference__simd4__float_8h.xml.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2009 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/xml/impl__reference__simd__double_8h.xml.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1837 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/xml/impl__reference__simd__float_8h.xml.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1886 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/xml/impl__reference__util__double_8h.xml.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1690 2025-11-22 16:49:29.000000 ./usr/share/doc/gromacs/html/doxygen/xml/impl__reference__util__float_8h.xml.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 4657 2025-11-22 16:49:29.000000 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.. │ │ │ -00002fe0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f . │ │ │ -00003020: 0a3c 7469 746c 653e 6d6f 6475 6c65 5f73 .module_s │ │ │ -00003030: 7263 5f67 726f 6d61 6373 5f6d 6474 7970 rc_gromacs_mdtyp │ │ │ -00003040: 6573 3c2f 7469 746c 653e 0a3c 656c 6c69 es. │ │ │ -000030a0: 0a3c 7465 7874 2074 6578 742d 616e 6368 .mdtype │ │ │ -00003100: 733c 2f74 6578 743e 0a3c 2f67 3e0a 3c21 s....module │ │ │ -00003180: 5f73 7263 5f67 726f 6d61 6373 5f72 6573 _src_gromacs_res │ │ │ -00003190: 7472 6169 6e74 2623 3435 3b26 6774 3b6d traint->m │ │ │ -000031a0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -000031b0: 735f 6d64 7479 7065 733c 2f74 6974 6c65 s_mdtypes... │ │ │ -000032d0: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 .. │ │ │ -00003310: 0a3c 7469 746c 653e 6d6f 6475 6c65 5f73 .module_s │ │ │ -00003320: 7263 5f67 726f 6d61 6373 5f67 6d78 6c69 rc_gromacs_gmxli │ │ │ -00003330: 623c 2f74 6974 6c65 3e0a 3c65 6c6c 6970 b.. │ │ │ -00003390: 3c74 6578 7420 7465 7874 2d61 6e63 686f gmxlib< │ │ │ -000033f0: 2f74 6578 743e 0a3c 2f67 3e0a 3c21 2d2d /text>.... │ │ │ -00003460: 3c74 6974 6c65 3e6d 6f64 756c 655f 7372 module_sr │ │ │ -00003470: 635f 6772 6f6d 6163 735f 7265 7374 7261 c_gromacs_restra │ │ │ -00003480: 696e 7426 2334 353b 2667 743b 6d6f 6475 int->modu │ │ │ -00003490: 6c65 5f73 7263 5f67 726f 6d61 6373 5f67 le_src_gromacs_g │ │ │ -000034a0: 6d78 6c69 623c 2f74 6974 6c65 3e0a 3c70 mxlib.

.

. │ │ │ -00003630: 3c2f 673e 0a3c 212d 2d20 6d6f 6475 6c65 ...module_src_grom │ │ │ -00003690: 6163 735f 616e 616c 7973 6973 6461 7461 acs_analysisdata │ │ │ -000036a0: 3c2f 7469 746c 653e 0a3c 6720 6964 3d22 ...analysisdata │ │ │ -000037d0: 3c2f 7465 7874 3e0a 3c2f 613e 0a3c 2f67 ......module_src_grom │ │ │ -00003ba0: 6163 735f 6770 755f 7574 696c 733c 2f74 acs_gpu_utils</t │ │ │ -00003bb0: 6974 6c65 3e0a 3c65 6c6c 6970 7365 2066 itle>.<ellipse f │ │ │ -00003bc0: 696c 6c3d 2223 6266 6266 6266 2220 7374 ill="#bfbfbf" st │ │ │ -00003bd0: 726f 6b65 3d22 626c 6163 6b22 2063 783d roke="black" cx= │ │ │ -00003be0: 2238 3236 2220 6379 3d22 2d39 322e 3331 "826" cy="-92.31 │ │ │ -00003bf0: 2220 7278 3d22 3339 2e37 2220 7279 3d22 " rx="39.7" ry=" │ │ │ -00003c00: 3133 2e33 3722 2f3e 0a3c 7465 7874 2074 13.37"/>.<text t │ │ │ -00003c10: 6578 742d 616e 6368 6f72 3d22 6d69 6464 ext-anchor="midd │ │ │ -00003c20: 6c65 2220 783d 2238 3236 2220 793d 222d le" x="826" y="- │ │ │ -00003c30: 3839 2e38 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..... │ │ │ -000062a0: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -000062b0: 6373 5f64 6f6d 6465 6326 2334 353b 2667 cs_domdec-&g │ │ │ -000062c0: 743b 6d6f 6475 6c65 5f73 7263 5f67 726f t;module_src_gro │ │ │ -000062d0: 6d61 6373 5f66 696c 6569 6f3c 2f74 6974 macs_fileio</tit │ │ │ -000062e0: 6c65 3e0a 3c70 6174 6820 6669 6c6c 3d22 le>.<path fill=" │ │ │ -000062f0: 6e6f 6e65 2220 7374 726f 6b65 3d22 2362 none" stroke="#b │ │ │ -00006300: 6662 6662 6622 2064 3d22 4d39 3938 2e39 fbfbf" d="M998.9 │ │ │ -00006310: 362c 2d38 3434 2e36 3343 3131 3332 2e32 6,-844.63C1132.2 │ │ │ -00006320: 362c 2d38 3430 2e33 2031 3539 372e 3933 6,-840.3 1597.93 │ │ │ -00006330: 2c2d 3832 332e 3632 2031 3734 342c 2d37 ,-823.62 1744,-7 │ │ │ -00006340: 3937 2e33 3120 3137 3437 2e32 322c 2d37 97.31 1747.22,-7 │ │ │ -00006350: 3936 2e37 3320 3137 3530 2e35 352c 2d37 96.73 1750.55,-7 │ │ │ -00006360: 3935 2e39 3820 3137 3533 2e38 342c 2d37 95.98 1753.84,-7 │ │ │ -00006370: 3935 2e31 3422 2f3e 0a3c 706f 6c79 676f 95.14"/>.<polygo │ │ │ -00006380: 6e20 6669 6c6c 3d22 2362 6662 6662 6622 n fill="#bfbfbf" │ │ │ -00006390: 2073 7472 6f6b 653d 2223 6266 6266 6266 stroke="#bfbfbf │ │ │ -000063a0: 2220 706f 696e 7473 3d22 3137 3534 2e38 " points="1754.8 │ │ │ -000063b0: 352c 2d37 3938 2e34 3920 3137 3633 2e35 5,-798.49 1763.5 │ │ │ -000063c0: 332c 2d37 3932 2e34 3120 3137 3532 2e39 3,-792.41 1752.9 │ │ │ -000063d0: 352c 2d37 3931 2e37 3620 3137 3534 2e38 5,-791.76 1754.8 │ │ │ -000063e0: 352c 2d37 3938 2e34 3922 2f3e 0a3c 2f67 5,-798.49"/>.</g │ │ │ -000063f0: 3e0a 3c21 2d2d 206d 6f64 756c 655f 7372 >.<!-- module_sr │ │ │ -00006400: 635f 6772 6f6d 6163 735f 7365 6c65 6374 c_gromacs_select │ │ │ -00006410: 696f 6e20 2d2d 3e0a 3c67 2069 643d 226e ion -->.<g id="n │ │ │ -00006420: 6f64 6538 2220 636c 6173 733d 226e 6f64 ode8" class="nod │ │ │ -00006430: 6522 3e0a 3c74 6974 6c65 3e6d 6f64 756c e">.<title>modul │ │ │ -00006440: 655f 7372 635f 6772 6f6d 6163 735f 7365 e_src_gromacs_se │ │ │ -00006450: 6c65 6374 696f 6e3c 2f74 6974 6c65 3e0a lection. │ │ │ -00006460: 3c67 2069 643d 2261 5f6e 6f64 6538 223e │ │ │ -00006470: 3c61 2078 6c69 6e6b 3a68 7265 663d 2267 .. │ │ │ -00006570: 7365 6c65 6374 696f 6e3c 2f74 6578 743e selection │ │ │ -00006580: 0a3c 2f61 3e0a 3c2f 673e 0a3c 2f67 3e0a .... │ │ │ -00006590: 3c21 2d2d 206d 6f64 756c 655f 7372 635f . │ │ │ -000065d0: 0a3c 7469 746c 653e 6d6f 6475 6c65 5f73 .module_s │ │ │ -000065e0: 7263 5f67 726f 6d61 6373 5f6f 7074 696f rc_gromacs_optio │ │ │ -000065f0: 6e73 3c2f 7469 746c 653e 0a3c 6720 6964 ns...optio │ │ │ -00006710: 6e73 3c2f 7465 7874 3e0a 3c2f 613e 0a3c ns..< │ │ │ -00006720: 2f67 3e0a 3c2f 673e 0a3c 212d 2d20 6d6f /g>....module │ │ │ -00006940: 5f73 7263 5f67 726f 6d61 6373 5f72 616e _src_gromacs_ran │ │ │ -00006950: 646f 6d3c 2f74 6974 6c65 3e0a 3c67 2069 dom...rando │ │ │ -00006a70: 6d3c 2f74 6578 743e 0a3c 2f61 3e0a 3c2f m..... │ │ │ -00006ad0: 3c67 2069 643d 2265 6467 6532 3122 2063 .module_src_g │ │ │ -00006b00: 726f 6d61 6373 5f73 656c 6563 7469 6f6e romacs_selection │ │ │ -00006b10: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ -00006b20: 7372 635f 6772 6f6d 6163 735f 7261 6e64 src_gromacs_rand │ │ │ -00006b30: 6f6d 3c2f 7469 746c 653e 0a3c 7061 7468 om.....< │ │ │ -00006d00: 6720 6964 3d22 6564 6765 3139 2220 636c g id="edge19" cl │ │ │ -00006d10: 6173 733d 2265 6467 6522 3e0a 3c74 6974 ass="edge">.module_src_gr │ │ │ -00006d30: 6f6d 6163 735f 7365 6c65 6374 696f 6e26 omacs_selection& │ │ │ -00006d40: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ -00006d50: 7263 5f67 726f 6d61 6373 5f6f 6e6c 696e rc_gromacs_onlin │ │ │ -00006d60: 6568 656c 703c 2f74 6974 6c65 3e0a 3c70 ehelp.

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..... │ │ │ +00002f70: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +00002f80: 6373 5f65 7761 6c64 3c2f 7469 746c 653e cs_ewald │ │ │ +00002f90: 0a3c 6720 6964 3d22 615f 6e6f 6465 3135 .. │ │ │ +00002ff0: 3c65 6c6c 6970 7365 2066 696c 6c3d 2223 .e │ │ │ +000030a0: 7761 6c64 3c2f 7465 7874 3e0a 3c2f 613e wald. │ │ │ +000030b0: 0a3c 2f67 3e0a 3c2f 673e 0a3c 212d 2d20 .....module_src_gro │ │ │ +00003130: 6d61 6373 5f6d 646c 6962 2623 3435 3b26 macs_mdlib-& │ │ │ +00003140: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ +00003150: 6f6d 6163 735f 6577 616c 643c 2f74 6974 omacs_ewald. │ │ │ +00003250: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 .....modul │ │ │ +00003310: 655f 7372 635f 6772 6f6d 6163 735f 6861 e_src_gromacs_ha │ │ │ +00003320: 7264 7761 7265 3c2f 7469 746c 653e 0a3c rdware.< │ │ │ +00003330: 656c 6c69 7073 6520 6669 6c6c 3d22 2362 ellipse fill="#b │ │ │ +00003340: 6662 6662 6622 2073 7472 6f6b 653d 2262 fbfbf" stroke="b │ │ │ +00003350: 6c61 636b 2220 6378 3d22 3230 3839 2220 lack" cx="2089" │ │ │ +00003360: 6379 3d22 2d39 322e 3331 2220 7278 3d22 cy="-92.31" rx=" │ │ │ +00003370: 3339 2e37 2220 7279 3d22 3133 2e33 3722 39.7" ry="13.37" │ │ │ +00003380: 2f3e 0a3c 7465 7874 2074 6578 742d 616e />.hardw │ │ │ +000033e0: 6172 653c 2f74 6578 743e 0a3c 2f67 3e0a are.. │ │ │ +000033f0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..module │ │ │ +00003460: 5f73 7263 5f67 726f 6d61 6373 5f6d 646c _src_gromacs_mdl │ │ │ +00003470: 6962 2623 3435 3b26 6774 3b6d 6f64 756c ib->modul │ │ │ +00003480: 655f 7372 635f 6772 6f6d 6163 735f 6861 e_src_gromacs_ha │ │ │ +00003490: 7264 7761 7265 3c2f 7469 746c 653e 0a3c rdware.< │ │ │ +000034a0: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ +000034b0: 2073 7472 6f6b 653d 2272 6564 2220 643d stroke="red" d= │ │ │ +000034c0: 224d 3134 3731 2e34 382c 2d39 3731 2e39 "M1471.48,-971.9 │ │ │ +000034d0: 3243 3135 3434 2e33 372c 2d39 3732 2e32 2C1544.37,-972.2 │ │ │ +000034e0: 3820 3137 3432 2e39 332c 2d39 3638 2e36 8 1742.93,-968.6 │ │ │ +000034f0: 3620 3139 3030 2c2d 3932 332e 3035 2032 6 1900,-923.05 2 │ │ │ +00003500: 3032 302e 3937 2c2d 3838 372e 3932 2032 020.97,-887.92 2 │ │ │ +00003510: 3038 352e 3133 2c2d 3930 322e 3738 2032 085.13,-902.78 2 │ │ │ +00003520: 3135 342c 2d37 3937 2e33 3120 3232 3333 154,-797.31 2233 │ │ │ +00003530: 2e34 392c 2d36 3735 2e35 3820 3231 3639 .49,-675.58 2169 │ │ │ +00003540: 2c2d 3631 352e 3932 2032 3136 392c 2d34 ,-615.92 2169,-4 │ │ │ +00003550: 3730 2e35 3320 3231 3639 2c2d 3437 302e 70.53 2169,-470. │ │ │ +00003560: 3533 2032 3136 392c 2d34 3730 2e35 3320 53 2169,-470.53 │ │ │ +00003570: 3231 3639 2c2d 3231 372e 3035 2032 3136 2169,-217.05 216 │ │ │ +00003580: 392c 2d31 3734 2e30 3720 3231 3334 2e35 9,-174.07 2134.5 │ │ │ +00003590: 342c 2d31 3334 2e32 2032 3131 302e 3836 4,-134.2 2110.86 │ │ │ +000035a0: 2c2d 3131 312e 3838 222f 3e0a 3c70 6f6c ,-111.88"/>.....module_src_gro │ │ │ +00003690: 6d61 6373 5f6d 646c 6962 2623 3435 3b26 macs_mdlib-& │ │ │ +000036a0: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ +000036b0: 6f6d 6163 735f 6d64 7479 7065 733c 2f74 omacs_mdtypes..

....module │ │ │ +000037f0: 5f73 7263 5f67 726f 6d61 6373 5f63 6f6d _src_gromacs_com │ │ │ +00003800: 7061 743c 2f74 6974 6c65 3e0a 3c65 6c6c pat. │ │ │ +00003860: 0a3c 7465 7874 2074 6578 742d 616e 6368 .compat │ │ │ +000038c0: 3c2f 7465 7874 3e0a 3c2f 673e 0a3c 212d .. │ │ │ +00003910: 0a3c 6720 6964 3d22 6564 6765 3136 2220 ..module_src_ │ │ │ +00003940: 6772 6f6d 6163 735f 6d64 6c69 6226 2334 gromacs_mdlib │ │ │ +00003950: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ +00003960: 5f67 726f 6d61 6373 5f63 6f6d 7061 743c _gromacs_compat< │ │ │ +00003970: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>.. │ │ │ +00003a90: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2223 ....m │ │ │ +00003b70: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +00003b80: 735f 6d64 6c69 6226 2334 353b 2667 743b s_mdlib-> │ │ │ +00003b90: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +00003ba0: 6373 5f66 696c 6569 6f3c 2f74 6974 6c65 cs_fileio......module_src_gro │ │ │ 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class= │ │ │ -000082e0: 2265 6467 6522 3e0a 3c74 6974 6c65 3e6d "edge">.<title>m │ │ │ -000082f0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -00008300: 735f 7461 736b 6173 7369 676e 6d65 6e74 s_taskassignment │ │ │ -00008310: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ -00008320: 7372 635f 6772 6f6d 6163 735f 6d64 7479 src_gromacs_mdty │ │ │ -00008330: 7065 733c 2f74 6974 6c65 3e0a 3c70 6174 pes......module_ │ │ │ -00008560: 7372 635f 6772 6f6d 6163 735f 7461 736b src_gromacs_task │ │ │ -00008570: 6173 7369 676e 6d65 6e74 2623 3435 3b26 assignment-& │ │ │ -00008580: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ -00008590: 6f6d 6163 735f 6d64 7275 6e75 7469 6c69 omacs_mdrunutili │ │ │ -000085a0: 7479 3c2f 7469 746c 653e 0a3c 7061 7468 ty......m │ │ │ -00008740: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -00008750: 735f 7461 736b 6173 7369 676e 6d65 6e74 s_taskassignment │ │ │ -00008760: 2623 3435 3b26 6774 3b6d 6f64 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.. │ │ │ -000088a0: 3c2f 673e 0a3c 212d 2d20 6d6f 6475 6c65 ...mod │ │ │ -00008920: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -00008930: 7461 736b 6173 7369 676e 6d65 6e74 2623 taskassignment&# │ │ │ -00008940: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ -00008950: 635f 6772 6f6d 6163 735f 6c69 7374 6564 c_gromacs_listed │ │ │ -00008960: 5f66 6f72 6365 733c 2f74 6974 6c65 3e0a _forces. │ │ │ -00008970: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 .....modu │ │ │ -00008b00: 6c65 5f73 7263 5f67 726f 6d61 6373 5f74 le_src_gromacs_t │ │ │ -00008b10: 6173 6b61 7373 6967 6e6d 656e 7426 2334 askassignment │ │ │ -00008b20: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ -00008b30: 5f67 726f 6d61 6373 5f65 7761 6c64 3c2f _gromacs_ewald</ │ │ │ -00008b40: 7469 746c 653e 0a3c 7061 7468 2066 696c title>.<path fil │ │ │ -00008b50: 6c3d 226e 6f6e 6522 2073 7472 6f6b 653d l="none" stroke= │ │ │ -00008b60: 2223 3238 3266 6363 2220 643d 224d 3933 "#282fcc" 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726f 6d61 6373 5f74 6173 6b61 7373 6967 romacs_taskassig │ │ │ -00008e90: 6e6d 656e 7426 2334 353b 2667 743b 6d6f nment->mo │ │ │ -00008ea0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -00008eb0: 5f68 6172 6477 6172 6520 2d2d 3e0a 3c67 _hardware -->..module_src_gro │ │ │ -00008ef0: 6d61 6373 5f74 6173 6b61 7373 6967 6e6d macs_taskassignm │ │ │ -00008f00: 656e 7426 2334 353b 2667 743b 6d6f 6475 ent->modu │ │ │ -00008f10: 6c65 5f73 7263 5f67 726f 6d61 6373 5f68 le_src_gromacs_h │ │ │ -00008f20: 6172 6477 6172 653c 2f74 6974 6c65 3e0a ardware. │ │ │ -00008f30: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 .....modul │ │ │ -000090d0: 655f 7372 635f 6772 6f6d 6163 735f 7461 e_src_gromacs_ta │ │ │ -000090e0: 736b 6173 7369 676e 6d65 6e74 2623 3435 skassignment- │ │ │ -000090f0: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -00009100: 6772 6f6d 6163 735f 6d64 6c69 623c 2f74 gromacs_mdlib</t │ │ │ -00009110: 6974 6c65 3e0a 3c70 6174 6820 6669 6c6c itle>.<path fill │ 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1318.19,-359.9 │ │ │ -00009560: 3722 2f3e 0a3c 2f67 3e0a 3c21 2d2d 206d 7"/>.</g>.<!-- m │ │ │ -00009570: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -00009580: 735f 6c69 6e65 6172 616c 6765 6272 6120 s_linearalgebra │ │ │ -00009590: 2d2d 3e0a 3c67 2069 643d 226e 6f64 6531 -->.<g id="node1 │ │ │ -000095a0: 3222 2063 6c61 7373 3d22 6e6f 6465 223e 2" class="node"> │ │ │ -000095b0: 0a3c 7469 746c 653e 6d6f 6475 6c65 5f73 .<title>module_s │ │ │ -000095c0: 7263 5f67 726f 6d61 6373 5f6c 696e 6561 rc_gromacs_linea │ │ │ -000095d0: 7261 6c67 6562 7261 3c2f 7469 746c 653e ralgebra │ │ │ -000095e0: 0a3c 656c 6c69 7073 6520 6669 6c6c 3d22 ..linearalgebra< │ │ │ -000096a0: 2f74 6578 743e 0a3c 2f67 3e0a 3c21 2d2d /text>....modu │ │ │ -00009720: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ -00009730: 6472 756e 7574 696c 6974 7926 2334 353b drunutility- │ │ │ -00009740: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ -00009750: 726f 6d61 6373 5f6d 6474 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is->modul │ │ │ -0000bc30: 655f 7372 635f 6772 6f6d 6163 735f 7374 e_src_gromacs_st │ │ │ -0000bc40: 6174 6973 7469 6373 202d 2d3e 0a3c 6720 atistics -->.<g │ │ │ -0000bc50: 6964 3d22 6564 6765 3534 2220 636c 6173 id="edge54" clas │ │ │ -0000bc60: 733d 2265 6467 6522 3e0a 3c74 6974 6c65 s="edge">.<title │ │ │ -0000bc70: 3e6d 6f64 756c 655f 7372 635f 6772 6f6d >module_src_grom │ │ │ -0000bc80: 6163 735f 7472 616a 6563 746f 7279 616e acs_trajectoryan │ │ │ -0000bc90: 616c 7973 6973 2623 3435 3b26 6774 3b6d alysis->m │ │ │ -0000bca0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -0000bcb0: 735f 7374 6174 6973 7469 6373 3c2f 7469 s_statistics</ti │ │ │ -0000bcc0: 746c 653e 0a3c 7061 7468 2066 696c 6c3d tle>.<path fill= │ │ │ -0000bcd0: 226e 6f6e 6522 2073 7472 6f6b 653d 2223 "none" stroke="# │ │ │ -0000bce0: 3238 3266 6363 2220 7374 726f 6b65 2d64 282fcc" stroke-d │ │ │ -0000bcf0: 6173 6861 7272 6179 3d22 352c 3222 2064 asharray="5,2" d │ │ │ -0000bd00: 3d22 4d32 3137 302e 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│ │ -0000bde0: 616c 7973 6973 2623 3435 3b26 6774 3b6d alysis->m │ │ │ -0000bdf0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -0000be00: 735f 636f 6d6d 616e 646c 696e 6520 2d2d s_commandline -- │ │ │ -0000be10: 3e0a 3c67 2069 643d 2265 6467 6535 3122 >.<g id="edge51" │ │ │ -0000be20: 2063 6c61 7373 3d22 6564 6765 223e 0a3c class="edge">.< │ │ │ -0000be30: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ -0000be40: 5f67 726f 6d61 6373 5f74 7261 6a65 6374 _gromacs_traject │ │ │ -0000be50: 6f72 7961 6e61 6c79 7369 7326 2334 353b oryanalysis- │ │ │ -0000be60: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ -0000be70: 726f 6d61 6373 5f63 6f6d 6d61 6e64 6c69 romacs_commandli │ │ │ -0000be80: 6e65 3c2f 7469 746c 653e 0a3c 7061 7468 ne.... │ │ │ -0000c050: 3c21 2d2d 206d 6f64 756c 655f 7372 635f │ │ │ -0000c0a0: 0a3c 6720 6964 3d22 6564 6765 3532 2220 ..module_src_ │ │ │ -0000c0d0: 6772 6f6d 6163 735f 7472 616a 6563 746f gromacs_trajecto │ │ │ 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5f67 726f 6d61 6373 5f67 6d78 _src_gromacs_gmx │ │ │ -0000c690: 616e 6126 2334 353b 2667 743b 6d6f 6475 ana->modu │ │ │ -0000c6a0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6c le_src_gromacs_l │ │ │ -0000c6b0: 6973 7465 645f 666f 7263 6573 202d 2d3e isted_forces --> │ │ │ -0000c6c0: 0a3c 6720 6964 3d22 6564 6765 3635 2220 .<g id="edge65" │ │ │ -0000c6d0: 636c 6173 733d 2265 6467 6522 3e0a 3c74 class="edge">.<t │ │ │ -0000c6e0: 6974 6c65 3e6d 6f64 756c 655f 7372 635f itle>module_src_ │ │ │ -0000c6f0: 6772 6f6d 6163 735f 676d 7861 6e61 2623 gromacs_gmxana&# │ │ │ -0000c700: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ -0000c710: 635f 6772 6f6d 6163 735f 6c69 7374 6564 c_gromacs_listed │ │ │ -0000c720: 5f66 6f72 6365 733c 2f74 6974 6c65 3e0a _forces. │ │ │ -0000c730: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 . │ │ │ -0000c8a0: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2223 . │ │ │ -0000c910: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 ...module │ │ │ -0000c980: 5f73 7263 5f67 726f 6d61 6373 5f67 6d78 _src_gromacs_gmx │ │ │ -0000c990: 616e 6126 2334 353b 2667 743b 6d6f 6475 ana->modu │ │ │ -0000c9a0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f72 le_src_gromacs_r │ │ │ -0000c9b0: 616e 646f 6d3c 2f74 6974 6c65 3e0a 3c70 andom.

. │ │ │ -0000cb30: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c ....m │ │ │ -0000cba0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -0000cbb0: 735f 676d 7861 6e61 2623 3435 3b26 6774 s_gmxana-> │ │ │ -0000cbc0: 3b6d 6f64 756c 655f 7372 635f 6772 6f6d ;module_src_grom │ │ │ -0000cbd0: 6163 735f 6d64 7370 616e 3c2f 7469 746c acs_mdspan</titl │ │ │ -0000cbe0: 653e 0a3c 7061 7468 2066 696c 6c3d 226e e>.<path fill="n │ │ │ -0000cbf0: 6f6e 6522 2073 7472 6f6b 653d 2223 3238 one" stroke="#28 │ │ │ -0000cc00: 3266 6363 2220 7374 726f 6b65 2d64 6173 2fcc" stroke-das │ │ │ -0000cc10: 6861 7272 6179 3d22 352c 3222 2064 3d22 harray="5,2" d=" │ │ │ -0000cc20: 4d31 3632 382e 332c 2d39 3730 2e39 3143 M1628.3,-970.91C │ │ │ -0000cc30: 3138 3035 2e38 362c 2d39 3637 2e35 3520 1805.86,-967.55 │ │ │ -0000cc40: 3235 3933 2c2d 3934 372e 3038 2032 3539 2593,-947.08 259 │ │ │ -0000cc50: 332c 2d38 3437 2e37 3520 3235 3933 2c2d 3,-847.75 2593,- │ │ │ -0000cc60: 3834 372e 3735 2032 3539 332c 2d38 3437 847.75 2593,-847 │ │ │ -0000cc70: 2e37 3520 3235 3933 2c2d 3732 302e 3031 .75 2593,-720.01 │ │ │ -0000cc80: 2032 3539 332c 2d34 3732 2e36 3820 3235 2593,-472.68 25 │ │ │ -0000cc90: 3436 2e39 2c2d 3431 342e 3234 2032 3531 46.9,-414.24 251 │ │ │ -0000cca0: 382c 2d31 3638 2e36 3120 3235 3135 2e39 8,-168.61 2515.9 │ │ │ -0000ccb0: 332c 2d31 3531 2e30 3520 3235 3134 2e31 3,-151.05 2514.1 │ │ │ -0000ccc0: 2c2d 3133 312e 3132 2032 3531 322e 3833 ,-131.12 2512.83 │ │ │ -0000ccd0: 2c2d 3131 362e 3138 222f 3e0a 3c70 6f6c ,-116.18"/>.<pol │ │ │ -0000cce0: 7967 6f6e 2066 696c 6c3d 2223 3238 3266 ygon fill="#282f │ │ │ -0000ccf0: 6363 2220 7374 726f 6b65 3d22 2332 3832 cc" stroke="#282 │ │ │ -0000cd00: 6663 6322 2070 6f69 6e74 733d 2232 3531 fcc" points="251 │ │ │ -0000cd10: 362e 3239 2c2d 3131 352e 3533 2032 3531 6.29,-115.53 251 │ │ │ -0000cd20: 312e 3938 2c2d 3130 352e 3835 2032 3530 1.98,-105.85 250 │ │ │ -0000cd30: 392e 3332 2c2d 3131 362e 3120 3235 3136 9.32,-116.1 2516 │ │ │ -0000cd40: 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-0000d010: 6d61 6373 5f67 6d78 616e 6126 2334 353b macs_gmxana- │ │ │ -0000d020: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ -0000d030: 726f 6d61 6373 5f73 7461 7469 7374 6963 romacs_statistic │ │ │ -0000d040: 733c 2f74 6974 6c65 3e0a 3c70 6174 6820 s....< │ │ │ -0000d170: 212d 2d20 6d6f 6475 6c65 5f73 7263 5f67 !-- module_src_g │ │ │ -0000d180: 726f 6d61 6373 5f66 6674 202d 2d3e 0a3c romacs_fft -->.< │ │ │ -0000d190: 6720 6964 3d22 6e6f 6465 3335 2220 636c g id="node35" cl │ │ │ -0000d1a0: 6173 733d 226e 6f64 6522 3e0a 3c74 6974 ass="node">.module_src_gr │ │ │ -0000d1c0: 6f6d 6163 735f 6666 743c 2f74 6974 6c65 omacs_fft..fft< │ │ │ -0000d280: 2f74 6578 743e 0a3c 2f67 3e0a 3c21 2d2d /text>....module_src_gro │ │ │ -0000d300: 6d61 6373 5f67 6d78 616e 6126 2334 353b macs_gmxana- │ │ │ -0000d310: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ -0000d320: 726f 6d61 6373 5f66 6674 3c2f 7469 746c romacs_fft...< │ │ │ -0000d4b0: 2f67 3e0a 3c21 2d2d 206d 6f64 756c 655f /g>...modu │ │ │ -0000d520: 6c65 5f73 7263 5f67 726f 6d61 6373 5f67 le_src_gromacs_g │ │ │ -0000d530: 6d78 616e 6126 2334 353b 2667 743b 6d6f mxana->mo │ │ │ -0000d540: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -0000d550: 5f6d 646c 6962 3c2f 7469 746c 653e 0a3c _mdlib.< │ │ │ -0000d560: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ -0000d570: 2073 7472 6f6b 653d 2223 6266 6266 6266 stroke="#bfbfbf │ │ │ -0000d580: 2220 643d 224d 3135 3537 2e39 392c 2d39 " d="M1557.99,-9 │ │ │ -0000d590: 3639 2e39 3543 3134 3738 2e38 332c 2d39 69.95C1478.83,-9 │ │ │ -0000d5a0: 3635 2e39 3620 3132 3838 2e36 332c 2d39 65.96 1288.63,-9 │ │ │ -0000d5b0: 3533 2e34 3220 3132 3333 2c2d 3932 332e 53.42 1233,-923. │ │ │ -0000d5c0: 3035 2031 3232 342e 3935 2c2d 3931 382e 05 1224.95,-918. │ │ │ -0000d5d0: 3636 2031 3133 312e 3635 2c2d 3830 342e 66 1131.65,-804. │ │ │ -0000d5e0: 3534 2031 3132 362c 2d37 3937 2e33 3120 54 1126,-797.31 │ │ │ -0000d5f0: 3131 3034 2e38 352c 2d37 3730 2e32 3320 1104.85,-770.23 │ │ │ -0000d600: 3130 3938 2e36 362c 2d37 3633 2e39 3220 1098.66,-763.92 │ │ │ -0000d610: 3130 3831 2c2d 3733 342e 3434 2031 3033 1081,-734.44 103 │ │ │ -0000d620: 312e 3338 2c2d 3635 312e 3539 2039 3934 1.38,-651.59 994 │ │ │ -0000d630: 2e32 322c 2d35 3935 2e35 3920 3130 3533 .22,-595.59 1053 │ │ │ -0000d640: 2c2d 3531 382e 3936 2031 3035 332e 3432 ,-518.96 1053.42 │ │ │ -0000d650: 2c2d 3531 382e 3431 2031 3139 332e 3937 ,-518.41 1193.97 │ │ │ -0000d660: 2c2d 3435 302e 3539 2031 3235 352e 3132 ,-450.59 1255.12 │ │ │ -0000d670: 2c2d 3432 312e 3122 2f3e 0a3c 706f 6c79 ,-421.1"/>.....module_src_grom │ │ │ -0000d770: 6163 735f 676d 7861 6e61 2623 3435 3b26 acs_gmxana-& │ │ │ -0000d780: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ -0000d790: 6f6d 6163 735f 636f 6d6d 616e 646c 696e omacs_commandlin │ │ │ -0000d7a0: 653c 2f74 6974 6c65 3e0a 3c70 6174 6820 e......module_src_grom │ │ │ -0000da20: 6163 735f 636f 7272 656c 6174 696f 6e66 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9,-735.77"/>.</g │ │ │ -0000e1a0: 3e0a 3c21 2d2d 206d 6f64 756c 655f 7372 >.<!-- module_sr │ │ │ -0000e1b0: 635f 6772 6f6d 6163 735f 746f 706f 6c6f c_gromacs_topolo │ │ │ -0000e1c0: 6779 202d 2d3e 0a3c 6720 6964 3d22 6e6f gy -->.<g id="no │ │ │ -0000e1d0: 6465 3137 2220 636c 6173 733d 226e 6f64 de17" class="nod │ │ │ -0000e1e0: 6522 3e0a 3c74 6974 6c65 3e6d 6f64 756c e">.<title>modul │ │ │ -0000e1f0: 655f 7372 635f 6772 6f6d 6163 735f 746f e_src_gromacs_to │ │ │ -0000e200: 706f 6c6f 6779 3c2f 7469 746c 653e 0a3c pology.< │ │ │ -0000e210: 656c 6c69 7073 6520 6669 6c6c 3d22 2362 ellipse fill="#b │ │ │ -0000e220: 6662 6662 6622 2073 7472 6f6b 653d 2262 fbfbf" stroke="b │ │ │ -0000e230: 6c61 636b 2220 6378 3d22 3535 3922 2063 lack" cx="559" c │ │ │ -0000e240: 793d 222d 3937 322e 3439 2220 7278 3d22 y="-972.49" rx=" │ │ │ -0000e250: 3337 2e34 3522 2072 793d 2231 332e 3337 37.45" ry="13.37 │ │ │ -0000e260: 222f 3e0a 3c74 6578 7420 7465 7874 2d61 "/>.topo │ │ │ -0000e2c0: 6c6f 6779 3c2f 7465 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│ │ -0000e5f0: 6573 7475 7469 6c73 3c2f 7465 7874 3e0a estutils. │ │ │ -0000e600: 3c2f 613e 0a3c 2f67 3e0a 3c2f 673e 0a3c ...< │ │ │ -0000e610: 212d 2d20 6d6f 6475 6c65 5f73 7263 5f67 !-- module_src_g │ │ │ -0000e620: 726f 6d61 6373 5f74 6f70 6f6c 6f67 7926 romacs_topology& │ │ │ -0000e630: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ -0000e640: 7263 5f74 6573 7475 7469 6c73 202d 2d3e rc_testutils --> │ │ │ -0000e650: 0a3c 6720 6964 3d22 6564 6765 3732 2220 ..module_src_ │ │ │ -0000e680: 6772 6f6d 6163 735f 746f 706f 6c6f 6779 gromacs_topology │ │ │ -0000e690: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ -0000e6a0: 7372 635f 7465 7374 7574 696c 733c 2f74 src_testutils.. │ │ │ -0000e760: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2272 ....module_ │ │ │ -0000e840: 7372 635f 6772 6f6d 6163 735f 746f 6f6c src_gromacs_tool │ │ │ -0000e850: 7326 2334 353b 2667 743b 6d6f 6475 6c65 s->module │ │ │ -0000e860: 5f73 7263 5f67 726f 6d61 6373 5f74 7261 _src_gromacs_tra │ │ │ 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735f 6669 6c65 696f 3c2f gromacs_fileio</ │ │ │ -00013320: 7469 746c 653e 0a3c 7061 7468 2066 696c title>.<path fil │ │ │ -00013330: 6c3d 226e 6f6e 6522 2073 7472 6f6b 653d l="none" stroke= │ │ │ -00013340: 2223 6266 6266 6266 2220 643d 224d 3139 "#bfbfbf" d="M19 │ │ │ -00013350: 3834 2e37 2c2d 3839 362e 3237 4331 3936 84.7,-896.27C196 │ │ │ -00013360: 382e 3035 2c2d 3838 302e 3120 3139 3336 8.05,-880.1 1936 │ │ │ -00013370: 2e38 352c 2d38 3531 2e36 3420 3139 3036 .85,-851.64 1906 │ │ │ -00013380: 2c2d 3833 332e 3331 2031 3837 372e 3632 ,-833.31 1877.62 │ │ │ -00013390: 2c2d 3831 362e 3435 2031 3834 322e 3238 ,-816.45 1842.28 │ │ │ -000133a0: 2c2d 3830 332e 3038 2031 3831 372e 3134 ,-803.08 1817.14 │ │ │ -000133b0: 2c2d 3739 342e 3639 222f 3e0a 3c70 6f6c ,-794.69"/>.<pol │ │ │ -000133c0: 7967 6f6e 2066 696c 6c3d 2223 6266 6266 ygon fill="#bfbf │ │ │ -000133d0: 6266 2220 7374 726f 6b65 3d22 2362 6662 bf" stroke="#bfb │ │ │ -000133e0: 6662 6622 2070 6f69 6e74 733d 2231 3831 fbf" points="181 │ │ │ -000133f0: 372e 3937 2c2d 3739 312e 3238 2031 3830 7.97,-791.28 180 │ │ │ -00013400: 372e 3338 2c2d 3739 312e 3531 2031 3831 7.38,-791.51 181 │ │ │ -00013410: 352e 382c 2d37 3937 2e39 3420 3138 3137 5.8,-797.94 1817 │ │ │ -00013420: 2e39 372c 2d37 3931 2e32 3822 2f3e 0a3c .97,-791.28"/>.< │ │ │ -00013430: 2f67 3e0a 3c21 2d2d 206d 6f64 756c 655f /g>.<!-- module_ │ │ │ -00013440: 7372 635f 6772 6f6d 6163 735f 7377 6170 src_gromacs_swap │ │ │ -00013450: 202d 2d3e 0a3c 6720 6964 3d22 6e6f 6465 -->.<g id="node │ │ │ -00013460: 3238 2220 636c 6173 733d 226e 6f64 6522 28" class="node" │ │ │ -00013470: 3e0a 3c74 6974 6c65 3e6d 6f64 756c 655f >.<title>module_ │ │ │ -00013480: 7372 635f 6772 6f6d 6163 735f 7377 6170 src_gromacs_swap │ │ │ -00013490: 3c2f 7469 746c 653e 0a3c 6720 6964 3d22 ...swap.< │ │ │ -000135b0: 2f61 3e0a 3c2f 673e 0a3c 2f67 3e0a 3c21 /a>... │ │ │ -00013600: 0a3c 6720 6964 3d22 6564 6765 3130 3922 ..< │ │ │ -00013620: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ -00013630: 5f67 726f 6d61 6373 5f73 7761 7026 2334 _gromacs_swap │ │ │ -00013640: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ -00013650: 5f67 726f 6d61 6373 5f64 6f6d 6465 633c _gromacs_domdec< │ │ │ -00013660: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>.... │ │ │ -000137d0: 0a3c 6720 6964 3d22 6564 6765 3131 3422 ..< │ │ │ -000137f0: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ -00013800: 5f67 726f 6d61 6373 5f73 7761 7026 2334 _gromacs_swap │ │ │ -00013810: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ -00013820: 5f67 726f 6d61 6373 5f6d 6474 7970 6573 _gromacs_mdtypes │ │ │ -00013830: 3c2f 7469 746c 653e 0a3c 7061 7468 2066 .... │ │ │ -000139a0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..mo │ │ │ -00013a10: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -00013a20: 5f73 7761 7026 2334 353b 2667 743b 6d6f _swap->mo │ │ │ -00013a30: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ 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6f6d 6163 735f 7377 6170 2623 3435 3b26 omacs_swap-& │ │ │ -00013c00: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ -00013c10: 6f6d 6163 735f 676d 786c 6962 3c2f 7469 omacs_gmxlib</ti │ │ │ -00013c20: 746c 653e 0a3c 7061 7468 2066 696c 6c3d tle>.<path fill= │ │ │ -00013c30: 226e 6f6e 6522 2073 7472 6f6b 653d 2223 "none" stroke="# │ │ │ -00013c40: 6266 6266 6266 2220 643d 224d 3135 3937 bfbfbf" d="M1597 │ │ │ -00013c50: 2e34 392c 2d35 3232 2e38 3443 3136 3332 .49,-522.84C1632 │ │ │ -00013c60: 2e31 372c 2d35 3036 2e31 3320 3137 3031 .17,-506.13 1701 │ │ │ -00013c70: 2c2d 3436 352e 3636 2031 3730 312c 2d34 ,-465.66 1701,-4 │ │ │ -00013c80: 3037 2e36 3620 3137 3031 2c2d 3430 372e 07.66 1701,-407. │ │ │ -00013c90: 3636 2031 3730 312c 2d34 3037 2e36 3620 66 1701,-407.66 │ │ │ -00013ca0: 3137 3031 2c2d 3237 392e 3932 2031 3730 1701,-279.92 170 │ │ │ -00013cb0: 312c 2d32 3434 2e35 3920 3136 3936 2e39 1,-244.59 1696.9 │ │ │ -00013cc0: 2c2d 3230 332e 3738 2031 3639 332e 3935 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3222 2063 6c61 7373 3d22 6564 6765 112" class="edge │ │ │ -00013db0: 223e 0a3c 7469 746c 653e 6d6f 6475 6c65 ">.<title>module │ │ │ -00013dc0: 5f73 7263 5f67 726f 6d61 6373 5f73 7761 _src_gromacs_swa │ │ │ -00013dd0: 7026 2334 353b 2667 743b 6d6f 6475 6c65 p->module │ │ │ -00013de0: 5f73 7263 5f67 726f 6d61 6373 5f6d 646c _src_gromacs_mdl │ │ │ -00013df0: 6962 3c2f 7469 746c 653e 0a3c 7061 7468 ib.... │ │ │ -00013f20: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..modu │ │ │ -00014170: 6c65 5f73 7263 5f67 726f 6d61 6373 5f69 le_src_gromacs_i │ │ │ -00014180: 6d64 2623 3435 3b26 6774 3b6d 6f64 756c md->modul │ │ │ -00014190: 655f 7372 635f 6772 6f6d 6163 735f 646f e_src_gromacs_do │ │ │ -000141a0: 6d64 6563 3c2f 7469 746c 653e 0a3c 7061 mdec......module_src_gr │ │ │ -00014370: 6f6d 6163 735f 696d 6426 2334 353b 2667 omacs_imd-&g │ │ │ -00014380: 743b 6d6f 6475 6c65 5f73 7263 5f67 726f t;module_src_gro │ │ │ -00014390: 6d61 6373 5f6d 6474 7970 6573 3c2f 7469 macs_mdtypes. │ │ │ -000144c0: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 ... │ │ │ -00014580: 0a3c 6720 6964 3d22 6564 6765 3132 3022 ..< │ │ │ -000145a0: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ -000145b0: 5f67 726f 6d61 6373 5f69 6d64 2623 3435 _gromacs_imd- │ │ │ -000145c0: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -000145d0: 6772 6f6d 6163 735f 6d64 7275 6e75 7469 gromacs_mdrunuti │ │ │ -000145e0: 6c69 7479 3c2f 7469 746c 653e 0a3c 7061 lity... │ │ │ -00014790: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 ...mo │ │ │ -000149b0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -000149c0: 5f69 6d64 2623 3435 3b26 6774 3b6d 6f64 _imd->mod │ │ │ -000149d0: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -000149e0: 6d64 6c69 623c 2f74 6974 6c65 3e0a 3c70 mdlib.

.....module_ │ │ │ -00014b40: 7372 635f 6772 6f6d 6163 735f 696d 6426 src_gromacs_imd& │ │ │ -00014b50: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ -00014b60: 7263 5f67 726f 6d61 6373 5f63 6f6d 6d61 rc_gromacs_comma │ │ │ -00014b70: 6e64 6c69 6e65 3c2f 7469 746c 653e 0a3c ndline.< │ │ │ -00014b80: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ -00014b90: 2073 7472 6f6b 653d 2262 6c61 636b 2220 stroke="black" │ │ │ -00014ba0: 7374 726f 6b65 2d64 6173 6861 7272 6179 stroke-dasharray │ │ │ -00014bb0: 3d22 352c 3222 2064 3d22 4d31 3834 302e ="5,2" d="M1840. │ │ │ -00014bc0: 3538 2c2d 3333 302e 3236 4331 3833 392e 58,-330.26C1839. │ │ │ -00014bd0: 3739 2c2d 3331 352e 3120 3138 3337 2e35 79,-315.1 1837.5 │ │ │ -00014be0: 322c 2d32 3838 2e39 3320 3138 3331 2c2d 2,-288.93 1831,- │ │ │ -00014bf0: 3236 372e 3438 2031 3831 302e 3332 2c2d 267.48 1810.32,- │ │ │ -00014c00: 3139 392e 3433 2031 3739 362e 3539 2c2d 199.43 1796.59,- │ │ │ -00014c10: 3137 312e 3532 2031 3733 322c 2d31 3431 171.52 1732,-141 │ │ │ -00014c20: 2e37 3420 3136 3731 2e35 362c 2d31 3133 .74 1671.56,-113 │ │ │ -00014c30: 2e38 3720 3134 3832 2e37 342c 2d31 3030 .87 1482.74,-100 │ │ │ -00014c40: 2e39 3220 3133 3834 2e32 312c 2d39 352e .92 1384.21,-95. │ │ │ -00014c50: 3933 222f 3e0a 3c70 6f6c 7967 6f6e 2066 93"/>. │ │ │ -00014cc0: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c ....mod │ │ │ -00014d30: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -00014d40: 696d 6426 2334 353b 2667 743b 6d6f 6475 imd->modu │ │ │ -00014d50: 6c65 5f73 7263 5f67 726f 6d61 6373 5f66 le_src_gromacs_f │ │ │ -00014d60: 696c 6569 6f3c 2f74 6974 6c65 3e0a 3c70 ileio.

.. │ │ │ -00014ed0: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 ...modu │ │ │ -00014f40: 6c65 5f73 7263 5f67 726f 6d61 6373 5f67 le_src_gromacs_g │ │ │ -00014f50: 6d78 6c69 6226 2334 353b 2667 743b 6d6f mxlib->mo │ │ │ -00014f60: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -00014f70: 5f6d 6474 7970 6573 3c2f 7469 746c 653e _mdtypes │ │ │ +0000ac10: 735f 6577 616c 6426 2334 353b 2667 743b s_ewald-> │ │ │ +0000ac20: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +0000ac30: 6373 5f64 6f6d 6465 6320 2d2d 3e0a 3c67 cs_domdec -->..module_src_gro │ │ │ +0000ac70: 6d61 6373 5f65 7761 6c64 2623 3435 3b26 macs_ewald-& │ │ │ +0000ac80: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ +0000ac90: 6f6d 6163 735f 646f 6d64 6563 3c2f 7469 omacs_domdec.... │ │ │ +0000ade0: 0a3c 6720 6964 3d22 6564 6765 3636 2220 ..module_src_ │ │ │ +0000ae10: 6772 6f6d 6163 735f 6577 616c 6426 2334 gromacs_ewald │ │ │ +0000ae20: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ +0000ae30: 5f67 726f 6d61 6373 5f6e 626e 786d 3c2f _gromacs_nbnxm......module_ │ │ │ +0000afb0: 7372 635f 6772 6f6d 6163 735f 6861 7264 src_gromacs_hard │ │ │ +0000afc0: 7761 7265 2623 3435 3b26 6774 3b6d 6f64 ware->mod │ │ │ +0000afd0: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +0000afe0: 6770 755f 7574 696c 733c 2f74 6974 6c65 gpu_utils......modul │ │ │ +0000b1e0: 655f 7372 635f 6772 6f6d 6163 735f 7574 e_src_gromacs_ut │ │ │ +0000b1f0: 696c 6974 7926 2334 353b 2667 743b 6d6f ility->mo │ │ │ +0000b200: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +0000b210: 5f67 7075 5f75 7469 6c73 3c2f 7469 746c _gpu_utils</titl │ │ │ +0000b220: 653e 0a3c 7061 7468 2066 696c 6c3d 226e e>.<path fill="n │ │ │ +0000b230: 6f6e 6522 2073 7472 6f6b 653d 2223 6266 one" stroke="#bf │ │ │ +0000b240: 6266 6266 2220 643d 224d 3137 3639 2e36 bfbf" d="M1769.6 │ │ │ +0000b250: 372c 2d31 3135 302e 3938 4331 3739 342e 7,-1150.98C1794. │ │ │ +0000b260: 3832 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gt;module_src_gr │ │ │ +0000b340: 6f6d 6163 735f 636f 6d70 6174 202d 2d3e omacs_compat --> │ │ │ +0000b350: 0a3c 6720 6964 3d22 6564 6765 3730 2220 .<g id="edge70" │ │ │ +0000b360: 636c 6173 733d 2265 6467 6522 3e0a 3c74 class="edge">.<t │ │ │ +0000b370: 6974 6c65 3e6d 6f64 756c 655f 7372 635f itle>module_src_ │ │ │ +0000b380: 6772 6f6d 6163 735f 7574 696c 6974 7926 gromacs_utility& │ │ │ +0000b390: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ +0000b3a0: 7263 5f67 726f 6d61 6373 5f63 6f6d 7061 rc_gromacs_compa │ │ │ +0000b3b0: 743c 2f74 6974 6c65 3e0a 3c70 6174 6820 t......module_src_grom │ │ │ +0000b520: 6163 735f 676d 7861 6e61 3c2f 7469 746c acs_gmxana</titl │ │ │ +0000b530: 653e 0a3c 656c 6c69 7073 6520 6669 6c6c e>.<ellipse fill │ │ │ +0000b540: 3d22 2362 6662 6662 6622 2073 7472 6f6b ="#bfbfbf" strok │ │ │ +0000b550: 653d 2262 6c61 636b 2220 6378 3d22 3434 e="black" cx="44 │ │ │ +0000b560: 3722 2063 793d 222d 3130 3938 2e32 3322 7" cy="-1098.23" │ │ │ +0000b570: 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class="e │ │ │ +0000b650: 6467 6522 3e0a 3c74 6974 6c65 3e6d 6f64 dge">.<title>mod │ │ │ +0000b660: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +0000b670: 676d 7861 6e61 2623 3435 3b26 6774 3b6d gmxana->m │ │ │ +0000b680: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +0000b690: 735f 6d64 6c69 623c 2f74 6974 6c65 3e0a s_mdlib. │ │ │ +0000b6a0: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 ..... │ │ │ +0000b810: 3c74 6974 6c65 3e6d 6f64 756c 655f 7372 module_sr │ │ │ +0000b820: 635f 6772 6f6d 6163 735f 676d 7861 6e61 c_gromacs_gmxana │ │ │ +0000b830: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ +0000b840: 7372 635f 6772 6f6d 6163 735f 676d 786c src_gromacs_gmxl │ │ │ +0000b850: 6962 3c2f 7469 746c 653e 0a3c 7061 7468 ib......mod │ │ │ +0000bcc0: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +0000bcd0: 676d 7861 6e61 2623 3435 3b26 6774 3b6d gmxana->m │ │ │ +0000bce0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ 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6373 5f67 6d78 616e rc_gromacs_gmxan │ │ │ +0000ce20: 6126 2334 353b 2667 743b 6d6f 6475 6c65 a->module │ │ │ +0000ce30: 5f73 7263 5f67 726f 6d61 6373 5f63 6f6d _src_gromacs_com │ │ │ +0000ce40: 6d61 6e64 6c69 6e65 3c2f 7469 746c 653e mandline │ │ │ +0000ce50: 0a3c 7061 7468 2066 696c 6c3d 226e 6f6e ......module_src_grom │ │ │ +0000d020: 6163 735f 676d 7861 6e61 2623 3435 3b26 acs_gmxana-& │ │ │ +0000d030: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ +0000d040: 6f6d 6163 735f 6170 706c 6965 645f 666f omacs_applied_fo │ │ │ +0000d050: 7263 6573 5f61 7768 3c2f 7469 746c 653e rces_awh │ │ │ +0000d060: 0a3c 7061 7468 2066 696c 6c3d 226e 6f6e .... │ │ │ +0000d1d0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..module_ │ │ │ +0000d240: 7372 635f 6772 6f6d 6163 735f 6d64 7479 src_gromacs_mdty │ │ │ +0000d250: 7065 7326 2334 353b 2667 743b 6d6f 6475 pes->modu │ │ │ +0000d260: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ +0000d270: 646c 6962 3c2f 7469 746c 653e 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nt.....< │ │ │ +00012ab0: 6720 6964 3d22 6e6f 6465 3236 2220 636c g id="node26" cl │ │ │ +00012ac0: 6173 733d 226e 6f64 6522 3e0a 3c74 6974 ass="node">.module_src_gr │ │ │ +00012ae0: 6f6d 6163 735f 6d69 6d69 633c 2f74 6974 omacs_mimic..mimic....modul │ │ │ +00012c20: 655f 7372 635f 6772 6f6d 6163 735f 6d64 e_src_gromacs_md │ │ │ +00012c30: 7275 6e26 2334 353b 2667 743b 6d6f 6475 run->modu │ │ │ +00012c40: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ +00012c50: 696d 6963 3c2f 7469 746c 653e 0a3c 7061 imic.. │ │ │ +00012cf0: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2223 ....modu │ │ │ +00012de0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ +00012df0: 6472 756e 2623 3435 3b26 6774 3b6d 6f64 drun->mod │ │ │ +00012e00: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +00012e10: 6d6f 6475 6c61 7273 696d 756c 6174 6f72 modularsimulator │ │ │ +00012e20: 3c2f 7469 746c 653e 0a3c 7061 7468 2066 ..... │ │ │ +00012f20: 3c67 2069 643d 226e 6f64 6532 3922 2063 .module_src_g │ │ │ +00012f50: 726f 6d61 6373 5f70 756c 6c69 6e67 3c2f romacs_pulling..pulling....module_src_gro │ │ │ +000130a0: 6d61 6373 5f6d 6472 756e 2623 3435 3b26 macs_mdrun-& │ │ │ +000130b0: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ +000130c0: 6f6d 6163 735f 7075 6c6c 696e 673c 2f74 omacs_pulling.. │ │ │ +00013180: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2223 .< │ │ │ +000131f0: 2f67 3e0a 3c21 2d2d 206d 6f64 756c 655f /g>...module_ │ │ │ +00013240: 7372 635f 6772 6f6d 6163 735f 7377 6170 src_gromacs_swap │ │ │ +00013250: 3c2f 7469 746c 653e 0a3c 6720 6964 3d22 ...swap......module_src_gr │ │ │ +000133f0: 6f6d 6163 735f 6d64 7275 6e26 2334 353b omacs_mdrun- │ │ │ +00013400: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ +00013410: 726f 6d61 6373 5f73 7761 703c 2f74 6974 romacs_swap.... │ │ │ +00013540: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..module_ │ │ │ +000135b0: 7372 635f 6772 6f6d 6163 735f 6d64 7275 src_gromacs_mdru │ │ │ +000135c0: 6e26 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│ │ │ +00013720: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c ... │ │ │ +00013770: 3c67 2069 643d 2265 6467 6531 3132 2220 .module_src_ │ │ │ +000137a0: 6772 6f6d 6163 735f 6d64 7275 6e26 2334 gromacs_mdrun │ │ │ +000137b0: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ +000137c0: 5f67 726f 6d61 6373 5f6d 6472 756e 7574 _gromacs_mdrunut │ │ │ +000137d0: 696c 6974 793c 2f74 6974 6c65 3e0a 3c70 ility.

.....modul │ │ │ +00013910: 655f 7372 635f 6772 6f6d 6163 735f 6170 e_src_gromacs_ap │ │ │ +00013920: 706c 6965 645f 666f 7263 6573 3c2f 7469 plied_forces</ti │ │ │ +00013930: 746c 653e 0a3c 656c 6c69 7073 6520 6669 tle>.<ellipse fi │ │ │ +00013940: 6c6c 3d22 2362 6662 6662 6622 2073 7472 ll="#bfbfbf" str │ │ │ +00013950: 6f6b 653d 2262 6c61 636b 2220 6378 3d22 oke="black" cx=" │ │ │ +00013960: 3135 3135 2220 6379 3d22 2d35 3332 2e34 1515" cy="-532.4 │ │ │ +00013970: 2220 7278 3d22 3536 2e36 3422 2072 793d " rx="56.64" ry= │ │ │ +00013980: 2231 332e 3337 222f 3e0a 3c74 6578 7420 "13.37"/>.<text │ │ │ +00013990: 7465 7874 2d61 6e63 686f 723d 226d 6964 text-anchor="mid │ │ │ +000139a0: 646c 6522 2078 3d22 3135 3135 2220 793d dle" x="1515" y= │ │ │ +000139b0: 222d 3532 392e 3922 2066 6f6e 742d 6661 "-529.9" font-fa │ │ │ +000139c0: 6d69 6c79 3d22 4672 6565 5361 6e73 2220 mily="FreeSans" │ │ │ +000139d0: 666f 6e74 2d73 697a 653d 2231 302e 3030 font-size="10.00 │ │ │ +000139e0: 223e 6170 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_mdrun->m │ │ │ +00014220: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +00014230: 735f 6170 706c 6965 645f 666f 7263 6573 s_applied_forces │ │ │ +00014240: 5f61 7768 3c2f 7469 746c 653e 0a3c 7061 _awh....< │ │ │ +00014340: 212d 2d20 6d6f 6475 6c65 5f73 7263 5f67 !-- module_src_g │ │ │ +00014350: 726f 6d61 6373 5f72 6573 7472 6169 6e74 romacs_restraint │ │ │ +00014360: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ +00014370: 7372 635f 6772 6f6d 6163 735f 676d 786c src_gromacs_gmxl │ │ │ +00014380: 6962 202d 2d3e 0a3c 6720 6964 3d22 6564 ib -->..modu │ │ │ +000143b0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f72 le_src_gromacs_r │ │ │ +000143c0: 6573 7472 6169 6e74 2623 3435 3b26 6774 estraint-> │ │ │ +000143d0: 3b6d 6f64 756c 655f 7372 635f 6772 6f6d ;module_src_grom │ │ │ +000143e0: 6163 735f 676d 786c 6962 3c2f 7469 746c acs_gmxlib</titl │ │ │ +000143f0: 653e 0a3c 7061 7468 2066 696c 6c3d 226e e>.<path fill="n │ │ │ +00014400: 6f6e 6522 2073 7472 6f6b 653d 2223 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│ │ │ +00014910: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c ....mo │ │ │ +00014980: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +00014990: 5f6d 696d 6963 2623 3435 3b26 6774 3b6d _mimic->m │ │ │ +000149a0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +000149b0: 735f 6d64 6c69 623c 2f74 6974 6c65 3e0a s_mdlib. │ │ │ +000149c0: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 ... │ │ │ +00014b10: 3c21 2d2d 206d 6f64 756c 655f 7372 635f .. │ │ │ +00014b80: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +00014b90: 6373 5f61 6e61 6c79 7369 7364 6174 6126 cs_analysisdata& │ │ │ +00014ba0: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ +00014bb0: 7263 5f67 726f 6d61 6373 5f66 696c 6569 rc_gromacs_filei │ │ │ +00014bc0: 6f3c 2f74 6974 6c65 3e0a 3c70 6174 6820 o..< │ │ │ +00014c30: 706f 6c79 676f 6e20 6669 6c6c 3d22 2362 polygon fill="#b │ │ │ +00014c40: 6662 6662 6622 2073 7472 6f6b 653d 2223 fbfbf" stroke="# │ │ │ +00014c50: 6266 6266 6266 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3c2f 7469 746c 653e 0a3c 7061 7468 2066 ......module_src_gr │ │ │ -00016480: 6f6d 6163 735f 676d 7870 7265 7072 6f63 omacs_gmxpreproc │ │ │ -00016490: 6573 7326 2334 353b 2667 743b 6d6f 6475 ess->modu │ │ │ -000164a0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f72 le_src_gromacs_r │ │ │ -000164b0: 616e 646f 6d3c 2f74 6974 6c65 3e0a 3c70 andom.

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cs_gmxpreprocess │ │ │ -00016ae0: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ -00016af0: 7372 635f 6772 6f6d 6163 735f 676d 786c src_gromacs_gmxl │ │ │ -00016b00: 6962 202d 2d3e 0a3c 6720 6964 3d22 6564 ib -->.<g id="ed │ │ │ -00016b10: 6765 3132 3922 2063 6c61 7373 3d22 6564 ge129" class="ed │ │ │ -00016b20: 6765 223e 0a3c 7469 746c 653e 6d6f 6475 ge">.<title>modu │ │ │ -00016b30: 6c65 5f73 7263 5f67 726f 6d61 6373 5f67 le_src_gromacs_g │ │ │ -00016b40: 6d78 7072 6570 726f 6365 7373 2623 3435 mxpreprocess- │ │ │ -00016b50: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -00016b60: 6772 6f6d 6163 735f 676d 786c 6962 3c2f gromacs_gmxlib</ │ │ │ -00016b70: 7469 746c 653e 0a3c 7061 7468 2066 696c title>.<path fil │ │ │ -00016b80: 6c3d 226e 6f6e 6522 2073 7472 6f6b 653d l="none" stroke= │ │ │ -00016b90: 2223 6266 6266 6266 2220 643d 224d 3132 "#bfbfbf" d="M12 │ │ │ -00016ba0: 3737 2e38 332c 2d31 3033 312e 3839 4331 77.83,-1031.89C1 │ │ │ -00016bb0: 3338 382e 3633 2c2d 3130 3236 2e35 3720 388.63,-1026.57 │ │ │ -00016bc0: 3136 3239 2e35 382c 2d31 3031 322e 3238 1629.58,-1012.28 │ │ │ -00016bd0: 2031 3730 382c 2d39 3835 2e39 3220 3137 1708,-985.92 17 │ │ │ -00016be0: 3137 2e35 312c 2d39 3832 2e37 3220 3230 17.51,-982.72 20 │ │ │ -00016bf0: 3039 2e31 392c 2d38 3034 2e36 3820 3230 09.19,-804.68 20 │ │ │ -00016c00: 3136 2c2d 3739 372e 3331 2032 3133 332e 16,-797.31 2133. │ │ │ -00016c10: 3633 2c2d 3637 302e 3034 2032 3030 312c 63,-670.04 2001, │ │ │ -00016c20: 2d35 3830 2e39 3620 3230 3031 2c2d 3430 -580.96 2001,-40 │ │ │ -00016c30: 372e 3636 2032 3030 312c 2d34 3037 2e36 7.66 2001,-407.6 │ │ │ -00016c40: 3620 3230 3031 2c2d 3430 372e 3636 2032 6 2001,-407.66 2 │ │ │ -00016c50: 3030 312c 2d32 3739 2e39 3220 3230 3031 001,-279.92 2001 │ │ │ -00016c60: 2c2d 3234 342e 3932 2032 3030 342e 3239 ,-244.92 2004.29 │ │ │ -00016c70: 2c2d 3232 372e 3731 2031 3937 382c 2d32 ,-227.71 1978,-2 │ │ │ -00016c80: 3034 2e36 3120 3139 3539 2e36 392c 2d31 04.61 1959.69,-1 │ │ │ -00016c90: 3838 2e35 3320 3138 3035 2e39 382c 2d31 88.53 1805.98,-1 │ │ │ -00016ca0: 3639 2e31 3820 3137 3331 2e33 352c 2d31 69.18 1731.35,-1 │ │ │ -00016cb0: 3630 2e36 3222 2f3e 0a3c 706f 6c79 676f 60.62"/>.<polygo │ │ │ -00016cc0: 6e20 6669 6c6c 3d22 2362 6662 6662 6622 n fill="#bfbfbf" │ │ │ -00016cd0: 2073 7472 6f6b 653d 2223 6266 6266 6266 stroke="#bfbfbf │ │ │ -00016ce0: 2220 706f 696e 7473 3d22 3137 3331 2e36 " points="1731.6 │ │ │ -00016cf0: 392c 2d31 3537 2e31 3320 3137 3231 2e33 9,-157.13 1721.3 │ │ │ -00016d00: 362c 2d31 3539 2e34 3820 3137 3330 2e39 6,-159.48 1730.9 │ │ │ -00016d10: 2c2d 3136 342e 3039 2031 3733 312e 3639 ,-164.09 1731.69 │ │ │ -00016d20: 2c2d 3135 372e 3133 222f 3e0a 3c2f 673e ,-157.13"/>.</g> │ │ │ -00016d30: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 .<!-- module_src │ │ │ -00016d40: 5f67 726f 6d61 6373 5f67 6d78 7072 6570 _gromacs_gmxprep │ │ │ -00016d50: 726f 6365 7373 2623 3435 3b26 6774 3b6d rocess->m │ │ │ +00014fa0: 6266 2220 643d 224d 3130 3039 2e38 332c bf" d="M1009.83, │ │ │ +00014fb0: 2d35 3138 2e37 3243 3939 312e 3131 2c2d -518.72C991.11,- │ │ │ +00014fc0: 3437 322e 3435 2039 3235 2e37 332c 2d33 472.45 925.73,-3 │ │ │ +00014fd0: 3038 2e31 3520 3838 342c 2d31 3638 2e36 08.15 884,-168.6 │ │ │ +00014fe0: 3120 3837 382e 3736 2c2d 3135 312e 3120 1 878.76,-151.1 │ │ │ +00014ff0: 3837 342e 3031 2c2d 3133 302e 3934 2038 874.01,-130.94 8 │ │ │ +00015000: 3730 2e37 312c 2d31 3135 2e38 3922 2f3e 70.71,-115.89"/> │ │ │ +00015010: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 .<polygon fill=" │ │ │ +00015020: 2362 6662 6662 6622 2073 7472 6f6b 653d #bfbfbf" stroke= │ │ │ +00015030: 2223 6266 6266 6266 2220 706f 696e 7473 "#bfbfbf" points │ │ │ +00015040: 3d22 3837 342e 3039 2c2d 3131 342e 3939 ="874.09,-114.99 │ │ │ +00015050: 2038 3638 2e35 372c 2d31 3035 2e39 3420 868.57,-105.94 │ │ │ +00015060: 3836 372e 3235 2c2d 3131 362e 3436 2038 867.25,-116.46 8 │ │ │ +00015070: 3734 2e30 392c 2d31 3134 2e39 3922 2f3e 74.09,-114.99"/> │ │ │ +00015080: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c .</g>.<!-- modul │ │ │ +00015090: 655f 7372 635f 6772 6f6d 6163 735f 6d6f e_src_gromacs_mo │ │ │ +000150a0: 6475 6c61 7273 696d 756c 6174 6f72 2623 dularsimulator&# │ │ │ +000150b0: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ +000150c0: 635f 6772 6f6d 6163 735f 6c69 7374 6564 c_gromacs_listed │ │ │ +000150d0: 5f66 6f72 6365 7320 2d2d 3e0a 3c67 2069 _forces -->.<g i │ │ │ +000150e0: 643d 2265 6467 6531 3438 2220 636c 6173 d="edge148" clas │ │ │ +000150f0: 733d 2265 6467 6522 3e0a 3c74 6974 6c65 s="edge">.<title │ │ │ +00015100: 3e6d 6f64 756c 655f 7372 635f 6772 6f6d >module_src_grom │ │ │ +00015110: 6163 735f 6d6f 6475 6c61 7273 696d 756c acs_modularsimul │ │ │ +00015120: 6174 6f72 2623 3435 3b26 6774 3b6d 6f64 ator->mod │ │ │ +00015130: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +00015140: 6c69 7374 6564 5f66 6f72 6365 733c 2f74 listed_forces</t │ │ │ +00015150: 6974 6c65 3e0a 3c70 6174 6820 6669 6c6c itle>.<path fill │ │ │ +00015160: 3d22 6e6f 6e65 2220 7374 726f 6b65 3d22 ="none" stroke=" │ │ │ +00015170: 2332 3832 6663 6322 2073 7472 6f6b 652d #282fcc" stroke- │ │ │ +00015180: 6461 7368 6172 7261 793d 2235 2c32 2220 dasharray="5,2" │ │ │ +00015190: 643d 224d 3130 3134 2e35 342c 2d35 3138 d="M1014.54,-518 │ │ │ +000151a0: 2e37 3343 3130 3133 2e34 392c 2d34 3838 .73C1013.49,-488 │ │ │ +000151b0: 2e35 3920 3130 3131 2c2d 3431 302e 3234 .59 1011,-410.24 │ │ │ +000151c0: 2031 3031 312c 2d33 3434 2e37 3920 3130 1011,-344.79 10 │ │ │ +000151d0: 3131 2c2d 3334 342e 3739 2031 3031 312c 11,-344.79 1011, │ │ │ +000151e0: 2d33 3434 2e37 3920 3130 3131 2c2d 3237 -344.79 1011,-27 │ │ │ +000151f0: 392e 3932 2031 3031 312c 2d32 3434 2e32 9.92 1011,-244.2 │ │ │ +00015200: 3920 3130 3137 2e32 2c2d 3230 332e 3331 9 1017.2,-203.31 │ │ │ +00015210: 2031 3032 312e 3633 2c2d 3137 382e 3539 1021.63,-178.59 │ │ │ +00015220: 222f 3e0a 3c70 6f6c 7967 6f6e 2066 696c "/>.<polygon fil │ │ │ 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6c65 s="edge">.<title │ │ │ +00015310: 3e6d 6f64 756c 655f 7372 635f 6772 6f6d >module_src_grom │ │ │ +00015320: 6163 735f 6d6f 6475 6c61 7273 696d 756c acs_modularsimul │ │ │ +00015330: 6174 6f72 2623 3435 3b26 6774 3b6d 6f64 ator->mod │ │ │ +00015340: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +00015350: 7261 6e64 6f6d 3c2f 7469 746c 653e 0a3c random.< │ │ │ +00015360: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ +00015370: 2073 7472 6f6b 653d 2262 6c61 636b 2220 stroke="black" │ │ │ +00015380: 7374 726f 6b65 2d64 6173 6861 7272 6179 stroke-dasharray │ │ │ +00015390: 3d22 352c 3222 2064 3d22 4d39 3539 2e31 ="5,2" d="M959.1 │ │ │ +000153a0: 312c 2d35 3235 2e34 3543 3834 352e 312c 1,-525.45C845.1, │ │ │ +000153b0: 2d35 3133 2e33 3220 3538 372e 3837 2c2d -513.32 587.87,- │ │ │ +000153c0: 3438 352e 3934 2034 3835 2e38 352c 2d34 485.94 485.85,-4 │ │ │ +000153d0: 3735 2e30 3922 2f3e 0a3c 706f 6c79 676f 75.09"/>.....mo │ │ │ +000154c0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +000154d0: 5f6d 6f64 756c 6172 7369 6d75 6c61 746f _modularsimulato │ │ │ +000154e0: 7226 2334 353b 2667 743b 6d6f 6475 6c65 r->module │ │ │ +000154f0: 5f73 7263 5f67 726f 6d61 6373 5f67 7075 _src_gromacs_gpu │ │ │ +00015500: 5f75 7469 6c73 3c2f 7469 746c 653e 0a3c _utils.< │ │ │ +00015510: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ +00015520: 2073 7472 6f6b 653d 2262 6c61 636b 2220 stroke="black" │ │ │ +00015530: 7374 726f 6b65 2d64 6173 6861 7272 6179 stroke-dasharray │ │ │ +00015540: 3d22 352c 3222 2064 3d22 4d31 3034 312e ="5,2" d="M1041. │ │ │ +00015550: 3033 2c2d 3534 342e 3731 4331 3132 372e 03,-544.71C1127. │ │ │ +00015560: 372c 2d35 3833 2e33 3520 3134 3131 2e31 7,-583.35 1411.1 │ │ │ +00015570: 392c 2d37 3137 2e36 3420 3135 3932 2c2d 9,-717.64 1592,- │ │ │ +00015580: 3839 362e 3138 2031 3635 302e 3736 2c2d 896.18 1650.76,- │ │ │ +00015590: 3935 342e 3231 2031 3632 392e 3539 2c2d 954.21 1629.59,- │ │ │ +000155a0: 3130 3032 2e35 3220 3136 3938 2c2d 3130 1002.52 1698,-10 │ │ │ +000155b0: 3438 2e37 3920 3137 3436 2e33 382c 2d31 48.79 1746.38,-1 │ │ │ +000155c0: 3038 312e 3531 2031 3831 332e 3737 2c2d 081.51 1813.77,- │ │ │ +000155d0: 3130 3932 2e33 3620 3138 3539 2e32 372c 1092.36 1859.27, │ │ │ +000155e0: 2d31 3039 352e 3832 222f 3e0a 3c70 6f6c -1095.82"/>.. │ │ │ +00015660: 3c2f 673e 0a3c 212d 2d20 6d6f 6475 6c65 ...module_src_grom │ │ │ +000156f0: 6163 735f 6d6f 6475 6c61 7273 696d 756c acs_modularsimul │ │ │ +00015700: 6174 6f72 2623 3435 3b26 6774 3b6d 6f64 ator->mod │ │ │ +00015710: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +00015720: 7461 736b 6173 7369 676e 6d65 6e74 3c2f taskassignment</ │ │ │ +00015730: 7469 746c 653e 0a3c 7061 7468 2066 696c title>.<path fil │ │ │ +00015740: 6c3d 226e 6f6e 6522 2073 7472 6f6b 653d l="none" stroke= │ │ │ +00015750: 2272 6564 2220 643d 224d 3130 3431 2e33 "red" d="M1041.3 │ │ │ +00015760: 382c 2d35 3230 2e30 3943 3130 3633 2e38 8,-520.09C1063.8 │ │ │ +00015770: 392c 2d35 3130 2e34 3420 3130 3936 2e34 9,-510.44 1096.4 │ │ │ +00015780: 382c 2d34 3936 2e34 3720 3131 3231 2e33 8,-496.47 1121.3 │ │ │ +00015790: 322c 2d34 3835 2e38 3222 2f3e 0a3c 706f 2,-485.82"/>.<po │ │ │ +000157a0: 6c79 676f 6e20 6669 6c6c 3d22 7265 6422 lygon fill="red" │ │ │ +000157b0: 2073 7472 6f6b 653d 2272 6564 2220 706f stroke="red" po │ │ │ +000157c0: 696e 7473 3d22 3131 3232 2e39 352c 2d34 ints="1122.95,-4 │ │ │ +000157d0: 3838 2e39 3320 3131 3330 2e37 362c 2d34 88.93 1130.76,-4 │ │ │ +000157e0: 3831 2e37 3720 3131 3230 2e31 392c 2d34 81.77 1120.19,-4 │ │ │ +000157f0: 3832 2e34 3920 3131 3232 2e39 352c 2d34 82.49 1122.95,-4 │ │ │ +00015800: 3838 2e39 3322 2f3e 0a3c 2f67 3e0a 3c21 88.93"/>.</g>.<! │ │ │ +00015810: 2d2d 206d 6f64 756c 655f 7372 635f 6772 -- module_src_gr │ │ │ +00015820: 6f6d 6163 735f 6d6f 6475 6c61 7273 696d omacs_modularsim │ │ │ +00015830: 756c 6174 6f72 2623 3435 3b26 6774 3b6d ulator->m │ │ │ +00015840: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +00015850: 735f 6577 616c 6420 2d2d 3e0a 3c67 2069 s_ewald -->.<g i │ │ │ +00015860: 643d 2265 6467 6531 3437 2220 636c 6173 d="edge147" clas │ │ │ +00015870: 733d 2265 6467 6522 3e0a 3c74 6974 6c65 s="edge">.<title │ │ │ +00015880: 3e6d 6f64 756c 655f 7372 635f 6772 6f6d >module_src_grom │ │ │ +00015890: 6163 735f 6d6f 6475 6c61 7273 696d 756c acs_modularsimul │ │ │ +000158a0: 6174 6f72 2623 3435 3b26 6774 3b6d 6f64 ator->mod │ │ │ +000158b0: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +000158c0: 6577 616c 643c 2f74 6974 6c65 3e0a 3c70 ewald.

..... │ │ │ +00015a70: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +00015a80: 6373 5f6d 6f64 756c 6172 7369 6d75 6c61 cs_modularsimula │ │ │ +00015a90: 746f 7226 2334 353b 2667 743b 6d6f 6475 tor->modu │ │ │ +00015aa0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ +00015ab0: 6474 7970 6573 3c2f 7469 746c 653e 0a3c dtypes.< │ │ │ +00015ac0: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ +00015ad0: 2073 7472 6f6b 653d 2272 6564 2220 643d stroke="red" d= │ │ │ +00015ae0: 224d 3130 3134 2e31 2c2d 3534 352e 3834 "M1014.1,-545.84 │ │ │ +00015af0: 4331 3031 322e 3834 2c2d 3537 312e 3331 C1012.84,-571.31 │ │ │ +00015b00: 2031 3031 322e 3937 2c2d 3633 302e 3437 1012.97,-630.47 │ │ │ +00015b10: 2031 3033 372c 2d36 3731 2e35 3720 3130 1037,-671.57 10 │ │ │ +00015b20: 3531 2e36 2c2d 3639 362e 3534 2031 3232 51.6,-696.54 122 │ │ │ +00015b30: 352e 3537 2c2d 3830 382e 3834 2031 3234 5.57,-808.84 124 │ │ │ +00015b40: 312c 2d38 3333 2e33 3120 3132 3431 2e33 1,-833.31 1241.3 │ │ │ +00015b50: 2c2d 3833 332e 3739 2031 3236 392e 3933 ,-833.79 1269.93 │ │ │ +00015b60: 2c2d 3935 392e 3432 2031 3238 312e 3837 ,-959.42 1281.87 │ │ │ +00015b70: 2c2d 3130 3131 2e38 3222 2f3e 0a3c 706f ,-1011.82"/>... │ │ │ +00015c40: 0a3c 6720 6964 3d22 6564 6765 3135 3122 ..< │ │ │ +00015c60: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ +00015c70: 5f67 726f 6d61 6373 5f6d 6f64 756c 6172 _gromacs_modular │ │ │ +00015c80: 7369 6d75 6c61 746f 7226 2334 353b 2667 simulator-&g │ │ │ +00015c90: 743b 6d6f 6475 6c65 5f73 7263 5f67 726f t;module_src_gro │ │ │ +00015ca0: 6d61 6373 5f63 6f6d 7061 743c 2f74 6974 macs_compat......module_src_gro │ │ │ +00015e30: 6d61 6373 5f6d 6f64 756c 6172 7369 6d75 macs_modularsimu │ │ │ +00015e40: 6c61 746f 7226 2334 353b 2667 743b 6d6f lator->mo │ │ │ +00015e50: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +00015e60: 5f66 696c 6569 6f3c 2f74 6974 6c65 3e0a _fileio. │ │ │ +00015e70: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 .....mo │ │ │ +00015fc0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +00015fd0: 5f6d 6f64 756c 6172 7369 6d75 6c61 746f _modularsimulato │ │ │ +00015fe0: 7226 2334 353b 2667 743b 6d6f 6475 6c65 r->module │ │ │ +00015ff0: 5f73 7263 5f67 726f 6d61 6373 5f6d 6472 _src_gromacs_mdr │ │ │ +00016000: 756e 3c2f 7469 746c 653e 0a3c 7061 7468 un.. │ │ │ +00016070: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2272 ..< │ │ │ +000160e0: 212d 2d20 6d6f 6475 6c65 5f73 7263 5f67 !-- module_src_g │ │ │ +000160f0: 726f 6d61 6373 5f6d 6f64 756c 6172 7369 romacs_modularsi │ │ │ +00016100: 6d75 6c61 746f 7226 2334 353b 2667 743b mulator-> │ │ │ +00016110: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +00016120: 6373 5f70 756c 6c69 6e67 202d 2d3e 0a3c cs_pulling -->.< │ │ │ +00016130: 6720 6964 3d22 6564 6765 3135 3322 2063 g id="edge153" c │ │ │ +00016140: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.module_src_g │ │ │ +00016160: 726f 6d61 6373 5f6d 6f64 756c 6172 7369 romacs_modularsi │ │ │ +00016170: 6d75 6c61 746f 7226 2334 353b 2667 743b mulator-> │ │ │ +00016180: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +00016190: 6373 5f70 756c 6c69 6e67 3c2f 7469 746c cs_pulling..< │ │ │ +00016220: 706f 6c79 676f 6e20 6669 6c6c 3d22 2332 polygon fill="#2 │ │ │ +00016230: 3832 6663 6322 2073 7472 6f6b 653d 2223 82fcc" stroke="# │ │ │ +00016240: 3238 3266 6363 2220 706f 696e 7473 3d22 282fcc" points=" │ │ │ +00016250: 3931 312e 3833 2c2d 3438 302e 3639 2039 911.83,-480.69 9 │ │ │ +00016260: 3031 2e32 382c 2d34 3739 2e37 3420 3930 01.28,-479.74 90 │ │ │ +00016270: 382e 3933 2c2d 3438 372e 3036 2039 3131 8.93,-487.06 911 │ │ │ +00016280: 2e38 332c 2d34 3830 2e36 3922 2f3e 0a3c .83,-480.69"/>.< │ │ │ +00016290: 2f67 3e0a 3c21 2d2d 206d 6f64 756c 655f /g>...m │ │ │ +00016500: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +00016510: 735f 6d6f 6475 6c61 7273 696d 756c 6174 s_modularsimulat │ │ │ 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6f69 ke="#282fcc" poi │ │ │ +00016600: 6e74 733d 2231 3037 362e 3934 2c2d 3633 nts="1076.94,-63 │ │ │ +00016610: 382e 3233 2031 3038 352e 3234 2c2d 3634 8.23 1085.24,-64 │ │ │ +00016620: 342e 3832 2031 3038 322e 3836 2c2d 3633 4.82 1082.86,-63 │ │ │ +00016630: 342e 3439 2031 3037 362e 3934 2c2d 3633 4.49 1076.94,-63 │ │ │ +00016640: 382e 3233 222f 3e0a 3c2f 673e 0a3c 212d 8.23"/>.</g>.<!- │ │ │ +00016650: 2d20 6d6f 6475 6c65 5f73 7263 5f67 726f - module_src_gro │ │ │ +00016660: 6d61 6373 5f6d 6f64 756c 6172 7369 6d75 macs_modularsimu │ │ │ +00016670: 6c61 746f 7226 2334 353b 2667 743b 6d6f lator->mo │ │ │ +00016680: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +00016690: 5f6e 626e 786d 202d 2d3e 0a3c 6720 6964 _nbnxm -->.<g id │ │ │ +000166a0: 3d22 6564 6765 3135 3022 2063 6c61 7373 ="edge150" class │ │ │ +000166b0: 3d22 6564 6765 223e 0a3c 7469 746c 653e ="edge">.<title> │ │ │ +000166c0: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +000166d0: 6373 5f6d 6f64 756c 6172 7369 6d75 6c61 cs_modularsimula │ │ │ +000166e0: 746f 7226 2334 353b 2667 743b 6d6f 6475 tor->modu │ │ │ +000166f0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6e le_src_gromacs_n │ │ │ +00016700: 626e 786d 3c2f 7469 746c 653e 0a3c 7061 bnxm......modul │ │ │ +000168b0: 655f 7372 635f 6772 6f6d 6163 735f 6d6f e_src_gromacs_mo │ │ │ +000168c0: 6475 6c61 7273 696d 756c 6174 6f72 2623 dularsimulator&# │ │ │ +000168d0: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ +000168e0: 635f 6772 6f6d 6163 735f 636f 6d6d 616e c_gromacs_comman │ │ │ +000168f0: 646c 696e 653c 2f74 6974 6c65 3e0a 3c70 dline.

.....module_src_grom │ │ │ +00016ab0: 6163 735f 7075 6c6c 696e 6726 2334 353b acs_pulling- │ │ │ +00016ac0: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ +00016ad0: 726f 6d61 6373 5f6d 646c 6962 3c2f 7469 romacs_mdlib</ti │ │ │ +00016ae0: 746c 653e 0a3c 7061 7468 2066 696c 6c3d tle>.<path fill= │ │ │ +00016af0: 226e 6f6e 6522 2073 7472 6f6b 653d 2223 "none" stroke="# │ │ │ +00016b00: 6266 6266 6266 2220 643d 224d 3837 362e bfbfbf" d="M876. │ │ │ +00016b10: 3232 2c2d 3438 332e 3037 4338 3732 2e37 22,-483.07C872.7 │ │ │ +00016b20: 352c 2d34 3932 2e37 3320 3836 382e 3239 5,-492.73 868.29 │ │ │ +00016b30: 2c2d 3530 362e 3439 2038 3636 2c2d 3531 ,-506.49 866,-51 │ │ │ +00016b40: 382e 3936 2038 3630 2e39 332c 2d35 3436 8.96 860.93,-546 │ │ │ +00016b50: 2e35 2038 3632 2e38 392c 2d35 3533 2e38 .5 862.89,-553.8 │ │ │ +00016b60: 3520 3836 322c 2d35 3831 2e38 3320 3835 5 862,-581.83 85 │ │ │ +00016b70: 382e 3736 2c2d 3638 332e 3738 2038 3633 8.76,-683.78 863 │ │ │ +00016b80: 2e31 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-952.89 1301.92, │ │ │ +00016c60: 2d39 3636 2e31 3920 3134 3034 2e35 322c -966.19 1404.52, │ │ │ +00016c70: 2d39 3730 2e31 3522 2f3e 0a3c 706f 6c79 -970.15"/>.<poly │ │ │ +00016c80: 676f 6e20 6669 6c6c 3d22 2362 6662 6662 gon fill="#bfbfb │ │ │ +00016c90: 6622 2073 7472 6f6b 653d 2223 6266 6266 f" stroke="#bfbf │ │ │ +00016ca0: 6266 2220 706f 696e 7473 3d22 3134 3034 bf" points="1404 │ │ │ +00016cb0: 2e36 332c 2d39 3733 2e36 3620 3134 3134 .63,-973.66 1414 │ │ │ +00016cc0: 2e37 352c 2d39 3730 2e35 3320 3134 3034 .75,-970.53 1404 │ │ │ +00016cd0: 2e38 392c 2d39 3636 2e36 3620 3134 3034 .89,-966.66 1404 │ │ │ +00016ce0: 2e36 332c 2d39 3733 2e36 3622 2f3e 0a3c .63,-973.66"/>.< │ │ │ +00016cf0: 2f67 3e0a 3c21 2d2d 206d 6f64 756c 655f /g>.<!-- module_ │ │ │ +00016d00: 7372 635f 6772 6f6d 6163 735f 7075 6c6c src_gromacs_pull │ │ │ +00016d10: 696e 6726 2334 353b 2667 743b 6d6f 6475 ing->modu │ │ │ +00016d20: 6c65 5f73 7263 5f67 726f 6d61 6373 5f67 le_src_gromacs_g │ │ │ +00016d30: 6d78 6c69 6220 2d2d 3e0a 3c67 2069 643d mxlib -->.<g id= │ │ │ +00016d40: 2265 6467 6531 3630 2220 636c 6173 733d "edge160" class= │ │ │ +00016d50: 2265 6467 6522 3e0a 3c74 6974 6c65 3e6d "edge">.<title>m │ │ │ 00016d60: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -00016d70: 735f 6d64 7275 6e20 2d2d 3e0a 3c67 2069 s_mdrun -->.<g i │ │ │ -00016d80: 643d 2265 6467 6531 3430 2220 636c 6173 d="edge140" clas │ │ │ -00016d90: 733d 2265 6467 6522 3e0a 3c74 6974 6c65 s="edge">.<title │ │ │ -00016da0: 3e6d 6f64 756c 655f 7372 635f 6772 6f6d >module_src_grom │ │ │ -00016db0: 6163 735f 676d 7870 7265 7072 6f63 6573 acs_gmxpreproces │ │ │ -00016dc0: 7326 2334 353b 2667 743b 6d6f 6475 6c65 s->module │ │ │ -00016dd0: 5f73 7263 5f67 726f 6d61 6373 5f6d 6472 _src_gromacs_mdr │ │ │ -00016de0: 756e 3c2f 7469 746c 653e 0a3c 7061 7468 un..... │ │ │ -00017420: 3c67 2069 643d 2265 6467 6531 3237 2220 .module_src_ │ │ │ -00017450: 6772 6f6d 6163 735f 676d 7870 7265 7072 gromacs_gmxprepr │ │ │ -00017460: 6f63 6573 7326 2334 353b 2667 743b 6d6f ocess->mo │ │ │ -00017470: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -00017480: 5f63 6f6d 6d61 6e64 6c69 6e65 3c2f 7469 _commandline.... │ │ │ -00017630: 3c21 2d2d 206d 6f64 756c 655f 7372 635f .. │ │ │ -000176a0: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -000176b0: 6373 5f67 6d78 7072 6570 726f 6365 7373 cs_gmxpreprocess │ │ │ -000176c0: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ -000176d0: 7372 635f 6772 6f6d 6163 735f 6e62 6e78 src_gromacs_nbnx │ │ │ -000176e0: 6d3c 2f74 6974 6c65 3e0a 3c70 6174 6820 m......module_src_grom │ │ │ -00017af0: 6163 735f 676d 7870 7265 7072 6f63 6573 acs_gmxpreproces │ │ │ -00017b00: 7326 2334 353b 2667 743b 6d6f 6475 6c65 s->module │ │ │ -00017b10: 5f73 7263 5f67 726f 6d61 6373 5f61 7070 _src_gromacs_app │ │ │ -00017b20: 6c69 6564 5f66 6f72 6365 735f 6177 683c lied_forces_awh< │ │ │ -00017b30: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>.<path fi │ │ │ -00017b40: 6c6c 3d22 6e6f 6e65 2220 7374 726f 6b65 ll="none" stroke │ │ │ -00017b50: 3d22 2332 3832 6663 6322 2073 7472 6f6b ="#282fcc" strok │ │ │ -00017b60: 652d 6461 7368 6172 7261 793d 2235 2c32 e-dasharray="5,2 │ │ │ -00017b70: 2220 643d 224d 3132 3738 2e30 342c 2d31 " d="M1278.04,-1 │ │ │ -00017b80: 3033 3243 3133 3830 2e37 2c2d 3130 3237 032C1380.7,-1027 │ │ │ -00017b90: 2e31 3120 3135 3932 2e32 322c 2d31 3031 .11 1592.22,-101 │ │ │ -00017ba0: 332e 3920 3136 3630 2c2d 3938 352e 3932 3.9 1660,-985.92 │ │ │ -00017bb0: 2031 3637 382e 3238 2c2d 3937 382e 3338 1678.28,-978.38 │ │ │ -00017bc0: 2031 3839 392e 3833 2c2d 3739 362e 3934 1899.83,-796.94 │ │ │ -00017bd0: 2031 3936 392e 392c 2d37 3339 2e33 3622 1969.9,-739.36" │ │ │ -00017be0: 2f3e 0a3c 706f 6c79 676f 6e20 6669 6c6c />.<polygon fill │ │ │ -00017bf0: 3d22 2332 3832 6663 6322 2073 7472 6f6b ="#282fcc" strok │ │ │ -00017c00: 653d 2223 3238 3266 6363 2220 706f 696e e="#282fcc" poin │ │ │ -00017c10: 7473 3d22 3139 3732 2e31 372c 2d37 3432 ts="1972.17,-742 │ │ │ -00017c20: 2e30 3320 3139 3737 2e36 372c 2d37 3332 .03 1977.67,-732 │ │ │ -00017c30: 2e39 3820 3139 3637 2e37 322c 2d37 3336 .98 1967.72,-736 │ │ │ -00017c40: 2e36 3220 3139 3732 2e31 372c 2d37 3432 .62 1972.17,-742 │ │ │ -00017c50: 2e30 3322 2f3e 0a3c 2f67 3e0a 3c21 2d2d .03"/>.</g>.<!-- │ │ │ -00017c60: 206d 6f64 756c 655f 7372 635f 6772 6f6d module_src_grom │ │ │ -00017c70: 6163 735f 676d 7870 7265 7072 6f63 6573 acs_gmxpreproces │ │ │ -00017c80: 7326 2334 353b 2667 743b 6d6f 6475 6c65 s->module │ │ │ -00017c90: 5f73 7263 5f74 6573 7475 7469 6c73 202d _src_testutils - │ │ │ -00017ca0: 2d3e 0a3c 6720 6964 3d22 6564 6765 3134 ->.<g id="edge14 │ │ │ -00017cb0: 3422 2063 6c61 7373 3d22 6564 6765 223e 4" class="edge"> │ │ │ -00017cc0: 0a3c 7469 746c 653e 6d6f 6475 6c65 5f73 .<title>module_s │ │ │ -00017cd0: 7263 5f67 726f 6d61 6373 5f67 6d78 7072 rc_gromacs_gmxpr │ │ │ -00017ce0: 6570 726f 6365 7373 2623 3435 3b26 6774 eprocess-> │ │ │ -00017cf0: 3b6d 6f64 756c 655f 7372 635f 7465 7374 ;module_src_test │ │ │ -00017d00: 7574 696c 733c 2f74 6974 6c65 3e0a 3c70 utils.

.....m │ │ │ -00017ec0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -00017ed0: 735f 6d64 7275 6e26 2334 353b 2667 743b s_mdrun-> │ │ │ -00017ee0: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -00017ef0: 6373 5f72 6573 7472 6169 6e74 3c2f 7469 cs_restraint</ti │ │ │ -00017f00: 746c 653e 0a3c 7061 7468 2066 696c 6c3d tle>.<path fill= │ │ │ -00017f10: 226e 6f6e 6522 2073 7472 6f6b 653d 2223 "none" stroke="# │ │ │ -00017f20: 3238 3266 6363 2220 7374 726f 6b65 2d64 282fcc" stroke-d │ │ │ -00017f30: 6173 6861 7272 6179 3d22 352c 3222 2064 asharray="5,2" d │ │ │ -00017f40: 3d22 4d31 3330 392e 3837 2c2d 3539 302e ="M1309.87,-590. │ │ │ -00017f50: 3038 4331 3338 322e 3236 2c2d 3537 392e 08C1382.26,-579. │ │ │ -00017f60: 3539 2031 3537 312e 3836 2c2d 3535 322e 59 1571.86,-552. │ │ │ -00017f70: 3131 2031 3635 372e 3638 2c2d 3533 392e 11 1657.68,-539. │ │ │ -00017f80: 3637 222f 3e0a 3c70 6f6c 7967 6f6e 2066 67"/>.<polygon f │ │ │ -00017f90: 696c 6c3d 2223 3238 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2d33 3633 .37 1389.61,-363 │ │ │ -0001a1c0: 2e32 3822 2f3e 0a3c 2f67 3e0a 3c21 2d2d .28"/>.</g>.<!-- │ │ │ -0001a1d0: 206d 6f64 756c 655f 7372 635f 6772 6f6d module_src_grom │ │ │ -0001a1e0: 6163 735f 6d64 7275 6e26 2334 353b 2667 acs_mdrun-&g │ │ │ -0001a1f0: 743b 6d6f 6475 6c65 5f73 7263 5f67 726f t;module_src_gro │ │ │ -0001a200: 6d61 6373 5f63 6f6d 6d61 6e64 6c69 6e65 macs_commandline │ │ │ -0001a210: 202d 2d3e 0a3c 6720 6964 3d22 6564 6765 -->.<g id="edge │ │ │ -0001a220: 3135 3122 2063 6c61 7373 3d22 6564 6765 151" class="edge │ │ │ -0001a230: 223e 0a3c 7469 746c 653e 6d6f 6475 6c65 ">.<title>module │ │ │ -0001a240: 5f73 7263 5f67 726f 6d61 6373 5f6d 6472 _src_gromacs_mdr │ │ │ -0001a250: 756e 2623 3435 3b26 6774 3b6d 6f64 756c un->modul │ │ │ -0001a260: 655f 7372 635f 6772 6f6d 6163 735f 636f e_src_gromacs_co │ │ │ -0001a270: 6d6d 616e 646c 696e 653c 2f74 6974 6c65 mmandline.... │ │ │ -0001a3b0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..modul │ │ │ -0001a5c0: 655f 7372 635f 6772 6f6d 6163 735f 7075 e_src_gromacs_pu │ │ │ -0001a5d0: 6c6c 696e 673c 2f74 6974 6c65 3e0a 3c65 lling..pul │ │ │ -0001a690: 6c69 6e67 3c2f 7465 7874 3e0a 3c2f 673e ling. │ │ │ -0001a6a0: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 ...modul │ │ │ -0001a710: 655f 7372 635f 6772 6f6d 6163 735f 6d64 e_src_gromacs_md │ │ │ -0001a720: 7275 6e26 2334 353b 2667 743b 6d6f 6475 run->modu │ │ │ -0001a730: 6c65 5f73 7263 5f67 726f 6d61 6373 5f70 le_src_gromacs_p │ │ │ -0001a740: 756c 6c69 6e67 3c2f 7469 746c 653e 0a3c ulling.< │ │ │ -0001a750: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ -0001a760: 2073 7472 6f6b 653d 2223 3238 3266 6363 stroke="#282fcc │ │ │ -0001a770: 2220 7374 726f 6b65 2d64 6173 6861 7272 " stroke-dasharr │ │ │ -0001a780: 6179 3d22 352c 3222 2064 3d22 4d31 3239 ay="5,2" d="M129 │ │ │ -0001a790: 342e 3134 2c2d 3538 322e 3735 4331 3330 4.14,-582.75C130 │ │ │ -0001a7a0: 352e 332c 2d35 3732 2e39 3520 3133 3231 5.3,-572.95 1321 │ │ │ -0001a7b0: 2e37 332c 2d35 3538 2e35 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6f6d >module_src_grom │ │ │ +00016f40: 6163 735f 7075 6c6c 696e 6726 2334 353b acs_pulling- │ │ │ +00016f50: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ +00016f60: 726f 6d61 6373 5f6d 6474 7970 6573 3c2f romacs_mdtypes</ │ │ │ +00016f70: 7469 746c 653e 0a3c 7061 7468 2066 696c title>.<path fil │ │ │ +00016f80: 6c3d 226e 6f6e 6522 2073 7472 6f6b 653d l="none" stroke= │ │ │ +00016f90: 2223 6266 6266 6266 2220 643d 224d 3837 "#bfbfbf" d="M87 │ │ │ +00016fa0: 332e 3733 2c2d 3438 322e 3738 4338 3638 3.73,-482.78C868 │ │ │ +00016fb0: 2e35 312c 2d34 3932 2e32 3820 3836 312e .51,-492.28 861. │ │ │ +00016fc0: 3932 2c2d 3530 352e 3938 2038 3539 2c2d 92,-505.98 859,- │ │ │ +00016fd0: 3531 382e 3936 2038 3434 2e31 322c 2d35 518.96 844.12,-5 │ │ │ +00016fe0: 3835 2e31 3420 3835 322e 3133 2c2d 3630 85.14 852.13,-60 │ │ │ +00016ff0: 3420 3835 382c 2d36 3731 2e35 3720 3836 4 858,-671.57 86 │ │ │ +00017000: 322e 3932 2c2d 3732 382e 3235 2038 3435 2.92,-728.25 845 │ │ │ +00017010: 2e38 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6772 6f6d 6163 735f 7075 6c6c src_gromacs_pull │ │ │ +000171d0: 696e 6726 2334 353b 2667 743b 6d6f 6475 ing->modu │ │ │ +000171e0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f66 le_src_gromacs_f │ │ │ +000171f0: 696c 6569 6f3c 2f74 6974 6c65 3e0a 3c70 ileio.

.....mod │ │ │ +00017370: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +00017380: 7075 6c6c 696e 6726 2334 353b 2667 743b pulling-> │ │ │ +00017390: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +000173a0: 6373 5f64 6f6d 6465 633c 2f74 6974 6c65 cs_domdec.. │ │ │ +000174d0: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c ....module_src_gr │ │ │ +00017730: 6f6d 6163 735f 7075 6c6c 696e 6726 2334 omacs_pulling │ │ │ +00017740: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ +00017750: 5f67 726f 6d61 6373 5f63 6f6d 6d61 6e64 _gromacs_command │ │ │ +00017760: 6c69 6e65 3c2f 7469 746c 653e 0a3c 7061 line......module_src_gr │ │ │ +00017900: 6f6d 6163 735f 7461 626c 6573 2623 3435 omacs_tables- │ │ │ +00017910: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ +00017920: 6772 6f6d 6163 735f 6d64 7479 7065 733c gromacs_mdtypes< │ │ │ +00017930: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>..

... │ │ │ +00017ad0: 3c67 2069 643d 2265 6467 6531 3634 2220 .module_src_ │ │ │ +00017b00: 6772 6f6d 6163 735f 7461 626c 6573 2623 gromacs_tables&# │ │ │ +00017b10: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ +00017b20: 635f 6772 6f6d 6163 735f 6669 6c65 696f c_gromacs_fileio │ │ │ +00017b30: 3c2f 7469 746c 653e 0a3c 7061 7468 2066 ......module_src_gr │ │ │ +00017d30: 6f6d 6163 735f 7461 626c 6573 2623 3435 omacs_tables- │ │ │ +00017d40: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ +00017d50: 6772 6f6d 6163 735f 6d64 7370 616e 3c2f gromacs_mdspan..< │ │ │ +00017de0: 706f 6c79 676f 6e20 6669 6c6c 3d22 2332 polygon fill="#2 │ │ │ +00017df0: 3832 6663 6322 2073 7472 6f6b 653d 2223 82fcc" stroke="# │ │ │ +00017e00: 3238 3266 6363 2220 706f 696e 7473 3d22 282fcc" points=" │ │ │ +00017e10: 3234 342e 3636 2c2d 3533 2e32 3520 3234 244.66,-53.25 24 │ │ │ +00017e20: 352e 3934 2c2d 3432 2e37 3320 3233 382e 5.94,-42.73 238. │ │ │ +00017e30: 3338 2c2d 3530 2e31 3620 3234 342e 3636 38,-50.16 244.66 │ │ │ +00017e40: 2c2d 3533 2e32 3522 2f3e 0a3c 2f67 3e0a ,-53.25"/>.. │ │ │ +00017e50: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..m │ │ │ +00017fe0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +00017ff0: 735f 746f 6f6c 7326 2334 353b 2667 743b s_tools-> │ │ │ +00018000: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +00018010: 6373 5f6d 646c 6962 3c2f 7469 746c 653e cs_mdlib │ │ │ +00018020: 0a3c 7061 7468 2066 696c 6c3d 226e 6f6e .... │ │ │ +00018170: 0a3c 6720 6964 3d22 6564 6765 3137 3522 ..< │ │ │ +00018190: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ +000181a0: 5f67 726f 6d61 6373 5f74 6f6f 6c73 2623 _gromacs_tools&# │ │ │ +000181b0: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ +000181c0: 635f 6772 6f6d 6163 735f 676d 786c 6962 c_gromacs_gmxlib │ │ │ +000181d0: 3c2f 7469 746c 653e 0a3c 7061 7468 2066 ... │ │ │ +000183b0: 3c2f 673e 0a3c 212d 2d20 6d6f 6475 6c65 .. │ │ │ +00018400: 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fill="#282fcc" s │ │ │ +0001a940: 7472 6f6b 653d 2223 3238 3266 6363 2220 troke="#282fcc" │ │ │ +0001a950: 706f 696e 7473 3d22 3130 3530 2e32 362c points="1050.26, │ │ │ +0001a960: 2d36 3438 2e37 3720 3130 3630 2e38 332c -648.77 1060.83, │ │ │ +0001a970: 2d36 3438 2e31 3120 3130 3532 2e31 352c -648.11 1052.15, │ │ │ +0001a980: 2d36 3432 2e30 3320 3130 3530 2e32 362c -642.03 1050.26, │ │ │ +0001a990: 2d36 3438 2e37 3722 2f3e 0a3c 2f67 3e0a -648.77"/>.</g>. │ │ │ +0001a9a0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f <!-- module_src_ │ │ │ +0001a9b0: 6772 6f6d 6163 735f 646f 6d64 6563 2623 gromacs_domdec&# │ │ │ +0001a9c0: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ +0001a9d0: 635f 6772 6f6d 6163 735f 696d 6420 2d2d c_gromacs_imd -- │ │ │ +0001a9e0: 3e0a 3c67 2069 643d 2265 6467 6531 3937 >.<g id="edge197 │ │ │ +0001a9f0: 2220 636c 6173 733d 2265 6467 6522 3e0a " class="edge">. │ │ │ +0001aa00: 3c74 6974 6c65 3e6d 6f64 756c 655f 7372 <title>module_sr │ │ │ +0001aa10: 635f 6772 6f6d 6163 735f 646f 6d64 6563 c_gromacs_domdec │ │ │ +0001aa20: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ +0001aa30: 7372 635f 6772 6f6d 6163 735f 696d 643c src_gromacs_imd< │ │ │ +0001aa40: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>.<path fi │ │ │ +0001aa50: 6c6c 3d22 6e6f 6e65 2220 7374 726f 6b65 ll="none" stroke │ │ │ +0001aa60: 3d22 2332 3832 6663 6322 2073 7472 6f6b ="#282fcc" strok │ │ │ +0001aa70: 652d 6461 7368 6172 7261 793d 2235 2c32 e-dasharray="5,2 │ │ │ +0001aa80: 2220 643d 224d 3135 3630 2e39 362c 2d33 " d="M1560.96,-3 │ │ │ +0001aa90: 3434 2e39 3143 3136 3030 2e35 322c 2d33 44.91C1600.52,-3 │ │ │ +0001aaa0: 3436 2e37 3620 3136 3632 2e35 352c 2d33 46.76 1662.55,-3 │ │ │ +0001aab0: 3535 2e37 3120 3136 3937 2c2d 3339 332e 55.71 1697,-393. │ │ │ +0001aac0: 3232 2031 3735 372e 3835 2c2d 3435 392e 22 1757.85,-459. │ │ │ +0001aad0: 3437 2031 3737 332e 3233 2c2d 3732 342e 47 1773.23,-724. │ │ │ +0001aae0: 3037 2031 3732 312c 2d37 3937 2e33 3120 07 1721,-797.31 │ │ │ +0001aaf0: 3136 3534 2e38 352c 2d38 3930 2e30 3620 1654.85,-890.06 │ │ │ +0001ab00: 3135 3034 2e37 372c 2d39 3036 2e30 3120 1504.77,-906.01 │ │ │ +0001ab10: 3134 3334 2e34 332c 2d39 3038 2e34 3122 1434.43,-908.41" │ │ │ +0001ab20: 2f3e 0a3c 706f 6c79 676f 6e20 6669 6c6c />.<polygon fill │ │ │ +0001ab30: 3d22 2332 3832 6663 6322 2073 7472 6f6b ="#282fcc" strok │ │ │ +0001ab40: 653d 2223 3238 3266 6363 2220 706f 696e e="#282fcc" poin │ │ │ +0001ab50: 7473 3d22 3134 3334 2e31 362c 2d39 3034 ts="1434.16,-904 │ │ │ +0001ab60: 2e39 3120 3134 3234 2e32 352c 2d39 3038 .91 1424.25,-908 │ │ │ +0001ab70: 2e36 3820 3134 3334 2e33 342c 2d39 3131 .68 1434.34,-911 │ │ │ +0001ab80: 2e39 3120 3134 3334 2e31 362c 2d39 3034 .91 1434.16,-904 │ │ │ +0001ab90: 2e39 3122 2f3e 0a3c 2f67 3e0a 3c21 2d2d .91"/>.</g>.<!-- │ │ │ +0001aba0: 206d 6f64 756c 655f 7372 635f 6772 6f6d module_src_grom │ │ │ +0001abb0: 6163 735f 646f 6d64 6563 2623 3435 3b26 acs_domdec-& │ │ │ +0001abc0: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ +0001abd0: 6f6d 6163 735f 6d64 6c69 6220 2d2d 3e0a omacs_mdlib -->. │ │ │ +0001abe0: 3c67 2069 643d 2265 6467 6531 3930 2220 <g id="edge190" │ │ │ +0001abf0: 636c 6173 733d 2265 6467 6522 3e0a 3c74 class="edge">.<t │ │ │ +0001ac00: 6974 6c65 3e6d 6f64 756c 655f 7372 635f itle>module_src_ │ │ │ +0001ac10: 6772 6f6d 6163 735f 646f 6d64 6563 2623 gromacs_domdec&# │ │ │ +0001ac20: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ +0001ac30: 635f 6772 6f6d 6163 735f 6d64 6c69 623c c_gromacs_mdlib< │ │ │ +0001ac40: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>.<path fi │ │ │ +0001ac50: 6c6c 3d22 6e6f 6e65 2220 7374 726f 6b65 ll="none" stroke │ │ │ +0001ac60: 3d22 2362 6662 6662 6622 2064 3d22 4d31 ="#bfbfbf" d="M1 │ │ │ +0001ac70: 3536 302e 3938 2c2d 3334 352e 3336 4331 560.98,-345.36C1 │ │ │ +0001ac80: 3630 322e 3036 2c2d 3334 372e 3633 2031 602.06,-347.63 1 │ │ │ +0001ac90: 3636 382e 3433 2c2d 3335 362e 3939 2031 668.43,-356.99 1 │ │ │ +0001aca0: 3731 302c 2d33 3933 2e32 3220 3137 3637 710,-393.22 1767 │ │ │ +0001acb0: 2e35 382c 2d34 3433 2e34 2031 3737 312e .58,-443.4 1771. │ │ │ +0001acc0: 3836 2c2d 3636 302e 3937 2031 3735 312c 86,-660.97 1751, │ │ │ +0001acd0: 2d37 3334 2e34 3420 3137 3231 2e39 372c -734.44 1721.97, │ │ │ +0001ace0: 2d38 3336 2e36 3820 3136 3937 2e34 342c -836.68 1697.44, │ │ │ +0001acf0: 2d38 3732 2e34 3220 3136 3034 2c2d 3932 -872.42 1604,-92 │ │ │ +0001ad00: 332e 3035 2031 3536 342e 3238 2c2d 3934 3.05 1564.28,-94 │ │ │ +0001ad10: 342e 3538 2031 3531 332e 3436 2c2d 3935 4.58 1513.46,-95 │ │ │ +0001ad20: 382e 3334 2031 3437 392e 3439 2c2d 3936 8.34 1479.49,-96 │ │ │ +0001ad30: 352e 3439 222f 3e0a 3c70 6f6c 7967 6f6e 5.49"/>.<polygon │ │ │ +0001ad40: 2066 696c 6c3d 2223 6266 6266 6266 2220 fill="#bfbfbf" │ │ │ +0001ad50: 7374 726f 6b65 3d22 2362 6662 6662 6622 stroke="#bfbfbf" │ │ │ +0001ad60: 2070 6f69 6e74 733d 2231 3437 382e 3633 points="1478.63 │ │ │ +0001ad70: 2c2d 3936 322e 3039 2031 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6d70 6174 3c2f 7469 746c 653e 0a3c 7061 mpat.... │ │ │ -0001af80: 3c21 2d2d 206d 6f64 756c 655f 7372 635f . │ │ │ -0001afd0: 3c67 2069 643d 2265 6467 6531 3535 2220 .module_src_ │ │ │ -0001b000: 6772 6f6d 6163 735f 6d64 7275 6e26 2334 gromacs_mdrun │ │ │ -0001b010: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ -0001b020: 5f67 726f 6d61 6373 5f61 7070 6c69 6564 _gromacs_applied │ │ │ -0001b030: 5f66 6f72 6365 735f 6177 683c 2f74 6974 _forces_awh......modu │ │ │ -0001b1b0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f68 le_src_gromacs_h │ │ │ -0001b1c0: 6172 6477 6172 6526 2334 353b 2667 743b ardware-> │ │ │ +0001adc0: 5f67 726f 6d61 6373 5f64 6f6d 6465 6326 _gromacs_domdec& │ │ │ +0001add0: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ +0001ade0: 7263 5f67 726f 6d61 6373 5f67 6d78 6c69 rc_gromacs_gmxli │ │ │ +0001adf0: 6220 2d2d 3e0a 3c67 2069 643d 2265 6467 b -->.<g id="edg │ │ │ +0001ae00: 6531 3837 2220 636c 6173 733d 2265 6467 e187" class="edg │ │ │ +0001ae10: 6522 3e0a 3c74 6974 6c65 3e6d 6f64 756c e">.<title>modul │ │ │ +0001ae20: 655f 7372 635f 6772 6f6d 6163 735f 646f e_src_gromacs_do │ │ │ +0001ae30: 6d64 6563 2623 3435 3b26 6774 3b6d 6f64 mdec->mod │ │ │ +0001ae40: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +0001ae50: 676d 786c 6962 3c2f 7469 746c 653e 0a3c gmxlib.< │ │ │ +0001ae60: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ +0001ae70: 2073 7472 6f6b 653d 2223 6266 6266 6266 stroke="#bfbfbf │ │ │ +0001ae80: 2220 643d 224d 3135 3230 2e38 312c 2d33 " d="M1520.81,-3 │ │ │ +0001ae90: 3330 2e32 3743 3135 3037 2e38 362c 2d32 30.27C1507.86,-2 │ │ │ +0001aea0: 3933 2e37 3220 3134 3634 2e36 2c2d 3138 93.72 1464.6,-18 │ │ │ +0001aeb0: 362e 3838 2031 3338 382c 2d31 3431 2e37 6.88 1388,-141.7 │ │ │ +0001aec0: 3420 3133 3037 2e30 392c 2d39 342e 3035 4 1307.09,-94.05 │ │ │ +0001aed0: 2031 3031 372e 3339 2c2d 3931 2e37 3820 1017.39,-91.78 │ │ │ +0001aee0: 3930 382e 3132 2c2d 3932 2e36 3822 2f3e 908.12,-92.68"/> │ │ │ +0001aef0: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 .....module_src_gr │ │ │ +0001afe0: 6f6d 6163 735f 646f 6d64 6563 2623 3435 omacs_domdec- │ │ │ +0001aff0: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ +0001b000: 6772 6f6d 6163 735f 6c69 7374 6564 5f66 gromacs_listed_f │ │ │ +0001b010: 6f72 6365 733c 2f74 6974 6c65 3e0a 3c70 orces.

.. │ │ │ +0001b140: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 ...mo │ │ │ +0001b1b0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +0001b1c0: 5f64 6f6d 6465 6326 2334 353b 2667 743b _domdec-> │ │ │ 0001b1d0: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ 0001b1e0: 6373 5f67 7075 5f75 7469 6c73 3c2f 7469 cs_gpu_utils</ti │ │ │ 0001b1f0: 746c 653e 0a3c 7061 7468 2066 696c 6c3d tle>.<path fill= │ │ │ 0001b200: 226e 6f6e 6522 2073 7472 6f6b 653d 2223 "none" stroke="# │ │ │ -0001b210: 6266 6266 6266 2220 643d 224d 3636 332e bfbfbf" d="M663. │ │ │ -0001b220: 3534 2c2d 3134 342e 3533 4336 3934 2e39 54,-144.53C694.9 │ │ │ -0001b230: 332c 2d31 3333 2e36 3220 3734 392e 3332 3,-133.62 749.32 │ │ │ -0001b240: 2c2d 3131 352e 3839 2037 3836 2e35 332c ,-115.89 786.53, │ │ │ -0001b250: 2d31 3034 2e34 3122 2f3e 0a3c 706f 6c79 -104.41"/>.<poly │ │ │ -0001b260: 676f 6e20 6669 6c6c 3d22 2362 6662 6662 gon fill="#bfbfb │ │ │ -0001b270: 6622 2073 7472 6f6b 653d 2223 6266 6266 f" stroke="#bfbf │ │ │ -0001b280: 6266 2220 706f 696e 7473 3d22 3738 382c bf" points="788, │ │ │ -0001b290: 2d31 3037 2e36 3220 3739 362e 3533 2c2d -107.62 796.53,- │ │ │ -0001b2a0: 3130 312e 3335 2037 3835 2e39 352c 2d31 101.35 785.95,-1 │ │ │ -0001b2b0: 3030 2e39 3320 3738 382c 2d31 3037 2e36 00.93 788,-107.6 │ │ │ -0001b2c0: 3222 2f3e 0a3c 2f67 3e0a 3c21 2d2d 206d 2"/>.</g>.<!-- m │ │ │ -0001b2d0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -0001b2e0: 735f 6666 7426 2334 353b 2667 743b 6d6f s_fft->mo │ │ │ -0001b2f0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -0001b300: 5f67 7075 5f75 7469 6c73 202d 2d3e 0a3c _gpu_utils -->.< │ │ │ -0001b310: 6720 6964 3d22 6564 6765 3137 3122 2063 g id="edge171" c │ │ │ -0001b320: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.<ti │ │ │ -0001b330: 746c 653e 6d6f 6475 6c65 5f73 7263 5f67 tle>module_src_g │ │ │ -0001b340: 726f 6d61 6373 5f66 6674 2623 3435 3b26 romacs_fft-& │ │ │ -0001b350: 6774 3b6d 6f64 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784.08,-104. │ │ │ -0001b430: 3537 2037 3837 2e31 372c 2d31 3033 2e38 57 787.17,-103.8 │ │ │ -0001b440: 3822 2f3e 0a3c 706f 6c79 676f 6e20 6669 8"/>.<polygon fi │ │ │ -0001b450: 6c6c 3d22 2332 3832 6663 6322 2073 7472 ll="#282fcc" str │ │ │ -0001b460: 6f6b 653d 2223 3238 3266 6363 2220 706f oke="#282fcc" po │ │ │ -0001b470: 696e 7473 3d22 3738 382e 3034 2c2d 3130 ints="788.04,-10 │ │ │ -0001b480: 372e 3237 2037 3936 2e39 362c 2d31 3031 7.27 796.96,-101 │ │ │ -0001b490: 2e35 3620 3738 362e 3432 2c2d 3130 302e .56 786.42,-100. │ │ │ -0001b4a0: 3436 2037 3838 2e30 342c 2d31 3037 2e32 46 788.04,-107.2 │ │ │ -0001b4b0: 3722 2f3e 0a3c 2f67 3e0a 3c21 2d2d 206d 7"/>.</g>.<!-- m │ │ │ -0001b4c0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -0001b4d0: 735f 6666 7426 2334 353b 2667 743b 6d6f s_fft->mo │ │ │ -0001b4e0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -0001b4f0: 5f68 6172 6477 6172 6520 2d2d 3e0a 3c67 _hardware -->.<g │ │ │ -0001b500: 2069 643d 2265 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6765 223e 9" class="edge"> │ │ │ -0001b6c0: 0a3c 7469 746c 653e 6d6f 6475 6c65 5f73 .<title>module_s │ │ │ -0001b6d0: 7263 5f67 726f 6d61 6373 5f6d 646c 6962 rc_gromacs_mdlib │ │ │ -0001b6e0: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ -0001b6f0: 7372 635f 6772 6f6d 6163 735f 7472 616a src_gromacs_traj │ │ │ -0001b700: 6563 746f 7279 3c2f 7469 746c 653e 0a3c ectory.< │ │ │ -0001b710: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ -0001b720: 2073 7472 6f6b 653d 2223 6266 6266 6266 stroke="#bfbfbf │ │ │ -0001b730: 2220 643d 224d 3133 3130 2e39 332c 2d34 " d="M1310.93,-4 │ │ │ -0001b740: 3033 2e35 3243 3134 3237 2e39 392c 2d33 03.52C1427.99,-3 │ │ │ -0001b750: 3934 2e36 2031 3837 392e 3932 2c2d 3336 94.6 1879.92,-36 │ │ │ -0001b760: 302e 3132 2032 3033 312e 3238 2c2d 3334 0.12 2031.28,-34 │ │ │ -0001b770: 382e 3538 222f 3e0a 3c70 6f6c 7967 6f6e 8.58"/>.. │ │ │ -0001b7f0: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 ...module │ │ │ -0001b860: 5f73 7263 5f67 726f 6d61 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2334 353b omacs_mdlib- │ │ │ -0001bc00: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ -0001bc10: 726f 6d61 6373 5f6d 6472 756e 7574 696c romacs_mdrunutil │ │ │ -0001bc20: 6974 7920 2d2d 3e0a 3c67 2069 643d 2265 ity -->.<g id="e │ │ │ -0001bc30: 6467 6531 3831 2220 636c 6173 733d 2265 dge181" class="e │ │ │ -0001bc40: 6467 6522 3e0a 3c74 6974 6c65 3e6d 6f64 dge">.<title>mod │ │ │ -0001bc50: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -0001bc60: 6d64 6c69 6226 2334 353b 2667 743b 6d6f mdlib->mo │ │ │ -0001bc70: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -0001bc80: 5f6d 6472 756e 7574 696c 6974 793c 2f74 _mdrunutility</t │ │ │ -0001bc90: 6974 6c65 3e0a 3c70 6174 6820 6669 6c6c itle>.<path fill │ │ │ -0001bca0: 3d22 6e6f 6e65 2220 7374 726f 6b65 3d22 ="none" stroke=" │ │ │ -0001bcb0: 2332 3832 6663 6322 2073 7472 6f6b 652d #282fcc" stroke- │ │ │ -0001bcc0: 6461 7368 6172 7261 793d 2235 2c32 2220 dasharray="5,2" │ │ │ -0001bcd0: 643d 224d 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-0001c310: 372c 2d33 3532 2e30 3320 3231 3430 2e37 7,-352.03 2140.7 │ │ │ -0001c320: 392c 2d33 3538 2e38 3222 2f3e 0a3c 2f67 9,-358.82"/>.</g │ │ │ -0001c330: 3e0a 3c21 2d2d 206d 6f64 756c 655f 7372 >.<!-- module_sr │ │ │ -0001c340: 635f 6772 6f6d 6163 735f 6d64 6c69 6226 c_gromacs_mdlib& │ │ │ -0001c350: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ -0001c360: 7263 5f67 726f 6d61 6373 5f6d 6473 7061 rc_gromacs_mdspa │ │ │ -0001c370: 6e20 2d2d 3e0a 3c67 2069 643d 2265 6467 n -->.<g id="edg │ │ │ -0001c380: 6531 3839 2220 636c 6173 733d 2265 6467 e189" class="edg │ │ │ -0001c390: 6522 3e0a 3c74 6974 6c65 3e6d 6f64 756c e">.<title>modul │ │ │ -0001c3a0: 655f 7372 635f 6772 6f6d 6163 735f 6d64 e_src_gromacs_md │ │ │ -0001c3b0: 6c69 6226 2334 353b 2667 743b 6d6f 6475 lib->modu │ │ │ -0001c3c0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ -0001c3d0: 6473 7061 6e3c 2f74 6974 6c65 3e0a 3c70 dspan.

....< │ │ │ -0001c550: 6720 6964 3d22 6564 6765 3138 3022 2063 g id="edge180" c │ │ │ -0001c560: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.module_src_g │ │ │ -0001c580: 726f 6d61 6373 5f6d 646c 6962 2623 3435 romacs_mdlib- │ │ │ -0001c590: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -0001c5a0: 6772 6f6d 6163 735f 6577 616c 643c 2f74 gromacs_ewald...< │ │ │ -0001c680: 2f67 3e0a 3c21 2d2d 206d 6f64 756c 655f /g>...module │ │ │ -0001c6f0: 5f73 7263 5f67 726f 6d61 6373 5f6d 646c _src_gromacs_mdl │ │ │ -0001c700: 6962 2623 3435 3b26 6774 3b6d 6f64 756c ib->modul │ │ │ -0001c710: 655f 7372 635f 6772 6f6d 6163 735f 696d e_src_gromacs_im │ │ │ -0001c720: 643c 2f74 6974 6c65 3e0a 3c70 6174 6820 d...< │ │ │ -0001c820: 2f67 3e0a 3c21 2d2d 206d 6f64 756c 655f /g>...mod │ │ │ -0001c890: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -0001c8a0: 6d64 6c69 6226 2334 353b 2667 743b 6d6f mdlib->mo │ │ │ -0001c8b0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -0001c8c0: 5f67 6d78 6c69 623c 2f74 6974 6c65 3e0a _gmxlib. │ │ │ -0001c8d0: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 ....< │ │ │ -0001ca50: 6720 6964 3d22 6564 6765 3138 3322 2063 g id="edge183" c │ │ │ -0001ca60: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.module_src_g │ │ │ -0001ca80: 726f 6d61 6373 5f6d 646c 6962 2623 3435 romacs_mdlib- │ │ │ -0001ca90: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -0001caa0: 6772 6f6d 6163 735f 6861 7264 7761 7265 gromacs_hardware │ │ │ -0001cab0: 3c2f 7469 746c 653e 0a3c 7061 7468 2066 ......modu │ │ │ -0001cc80: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ -0001cc90: 646c 6962 2623 3435 3b26 6774 3b6d 6f64 dlib->mod │ │ │ -0001cca0: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -0001ccb0: 6573 7365 6e74 6961 6c64 796e 616d 6963 essentialdynamic │ │ │ -0001ccc0: 733c 2f74 6974 6c65 3e0a 3c70 6174 6820 s......module_src_grom │ │ │ -0001ce40: 6163 735f 6d64 6c69 6226 2334 353b 2667 acs_mdlib-&g │ │ │ +0001b210: 6266 6266 6266 2220 643d 224d 3135 3631 bfbfbf" d="M1561 │ │ │ +0001b220: 2e31 322c 2d33 3434 2e35 3843 3136 3331 .12,-344.58C1631 │ │ │ +0001b230: 2e36 352c 2d33 3436 2e33 3620 3137 3837 .65,-346.36 1787 │ │ │ +0001b240: 2e30 392c 2d33 3631 2e34 3320 3138 3539 .09,-361.43 1859 │ │ │ +0001b250: 2c2d 3435 362e 3039 2031 3937 312e 3935 ,-456.09 1971.95 │ │ │ +0001b260: 2c2d 3630 342e 3738 2031 3939 342e 3432 ,-604.78 1994.42 │ │ │ +0001b270: 2c2d 3637 342e 3537 2031 3937 342c 2d38 ,-674.57 1974,-8 │ │ │ +0001b280: 3630 2e31 3820 3139 3635 2e30 352c 2d39 60.18 1965.05,-9 │ │ │ +0001b290: 3431 2e35 3220 3139 3333 2e30 342c 2d31 41.52 1933.04,-1 │ │ │ +0001b2a0: 3033 3420 3139 3137 2e35 342c 2d31 3037 034 1917.54,-107 │ │ │ +0001b2b0: 352e 3322 2f3e 0a3c 706f 6c79 676f 6e20 5.3"/>.<polygon │ │ │ +0001b2c0: 6669 6c6c 3d22 2362 6662 6662 6622 2073 fill="#bfbfbf" s │ │ │ +0001b2d0: 7472 6f6b 653d 2223 6266 6266 6266 2220 troke="#bfbfbf" │ │ │ 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6d6f omdec->mo │ │ │ +0001b3c0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +0001b3d0: 5f65 7761 6c64 3c2f 7469 746c 653e 0a3c _ewald.< │ │ │ +0001b3e0: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ +0001b3f0: 2073 7472 6f6b 653d 2272 6564 2220 643d stroke="red" d= │ │ │ +0001b400: 224d 3135 3538 2e33 322c 2d33 3338 2e33 "M1558.32,-338.3 │ │ │ +0001b410: 3143 3136 3438 2e33 382c 2d33 3236 2e39 1C1648.38,-326.9 │ │ │ +0001b420: 3420 3138 3935 2e36 312c 2d32 3937 2e30 4 1895.61,-297.0 │ │ │ +0001b430: 3920 3139 3930 2e39 342c 2d32 3836 2e30 9 1990.94,-286.0 │ │ │ +0001b440: 3722 2f3e 0a3c 706f 6c79 676f 6e20 6669 7"/>.....m │ │ │ +0001b520: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +0001b530: 735f 646f 6d64 6563 2623 3435 3b26 6774 s_domdec-> │ │ │ +0001b540: 3b6d 6f64 756c 655f 7372 635f 6772 6f6d ;module_src_grom │ │ │ +0001b550: 6163 735f 6861 7264 7761 7265 3c2f 7469 acs_hardware</ti │ │ │ +0001b560: 746c 653e 0a3c 7061 7468 2066 696c 6c3d tle>.<path fill= │ │ │ +0001b570: 226e 6f6e 6522 2073 7472 6f6b 653d 2223 "none" stroke="# │ │ │ +0001b580: 6266 6266 6266 2220 643d 224d 3135 3234 bfbfbf" d="M1524 │ │ │ +0001b590: 2e33 392c 2d33 3330 2e33 3543 3135 3233 .39,-330.35C1523 │ │ │ +0001b5a0: 2e33 392c 2d32 3934 2e34 3920 3135 3235 .39,-294.49 1525 │ │ │ +0001b5b0: 2e39 322c 2d31 3930 2e33 3320 3135 3835 .92,-190.33 1585 │ │ │ +0001b5c0: 2c2d 3134 312e 3734 2031 3631 392e 3637 ,-141.74 1619.67 │ │ │ +0001b5d0: 2c2d 3131 332e 3232 2031 3931 392e 3938 ,-113.22 1919.98 │ │ │ +0001b5e0: 2c2d 3939 2e33 3720 3230 3339 2e38 372c ,-99.37 2039.87, │ │ │ +0001b5f0: 2d39 342e 3934 222f 3e0a 3c70 6f6c 7967 -94.94"/>.<polyg │ │ │ +0001b600: 6f6e 2066 696c 6c3d 2223 6266 6266 6266 on fill="#bfbfbf │ │ │ +0001b610: 2220 7374 726f 6b65 3d22 2362 6662 6662 " stroke="#bfbfb │ │ │ +0001b620: 6622 2070 6f69 6e74 733d 2232 3034 302e f" points="2040. │ │ │ +0001b630: 3032 2c2d 3938 2e34 3420 3230 3439 2e38 02,-98.44 2049.8 │ │ │ +0001b640: 382c 2d39 342e 3538 2032 3033 392e 3736 8,-94.58 2039.76 │ │ │ +0001b650: 2c2d 3931 2e34 3520 3230 3430 2e30 322c ,-91.45 2040.02, │ │ │ +0001b660: 2d39 382e 3434 222f 3e0a 3c2f 673e 0a3c -98.44"/>.</g>.< │ │ │ +0001b670: 212d 2d20 6d6f 6475 6c65 5f73 7263 5f67 !-- module_src_g │ │ │ +0001b680: 726f 6d61 6373 5f64 6f6d 6465 6326 2334 romacs_domdec │ │ │ +0001b690: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ +0001b6a0: 5f67 726f 6d61 6373 5f6d 6474 7970 6573 _gromacs_mdtypes │ │ │ +0001b6b0: 202d 2d3e 0a3c 6720 6964 3d22 6564 6765 -->.<g id="edge │ │ │ +0001b6c0: 3138 3922 2063 6c61 7373 3d22 6564 6765 189" class="edge │ │ │ +0001b6d0: 223e 0a3c 7469 746c 653e 6d6f 6475 6c65 ">.<title>module │ │ │ +0001b6e0: 5f73 7263 5f67 726f 6d61 6373 5f64 6f6d _src_gromacs_dom │ │ │ +0001b6f0: 6465 6326 2334 353b 2667 743b 6d6f 6475 dec->modu │ │ │ +0001b700: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ +0001b710: 6474 7970 6573 3c2f 7469 746c 653e 0a3c dtypes.< │ │ │ +0001b720: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ +0001b730: 2073 7472 6f6b 653d 2223 6266 6266 6266 stroke="#bfbfbf │ │ │ +0001b740: 2220 643d 224d 3135 3433 2e30 332c 2d33 " d="M1543.03,-3 │ │ │ +0001b750: 3535 2e36 3343 3135 3738 2e36 362c 2d33 55.63C1578.66,-3 │ │ │ +0001b760: 3831 2e33 3720 3136 3537 2e34 312c 2d34 81.37 1657.41,-4 │ │ │ +0001b770: 3439 2e32 3620 3137 3038 2c2d 3531 382e 49.26 1708,-518. │ │ │ +0001b780: 3936 2031 3835 392e 352c 2d37 3237 2e36 96 1859.5,-727.6 │ │ │ +0001b790: 3820 3138 3833 2e37 312c 2d38 3336 2e31 8 1883.71,-836.1 │ │ │ +0001b7a0: 3220 3138 3638 2c2d 3836 302e 3138 2031 2 1868,-860.18 1 │ │ │ +0001b7b0: 3830 382e 3139 2c2d 3935 312e 3831 2031 808.19,-951.81 1 │ │ │ +0001b7c0: 3435 382e 3936 2c2d 3130 3130 2e36 3520 458.96,-1010.65 │ │ │ +0001b7d0: 3133 3332 2e35 342c 2d31 3032 382e 3536 1332.54,-1028.56 │ │ │ +0001b7e0: 222f 3e0a 3c70 6f6c 7967 6f6e 2066 696c "/>... │ │ │ +0001b860: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..module │ │ │ +0001b8d0: 5f73 7263 5f67 726f 6d61 6373 5f64 6f6d _src_gromacs_dom │ │ │ +0001b8e0: 6465 6326 2334 353b 2667 743b 6d6f 6475 dec->modu │ │ │ +0001b8f0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f66 le_src_gromacs_f │ │ │ +0001b900: 696c 6569 6f3c 2f74 6974 6c65 3e0a 3c70 ileio.

│ │ │ +0001ba20: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 .. │ │ │ +0001ba90: 3c2f 673e 0a3c 212d 2d20 6d6f 6475 6c65 ...mo │ │ │ +0001bb00: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +0001bb10: 5f64 6f6d 6465 6326 2334 353b 2667 743b _domdec-> │ │ │ +0001bb20: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +0001bb30: 6373 5f6d 6472 756e 3c2f 7469 746c 653e cs_mdrun │ │ │ +0001bb40: 0a3c 7061 7468 2066 696c 6c3d 226e 6f6e ...< │ │ │ +0001bc90: 2f67 3e0a 3c21 2d2d 206d 6f64 756c 655f /g>..< │ │ │ +0001bce0: 6720 6964 3d22 6564 6765 3139 3622 2063 g id="edge196" c │ │ │ +0001bcf0: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.module_src_g │ │ │ +0001bd10: 726f 6d61 6373 5f64 6f6d 6465 6326 2334 romacs_domdec │ │ │ +0001bd20: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ +0001bd30: 5f67 726f 6d61 6373 5f6d 6472 756e 7574 _gromacs_mdrunut │ │ │ +0001bd40: 696c 6974 793c 2f74 6974 6c65 3e0a 3c70 ility.

... │ │ │ +0001beb0: 0a3c 6720 6964 3d22 6564 6765 3139 3222 ..< │ │ │ +0001bed0: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ +0001bee0: 5f67 726f 6d61 6373 5f64 6f6d 6465 6326 _gromacs_domdec& │ │ │ +0001bef0: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ +0001bf00: 7263 5f67 726f 6d61 6373 5f6e 626e 786d rc_gromacs_nbnxm │ │ │ +0001bf10: 3c2f 7469 746c 653e 0a3c 7061 7468 2066 ..

..< │ │ │ +0001bff0: 212d 2d20 6d6f 6475 6c65 5f73 7263 5f67 !-- module_src_g │ │ │ +0001c000: 726f 6d61 6373 5f6d 6472 756e 7574 696c romacs_mdrunutil │ │ │ +0001c010: 6974 7926 2334 353b 2667 743b 6d6f 6475 ity->modu │ │ │ +0001c020: 6c65 5f73 7263 5f67 726f 6d61 6373 5f67 le_src_gromacs_g │ │ │ +0001c030: 6d78 6c69 6220 2d2d 3e0a 3c67 2069 643d mxlib -->..m │ │ │ +0001c060: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +0001c070: 735f 6d64 7275 6e75 7469 6c69 7479 2623 s_mdrunutility&# │ │ │ +0001c080: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ +0001c090: 635f 6772 6f6d 6163 735f 676d 786c 6962 c_gromacs_gmxlib │ │ │ +0001c0a0: 3c2f 7469 746c 653e 0a3c 7061 7468 2066 ...... │ │ │ +0001c260: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +0001c270: 6373 5f6d 6472 756e 7574 696c 6974 7926 cs_mdrunutility& │ │ │ +0001c280: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ +0001c290: 7263 5f67 726f 6d61 6373 5f68 6172 6477 rc_gromacs_hardw │ │ │ +0001c2a0: 6172 653c 2f74 6974 6c65 3e0a 3c70 6174 are.. │ │ │ +0001c360: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2223 ....module │ │ │ +0001c450: 5f73 7263 5f67 726f 6d61 6373 5f6d 6472 _src_gromacs_mdr │ │ │ +0001c460: 756e 7574 696c 6974 7926 2334 353b 2667 unutility-&g │ │ │ +0001c470: 743b 6d6f 6475 6c65 5f73 7263 5f67 726f t;module_src_gro │ │ │ +0001c480: 6d61 6373 5f6d 6474 7970 6573 3c2f 7469 macs_mdtypes</ti │ │ │ +0001c490: 746c 653e 0a3c 7061 7468 2066 696c 6c3d tle>.<path fill= │ │ │ +0001c4a0: 226e 6f6e 6522 2073 7472 6f6b 653d 2223 "none" stroke="# │ │ │ +0001c4b0: 6266 6266 6266 2220 643d 224d 3131 3036 bfbfbf" d="M1106 │ │ │ +0001c4c0: 2e30 362c 2d36 3731 2e31 3243 3131 3431 .06,-671.12C1141 │ │ │ +0001c4d0: 2e33 332c 2d37 3033 2e38 2031 3233 372e .33,-703.8 1237. │ │ │ +0001c4e0: 3136 2c2d 3739 342e 3538 2031 3235 362c 16,-794.58 1256, │ │ │ +0001c4f0: 2d38 3333 2e33 3120 3132 3731 2e31 362c -833.31 1271.16, │ │ │ +0001c500: 2d38 3634 2e34 3920 3132 3831 2e33 2c2d -864.49 1281.3,- │ │ │ +0001c510: 3936 362e 3037 2031 3238 352e 322c 2d31 966.07 1285.2,-1 │ │ │ +0001c520: 3031 312e 3735 222f 3e0a 3c70 6f6c 7967 011.75"/>.<polyg │ │ │ +0001c530: 6f6e 2066 696c 6c3d 2223 6266 6266 6266 on fill="#bfbfbf │ │ │ +0001c540: 2220 7374 726f 6b65 3d22 2362 6662 6662 " stroke="#bfbfb │ │ │ +0001c550: 6622 2070 6f69 6e74 733d 2231 3238 312e f" points="1281. │ │ │ +0001c560: 3732 2c2d 3130 3132 2e31 3620 3132 3836 72,-1012.16 1286 │ │ │ +0001c570: 2e30 342c 2d31 3032 312e 3834 2031 3238 .04,-1021.84 128 │ │ │ +0001c580: 382e 372c 2d31 3031 312e 3538 2031 3238 8.7,-1011.58 128 │ │ │ +0001c590: 312e 3732 2c2d 3130 3132 2e31 3622 2f3e 1.72,-1012.16"/> │ │ │ +0001c5a0: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c .</g>.<!-- modul │ │ │ +0001c5b0: 655f 7372 635f 6772 6f6d 6163 735f 6d64 e_src_gromacs_md │ │ │ +0001c5c0: 7275 6e75 7469 6c69 7479 2623 3435 3b26 runutility-& │ │ │ +0001c5d0: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ +0001c5e0: 6f6d 6163 735f 6669 6c65 696f 202d 2d3e omacs_fileio --> │ │ │ +0001c5f0: 0a3c 6720 6964 3d22 6564 6765 3139 3922 .<g id="edge199" │ │ │ +0001c600: 2063 6c61 7373 3d22 6564 6765 223e 0a3c class="edge">.< │ │ │ +0001c610: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ +0001c620: 5f67 726f 6d61 6373 5f6d 6472 756e 7574 _gromacs_mdrunut │ │ │ +0001c630: 696c 6974 7926 2334 353b 2667 743b 6d6f ility->mo │ │ │ +0001c640: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +0001c650: 5f66 696c 6569 6f3c 2f74 6974 6c65 3e0a _fileio. │ │ │ +0001c660: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 .....module_ │ │ │ +0001c7b0: 7372 635f 6772 6f6d 6163 735f 6d64 7275 src_gromacs_mdru │ │ │ +0001c7c0: 6e75 7469 6c69 7479 2623 3435 3b26 6774 nutility-> │ │ │ +0001c7d0: 3b6d 6f64 756c 655f 7372 635f 6772 6f6d ;module_src_grom │ │ │ +0001c7e0: 6163 735f 6d64 7275 6e3c 2f74 6974 6c65 acs_mdrun.. │ │ │ +0001c8c0: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c ....modul │ │ │ +0001c940: 655f 7372 635f 6772 6f6d 6163 735f 6d64 e_src_gromacs_md │ │ │ +0001c950: 7275 6e75 7469 6c69 7479 2623 3435 3b26 runutility-& │ │ │ +0001c960: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ +0001c970: 6f6d 6163 735f 636f 6d6d 616e 646c 696e omacs_commandlin │ │ │ +0001c980: 653c 2f74 6974 6c65 3e0a 3c70 6174 6820 e.... │ │ │ +0001caf0: 0a3c 6720 6964 3d22 6564 6765 3231 3522 ..< │ │ │ +0001cb10: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ +0001cb20: 5f67 726f 6d61 6373 5f67 6d78 7072 6570 _gromacs_gmxprep │ │ │ +0001cb30: 726f 6365 7373 2623 3435 3b26 6774 3b6d rocess->m │ │ │ +0001cb40: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +0001cb50: 735f 696d 643c 2f74 6974 6c65 3e0a 3c70 s_imd.

│ │ │ +0001cbe0: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 .....mod │ │ │ -0001d030: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -0001d040: 6d64 6c69 6226 2334 353b 2667 743b 6d6f mdlib->mo │ │ │ -0001d050: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -0001d060: 5f74 6162 6c65 733c 2f74 6974 6c65 3e0a _tables. │ │ │ -0001d070: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 .....modul │ │ │ -0001d200: 655f 7372 635f 6772 6f6d 6163 735f 6d64 e_src_gromacs_md │ │ │ -0001d210: 6c69 6226 2334 353b 2667 743b 6d6f 6475 lib->modu │ │ │ -0001d220: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6e le_src_gromacs_n │ │ │ -0001d230: 626e 786d 3c2f 7469 746c 653e 0a3c 7061 bnxm......module_src_gro │ │ │ -0001d400: 6d61 6373 5f6d 646c 6962 2623 3435 3b26 macs_mdlib-& │ │ │ -0001d410: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ -0001d420: 6f6d 6163 735f 6669 6c65 696f 3c2f 7469 omacs_fileio..... │ │ │ -0001d5e0: 3c67 2069 643d 2265 6467 6531 3832 2220 .module_src_ │ │ │ -0001d610: 6772 6f6d 6163 735f 6d64 6c69 6226 2334 gromacs_mdlib │ │ │ -0001d620: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ -0001d630: 5f67 726f 6d61 6373 5f63 6f6d 7061 743c _gromacs_compat< │ │ │ -0001d640: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>......mod │ │ │ -0001d7a0: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -0001d7b0: 6d64 6c69 6226 2334 353b 2667 743b 6d6f mdlib->mo │ │ │ -0001d7c0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -0001d7d0: 5f61 7070 6c69 6564 5f66 6f72 6365 735f _applied_forces_ │ │ │ -0001d7e0: 6177 683c 2f74 6974 6c65 3e0a 3c70 6174 awh......mod │ │ │ -0001d9d0: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -0001d9e0: 6d64 6c69 6226 2334 353b 2667 743b 6d6f mdlib->mo │ │ │ -0001d9f0: 6475 6c65 5f73 7263 5f74 6573 7475 7469 dule_src_testuti │ │ │ -0001da00: 6c73 3c2f 7469 746c 653e 0a3c 7061 7468 ls...< │ │ │ -0001db00: 2f67 3e0a 3c21 2d2d 206d 6f64 756c 655f /g>..< │ │ │ -0001df20: 6720 6964 3d22 6564 6765 3230 3422 2063 g id="edge204" c │ │ │ -0001df30: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.module_src_g │ │ │ -0001df50: 726f 6d61 6373 5f6d 6f64 756c 6172 7369 romacs_modularsi │ │ │ -0001df60: 6d75 6c61 746f 7226 2334 353b 2667 743b mulator-> │ │ │ -0001df70: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -0001df80: 6373 5f74 6173 6b61 7373 6967 6e6d 656e cs_taskassignmen │ │ │ -0001df90: 743c 2f74 6974 6c65 3e0a 3c70 6174 6820 t.. │ │ │ -0001e000: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2272 .. │ │ │ -0001e070: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..module │ │ │ -0001e0f0: 5f73 7263 5f67 726f 6d61 6373 5f6d 6f64 _src_gromacs_mod │ │ │ -0001e100: 756c 6172 7369 6d75 6c61 746f 7226 2334 ularsimulator │ │ │ -0001e110: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ -0001e120: 5f67 726f 6d61 6373 5f6d 6472 756e 7574 _gromacs_mdrunut │ │ │ -0001e130: 696c 6974 793c 2f74 6974 6c65 3e0a 3c70 ility.

.....module_ │ │ │ -0001e2e0: 7372 635f 6772 6f6d 6163 735f 6d6f 6475 src_gromacs_modu │ │ │ -0001e2f0: 6c61 7273 696d 756c 6174 6f72 2623 3435 larsimulator- │ │ │ -0001e300: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -0001e310: 6772 6f6d 6163 735f 6770 755f 7574 696c gromacs_gpu_util │ │ │ -0001e320: 733c 2f74 6974 6c65 3e0a 3c70 6174 6820 s. │ │ │ -0001e3d0: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 .....module_ │ │ │ -0001e4c0: 7372 635f 6772 6f6d 6163 735f 6d6f 6475 src_gromacs_modu │ │ │ -0001e4d0: 6c61 7273 696d 756c 6174 6f72 2623 3435 larsimulator- │ │ │ -0001e4e0: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -0001e4f0: 6772 6f6d 6163 735f 6c69 7374 6564 5f66 gromacs_listed_f │ │ │ -0001e500: 6f72 6365 733c 2f74 6974 6c65 3e0a 3c70 orces.

..... │ │ │ -0001e6a0: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -0001e6b0: 6373 5f6d 6f64 756c 6172 7369 6d75 6c61 cs_modularsimula │ │ │ -0001e6c0: 746f 7226 2334 353b 2667 743b 6d6f 6475 tor->modu │ │ │ -0001e6d0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f72 le_src_gromacs_r │ │ │ -0001e6e0: 616e 646f 6d3c 2f74 6974 6c65 3e0a 3c70 andom.

.....mo │ │ │ -0001e8b0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -0001e8c0: 5f6d 6f64 756c 6172 7369 6d75 6c61 746f _modularsimulato │ │ │ -0001e8d0: 7226 2334 353b 2667 743b 6d6f 6475 6c65 r->module │ │ │ -0001e8e0: 5f73 7263 5f67 726f 6d61 6373 5f65 7761 _src_gromacs_ewa │ │ │ -0001e8f0: 6c64 3c2f 7469 746c 653e 0a3c 7061 7468 ld..

....m │ │ │ -0001ea90: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -0001eaa0: 735f 6d6f 6475 6c61 7273 696d 756c 6174 s_modularsimulat │ │ │ -0001eab0: 6f72 2623 3435 3b26 6774 3b6d 6f64 756c or->modul │ │ │ -0001eac0: 655f 7372 635f 6772 6f6d 6163 735f 676d e_src_gromacs_gm │ │ │ -0001ead0: 786c 6962 3c2f 7469 746c 653e 0a3c 7061 xlib.. │ │ │ -0001ec40: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c ....module_ │ │ │ -0001ecc0: 7372 635f 6772 6f6d 6163 735f 6d6f 6475 src_gromacs_modu │ │ │ -0001ecd0: 6c61 7273 696d 756c 6174 6f72 2623 3435 larsimulator- │ │ │ -0001ece0: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -0001ecf0: 6772 6f6d 6163 735f 6d64 7275 6e3c 2f74 gromacs_mdrun</t │ │ │ -0001ed00: 6974 6c65 3e0a 3c70 6174 6820 6669 6c6c itle>.<path fill │ │ │ -0001ed10: 3d22 6e6f 6e65 2220 7374 726f 6b65 3d22 ="none" stroke=" │ │ │ -0001ed20: 7265 6422 2064 3d22 4d31 3137 362e 3636 red" d="M1176.66 │ │ │ -0001ed30: 2c2d 3534 342e 3434 4331 3230 302e 3039 ,-544.44C1200.09 │ │ │ -0001ed40: 2c2d 3535 342e 3332 2031 3233 322e 3237 ,-554.32 1232.27 │ │ │ -0001ed50: 2c2d 3536 382e 3836 2031 3235 342e 3737 ,-568.86 1254.77 │ │ │ -0001ed60: 2c2d 3537 392e 3639 222f 3e0a 3c70 6f6c ,-579.69"/>.<pol │ │ │ -0001ed70: 7967 6f6e 2066 696c 6c3d 2272 6564 2220 ygon fill="red" │ │ │ -0001ed80: 7374 726f 6b65 3d22 7265 6422 2070 6f69 stroke="red" poi │ │ │ -0001ed90: 6e74 733d 2231 3235 332e 3234 2c2d 3538 nts="1253.24,-58 │ │ │ -0001eda0: 322e 3834 2031 3236 332e 3736 2c2d 3538 2.84 1263.76,-58 │ │ │ -0001edb0: 342e 3038 2031 3235 362e 3331 2c2d 3537 4.08 1256.31,-57 │ │ │ -0001edc0: 362e 3535 2031 3235 332e 3234 2c2d 3538 6.55 1253.24,-58 │ │ │ -0001edd0: 322e 3834 222f 3e0a 3c2f 673e 0a3c 212d 2.84"/>.</g>.<!- │ │ │ -0001ede0: 2d20 6d6f 6475 6c65 5f73 7263 5f67 726f - module_src_gro │ │ │ -0001edf0: 6d61 6373 5f6d 6f64 756c 6172 7369 6d75 macs_modularsimu │ │ │ -0001ee00: 6c61 746f 7226 2334 353b 2667 743b 6d6f lator->mo │ │ │ -0001ee10: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -0001ee20: 5f6d 646c 6962 202d 2d3e 0a3c 6720 6964 _mdlib -->.<g id │ │ │ -0001ee30: 3d22 6564 6765 3139 3322 2063 6c61 7373 ="edge193" class │ │ │ -0001ee40: 3d22 6564 6765 223e 0a3c 7469 746c 653e ="edge">.<title> │ │ │ -0001ee50: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -0001ee60: 6373 5f6d 6f64 756c 6172 7369 6d75 6c61 cs_modularsimula │ │ │ -0001ee70: 746f 7226 2334 353b 2667 743b 6d6f 6475 tor->modu │ │ │ -0001ee80: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ -0001ee90: 646c 6962 3c2f 7469 746c 653e 0a3c 7061 dlib..< │ │ │ -0001ef30: 706f 6c79 676f 6e20 6669 6c6c 3d22 7265 polygon fill="re │ │ │ -0001ef40: 6422 2073 7472 6f6b 653d 2272 6564 2220 d" stroke="red" │ │ │ -0001ef50: 706f 696e 7473 3d22 3132 3837 2e34 322c points="1287.42, │ │ │ -0001ef60: 2d34 3330 2e31 3120 3132 3833 2e39 322c -430.11 1283.92, │ │ │ -0001ef70: 2d34 3230 2e31 3120 3132 3830 2e34 322c -420.11 1280.42, │ │ │ -0001ef80: 2d34 3330 2e31 3120 3132 3837 2e34 322c -430.11 1287.42, │ │ │ -0001ef90: 2d34 3330 2e31 3122 2f3e 0a3c 2f67 3e0a -430.11"/>.. │ │ │ -0001efa0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..module_ │ │ │ -0001f020: 7372 635f 6772 6f6d 6163 735f 6d6f 6475 src_gromacs_modu │ │ │ -0001f030: 6c61 7273 696d 756c 6174 6f72 2623 3435 larsimulator- │ │ │ -0001f040: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -0001f050: 6772 6f6d 6163 735f 636f 6d6d 616e 646c gromacs_commandl │ │ │ -0001f060: 696e 653c 2f74 6974 6c65 3e0a 3c70 6174 ine...... │ │ │ -0001f220: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -0001f230: 6373 5f6d 6f64 756c 6172 7369 6d75 6c61 cs_modularsimula │ │ │ -0001f240: 746f 7226 2334 353b 2667 743b 6d6f 6475 tor->modu │ │ │ -0001f250: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6e le_src_gromacs_n │ │ │ -0001f260: 626e 786d 3c2f 7469 746c 653e 0a3c 7061 bnxm......m │ │ │ -0001f400: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -0001f410: 735f 6d6f 6475 6c61 7273 696d 756c 6174 s_modularsimulat │ │ │ -0001f420: 6f72 2623 3435 3b26 6774 3b6d 6f64 756c or->modul │ │ │ -0001f430: 655f 7372 635f 6772 6f6d 6163 735f 7075 e_src_gromacs_pu │ │ │ -0001f440: 6c6c 696e 673c 2f74 6974 6c65 3e0a 3c70 lling.

... │ │ │ -0001f5c0: 0a3c 6720 6964 3d22 6564 6765 3230 3822 ..< │ │ │ -0001f5e0: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ -0001f5f0: 5f67 726f 6d61 6373 5f6d 6f64 756c 6172 _gromacs_modular │ │ │ -0001f600: 7369 6d75 6c61 746f 7226 2334 353b 2667 simulator-&g │ │ │ -0001f610: 743b 6d6f 6475 6c65 5f73 7263 5f67 726f t;module_src_gro │ │ │ -0001f620: 6d61 6373 5f66 696c 6569 6f3c 2f74 6974 macs_fileio.... │ │ │ -0001f770: 3c21 2d2d 206d 6f64 756c 655f 7372 635f .< │ │ │ -0001f7c0: 6720 6964 3d22 6564 6765 3230 3322 2063 g id="edge203" c │ │ │ -0001f7d0: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.module_src_g │ │ │ -0001f7f0: 726f 6d61 6373 5f6d 6f64 756c 6172 7369 romacs_modularsi │ │ │ -0001f800: 6d75 6c61 746f 7226 2334 353b 2667 743b mulator-> │ │ │ -0001f810: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -0001f820: 6373 5f63 6f6d 7061 743c 2f74 6974 6c65 cs_compat... │ │ │ -0001f9b0: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 . │ │ │ -0001fa00: 0a3c 6720 6964 3d22 6564 6765 3231 3022 ..< │ │ │ -0001fa20: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ -0001fa30: 5f67 726f 6d61 6373 5f65 7373 656e 7469 _gromacs_essenti │ │ │ -0001fa40: 616c 6479 6e61 6d69 6373 2623 3435 3b26 aldynamics-& │ │ │ -0001fa50: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ -0001fa60: 6f6d 6163 735f 646f 6d64 6563 3c2f 7469 omacs_domdec......mod │ │ │ -0001fd10: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -0001fd20: 6573 7365 6e74 6961 6c64 796e 616d 6963 essentialdynamic │ │ │ -0001fd30: 7326 2334 353b 2667 743b 6d6f 6475 6c65 s->module │ │ │ -0001fd40: 5f73 7263 5f67 726f 6d61 6373 5f6d 6474 _src_gromacs_mdt │ │ │ -0001fd50: 7970 6573 3c2f 7469 746c 653e 0a3c 7061 ypes......mod │ │ │ -000201e0: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -000201f0: 6573 7365 6e74 6961 6c64 796e 616d 6963 essentialdynamic │ │ │ -00020200: 7326 2334 353b 2667 743b 6d6f 6475 6c65 s->module │ │ │ -00020210: 5f73 7263 5f67 726f 6d61 6373 5f67 6d78 _src_gromacs_gmx │ │ │ -00020220: 6c69 623c 2f74 6974 6c65 3e0a 3c70 6174 lib......m │ │ │ -000203b0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -000203c0: 735f 6573 7365 6e74 6961 6c64 796e 616d s_essentialdynam │ │ │ -000203d0: 6963 7326 2334 353b 2667 743b 6d6f 6475 ics->modu │ │ │ -000203e0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ -000203f0: 646c 6962 3c2f 7469 746c 653e 0a3c 7061 dlib.... │ │ │ -000204e0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..module │ │ │ -00020560: 5f73 7263 5f67 726f 6d61 6373 5f65 7373 _src_gromacs_ess │ │ │ -00020570: 656e 7469 616c 6479 6e61 6d69 6373 2623 entialdynamics&# │ │ │ -00020580: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ -00020590: 635f 6772 6f6d 6163 735f 636f 6d6d 616e c_gromacs_comman │ │ │ -000205a0: 646c 696e 653c 2f74 6974 6c65 3e0a 3c70 dline.

...< │ │ │ -000206d0: 212d 2d20 6d6f 6475 6c65 5f73 7263 5f67 !-- module_src_g │ │ │ -000206e0: 726f 6d61 6373 5f65 7373 656e 7469 616c romacs_essential │ │ │ -000206f0: 6479 6e61 6d69 6373 2623 3435 3b26 6774 dynamics-> │ │ │ -00020700: 3b6d 6f64 756c 655f 7372 635f 6772 6f6d ;module_src_grom │ │ │ -00020710: 6163 735f 6669 6c65 696f 202d 2d3e 0a3c acs_fileio -->.< │ │ │ -00020720: 6720 6964 3d22 6564 6765 3231 3122 2063 g id="edge211" c │ │ │ -00020730: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.module_src_g │ │ │ -00020750: 726f 6d61 6373 5f65 7373 656e 7469 616c romacs_essential │ │ │ -00020760: 6479 6e61 6d69 6373 2623 3435 3b26 6774 dynamics-> │ │ │ -00020770: 3b6d 6f64 756c 655f 7372 635f 6772 6f6d ;module_src_grom │ │ │ -00020780: 6163 735f 6669 6c65 696f 3c2f 7469 746c acs_fileio......module_src_gro │ │ │ -00020970: 6d61 6373 5f63 6f6d 6d61 6e64 6c69 6e65 macs_commandline │ │ │ -00020980: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ -00020990: 7372 635f 6772 6f6d 6163 735f 6f70 7469 src_gromacs_opti │ │ │ -000209a0: 6f6e 733c 2f74 6974 6c65 3e0a 3c70 6174 ons...... │ │ │ -00020b10: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -00020b20: 6373 5f63 6f6d 6d61 6e64 6c69 6e65 2623 cs_commandline&# │ │ │ -00020b30: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ -00020b40: 635f 6772 6f6d 6163 735f 6f6e 6c69 6e65 c_gromacs_online │ │ │ -00020b50: 6865 6c70 3c2f 7469 746c 653e 0a3c 7061 help. │ │ │ -00020bc0: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 .....module_src_grom │ │ │ -00020cb0: 6163 735f 636f 6d6d 616e 646c 696e 6526 acs_commandline& │ │ │ -00020cc0: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ -00020cd0: 7263 5f67 726f 6d61 6373 5f66 696c 6569 rc_gromacs_filei │ │ │ -00020ce0: 6f3c 2f74 6974 6c65 3e0a 3c70 6174 6820 o.... │ │ │ -00020ec0: 0a3c 6720 6964 3d22 6564 6765 3232 3122 ..< │ │ │ -00020ee0: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ -00020ef0: 5f67 726f 6d61 6373 5f74 6162 6c65 7326 _gromacs_tables& │ │ │ -00020f00: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ -00020f10: 7263 5f67 726f 6d61 6373 5f6d 6474 7970 rc_gromacs_mdtyp │ │ │ -00020f20: 6573 3c2f 7469 746c 653e 0a3c 7061 7468 es... │ │ │ -000210e0: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 ...modul │ │ │ -00021150: 655f 7372 635f 6772 6f6d 6163 735f 7461 e_src_gromacs_ta │ │ │ -00021160: 626c 6573 2623 3435 3b26 6774 3b6d 6f64 bles->mod │ │ │ -00021170: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -00021180: 6d64 7370 616e 3c2f 7469 746c 653e 0a3c mdspan.< │ │ │ -00021190: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ -000211a0: 2073 7472 6f6b 653d 2223 3238 3266 6363 stroke="#282fcc │ │ │ -000211b0: 2220 7374 726f 6b65 2d64 6173 6861 7272 " stroke-dasharr │ │ │ -000211c0: 6179 3d22 352c 3222 2064 3d22 4d32 3434 ay="5,2" d="M244 │ │ │ -000211d0: 362e 3439 2c2d 3134 332e 3031 4332 3435 6.49,-143.01C245 │ │ │ -000211e0: 382e 3131 2c2d 3133 342e 3036 2032 3437 8.11,-134.06 247 │ │ │ -000211f0: 342e 3633 2c2d 3132 312e 3332 2032 3438 4.63,-121.32 248 │ │ │ -00021200: 382e 3035 2c2d 3131 302e 3939 222f 3e0a 8.05,-110.99"/>. │ │ │ -00021210: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2223 ....module_src_gro │ │ │ -00021300: 6d61 6373 5f74 6162 6c65 7326 2334 353b macs_tables- │ │ │ -00021310: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ -00021320: 726f 6d61 6373 5f66 696c 6569 6f3c 2f74 romacs_fileio.... │ │ │ -000214e0: 0a3c 6720 6964 3d22 6564 6765 3232 3622 ..< │ │ │ -00021500: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ -00021510: 5f67 726f 6d61 6373 5f6e 626e 786d 2623 _gromacs_nbnxm&# │ │ │ -00021520: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ -00021530: 635f 6772 6f6d 6163 735f 646f 6d64 6563 c_gromacs_domdec │ │ │ -00021540: 3c2f 7469 746c 653e 0a3c 7061 7468 2066 .. │ │ │ -00021660: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2223 . │ │ │ -000216d0: 3c2f 673e 0a3c 212d 2d20 6d6f 6475 6c65 ...m │ │ │ -00021740: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -00021750: 735f 6e62 6e78 6d26 2334 353b 2667 743b s_nbnxm-> │ │ │ -00021760: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -00021770: 6373 5f6d 6474 7970 6573 3c2f 7469 746c cs_mdtypes</titl │ │ │ -00021780: 653e 0a3c 7061 7468 2066 696c 6c3d 226e e>.<path fill="n │ │ │ -00021790: 6f6e 6522 2073 7472 6f6b 653d 2272 6564 one" stroke="red │ │ │ -000217a0: 2220 643d 224d 3639 342e 3436 2c2d 3239 " d="M694.46,-29 │ │ │ -000217b0: 322e 3735 4336 3433 2e35 332c 2d33 3237 2.75C643.53,-327 │ │ │ -000217c0: 2e33 3320 3438 392e 3631 2c2d 3434 312e .33 489.61,-441. │ │ │ -000217d0: 3033 2034 3432 2c2d 3538 312e 3833 2034 03 442,-581.83 4 │ │ │ -000217e0: 3230 2e31 2c2d 3634 362e 3539 2035 3135 20.1,-646.59 515 │ │ │ -000217f0: 2e36 362c 2d38 3232 2e39 3520 3537 332c .66,-822.95 573, │ │ │ -00021800: 2d38 3630 2e31 3820 3632 372e 3932 2c2d -860.18 627.92,- │ │ │ -00021810: 3839 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-->.< │ │ │ -000218f0: 6720 6964 3d22 6564 6765 3232 3222 2063 g id="edge222" c │ │ │ -00021900: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.<ti │ │ │ -00021910: 746c 653e 6d6f 6475 6c65 5f73 7263 5f67 tle>module_src_g │ │ │ -00021920: 726f 6d61 6373 5f6e 626e 786d 2623 3435 romacs_nbnxm- │ │ │ -00021930: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ -00021940: 6772 6f6d 6163 735f 6770 755f 7574 696c gromacs_gpu_util │ │ │ -00021950: 733c 2f74 6974 6c65 3e0a 3c70 6174 6820 s.. │ │ │ -00021a20: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c .. │ │ │ -00021a70: 0a3c 6720 6964 3d22 6564 6765 3232 3822 ..< │ │ │ -00021a90: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ -00021aa0: 5f67 726f 6d61 6373 5f6e 626e 786d 2623 _gromacs_nbnxm&# │ │ │ -00021ab0: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ -00021ac0: 635f 6772 6f6d 6163 735f 6c69 7374 6564 c_gromacs_listed │ │ │ -00021ad0: 5f66 6f72 6365 733c 2f74 6974 6c65 3e0a _forces. │ │ │ 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9,-175.33"/>.</g │ │ │ -000220a0: 3e0a 3c21 2d2d 206d 6f64 756c 655f 7372 >.<!-- module_sr │ │ │ -000220b0: 635f 6772 6f6d 6163 735f 6e62 6e78 6d26 c_gromacs_nbnxm& │ │ │ -000220c0: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ -000220d0: 7263 5f67 726f 6d61 6373 5f6d 646c 6962 rc_gromacs_mdlib │ │ │ -000220e0: 202d 2d3e 0a3c 6720 6964 3d22 6564 6765 -->.<g id="edge │ │ │ -000220f0: 3232 3422 2063 6c61 7373 3d22 6564 6765 224" class="edge │ │ │ -00022100: 223e 0a3c 7469 746c 653e 6d6f 6475 6c65 ">.<title>module │ │ │ -00022110: 5f73 7263 5f67 726f 6d61 6373 5f6e 626e _src_gromacs_nbn │ │ │ -00022120: 786d 2623 3435 3b26 6774 3b6d 6f64 756c xm->modul │ │ │ -00022130: 655f 7372 635f 6772 6f6d 6163 735f 6d64 e_src_gromacs_md │ │ │ -00022140: 6c69 623c 2f74 6974 6c65 3e0a 3c70 6174 lib..< │ │ │ -00022230: 706f 6c79 676f 6e20 6669 6c6c 3d22 2362 polygon fill="#b │ │ │ -00022240: 6662 6662 6622 2073 7472 6f6b 653d 2223 fbfbf" stroke="# │ │ │ -00022250: 6266 6266 6266 2220 706f 696e 7473 3d22 bfbfbf" points=" │ │ │ -00022260: 3132 3434 2e38 382c 2d34 3036 2e37 3920 1244.88,-406.79 │ │ │ -00022270: 3132 3535 2e31 2c2d 3430 342e 3031 2031 1255.1,-404.01 1 │ │ │ -00022280: 3234 352e 3337 2c2d 3339 392e 3831 2031 245.37,-399.81 1 │ │ │ -00022290: 3234 342e 3838 2c2d 3430 362e 3739 222f 244.88,-406.79"/ │ │ │ -000222a0: 3e0a 3c2f 673e 0a3c 212d 2d20 6d6f 6475 >....m │ │ │ -00022310: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -00022320: 735f 6d61 7468 2623 3435 3b26 6774 3b6d s_math->m │ │ │ -00022330: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -00022340: 735f 6d64 7370 616e 3c2f 7469 746c 653e s_mdspan │ │ │ -00022350: 0a3c 7061 7468 2066 696c 6c3d 226e 6f6e ......modu │ │ │ -000224a0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f63 le_src_gromacs_c │ │ │ -000224b0: 6f72 7265 6c61 7469 6f6e 6675 6e63 7469 orrelationfuncti │ │ │ -000224c0: 6f6e 7326 2334 353b 2667 743b 6d6f 6475 ons->modu │ │ │ -000224d0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f66 le_src_gromacs_f │ │ │ -000224e0: 6674 3c2f 7469 746c 653e 0a3c 7061 7468 ft......modul │ │ │ -00022670: 655f 7372 635f 6772 6f6d 6163 735f 636f e_src_gromacs_co │ │ │ -00022680: 7272 656c 6174 696f 6e66 756e 6374 696f rrelationfunctio │ │ │ -00022690: 6e73 2623 3435 3b26 6774 3b6d 6f64 756c ns->modul │ │ │ -000226a0: 655f 7372 635f 6772 6f6d 6163 735f 636f e_src_gromacs_co │ │ │ -000226b0: 6d6d 616e 646c 696e 653c 2f74 6974 6c65 mmandline.... │ │ │ -00022890: 3c21 2d2d 206d 6f64 756c 655f 7372 635f . │ │ │ -00022a80: 3c67 2069 643d 2265 6467 6532 3334 2220 .module_src_ │ │ │ -00022ab0: 6772 6f6d 6163 735f 7075 6c6c 696e 6726 gromacs_pulling& │ │ │ -00022ac0: 2334 353b 2667 743b 6d6f 6475 6c65 5f73 #45;>module_s │ │ │ -00022ad0: 7263 5f67 726f 6d61 6373 5f64 6f6d 6465 rc_gromacs_domde │ │ │ -00022ae0: 633c 2f74 6974 6c65 3e0a 3c70 6174 6820 c..

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│ │ -00023000: 2f3e 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 />....module_src_gr │ │ │ -00023080: 6f6d 6163 735f 7075 6c6c 696e 6726 2334 omacs_pulling │ │ │ -00023090: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ -000230a0: 5f67 726f 6d61 6373 5f67 6d78 6c69 623c _gromacs_gmxlib< │ │ │ -000230b0: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>... │ │ │ -000231e0: 3c2f 673e 0a3c 212d 2d20 6d6f 6475 6c65 .. │ │ │ +0001ce70: 3c67 2069 643d 2265 6467 6532 3037 2220 .module_src_ │ │ │ +0001cea0: 6772 6f6d 6163 735f 676d 7870 7265 7072 gromacs_gmxprepr │ │ │ +0001ceb0: 6f63 6573 7326 2334 353b 2667 743b 6d6f ocess->mo │ │ │ +0001cec0: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ +0001ced0: 5f67 6d78 6c69 623c 2f74 6974 6c65 3e0a _gmxlib. │ │ │ +0001cee0: 3c70 6174 6820 6669 6c6c 3d22 6e6f 6e65 . │ │ │ +0001cff0: 3c70 6f6c 7967 6f6e 2066 696c 6c3d 2223 . │ │ │ +0001d060: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 ...module_ │ │ │ +0001d0e0: 7372 635f 6772 6f6d 6163 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5f67 726f 6d61 6373 5f6f 7074 696f rc_gromacs_optio │ │ │ +0001d560: 6e73 202d 2d3e 0a3c 6720 6964 3d22 6564 ns -->.<g id="ed │ │ │ +0001d570: 6765 3231 3922 2063 6c61 7373 3d22 6564 ge219" class="ed │ │ │ +0001d580: 6765 223e 0a3c 7469 746c 653e 6d6f 6475 ge">.<title>modu │ │ │ +0001d590: 6c65 5f73 7263 5f67 726f 6d61 6373 5f67 le_src_gromacs_g │ │ │ +0001d5a0: 6d78 7072 6570 726f 6365 7373 2623 3435 mxpreprocess- │ │ │ +0001d5b0: 3b26 6774 3b6d 6f64 756c 655f 7372 635f ;>module_src_ │ │ │ +0001d5c0: 6772 6f6d 6163 735f 6f70 7469 6f6e 733c gromacs_options< │ │ │ +0001d5d0: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>.<path fi │ │ │ +0001d5e0: 6c6c 3d22 6e6f 6e65 2220 7374 726f 6b65 ll="none" stroke │ │ │ +0001d5f0: 3d22 2332 3832 6663 6322 2073 7472 6f6b ="#282fcc" strok │ │ │ +0001d600: 652d 6461 7368 6172 7261 793d 2235 2c32 e-dasharray="5,2 │ │ │ +0001d610: 2220 643d 224d 3134 3139 2e38 342c 2d31 " d="M1419.84,-1 │ │ │ +0001d620: 3135 332e 3232 4331 3436 342e 3334 2c2d 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6365 7373 2623 3435 3b26 preprocess-& │ │ │ +0001da70: 6774 3b6d 6f64 756c 655f 7372 635f 6772 gt;module_src_gr │ │ │ +0001da80: 6f6d 6163 735f 676d 7861 6e61 202d 2d3e omacs_gmxana --> │ │ │ +0001da90: 0a3c 6720 6964 3d22 6564 6765 3232 3022 .<g id="edge220" │ │ │ +0001daa0: 2063 6c61 7373 3d22 6564 6765 223e 0a3c class="edge">.< │ │ │ +0001dab0: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ +0001dac0: 5f67 726f 6d61 6373 5f67 6d78 7072 6570 _gromacs_gmxprep │ │ │ +0001dad0: 726f 6365 7373 2623 3435 3b26 6774 3b6d rocess->m │ │ │ +0001dae0: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ +0001daf0: 735f 676d 7861 6e61 3c2f 7469 746c 653e s_gmxana │ │ │ +0001db00: 0a3c 7061 7468 2066 696c 6c3d 226e 6f6e .. │ │ │ +0001dbe0: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c .... │ │ │ +0001de30: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +0001de40: 6373 5f67 6d78 7072 6570 726f 6365 7373 cs_gmxpreprocess │ │ │ +0001de50: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ +0001de60: 7372 635f 6772 6f6d 6163 735f 6669 6c65 src_gromacs_file │ │ │ +0001de70: 696f 3c2f 7469 746c 653e 0a3c 7061 7468 io......mod │ │ │ +0001e020: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +0001e030: 676d 7870 7265 7072 6f63 6573 7326 2334 gmxpreprocess │ │ │ +0001e040: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ +0001e050: 5f67 726f 6d61 6373 5f6d 6472 756e 3c2f _gromacs_mdrun</ │ │ │ +0001e060: 7469 746c 653e 0a3c 7061 7468 2066 696c title>.<path fil │ │ │ +0001e070: 6c3d 226e 6f6e 6522 2073 7472 6f6b 653d l="none" stroke= │ │ │ +0001e080: 2223 3238 3266 6363 2220 7374 726f 6b65 "#282fcc" stroke │ │ │ +0001e090: 2d64 6173 6861 7272 6179 3d22 352c 3222 -dasharray="5,2" │ │ │ +0001e0a0: 2064 3d22 4d31 3431 352e 3334 2c2d 3131 d="M1415.34,-11 │ │ │ +0001e0b0: 3532 4331 3437 312e 3639 2c2d 3131 3338 52C1471.69,-1138 │ │ │ +0001e0c0: 2e36 3720 3135 3633 2c2d 3131 3036 2e32 .67 1563,-1106.2 │ │ │ +0001e0d0: 3920 3135 3633 2c2d 3130 3336 2e33 3620 9 1563,-1036.36 │ │ │ +0001e0e0: 3135 3633 2c2d 3130 3336 2e33 3620 3135 1563,-1036.36 15 │ │ │ +0001e0f0: 3633 2c2d 3130 3336 2e33 3620 3135 3633 63,-1036.36 1563 │ │ │ +0001e100: 2c2d 3937 312e 3439 2031 3536 332c 2d39 ,-971.49 1563,-9 │ │ │ +0001e110: 3237 2e35 3920 3133 3732 2e31 312c 2d36 27.59 1372.11,-6 │ │ │ +0001e120: 3735 2e36 3720 3133 3431 2c2d 3634 342e 75.67 1341,-644. │ │ │ +0001e130: 3720 3133 3237 2e38 362c 2d36 3331 2e36 7 1327.86,-631.6 │ │ │ +0001e140: 3220 3133 3130 2e37 322c 2d36 3139 2e39 2 1310.72,-619.9 │ │ │ +0001e150: 3320 3132 3936 2e34 362c 2d36 3131 2e33 3 1296.46,-611.3 │ │ │ +0001e160: 3122 2f3e 0a3c 706f 6c79 676f 6e20 6669 1"/>.<polygon fi │ │ │ +0001e170: 6c6c 3d22 2332 3832 6663 6322 2073 7472 ll="#282fcc" str │ │ │ +0001e180: 6f6b 653d 2223 3238 3266 6363 2220 706f oke="#282fcc" po │ │ │ +0001e190: 696e 7473 3d22 3132 3937 2e39 372c 2d36 ints="1297.97,-6 │ │ │ +0001e1a0: 3038 2e31 3420 3132 3837 2e35 372c 2d36 08.14 1287.57,-6 │ │ │ +0001e1b0: 3036 2e31 2031 3239 342e 3433 2c2d 3631 06.1 1294.43,-61 │ │ │ +0001e1c0: 342e 3138 2031 3239 372e 3937 2c2d 3630 4.18 1297.97,-60 │ │ │ +0001e1d0: 382e 3134 222f 3e0a 3c2f 673e 0a3c 212d 8.14"/>.</g>.<!- │ │ │ +0001e1e0: 2d20 6d6f 6475 6c65 5f73 7263 5f67 726f - module_src_gro │ │ │ +0001e1f0: 6d61 6373 5f67 6d78 7072 6570 726f 6365 macs_gmxpreproce │ │ │ +0001e200: 7373 2623 3435 3b26 6774 3b6d 6f64 756c ss->modul │ │ │ +0001e210: 655f 7372 635f 6772 6f6d 6163 735f 6666 e_src_gromacs_ff │ │ │ +0001e220: 7420 2d2d 3e0a 3c67 2069 643d 2265 6467 t -->.<g id="edg │ │ │ +0001e230: 6532 3134 2220 636c 6173 733d 2265 6467 e214" class="edg │ │ │ +0001e240: 6522 3e0a 3c74 6974 6c65 3e6d 6f64 756c e">.<title>modul │ │ │ +0001e250: 655f 7372 635f 6772 6f6d 6163 735f 676d e_src_gromacs_gm │ │ │ +0001e260: 7870 7265 7072 6f63 6573 7326 2334 353b xpreprocess- │ │ │ +0001e270: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ +0001e280: 726f 6d61 6373 5f66 6674 3c2f 7469 746c romacs_fft</titl │ │ │ +0001e290: 653e 0a3c 7061 7468 2066 696c 6c3d 226e e>.<path fill="n │ │ │ +0001e2a0: 6f6e 6522 2073 7472 6f6b 653d 2223 6266 one" stroke="#bf │ │ │ +0001e2b0: 6266 6266 2220 643d 224d 3134 3239 2e31 bfbf" d="M1429.1 │ │ │ +0001e2c0: 362c 2d31 3135 372e 3932 4331 3631 342e 6,-1157.92C1614. │ │ │ +0001e2d0: 3536 2c2d 3131 3530 2e37 3120 3231 3839 56,-1150.71 2189 │ │ │ +0001e2e0: 2e33 352c 2d31 3132 372e 3232 2032 3232 .35,-1127.22 222 │ │ │ +0001e2f0: 362c 2d31 3131 312e 3636 2032 3239 312e 6,-1111.66 2291. │ │ │ +0001e300: 3934 2c2d 3130 3833 2e36 3720 3233 3039 94,-1083.67 2309 │ │ │ +0001e310: 2c2d 3130 3435 2e31 3220 3233 3039 2c2d ,-1045.12 2309,- │ │ │ +0001e320: 3937 332e 3439 2032 3330 392c 2d39 3733 973.49 2309,-973 │ │ │ +0001e330: 2e34 3920 3233 3039 2c2d 3937 332e 3439 .49 2309,-973.49 │ │ │ +0001e340: 2032 3330 392c 2d36 3537 2e31 3420 3233 2309,-657.14 23 │ │ │ +0001e350: 3039 2c2d 3439 342e 3236 2032 3234 362e 09,-494.26 2246. │ │ │ +0001e360: 3132 2c2d 3330 342e 3734 2032 3232 332e 12,-304.74 2223. │ │ │ +0001e370: 3231 2c2d 3234 312e 3133 222f 3e0a 3c70 21,-241.13"/>.<p │ │ │ +0001e380: 6f6c 7967 6f6e 2066 696c 6c3d 2223 6266 olygon fill="#bf │ │ │ +0001e390: 6266 6266 2220 7374 726f 6b65 3d22 2362 bfbf" stroke="#b │ │ │ +0001e3a0: 6662 6662 6622 2070 6f69 6e74 733d 2232 fbfbf" points="2 │ │ │ +0001e3b0: 3232 362e 3337 2c2d 3233 392e 3538 2032 226.37,-239.58 2 │ │ │ +0001e3c0: 3231 392e 3636 2c2d 3233 312e 3338 2032 219.66,-231.38 2 │ │ │ +0001e3d0: 3231 392e 382c 2d32 3431 2e39 3820 3232 219.8,-241.98 22 │ │ │ +0001e3e0: 3236 2e33 372c 2d32 3339 2e35 3822 2f3e 26.37,-239.58"/> │ │ │ +0001e3f0: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c .</g>.<!-- modul │ │ │ +0001e400: 655f 7372 635f 6772 6f6d 6163 735f 676d e_src_gromacs_gm │ │ │ +0001e410: 7870 7265 7072 6f63 6573 7326 2334 353b xpreprocess- │ │ │ +0001e420: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ +0001e430: 726f 6d61 6373 5f64 6f6d 6465 6320 2d2d romacs_domdec -- │ │ │ +0001e440: 3e0a 3c67 2069 643d 2265 6467 6532 3039 >.<g id="edge209 │ │ │ +0001e450: 2220 636c 6173 733d 2265 6467 6522 3e0a " class="edge">. │ │ │ +0001e460: 3c74 6974 6c65 3e6d 6f64 756c 655f 7372 <title>module_sr │ │ │ +0001e470: 635f 6772 6f6d 6163 735f 676d 7870 7265 c_gromacs_gmxpre │ │ │ +0001e480: 7072 6f63 6573 7326 2334 353b 2667 743b process-> │ │ │ +0001e490: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +0001e4a0: 6373 5f64 6f6d 6465 633c 2f74 6974 6c65 cs_domdec..< │ │ │ +0001e5c0: 706f 6c79 676f 6e20 6669 6c6c 3d22 2332 polygon fill="#2 │ │ │ +0001e5d0: 3832 6663 6322 2073 7472 6f6b 653d 2223 82fcc" stroke="# │ │ │ +0001e5e0: 3238 3266 6363 2220 706f 696e 7473 3d22 282fcc" points=" │ │ │ +0001e5f0: 3135 3731 2e33 322c 2d33 3431 2e39 3120 1571.32,-341.91 │ │ │ +0001e600: 3135 3631 2e31 342c 2d33 3434 2e38 3320 1561.14,-344.83 │ │ │ +0001e610: 3135 3730 2e39 322c 2d33 3438 2e39 2031 1570.92,-348.9 1 │ │ │ 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351,-1077.54 135 │ │ │ +0001e770: 312c 2d31 3033 362e 3336 2031 3335 312c 1,-1036.36 1351, │ │ │ +0001e780: 2d31 3033 362e 3336 2031 3335 312c 2d31 -1036.36 1351,-1 │ │ │ +0001e790: 3033 362e 3336 2031 3335 312c 2d39 3731 036.36 1351,-971 │ │ │ +0001e7a0: 2e34 3920 3133 3531 2c2d 3934 352e 3533 .49 1351,-945.53 │ │ │ +0001e7b0: 2031 3234 382e 3435 2c2d 3739 302e 3532 1248.45,-790.52 │ │ │ +0001e7c0: 2031 3233 322c 2d37 3730 2e34 3420 3132 1232,-770.44 12 │ │ │ +0001e7d0: 3136 2e38 352c 2d37 3531 2e39 3420 3132 16.85,-751.94 12 │ │ │ +0001e7e0: 3039 2e36 362c 2d37 3530 2e35 3720 3131 09.66,-750.57 11 │ │ │ +0001e7f0: 3932 2c2d 3733 342e 3434 2031 3137 392e 92,-734.44 1179. │ │ │ +0001e800: 3032 2c2d 3732 322e 3539 2031 3137 362e 02,-722.59 1176. │ │ │ +0001e810: 372c 2d37 3138 2e35 3720 3131 3633 2c2d 7,-718.57 1163,- │ │ │ +0001e820: 3730 372e 3537 2031 3134 392e 3233 2c2d 707.57 1149.23,- │ │ │ +0001e830: 3639 362e 3532 2031 3133 332e 3038 2c2d 696.52 1133.08,- │ │ │ +0001e840: 3638 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module │ │ │ +000242e0: 5f73 7263 5f67 726f 6d61 6373 5f63 6f6d _src_gromacs_com │ │ │ +000242f0: 6d61 6e64 6c69 6e65 2623 3435 3b26 6774 mandline-> │ │ │ +00024300: 3b6d 6f64 756c 655f 7372 635f 6772 6f6d ;module_src_grom │ │ │ +00024310: 6163 735f 6f70 7469 6f6e 7320 2d2d 3e0a acs_options -->. │ │ │ +00024320: 3c67 2069 643d 2265 6467 6532 3632 2220 <g id="edge262" │ │ │ +00024330: 636c 6173 733d 2265 6467 6522 3e0a 3c74 class="edge">.<t │ │ │ +00024340: 6974 6c65 3e6d 6f64 756c 655f 7372 635f itle>module_src_ │ │ │ +00024350: 6772 6f6d 6163 735f 636f 6d6d 616e 646c gromacs_commandl │ │ │ +00024360: 696e 6526 2334 353b 2667 743b 6d6f 6475 ine->modu │ │ │ +00024370: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6f le_src_gromacs_o │ │ │ +00024380: 7074 696f 6e73 3c2f 7469 746c 653e 0a3c ptions.< │ │ │ +00024390: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ +000243a0: 2073 7472 6f6b 653d 2223 3238 3266 6363 stroke="#282fcc │ │ │ +000243b0: 2220 7374 726f 6b65 2d64 6173 6861 7272 " stroke-dasharr │ │ │ +000243c0: 6179 3d22 352c 3222 2064 3d22 4d31 3233 ay="5,2" d="M123 │ │ │ +000243d0: 312e 3633 2c2d 3834 342e 3237 4331 3335 1.63,-844.27C135 │ │ │ +000243e0: 382e 3331 2c2d 3834 302e 3231 2031 3637 8.31,-840.21 167 │ │ │ +000243f0: 362e 3839 2c2d 3832 372e 3131 2031 3731 6.89,-827.11 171 │ │ │ +00024400: 342c 2d37 3937 2e33 3120 3137 3633 2e30 4,-797.31 1763.0 │ │ │ +00024410: 352c 2d37 3537 2e39 3220 3138 3030 2e37 5,-757.92 1800.7 │ │ │ +00024420: 332c 2d35 3630 2e31 3820 3138 3132 2e33 3,-560.18 1812.3 │ │ │ +00024430: 2c2d 3439 322e 3934 222f 3e0a 3c70 6f6c ,-492.94"/>.. │ │ │ +000244b0: 3c2f 673e 0a3c 212d 2d20 6d6f 6475 6c65 ..< │ │ │ +00024500: 6720 6964 3d22 6564 6765 3236 3422 2063 g id="edge264" c │ │ │ +00024510: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.module_src_g │ │ │ +00024530: 726f 6d61 6373 5f63 6f6d 6d61 6e64 6c69 romacs_commandli │ │ │ +00024540: 6e65 2623 3435 3b26 6774 3b6d 6f64 756c ne->modul │ │ │ +00024550: 655f 7372 635f 6772 6f6d 6163 735f 6669 e_src_gromacs_fi │ │ │ +00024560: 6c65 696f 3c2f 7469 746c 653e 0a3c 7061 leio.... │ │ │ +00024670: 3c21 2d2d 206d 6f64 756c 655f 7372 635f │ │ │ +000246c0: 0a3c 6720 6964 3d22 6564 6765 3237 3022 ..< │ │ │ +000246e0: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ +000246f0: 5f67 726f 6d61 6373 5f61 7070 6c69 6564 _gromacs_applied │ │ │ +00024700: 5f66 6f72 6365 735f 6177 6826 2334 353b _forces_awh- │ │ │ +00024710: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ +00024720: 726f 6d61 6373 5f67 6d78 6c69 623c 2f74 romacs_gmxlib... │ │ │ +00024870: 3c2f 673e 0a3c 212d 2d20 6d6f 6475 6c65 ...modul │ │ │ +000248f0: 655f 7372 635f 6772 6f6d 6163 735f 6170 e_src_gromacs_ap │ │ │ +00024900: 706c 6965 645f 666f 7263 6573 5f61 7768 plied_forces_awh │ │ │ +00024910: 2623 3435 3b26 6774 3b6d 6f64 756c 655f ->module_ │ │ │ +00024920: 7372 635f 6772 6f6d 6163 735f 7261 6e64 src_gromacs_rand │ │ │ +00024930: 6f6d 3c2f 7469 746c 653e 0a3c 7061 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. │ │ │ +00024bf0: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c ....mod │ │ │ +00024c70: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ +00024c80: 6170 706c 6965 645f 666f 7263 6573 5f61 applied_forces_a │ │ │ +00024c90: 7768 2623 3435 3b26 6774 3b6d 6f64 756c wh->modul │ │ │ +00024ca0: 655f 7372 635f 6772 6f6d 6163 735f 6d64 e_src_gromacs_md │ │ │ +00024cb0: 7479 7065 733c 2f74 6974 6c65 3e0a 3c70 types.

... │ │ │ +00024dd0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f │ │ │ +00024e20: 0a3c 6720 6964 3d22 6564 6765 3237 3222 ..< │ │ │ +00024e40: 7469 746c 653e 6d6f 6475 6c65 5f73 7263 title>module_src │ │ │ +00024e50: 5f67 726f 6d61 6373 5f61 7070 6c69 6564 _gromacs_applied │ │ │ +00024e60: 5f66 6f72 6365 735f 6177 6826 2334 353b _forces_awh- │ │ │ +00024e70: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ +00024e80: 726f 6d61 6373 5f66 696c 6569 6f3c 2f74 romacs_fileio. │ │ │ +00024f20: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 . │ │ │ +00024f90: 0a3c 2f67 3e0a 3c21 2d2d 206d 6f64 756c ....module_src_gro │ │ │ +00025020: 6d61 6373 5f61 7070 6c69 6564 5f66 6f72 macs_applied_for │ │ │ +00025030: 6365 735f 6177 6826 2334 353b 2667 743b ces_awh-> │ │ │ +00025040: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ +00025050: 6373 5f6d 6472 756e 7574 696c 6974 793c cs_mdrunutility< │ │ │ +00025060: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>......module_src_gro │ │ │ 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45;>module_sr │ │ │ +000257e0: 635f 6772 6f6d 6163 735f 6861 7264 7761 c_gromacs_hardwa │ │ │ +000257f0: 7265 3c2f 7469 746c 653e 0a3c 7061 7468 re..< │ │ │ +000258b0: 706f 6c79 676f 6e20 6669 6c6c 3d22 7265 polygon fill="re │ │ │ +000258c0: 6422 2073 7472 6f6b 653d 2272 6564 2220 d" stroke="red" │ │ │ +000258d0: 706f 696e 7473 3d22 3231 3336 2e34 322c points="2136.42, │ │ │ +000258e0: 2d39 342e 3938 2032 3132 362e 3037 2c2d -94.98 2126.07,- │ │ │ +000258f0: 3937 2e32 3620 3231 3335 2e35 382c 2d31 97.26 2135.58,-1 │ │ │ +00025900: 3031 2e39 3320 3231 3336 2e34 322c 2d39 01.93 2136.42,-9 │ │ │ +00025910: 342e 3938 222f 3e0a 3c2f 673e 0a3c 212d 4.98"/>....module_ │ │ │ +00025990: 7372 635f 7465 7374 7574 696c 7326 2334 src_testutils │ │ │ +000259a0: 353b 2667 743b 6d6f 6475 6c65 5f73 7263 5;>module_src │ │ │ +000259b0: 5f67 726f 6d61 6373 5f67 6d78 7072 6570 _gromacs_gmxprep │ │ │ +000259c0: 726f 6365 7373 3c2f 7469 746c 653e 0a3c rocess.< │ │ │ +000259d0: 7061 7468 2066 696c 6c3d 226e 6f6e 6522 path fill="none" │ │ │ +000259e0: 2073 7472 6f6b 653d 2223 6266 6266 6266 stroke="#bfbfbf │ │ │ +000259f0: 2220 643d 224d 3233 3734 2e36 312c 2d31 " d="M2374.61,-1 │ │ │ +00025a00: 3034 382e 3438 4332 3336 302e 3134 2c2d 048.48C2360.14,- │ │ │ +00025a10: 3130 3636 2e31 2032 3333 302e 3534 2c2d 1066.1 2330.54,- │ │ │ +00025a20: 3130 3938 2e31 3520 3232 3937 2c2d 3131 1098.15 2297,-11 │ │ │ +00025a30: 3131 2e36 3620 3232 3537 2e33 372c 2d31 11.66 2257.37,-1 │ │ │ +00025a40: 3132 372e 3632 2031 3634 352e 3937 2c2d 127.62 1645.97,- │ │ │ +00025a50: 3131 3530 2e34 3720 3134 3339 2e35 312c 1150.47 1439.51, │ │ │ +00025a60: 2d31 3135 372e 3736 222f 3e0a 3c70 6f6c -1157.76"/>.....module_src_tes │ │ │ +00025b60: 7475 7469 6c73 2623 3435 3b26 6774 3b6d tutils->m │ │ │ 00025b70: 6f64 756c 655f 7372 635f 6772 6f6d 6163 odule_src_gromac │ │ │ -00025b80: 735f 676d 7870 7265 7072 6f63 6573 733c s_gmxpreprocess< │ │ │ -00025b90: 2f74 6974 6c65 3e0a 3c70 6174 6820 6669 /title>.... │ │ │ -00025cf0: 3c21 2d2d 206d 6f64 756c 655f 7372 635f .< │ │ │ -00025d40: 6720 6964 3d22 6564 6765 3236 3422 2063 g id="edge264" c │ │ │ -00025d50: 6c61 7373 3d22 6564 6765 223e 0a3c 7469 lass="edge">.module_src_g │ │ │ -00025d70: 726f 6d61 6373 5f61 7070 6c69 6564 5f66 romacs_applied_f │ │ │ -00025d80: 6f72 6365 7326 2334 353b 2667 743b 6d6f orces->mo │ │ │ -00025d90: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -00025da0: 5f68 6172 6477 6172 653c 2f74 6974 6c65 _hardware... │ │ │ -00025f30: 0a3c 212d 2d20 6d6f 6475 6c65 5f73 7263 ...module_src_gro │ │ │ -00025fb0: 6d61 6373 5f61 7070 6c69 6564 5f66 6f72 macs_applied_for │ │ │ -00025fc0: 6365 7326 2334 353b 2667 743b 6d6f 6475 ces->modu │ │ │ -00025fd0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f6d le_src_gromacs_m │ │ │ -00025fe0: 646c 6962 3c2f 7469 746c 653e 0a3c 7061 dlib......module │ │ │ -00026190: 5f73 7263 5f67 726f 6d61 6373 5f61 7070 _src_gromacs_app │ │ │ -000261a0: 6c69 6564 5f66 6f72 6365 7326 2334 353b lied_forces- │ │ │ -000261b0: 2667 743b 6d6f 6475 6c65 5f73 7263 5f67 >module_src_g │ │ │ -000261c0: 726f 6d61 6373 5f63 6f6d 6d61 6e64 6c69 romacs_commandli │ │ │ -000261d0: 6e65 3c2f 7469 746c 653e 0a3c 7061 7468 ne. │ │ │ -000262b0: 0a3c 706f 6c79 676f 6e20 6669 6c6c 3d22 ... │ │ │ -00026320: 3c21 2d2d 206d 6f64 756c 655f 7372 635f ..module_src_gro │ │ │ -000263a0: 6d61 6373 5f61 7070 6c69 6564 5f66 6f72 macs_applied_for │ │ │ -000263b0: 6365 7326 2334 353b 2667 743b 6d6f 6475 ces->modu │ │ │ -000263c0: 6c65 5f73 7263 5f67 726f 6d61 6373 5f66 le_src_gromacs_f │ │ │ -000263d0: 696c 6569 6f3c 2f74 6974 6c65 3e0a 3c70 ileio.

.....mod │ │ │ -00026610: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -00026620: 6170 706c 6965 645f 666f 7263 6573 2623 applied_forces&# │ │ │ -00026630: 3435 3b26 6774 3b6d 6f64 756c 655f 7372 45;>module_sr │ │ │ -00026640: 635f 6772 6f6d 6163 735f 636f 6d70 6174 c_gromacs_compat │ │ │ -00026650: 3c2f 7469 746c 653e 0a3c 7061 7468 2066 ......mod │ │ │ -000267d0: 756c 655f 7372 635f 6772 6f6d 6163 735f ule_src_gromacs_ │ │ │ -000267e0: 6170 706c 6965 645f 666f 7263 6573 5f61 applied_forces_a │ │ │ -000267f0: 7768 2623 3435 3b26 6774 3b6d 6f64 756c wh->modul │ │ │ -00026800: 655f 7372 635f 6772 6f6d 6163 735f 7472 e_src_gromacs_tr │ │ │ -00026810: 616a 6563 746f 7279 3c2f 7469 746c 653e ajectory │ │ │ -00026820: 0a3c 7061 7468 2066 696c 6c3d 226e 6f6e ......module_src_gro │ │ │ -00026a10: 6d61 6373 5f61 7070 6c69 6564 5f66 6f72 macs_applied_for │ │ │ -00026a20: 6365 735f 6177 6826 2334 353b 2667 743b ces_awh-> │ │ │ -00026a30: 6d6f 6475 6c65 5f73 7263 5f67 726f 6d61 module_src_groma │ │ │ -00026a40: 6373 5f6d 6474 7970 6573 3c2f 7469 746c cs_mdtypes......mo │ │ │ -00026e00: 6475 6c65 5f73 7263 5f67 726f 6d61 6373 dule_src_gromacs │ │ │ -00026e10: 5f61 7070 6c69 6564 5f66 6f72 6365 735f _applied_forces_ │ │ │ -00026e20: 6177 6826 2334 353b 2667 743b 6d6f 6475 awh->modu │ │ │ -00026e30: 6c65 5f73 7263 5f67 726f 6d61 6373 5f72 le_src_gromacs_r │ │ │ -00026e40: 616e 646f 6d3c 2f74 6974 6c65 3e0a 3c70 andom.

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│ │ │ +000272a0: 0a3c 2f67 3e0a 3c2f 673e 0a3c 2f73 7667 .... │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/page_modulegraph.xhtml │ │ │ @@ -74,15 +74,15 @@ │ │ │ │ │ │

│ │ │
Module dependency graph
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The graph below shows the dependencies between the source code modules, computed from include statements in the code. For documented modules (those that do not have a gray background), clicking on the module takes you to the module documentation. Legend for the graph can be found below the graph.

│ │ │
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│ │ │ Legend

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The graph below annotates the colors and line styles used in the module dependency graph above. More detailed textual annotation is below the graph.

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Node colors:

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gray background
│ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_10.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -133,16 +133,16 @@ │ │ │ │ ['makeunperturbedlj14params_97', ['makeUnperturbedLJ14Params', ['../namespacegmx_1_1test_1_1anonymous__namespace_02topsort_8cpp_03.xhtml#a2808faea96c2b64e53ffd7a46782d459', 1, 'gmx::test::anonymous_namespace{topsort.cpp}']]], │ │ │ │ ['makeupdategroupingspermoleculetype_98', ['makeupdategroupingspermoleculetype', ['../namespacegmx.xhtml#aa51b331e6dc5454e57b96838b2d503af', 1, 'gmx::makeUpdateGroupingsPerMoleculeType(const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)'], │ │ │ │ ['../namespacegmx.xhtml#a716fe4766d0dbb653552d9287feb563f', 1, 'gmx::makeUpdateGroupingsPerMoleculeType(const gmx_mtop_t &mtop)'] │ │ │ │ ]], │ │ │ │ ['makeupdategroups_99', ['makeUpdateGroups', ['../namespacegmx.xhtml#a2dc1261c727390c49373b57c3581f1af', 1, 'gmx']]], │ │ │ │ ['makevendorflavorchoice_100', ['makeVendorFlavorChoice', ['../ocl__compiler_8cpp.xhtml#ab7da5ff7c4af27a4a1789dbd342a8966', 1, 'gmx::ocl']]], │ │ │ │ ['makevirtualsiteshandler_101', ['makeVirtualSitesHandler', ['../namespacegmx.xhtml#ad59dd2687a751a26481a0a774f51146a', 1, 'gmx']]], │ │ │ │ - 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['../classgmx_1_1layout__right_1_1mapping.xhtml#a80905ecdaf35273d7f7c303e7d2ff909', 1, 'gmx::layout_right::mapping::mapping() noexcept=default'] │ │ │ │ + ['../classgmx_1_1layout__right_1_1mapping.xhtml#ad632683c77288c28df614ea7915917ce', 1, 'gmx::layout_right::mapping::mapping(const mapping &) noexcept=default'] │ │ │ │ ]], │ │ │ │ ['mapping_5ftype_130', ['mapping_type', ['../classgmx_1_1basic__mdspan.xhtml#a41c0126e07c9b922b4b838b578af7888', 1, 'gmx::basic_mdspan']]], │ │ │ │ ['maptoframeatoms_5f_131', ['mapToFrameAtoms_', ['../classgmx_1_1PositionCalculationCollection_1_1Impl.xhtml#a028b638ac6bf4c5c76f4c78819d94cff', 1, 'gmx::PositionCalculationCollection::Impl']]], │ │ │ │ ['maptype_132', ['MapType', ['../classgmx_1_1EnergyFrame.xhtml#ae7cbc6aabfeacd2447563d8f137045f4', 1, 'gmx::EnergyFrame']]], │ │ │ │ ['mark_5fsubexpr_5fdynamic_133', ['mark_subexpr_dynamic', ['../compiler_8cpp.xhtml#a2ce676e6caff3877910cd9cfc27cb955', 1, 'compiler.cpp']]], │ │ │ │ ['mark_5fsurface_5fcovered_134', ['mark_surface_covered', ['../sm__insolidangle_8cpp.xhtml#ad016ba6ae3e4a77948222f08f4004e4f', 1, 'sm_insolidangle.cpp']]], │ │ │ │ ['markasreadytoreduce_135', ['markAsReadyToReduce', ['../classgmx_1_1ObservablesReducer.xhtml#aa76fb912aca1c30275e567685626f515', 1, 'gmx::ObservablesReducer']]], │ │ │ │ ['markasset_136', ['markAsSet', ['../classgmx_1_1AbstractOptionStorage.xhtml#af02f972186bba8ff52f0e789e7d6fedc', 1, 'gmx::AbstractOptionStorage']]], │ │ │ │ ['marknotified_137', ['markNotified', ['../classgmx_1_1internal_1_1AnalysisDataStorageFrameData.xhtml#a2e4ff0da40c2d126b1dd4539cc1d8d99', 1, 'gmx::internal::AnalysisDataStorageFrameData']]], │ │ │ │ ['markup_138', ['markup', ['../page_onlinehelp.xhtml#autotoc_md91', 1, 'Formatting markup'], │ │ │ │ ['../page_onlinehelp.xhtml#autotoc_md93', 1, 'GROMACS-specific markup'] │ │ │ │ ]], │ │ │ │ ['mask_139', ['mask', ['../classgmx_1_1test_1_1AllocatorTest.xhtml#a3b860b1af26fe4dce4d932a100a1d1ab', 1, 'gmx::test::AllocatorTest']]], │ │ │ │ - ['maskadd_140', ['maskadd', ['../namespacegmx.xhtml#a0178a127dde331652ab015323ae622f2', 1, 'gmx::maskAdd(float a, float b, float m)'], │ │ │ │ - ['../group__module__simd.xhtml#ga766a313a4a158cfcb0eed0373dd82dfc', 1, 'gmx::maskAdd(SimdFloat a, SimdFloat b, SimdFBool m)'], │ │ │ │ - ['../group__module__simd.xhtml#gadab86e04bd62248ab68039d8983a9206', 1, 'gmx::maskAdd(SimdDouble a, SimdDouble b, SimdDBool m)'], │ │ │ │ - ['../namespacegmx.xhtml#a68b090d0e3ab5695c508453406ee43c8', 1, 'gmx::maskAdd(double a, double b, double m)'] │ │ │ │ + ['maskadd_140', ['maskadd', ['../group__module__simd.xhtml#ga766a313a4a158cfcb0eed0373dd82dfc', 1, 'gmx::maskAdd(SimdFloat a, SimdFloat b, SimdFBool m)'], │ │ │ │ + ['../namespacegmx.xhtml#a0178a127dde331652ab015323ae622f2', 1, 'gmx::maskAdd(float a, float b, float m)'], │ │ │ │ + ['../namespacegmx.xhtml#a68b090d0e3ab5695c508453406ee43c8', 1, 'gmx::maskAdd(double a, double b, double m)'], │ │ │ │ + ['../group__module__simd.xhtml#gadab86e04bd62248ab68039d8983a9206', 1, 'gmx::maskAdd(SimdDouble a, SimdDouble b, SimdDBool m)'] │ │ │ │ ]], │ │ │ │ ['maskarray_141', ['maskarray', ['../classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsHalfISize_01_4.xhtml#aa09948a382ac9009e878a3bf5081abd5', 1, 'gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize >::maskArray()'], │ │ │ │ - ['../classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4.xhtml#a42fcf1ef011c98c6dca2d5fb14a4ff53', 1, 'gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize >::maskArray()'], │ │ │ │ - ['../classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4.xhtml#a45e2188c94bad5c65ddfbf1802dd7a81', 1, 'gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize >::maskArray()'] │ │ │ │ + ['../classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeIsDoubleISize_01_4.xhtml#a45e2188c94bad5c65ddfbf1802dd7a81', 1, 'gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize >::maskArray()'], │ │ │ │ + ['../classgmx_1_1DiagonalMasker_3_01nR_00_01kernelLayout_00_01KernelLayoutClusterRatio_1_1JSizeEqualsISize_01_4.xhtml#a42fcf1ef011c98c6dca2d5fb14a4ff53', 1, 'gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize >::maskArray()'] │ │ │ │ ]], │ │ │ │ - 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['gmx_5fpme_5fcomm_5fn_5fbox_5ft_945', ['gmx_pme_comm_n_box_t', ['../structgmx__pme__comm__n__box__t.xhtml', 1, '']]], │ │ │ │ ['gmx_5fpme_5fcomm_5fvir_5fene_5ft_946', ['gmx_pme_comm_vir_ene_t', ['../structgmx__pme__comm__vir__ene__t.xhtml', 1, '']]], │ │ │ │ - ['gmx_5fpme_5fdestroy_947', ['gmx_pme_destroy', ['../pme_8h.xhtml#afb9db2681fc072d6b4176febca9831c6', 1, 'gmx_pme_destroy(gmx_pme_t *pme, bool destroyGpuData): pme.cpp'], │ │ │ │ - ['../pme_8h.xhtml#ac5a75a2d477885fcb0260908f6e7b2f2', 1, 'gmx_pme_destroy(gmx_pme_t *pme): pme.cpp'], │ │ │ │ + ['gmx_5fpme_5fdestroy_947', ['gmx_pme_destroy', ['../pme_8cpp.xhtml#ac5a75a2d477885fcb0260908f6e7b2f2', 1, 'gmx_pme_destroy(gmx_pme_t *pme): pme.cpp'], │ │ │ │ ['../pme_8cpp.xhtml#afb9db2681fc072d6b4176febca9831c6', 1, 'gmx_pme_destroy(gmx_pme_t *pme, bool destroyGpuData): pme.cpp'], │ │ │ │ - ['../pme_8cpp.xhtml#ac5a75a2d477885fcb0260908f6e7b2f2', 1, 'gmx_pme_destroy(gmx_pme_t *pme): pme.cpp'] │ │ │ │ + ['../pme_8h.xhtml#ac5a75a2d477885fcb0260908f6e7b2f2', 1, 'gmx_pme_destroy(gmx_pme_t *pme): pme.cpp'], │ │ │ │ + ['../pme_8h.xhtml#afb9db2681fc072d6b4176febca9831c6', 1, 'gmx_pme_destroy(gmx_pme_t *pme, bool destroyGpuData): pme.cpp'] │ │ │ │ ]], │ │ │ │ - ['gmx_5fpme_5fdo_948', ['gmx_pme_do', ['../pme_8h.xhtml#ae9d5a3c227bbe220bd732be51ec92d9b', 1, 'gmx_pme_do(struct gmx_pme_t *pme, gmx::ArrayRef< const gmx::RVec > coordinates, gmx::ArrayRef< gmx::RVec > forces, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const real > c6A, gmx::ArrayRef< const real > c6B, gmx::ArrayRef< const real > sigmaA, gmx::ArrayRef< const real > sigmaB, const matrix box, const t_commrec *cr, int maxshift_x, int maxshift_y, t_nrnb *nrnb, gmx_wallcycle *wcycle, matrix vir_q, matrix vir_lj, real *energy_q, real *energy_lj, real lambda_q, real lambda_lj, real *dvdlambda_q, real *dvdlambda_lj, const gmx::StepWorkload &stepWork): pme.cpp'], │ │ │ │ - ['../pme_8cpp.xhtml#ae9d5a3c227bbe220bd732be51ec92d9b', 1, 'gmx_pme_do(struct gmx_pme_t *pme, gmx::ArrayRef< const gmx::RVec > coordinates, gmx::ArrayRef< gmx::RVec > forces, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const real > c6A, gmx::ArrayRef< const real > c6B, gmx::ArrayRef< const real > sigmaA, gmx::ArrayRef< const real > sigmaB, const matrix box, const t_commrec *cr, int maxshift_x, int maxshift_y, t_nrnb *nrnb, gmx_wallcycle *wcycle, matrix vir_q, matrix vir_lj, real *energy_q, real *energy_lj, real lambda_q, real lambda_lj, real *dvdlambda_q, real *dvdlambda_lj, const gmx::StepWorkload &stepWork): pme.cpp'] │ │ │ │ + ['gmx_5fpme_5fdo_948', ['gmx_pme_do', ['../pme_8cpp.xhtml#ae9d5a3c227bbe220bd732be51ec92d9b', 1, 'gmx_pme_do(struct gmx_pme_t *pme, gmx::ArrayRef< const gmx::RVec > coordinates, gmx::ArrayRef< gmx::RVec > forces, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const real > c6A, gmx::ArrayRef< const real > c6B, gmx::ArrayRef< const real > sigmaA, gmx::ArrayRef< const real > sigmaB, const matrix box, const t_commrec *cr, int maxshift_x, int maxshift_y, t_nrnb *nrnb, gmx_wallcycle *wcycle, matrix vir_q, matrix vir_lj, real *energy_q, real *energy_lj, real lambda_q, real lambda_lj, real *dvdlambda_q, real *dvdlambda_lj, const gmx::StepWorkload &stepWork): pme.cpp'], │ │ │ │ + ['../pme_8h.xhtml#ae9d5a3c227bbe220bd732be51ec92d9b', 1, 'gmx_pme_do(struct gmx_pme_t *pme, gmx::ArrayRef< const gmx::RVec > coordinates, gmx::ArrayRef< gmx::RVec > forces, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const real > c6A, gmx::ArrayRef< const real > c6B, gmx::ArrayRef< const real > sigmaA, gmx::ArrayRef< const real > sigmaB, const matrix box, const t_commrec *cr, int maxshift_x, int maxshift_y, t_nrnb *nrnb, gmx_wallcycle *wcycle, matrix vir_q, matrix vir_lj, real *energy_q, real *energy_lj, real lambda_q, real lambda_lj, real *dvdlambda_q, real *dvdlambda_lj, const gmx::StepWorkload &stepWork): pme.cpp'] │ │ │ │ ]], │ │ │ │ - ['gmx_5fpme_5fgrid_5fmatches_949', ['gmx_pme_grid_matches', ['../pme_8cpp.xhtml#a90e8466d51fc7f91409cce40287f1d14', 1, 'gmx_pme_grid_matches(const gmx_pme_t &pme, const ivec grid_size): pme.cpp'], │ │ │ │ - ['../pme_8h.xhtml#a90e8466d51fc7f91409cce40287f1d14', 1, 'gmx_pme_grid_matches(const gmx_pme_t &pme, const ivec grid_size): pme.cpp'] │ │ │ │ + ['gmx_5fpme_5fgrid_5fmatches_949', ['gmx_pme_grid_matches', ['../pme_8h.xhtml#a90e8466d51fc7f91409cce40287f1d14', 1, 'gmx_pme_grid_matches(const gmx_pme_t &pme, const ivec grid_size): pme.cpp'], │ │ │ │ + ['../pme_8cpp.xhtml#a90e8466d51fc7f91409cce40287f1d14', 1, 'gmx_pme_grid_matches(const gmx_pme_t &pme, const ivec grid_size): pme.cpp'] │ │ │ │ ]], │ │ │ │ - ['gmx_5fpme_5finit_950', ['gmx_pme_init', ['../pme_8cpp.xhtml#a39e800d9a258e0c8a553fa7b71e10dcf', 1, 'gmx_pme_init(const t_commrec *cr, const NumPmeDomains &numPmeDomains, const t_inputrec *ir, const matrix box, real haloExtentForAtomDisplacement, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, real ewaldcoeff_q, real ewaldcoeff_lj, int nthread, PmeRunMode runMode, PmeGpu *pmeGpu, const DeviceContext *deviceContext, const DeviceStream *deviceStream, const PmeGpuProgram *pmeGpuProgram, const gmx::MDLogger &mdlog, std::shared_ptr< PmeGridsStorage > pmeGridsStoragePtr): pme.cpp'], │ │ │ │ - ['../pme_8h.xhtml#a39e800d9a258e0c8a553fa7b71e10dcf', 1, 'gmx_pme_init(const t_commrec *cr, const NumPmeDomains &numPmeDomains, const t_inputrec *ir, const matrix box, real haloExtentForAtomDisplacement, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, real ewaldcoeff_q, real ewaldcoeff_lj, int nthread, PmeRunMode runMode, PmeGpu *pmeGpu, const DeviceContext *deviceContext, const DeviceStream *deviceStream, const PmeGpuProgram *pmeGpuProgram, const gmx::MDLogger &mdlog, std::shared_ptr< PmeGridsStorage > pmeGridsStoragePtr): pme.cpp'] │ │ │ │ + ['gmx_5fpme_5finit_950', ['gmx_pme_init', ['../pme_8h.xhtml#a39e800d9a258e0c8a553fa7b71e10dcf', 1, 'gmx_pme_init(const t_commrec *cr, const NumPmeDomains &numPmeDomains, const t_inputrec *ir, const matrix box, real haloExtentForAtomDisplacement, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, real ewaldcoeff_q, real ewaldcoeff_lj, int nthread, PmeRunMode runMode, PmeGpu *pmeGpu, const DeviceContext *deviceContext, const DeviceStream *deviceStream, const PmeGpuProgram *pmeGpuProgram, const gmx::MDLogger &mdlog, std::shared_ptr< PmeGridsStorage > pmeGridsStoragePtr): pme.cpp'], │ │ │ │ + ['../pme_8cpp.xhtml#a39e800d9a258e0c8a553fa7b71e10dcf', 1, 'gmx_pme_init(const t_commrec *cr, const NumPmeDomains &numPmeDomains, const t_inputrec *ir, const matrix box, real haloExtentForAtomDisplacement, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, real ewaldcoeff_q, real ewaldcoeff_lj, int nthread, PmeRunMode runMode, PmeGpu *pmeGpu, const DeviceContext *deviceContext, const DeviceStream *deviceStream, const PmeGpuProgram *pmeGpuProgram, const gmx::MDLogger &mdlog, std::shared_ptr< PmeGridsStorage > pmeGridsStoragePtr): pme.cpp'] │ │ │ │ ]], │ │ │ │ ['gmx_5fpme_5fpp_951', ['gmx_pme_pp', ['../structgmx__pme__pp.xhtml', 1, '']]], │ │ │ │ - ['gmx_5fpme_5freceive_5ff_952', ['gmx_pme_receive_f', ['../pme__pp_8cpp.xhtml#ac80dc53aeed084dcf80cf5a3581df28b', 1, 'gmx_pme_receive_f(gmx::PmePpCommGpu *pmePpCommGpu, const t_commrec *cr, gmx::ForceWithVirial *forceWithVirial, real *energy_q, real *energy_lj, real *dvdlambda_q, real *dvdlambda_lj, bool useGpuPmePpComms, bool receivePmeForceToGpu, float *pme_cycles): pme_pp.cpp'], │ │ │ │ - ['../pme__pp_8h.xhtml#ac80dc53aeed084dcf80cf5a3581df28b', 1, 'gmx_pme_receive_f(gmx::PmePpCommGpu *pmePpCommGpu, const t_commrec *cr, gmx::ForceWithVirial *forceWithVirial, real *energy_q, real *energy_lj, real *dvdlambda_q, real *dvdlambda_lj, bool useGpuPmePpComms, bool receivePmeForceToGpu, float *pme_cycles): pme_pp.cpp'] │ │ │ │ + ['gmx_5fpme_5freceive_5ff_952', ['gmx_pme_receive_f', ['../pme__pp_8h.xhtml#ac80dc53aeed084dcf80cf5a3581df28b', 1, 'gmx_pme_receive_f(gmx::PmePpCommGpu *pmePpCommGpu, const t_commrec *cr, gmx::ForceWithVirial *forceWithVirial, real *energy_q, real *energy_lj, real *dvdlambda_q, real *dvdlambda_lj, bool useGpuPmePpComms, bool receivePmeForceToGpu, float *pme_cycles): pme_pp.cpp'], │ │ │ │ + ['../pme__pp_8cpp.xhtml#ac80dc53aeed084dcf80cf5a3581df28b', 1, 'gmx_pme_receive_f(gmx::PmePpCommGpu *pmePpCommGpu, const t_commrec *cr, gmx::ForceWithVirial *forceWithVirial, real *energy_q, real *energy_lj, real *dvdlambda_q, real *dvdlambda_lj, bool useGpuPmePpComms, bool receivePmeForceToGpu, float *pme_cycles): pme_pp.cpp'] │ │ │ │ ]], │ │ │ │ - ['gmx_5fpme_5freinit_953', ['gmx_pme_reinit', ['../pme_8h.xhtml#addb051f62c492eb3a5720c8cbf4332c6', 1, 'gmx_pme_reinit(gmx_pme_t **pmedata, const t_commrec *cr, gmx_pme_t *pme_src, const t_inputrec *ir, const ivec grid_size, real ewaldcoeff_q, real ewaldcoeff_lj): pme.cpp'], │ │ │ │ - ['../pme_8cpp.xhtml#ab1d5c3f2e6e75de3f38107c0acd92c6d', 1, 'gmx_pme_reinit(struct gmx_pme_t **pmedata, const t_commrec *cr, struct gmx_pme_t *pme_src, const t_inputrec *ir, const ivec grid_size, real ewaldcoeff_q, real ewaldcoeff_lj): pme.cpp'] │ │ │ │ + ['gmx_5fpme_5freinit_953', ['gmx_pme_reinit', ['../pme_8cpp.xhtml#ab1d5c3f2e6e75de3f38107c0acd92c6d', 1, 'gmx_pme_reinit(struct gmx_pme_t **pmedata, const t_commrec *cr, struct gmx_pme_t *pme_src, const t_inputrec *ir, const ivec grid_size, real ewaldcoeff_q, real ewaldcoeff_lj): pme.cpp'], │ │ │ │ + ['../pme_8h.xhtml#addb051f62c492eb3a5720c8cbf4332c6', 1, 'gmx_pme_reinit(gmx_pme_t **pmedata, const t_commrec *cr, gmx_pme_t *pme_src, const t_inputrec *ir, const ivec grid_size, real ewaldcoeff_q, real ewaldcoeff_lj): pme.cpp'] │ │ │ │ ]], │ │ │ │ - ['gmx_5fpme_5freinit_5fatoms_954', ['gmx_pme_reinit_atoms', ['../pme_8h.xhtml#a05afbf020b612d12ae1007b79a737edb', 1, 'gmx_pme_reinit_atoms(gmx_pme_t *pme, int numAtoms, gmx::ArrayRef< const real > chargesA, gmx::ArrayRef< const real > chargesB): pme.cpp'], │ │ │ │ - ['../pme_8cpp.xhtml#a1502bc293ce8fb854adf4648a1d2d4c7', 1, 'gmx_pme_reinit_atoms(gmx_pme_t *pme, const int numAtoms, gmx::ArrayRef< const real > chargesA, gmx::ArrayRef< const real > chargesB): pme.cpp'] │ │ │ │ + ['gmx_5fpme_5freinit_5fatoms_954', ['gmx_pme_reinit_atoms', ['../pme_8cpp.xhtml#a1502bc293ce8fb854adf4648a1d2d4c7', 1, 'gmx_pme_reinit_atoms(gmx_pme_t *pme, const int numAtoms, gmx::ArrayRef< const real > chargesA, gmx::ArrayRef< const real > chargesB): pme.cpp'], │ │ │ │ + ['../pme_8h.xhtml#a05afbf020b612d12ae1007b79a737edb', 1, 'gmx_pme_reinit_atoms(gmx_pme_t *pme, int numAtoms, gmx::ArrayRef< const real > chargesA, gmx::ArrayRef< const real > chargesB): pme.cpp'] │ │ │ │ ]], │ │ │ │ ['gmx_5fpme_5fsend_5fcoeffs_5fcoords_955', ['gmx_pme_send_coeffs_coords', ['../pme__pp_8cpp.xhtml#a810bd87c033d0b7544a243693e1b53d2', 1, 'pme_pp.cpp']]], │ │ │ │ ['gmx_5fpme_5fsend_5fcoeffs_5fcoords_5fwait_956', ['gmx_pme_send_coeffs_coords_wait', ['../pme__pp_8cpp.xhtml#a8b23b61fb70dc499495370bccce186fe', 1, 'pme_pp.cpp']]], │ │ │ │ ['gmx_5fpme_5fsend_5fcoordinates_957', ['gmx_pme_send_coordinates', ['../pme__pp_8cpp.xhtml#ab646bb77e2d8189a87259663e98a3aac', 1, 'gmx_pme_send_coordinates(t_forcerec *fr, const t_commrec *cr, const matrix box, gmx::ArrayRef< const gmx::RVec > x, real lambda_q, real lambda_lj, bool computeEnergyAndVirial, int64_t step, bool useGpuPmePpComms, bool receiveCoordinateAddressFromPme, bool sendCoordinatesFromGpu, bool receiveForcesToGpu, GpuEventSynchronizer *coordinatesReadyOnDeviceEvent, bool useMdGpuGraph, gmx_wallcycle *wcycle): pme_pp.cpp'], │ │ │ │ ['../pme__pp_8h.xhtml#a56a70e5ba4d08896460c86b77914dfb3', 1, 'gmx_pme_send_coordinates(t_forcerec *fr, const t_commrec *cr, const matrix box, gmx::ArrayRef< const gmx::RVec > x, real lambda_q, real lambda_lj, bool computeEnergyAndVirial, int64_t step, bool useGpuPmePpComms, bool reinitGpuPmePpComms, bool sendCoordinatesFromGpu, bool receiveForcesToGpu, GpuEventSynchronizer *coordinatesReadyOnDeviceEvent, bool useMdGpuGraph, gmx_wallcycle *wcycle): pme_pp.cpp'] │ │ │ │ ]], │ │ │ │ ['gmx_5fpme_5fsend_5ffinish_958', ['gmx_pme_send_finish', ['../pme__pp_8cpp.xhtml#a4daff17a719886efa0309286a8278bcc', 1, 'gmx_pme_send_finish(const t_commrec *cr): pme_pp.cpp'], │ │ │ │ @@ -1541,16 +1541,16 @@ │ │ │ │ ['gpp_5fatomtype_2eh_1116', ['gpp_atomtype.h', ['../gpp__atomtype_8h.xhtml', 1, '']]], │ │ │ │ ['gpp_5fbond_5fatomtype_2ecpp_1117', ['gpp_bond_atomtype.cpp', ['../tests_2gpp__bond__atomtype_8cpp.xhtml', 1, '']]], │ │ │ │ ['gpp_5fbond_5fatomtype_2eh_1118', ['gpp_bond_atomtype.h', ['../gpp__bond__atomtype_8h.xhtml', 1, '']]], │ │ │ │ ['gpu_1119', ['gpu', ['../namespacegmx.xhtml#a3f42ed0b9f4da1face257003c06bfddba3432ca64f06615abf07ab44c10cada38', 1, 'gmx::Gpu'], │ │ │ │ ['../pme_8h.xhtml#adc082ed1af9a4868af13352373ed3791a52f9ec21735243ad9917cda3ca077d32', 1, 'GPU: pme.h'], │ │ │ │ ['../namespacegmx_1_1test.xhtml#a12502ff6638f23aeff85ad081f6a0a1ca52f9ec21735243ad9917cda3ca077d32', 1, 'gmx::test::GPU'] │ │ │ │ ]], │ │ │ │ - ['gpu3dfft_1120', ['gpu3dfft', ['../classgmx_1_1Gpu3dFft.xhtml', 1, 'gmx::Gpu3dFft'], │ │ │ │ - ['../classgmx_1_1Gpu3dFft.xhtml#a601de47c00396f7f8bb2df3fb91a65f0', 1, 'gmx::Gpu3dFft::Gpu3dFft()'] │ │ │ │ + ['gpu3dfft_1120', ['gpu3dfft', ['../classgmx_1_1Gpu3dFft.xhtml#a601de47c00396f7f8bb2df3fb91a65f0', 1, 'gmx::Gpu3dFft::Gpu3dFft()'], │ │ │ │ + ['../classgmx_1_1Gpu3dFft.xhtml', 1, 'gmx::Gpu3dFft'] │ │ │ │ ]], │ │ │ │ ['gpu_5f3dfft_2ecpp_1121', ['gpu_3dfft.cpp', ['../gpu__3dfft_8cpp.xhtml', 1, '']]], │ │ │ │ ['gpu_5f3dfft_2eh_1122', ['gpu_3dfft.h', ['../gpu__3dfft_8h.xhtml', 1, '']]], │ │ │ │ ['gpu_5f3dfft_5fcufft_2eh_1123', ['gpu_3dfft_cufft.h', ['../gpu__3dfft__cufft_8h.xhtml', 1, '']]], │ │ │ │ ['gpu_5f3dfft_5fcufftmp_2ecpp_1124', ['gpu_3dfft_cufftmp.cpp', ['../gpu__3dfft__cufftmp_8cpp.xhtml', 1, '']]], │ │ │ │ ['gpu_5f3dfft_5fcufftmp_2eh_1125', ['gpu_3dfft_cufftmp.h', ['../gpu__3dfft__cufftmp_8h.xhtml', 1, '']]], │ │ │ │ ['gpu_5f3dfft_5fheffte_2ecpp_1126', ['gpu_3dfft_heffte.cpp', ['../gpu__3dfft__heffte_8cpp.xhtml', 1, '']]], │ │ │ │ @@ -1575,37 +1575,37 @@ │ │ │ │ ['gpu_5f3dfft_5fsycl_5frocfft_2eh_1145', ['gpu_3dfft_sycl_rocfft.h', ['../gpu__3dfft__sycl__rocfft_8h.xhtml', 1, '']]], │ │ │ │ ['gpu_5f3dfft_5fsycl_5fvkfft_2ecpp_1146', ['gpu_3dfft_sycl_vkfft.cpp', ['../gpu__3dfft__sycl__vkfft_8cpp.xhtml', 1, '']]], │ │ │ │ ['gpu_5f3dfft_5fsycl_5fvkfft_2eh_1147', ['gpu_3dfft_sycl_vkfft.h', ['../gpu__3dfft__sycl__vkfft_8h.xhtml', 1, '']]], │ │ │ │ ['gpu_5faccumulate_5ftimings_1148', ['gpu_accumulate_timings', ['../namespacegmx.xhtml#ac59e98cb9d0f58b6a86541d252a1f6db', 1, 'gmx']]], │ │ │ │ ['gpu_5fclear_5foutputs_1149', ['gpu_clear_outputs', ['../namespacegmx.xhtml#a7ce8d46cf4d31f5615aafa09502b9885', 1, 'gmx']]], │ │ │ │ ['gpu_5fcommon_2eh_1150', ['gpu_common.h', ['../gpu__common_8h.xhtml', 1, '']]], │ │ │ │ ['gpu_5fcommon_5futils_2eh_1151', ['gpu_common_utils.h', ['../gpu__common__utils_8h.xhtml', 1, '']]], │ │ │ │ - ['gpu_5fcopy_5fxq_5fto_5fgpu_1152', ['gpu_copy_xq_to_gpu', ['../namespacegmx.xhtml#ab38729f4217d6e32d04e32b877e8c3c6', 1, 'gmx::gpu_copy_xq_to_gpu(NbnxmGpu gmx_unused *nb, const struct nbnxn_atomdata_t gmx_unused *nbdata, AtomLocality gmx_unused aloc)'], │ │ │ │ - ['../namespacegmx.xhtml#a81682a6299331fb76b415a8fd0d6bb4c', 1, 'gmx::gpu_copy_xq_to_gpu(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom, const AtomLocality atomLocality)'] │ │ │ │ + ['gpu_5fcopy_5fxq_5fto_5fgpu_1152', ['gpu_copy_xq_to_gpu', ['../namespacegmx.xhtml#a81682a6299331fb76b415a8fd0d6bb4c', 1, 'gmx::gpu_copy_xq_to_gpu(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom, const AtomLocality atomLocality)'], │ │ │ │ + ['../namespacegmx.xhtml#ab38729f4217d6e32d04e32b877e8c3c6', 1, 'gmx::gpu_copy_xq_to_gpu(NbnxmGpu gmx_unused *nb, const struct nbnxn_atomdata_t gmx_unused *nbdata, AtomLocality gmx_unused aloc)'] │ │ │ │ ]], │ │ │ │ ['gpu_5fdata_5fmgmt_2eh_1153', ['gpu_data_mgmt.h', ['../gpu__data__mgmt_8h.xhtml', 1, '']]], │ │ │ │ ['gpu_5ffree_1154', ['gpu_free', ['../namespacegmx.xhtml#af96be16f42d67a9ddb29abe7810a48ba', 1, 'gmx::gpu_free(NbnxmGpu gmx_unused *nb)'], │ │ │ │ ['../namespacegmx.xhtml#ac31ed3e4c02494575fe3d85683ed95a4', 1, 'gmx::gpu_free(NbnxmGpu *nb)'] │ │ │ │ ]], │ │ │ │ ['gpu_5ffree_5fplatform_5fspecific_1155', ['gpu_free_platform_specific', ['../namespacegmx.xhtml#a0c9945e49d8977c64f9514ab048fffb7', 1, 'gmx']]], │ │ │ │ ['gpu_5fget_5ff_1156', ['gpu_get_f', ['../namespacegmx.xhtml#a3f4aa560b48378f9e8ab275ff326b4da', 1, 'gmx']]], │ │ │ │ - ['gpu_5fget_5ftimings_1157', ['gpu_get_timings', ['../namespacegmx.xhtml#ab7a59287bd253fd4feccbc55b49dd6c7', 1, 'gmx::gpu_get_timings(NbnxmGpu gmx_unused *nb)'], │ │ │ │ - ['../namespacegmx.xhtml#adc6c6fd8f6ed6f95bf9137379d020b76', 1, 'gmx::gpu_get_timings(NbnxmGpu *nb)'] │ │ │ │ + ['gpu_5fget_5ftimings_1157', ['gpu_get_timings', ['../namespacegmx.xhtml#adc6c6fd8f6ed6f95bf9137379d020b76', 1, 'gmx::gpu_get_timings(NbnxmGpu *nb)'], │ │ │ │ + ['../namespacegmx.xhtml#ab7a59287bd253fd4feccbc55b49dd6c7', 1, 'gmx::gpu_get_timings(NbnxmGpu gmx_unused *nb)'] │ │ │ │ ]], │ │ │ │ ['gpu_5finit_1158', ['gpu_init', ['../namespacegmx.xhtml#ab372371672d176090085a7d51bfa0fe8', 1, 'gmx']]], │ │ │ │ ['gpu_5finit_5fatomdata_1159', ['gpu_init_atomdata', ['../namespacegmx.xhtml#aed87fa557eeacefe44d14a79f92a13e5', 1, 'gmx']]], │ │ │ │ - ['gpu_5finit_5fpairlist_1160', ['gpu_init_pairlist', ['../namespacegmx.xhtml#acd25525982179407dd080639bb19f06d', 1, 'gmx::gpu_init_pairlist(NbnxmGpu gmx_unused *nb, const struct NbnxnPairlistGpu gmx_unused *h_nblist, InteractionLocality gmx_unused iloc)'], │ │ │ │ - ['../namespacegmx.xhtml#a76b7889defa44d4b0e3c97d5ce6a4988', 1, 'gmx::gpu_init_pairlist(NbnxmGpu *nb, const NbnxnPairlistGpu *h_plist, const InteractionLocality iloc)'] │ │ │ │ + ['gpu_5finit_5fpairlist_1160', ['gpu_init_pairlist', ['../namespacegmx.xhtml#a76b7889defa44d4b0e3c97d5ce6a4988', 1, 'gmx::gpu_init_pairlist(NbnxmGpu *nb, const NbnxnPairlistGpu *h_plist, const InteractionLocality iloc)'], │ │ │ │ + ['../namespacegmx.xhtml#acd25525982179407dd080639bb19f06d', 1, 'gmx::gpu_init_pairlist(NbnxmGpu gmx_unused *nb, const struct NbnxnPairlistGpu gmx_unused *h_nblist, InteractionLocality gmx_unused iloc)'] │ │ │ │ ]], │ │ │ │ ['gpu_5finit_5fplatform_5fspecific_1161', ['gpu_init_platform_specific', ['../namespacegmx.xhtml#a103fd146a3d324aaa3f78d11d51d312d', 1, 'gmx']]], │ │ │ │ ['gpu_5fis_5fkernel_5fewald_5fanalytical_1162', ['gpu_is_kernel_ewald_analytical', ['../namespacegmx.xhtml#a366c2a577ce32bcf2ebe44221c22c9a7', 1, 'gmx']]], │ │ │ │ ['gpu_5fjit_5fsupport_2eh_1163', ['gpu_jit_support.h', ['../gpu__jit__support_8h.xhtml', 1, '']]], │ │ │ │ ['gpu_5fkernel_5futils_2eh_1164', ['gpu_kernel_utils.h', ['../gpu__kernel__utils_8h.xhtml', 1, '']]], │ │ │ │ - ['gpu_5flaunch_5fcpyback_1165', ['gpu_launch_cpyback', ['../namespacegmx.xhtml#a7f597489a21ec7526af49e30af3dd413', 1, 'gmx::gpu_launch_cpyback(NbnxmGpu *nb, struct nbnxn_atomdata_t *nbatom, const StepWorkload &stepWork, const AtomLocality atomLocality)'], │ │ │ │ - ['../namespacegmx.xhtml#a7e44b47b3129712b572de33e51614622', 1, 'gmx::gpu_launch_cpyback(NbnxmGpu gmx_unused *nb, nbnxn_atomdata_t gmx_unused *nbatom, const StepWorkload gmx_unused &stepWork, AtomLocality gmx_unused aloc)'] │ │ │ │ + ['gpu_5flaunch_5fcpyback_1165', ['gpu_launch_cpyback', ['../namespacegmx.xhtml#a7e44b47b3129712b572de33e51614622', 1, 'gmx::gpu_launch_cpyback(NbnxmGpu gmx_unused *nb, nbnxn_atomdata_t gmx_unused *nbatom, const StepWorkload gmx_unused &stepWork, AtomLocality gmx_unused aloc)'], │ │ │ │ + ['../namespacegmx.xhtml#a7f597489a21ec7526af49e30af3dd413', 1, 'gmx::gpu_launch_cpyback(NbnxmGpu *nb, struct nbnxn_atomdata_t *nbatom, const StepWorkload &stepWork, const AtomLocality atomLocality)'] │ │ │ │ ]], │ │ │ │ ['gpu_5flaunch_5fkernel_1166', ['gpu_launch_kernel', ['../namespacegmx.xhtml#a723c08560acc1da48993827cb2329fe2', 1, 'gmx::gpu_launch_kernel(NbnxmGpu gmx_unused *nb, const StepWorkload gmx_unused &stepWork, InteractionLocality gmx_unused iloc)'], │ │ │ │ ['../namespacegmx.xhtml#aeb2f9e9167216ea83e7c738b8fec38e3', 1, 'gmx::gpu_launch_kernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc)'] │ │ │ │ ]], │ │ │ │ ['gpu_5flaunch_5fkernel_5fpruneonly_1167', ['gpu_launch_kernel_pruneonly', ['../namespacegmx.xhtml#a265dfa2c107a06f8e50dab59e6719258', 1, 'gmx::gpu_launch_kernel_pruneonly(NbnxmGpu gmx_unused *nb, InteractionLocality gmx_unused iloc, int gmx_unused numParts)'], │ │ │ │ ['../namespacegmx.xhtml#a36f047b90a00b500a201854cfc3afeea', 1, 'gmx::gpu_launch_kernel_pruneonly(NbnxmGpu *nb, const InteractionLocality iloc, const int numParts)'] │ │ │ │ ]], │ │ │ │ @@ -1702,52 +1702,52 @@ │ │ │ │ ['../classgmx_1_1DensitySimilarityMeasure.xhtml#a695fef9b730f4e653f43abb2247f84aa', 1, 'gmx::DensitySimilarityMeasure::gradient()'] │ │ │ │ ]], │ │ │ │ ['graph_1228', ['Module dependency graph', ['../page_modulegraph.xhtml', 1, 'index']]], │ │ │ │ ['graphiscapturingthisstep_1229', ['graphIsCapturingThisStep', ['../classgmx_1_1MdGpuGraph_1_1Impl.xhtml#ab56ed8da0231e7f6b26e990ee8090dcb', 1, 'gmx::MdGpuGraph::Impl']]], │ │ │ │ ['graphstate_1230', ['GraphState', ['../namespacegmx.xhtml#a936952a1a6d4f2d24c06259e1b03647b', 1, 'gmx']]], │ │ │ │ ['greatestcommondivisor_1231', ['greatestCommonDivisor', ['../namespacegmx.xhtml#a87a820e81baebe1c30a4190eb2aa2a64', 1, 'gmx']]], │ │ │ │ ['gref_1232', ['gref', ['../classgmx_1_1SelectionTreeElement.xhtml#a64f582fc2e944f96cac7137a7d9ebe93', 1, 'gmx::SelectionTreeElement']]], │ │ │ │ - ['grid_1233', ['grid', ['../classgmx_1_1GridSet.xhtml#a9a5d13e20a107e66f6dbe4f84adc7a5e', 1, 'gmx::GridSet::grid()'], │ │ │ │ - ['../structpme__setup__t.xhtml#a802011c5154d75f85f8350703a3cc57a', 1, 'pme_setup_t::grid'], │ │ │ │ - ['../structPmeGpuKernelParamsBase.xhtml#aaf6a2003a41a087df8b48308103d4f65', 1, 'PmeGpuKernelParamsBase::grid'], │ │ │ │ + ['grid_1233', ['grid', ['../structPmeGpuKernelParamsBase.xhtml#aaf6a2003a41a087df8b48308103d4f65', 1, 'PmeGpuKernelParamsBase::grid'], │ │ │ │ ['../classgmx_1_1Grid.xhtml#af86034f1ac6c91d92ca3c9d24118246f', 1, 'gmx::Grid::Grid()'], │ │ │ │ - ['../classgmx_1_1Grid.xhtml', 1, 'gmx::Grid'] │ │ │ │ + ['../classgmx_1_1Grid.xhtml', 1, 'gmx::Grid'], │ │ │ │ + ['../structpme__setup__t.xhtml#a802011c5154d75f85f8350703a3cc57a', 1, 'pme_setup_t::grid'], │ │ │ │ + ['../classgmx_1_1GridSet.xhtml#a9a5d13e20a107e66f6dbe4f84adc7a5e', 1, 'gmx::GridSet::grid()'] │ │ │ │ ]], │ │ │ │ ['grid_2ecpp_1234', ['grid.cpp', ['../grid_8cpp.xhtml', 1, '']]], │ │ │ │ ['grid_2eh_1235', ['grid.h', ['../grid_8h.xhtml', 1, '']]], │ │ │ │ ['grid_5fefficiency_1236', ['grid_efficiency', ['../structpme__setup__t.xhtml#af9bc7fe8d120a9ce09fb34dbb13c5e02', 1, 'pme_setup_t']]], │ │ │ │ ['grid_5fjump_5flimit_1237', ['grid_jump_limit', ['../cellsizes_8h.xhtml#af6352e0cf904a7706ee1bfa26da92fd1', 1, 'cellsizes.cpp']]], │ │ │ │ ['grid_5fsize_1238', ['grid_size', ['../structgmx__pme__comm__n__box__t.xhtml#ab5017f2825236c1b6b25bae434c54285', 1, 'gmx_pme_comm_n_box_t']]], │ │ │ │ ['grid_5fspacing_1239', ['grid_spacing', ['../structgmx__cmap__t.xhtml#a33fff24fdd8af811e3cab88f85a684d4', 1, 'gmx_cmap_t']]], │ │ │ │ ['gridatomdensity_1240', ['gridAtomDensity', ['../namespacegmx.xhtml#a24ee8f0a42321d5cc9b56695d1104851', 1, 'gmx']]], │ │ │ │ - ['gridaxis_1241', ['gridaxis', ['../classgmx_1_1GridAxis.xhtml#ac25fe4a7ae54ee244af76de43849981a', 1, 'gmx::GridAxis::GridAxis()'], │ │ │ │ - ['../classgmx_1_1GridAxis.xhtml', 1, 'gmx::GridAxis'], │ │ │ │ - ['../classgmx_1_1GridAxis.xhtml#a02a3470e94373965d0384ec553def815', 1, 'gmx::GridAxis::GridAxis()'] │ │ │ │ + ['gridaxis_1241', ['gridaxis', ['../classgmx_1_1GridAxis.xhtml#ac25fe4a7ae54ee244af76de43849981a', 1, 'gmx::GridAxis::GridAxis(double origin, double end, double period, int numPoints, bool isFepLambdaAxis)'], │ │ │ │ + ['../classgmx_1_1GridAxis.xhtml#a02a3470e94373965d0384ec553def815', 1, 'gmx::GridAxis::GridAxis(double origin, double end, double period, double pointDensity)'], │ │ │ │ + ['../classgmx_1_1GridAxis.xhtml', 1, 'gmx::GridAxis'] │ │ │ │ ]], │ │ │ │ ['gridcolumns_1242', ['GridColumns', ['../namespacegmx.xhtml#aa1992b14265329250b7e14d817e7bb92a8b6df887946357351b1d8e05660d1eea', 1, 'gmx']]], │ │ │ │ ['gridconverter_1243', ['GridConverter', ['../classGridConverter.xhtml', 1, '']]], │ │ │ │ - ['griddimensions_1244', ['griddimensions', ['../structgmx_1_1GridDimensions.xhtml', 1, 'gmx::GridDimensions'], │ │ │ │ - ['../namespacegmx.xhtml#aa1992b14265329250b7e14d817e7bb92a989dff161ffe2f1603b6508fd3ce5be9', 1, 'gmx::GridDimensions'] │ │ │ │ + ['griddimensions_1244', ['griddimensions', ['../namespacegmx.xhtml#aa1992b14265329250b7e14d817e7bb92a989dff161ffe2f1603b6508fd3ce5be9', 1, 'gmx::GridDimensions'], │ │ │ │ + ['../structgmx_1_1GridDimensions.xhtml', 1, 'gmx::GridDimensions'] │ │ │ │ ]], │ │ │ │ ['griddimx_5f_1245', ['gridDimX_', ['../structgmx_1_1nvshmemHaloExchangeOps.xhtml#a042f4f0d3108190438aac4d3682784b5', 1, 'gmx::nvshmemHaloExchangeOps']]], │ │ │ │ ['gridhalo_1246', ['gridHalo', ['../structPmeShared.xhtml#aaf3451df7d0cc668d77d528d6b5faa7a', 1, 'PmeShared']]], │ │ │ │ ['gridlineindices_1247', ['gridLineIndices', ['../structgmx_1_1test_1_1anonymous__namespace_02pmegathertest_8cpp_03_1_1TestSystem.xhtml#ae3f59f14fe82da742d0c9a3421992d91', 1, 'gmx::test::anonymous_namespace{pmegathertest.cpp}::TestSystem']]], │ │ │ │ ['gridlineindicessize_1248', ['gridlineIndicesSize', ['../structPmeGpuSpecific.xhtml#a247c98c89be390d46866794581b48a85', 1, 'PmeGpuSpecific']]], │ │ │ │ ['gridlineindicessizealloc_1249', ['gridlineIndicesSizeAlloc', ['../structPmeGpuSpecific.xhtml#ab74e57d8c216e197a7b975b4c3db3cc0', 1, 'PmeGpuSpecific']]], │ │ │ │ ['gridlineindicestabletexture_1250', ['gridlineIndicesTableTexture', ['../structPmeGpuKernelParamsBase.xhtml#a3691d83fd3e630b2e0fbe6164fc585ed', 1, 'PmeGpuKernelParamsBase']]], │ │ │ │ ['gridlineindicesvector_1251', ['GridLineIndicesVector', ['../namespacegmx_1_1test.xhtml#a1767f5a0dc16317f3850673f9dcb2774', 1, 'gmx::test']]], │ │ │ │ ['gridordering_1252', ['GridOrdering', ['../pme__gpu__internal_8h.xhtml#a68be0dbcc0dc3960694fc024c5996d79', 1, 'pme_gpu_internal.h']]], │ │ │ │ ['gridpoint_1253', ['GridPoint', ['../structgmx_1_1GridPoint.xhtml', 1, 'gmx']]], │ │ │ │ ['gridpointindex_1254', ['gridpointIndex', ['../classgmx_1_1CoordState.xhtml#a0e9bd167b43dd6d3a80babaf588b8952', 1, 'gmx::CoordState']]], │ │ │ │ ['gridpointsscalefactor_1255', ['gridpointsScaleFactor', ['../pme__load__balancing_8cpp.xhtml#ac64134c8b30aafc2d8b58015b998586e', 1, 'pme_load_balancing.cpp']]], │ │ │ │ ['gridpointvaluestring_1256', ['gridPointValueString', ['../namespacegmx_1_1anonymous__namespace_02biasstate_8cpp_03.xhtml#a10f5abe6e41fdca2972f2b8f461483cc', 1, 'gmx::anonymous_namespace{biasstate.cpp}']]], │ │ │ │ ['grids_1257', ['grids', ['../classgmx_1_1GridSet.xhtml#aea347c9d831801e363fab59cfd2e4a45', 1, 'gmx::GridSet']]], │ │ │ │ - ['gridset_1258', ['gridset', ['../classgmx_1_1PairSearch.xhtml#a9a2e96afcf5b46048f3af516949fc838', 1, 'gmx::PairSearch::gridSet()'], │ │ │ │ - ['../classgmx_1_1GridSet.xhtml#a9c99b919b71c2d3b740cf85d0c026b1b', 1, 'gmx::GridSet::GridSet()'], │ │ │ │ - ['../classgmx_1_1GridSet.xhtml', 1, 'gmx::GridSet'] │ │ │ │ + ['gridset_1258', ['gridset', ['../classgmx_1_1GridSet.xhtml', 1, 'gmx::GridSet'], │ │ │ │ + ['../classgmx_1_1PairSearch.xhtml#a9a2e96afcf5b46048f3af516949fc838', 1, 'gmx::PairSearch::gridSet()'], │ │ │ │ + ['../classgmx_1_1GridSet.xhtml#a9c99b919b71c2d3b740cf85d0c026b1b', 1, 'gmx::GridSet::GridSet()'] │ │ │ │ ]], │ │ │ │ ['gridset_2ecpp_1259', ['gridset.cpp', ['../gridset_8cpp.xhtml', 1, '']]], │ │ │ │ ['gridset_2eh_1260', ['gridset.h', ['../gridset_8h.xhtml', 1, '']]], │ │ │ │ ['gridsetdata_1261', ['GridSetData', ['../structgmx_1_1GridSetData.xhtml', 1, 'gmx']]], │ │ │ │ ['gridsetdata_2eh_1262', ['gridsetdata.h', ['../gridsetdata_8h.xhtml', 1, '']]], │ │ │ │ ['gridsize_1263', ['gridsize', ['../structgmx_1_1GridDimensions.xhtml#a745bf70fcdd7bcb1e850f328be33b622', 1, 'gmx::GridDimensions::gridSize'], │ │ │ │ ['../structKernelLaunchConfig.xhtml#a3624b5c69309eb75970d57a6b80b6dae', 1, 'KernelLaunchConfig::gridSize'] │ │ │ │ @@ -1760,16 +1760,16 @@ │ │ │ │ ['../page_analysistemplate.xhtml#autotoc_md88', 1, 'Tools within GROMACS'] │ │ │ │ ]], │ │ │ │ ['gromacs_20api_1269', ['Notes on GROMACS API', ['../page_usinglibrary.xhtml#autotoc_md105', 1, '']]], │ │ │ │ ['gromacs_20as_20a_20library_1270', ['Using GROMACS as a library', ['../page_usinglibrary.xhtml', 1, 'index']]], │ │ │ │ ['gromacs_20simd_20module_1271', ['Design of the GROMACS SIMD module', ['../page_simd.xhtml#autotoc_md57', 1, '']]], │ │ │ │ ['gromacs_20specific_20markup_1272', ['GROMACS-specific markup', ['../page_onlinehelp.xhtml#autotoc_md93', 1, '']]], │ │ │ │ ['gromacs_20tt_20details_1273', ['CMake <tt>find_package(GROMACS)</tt> details', ['../page_usinglibrary.xhtml#autotoc_md104', 1, '']]], │ │ │ │ - ['gromacsexception_1274', ['gromacsexception', ['../classgmx_1_1GromacsException.xhtml#a1a17194de13545be2ae61aa7d95479e6', 1, 'gmx::GromacsException::GromacsException()'], │ │ │ │ - ['../classgmx_1_1GromacsException.xhtml', 1, 'gmx::GromacsException'] │ │ │ │ + ['gromacsexception_1274', ['gromacsexception', ['../classgmx_1_1GromacsException.xhtml', 1, 'gmx::GromacsException'], │ │ │ │ + ['../classgmx_1_1GromacsException.xhtml#a1a17194de13545be2ae61aa7d95479e6', 1, 'gmx::GromacsException::GromacsException()'] │ │ │ │ ]], │ │ │ │ ['grompp_2ecpp_1275', ['grompp.cpp', ['../programs_2mdrun_2tests_2grompp_8cpp.xhtml', 1, '']]], │ │ │ │ ['grompp_5fdirectives_2ecpp_1276', ['grompp_directives.cpp', ['../grompp__directives_8cpp.xhtml', 1, '']]], │ │ │ │ ['gromppmtsopts_1277', ['GromppMtsOpts', ['../structgmx_1_1GromppMtsOpts.xhtml', 1, 'gmx']]], │ │ │ │ ['grompptest_1278', ['GromppTest', ['../classanonymous__namespace_02grompp_8cpp_03_1_1GromppTest.xhtml', 1, 'anonymous_namespace{grompp.cpp}']]], │ │ │ │ ['group_1279', ['group', ['../classgmx_1_1internal_1_1OptionSectionImpl_1_1Group.xhtml', 1, 'gmx::internal::OptionSectionImpl::Group'], │ │ │ │ ['../classgmx_1_1internal_1_1OptionSectionImpl_1_1Group.xhtml#a4acd2ced9bfdabb539a488ba3637b289', 1, 'gmx::internal::OptionSectionImpl::Group::Group()'], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/all_b.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -180,16 +180,16 @@ │ │ │ │ ['haveppdomaindecomposition_136', ['havePpDomainDecomposition', ['../classgmx_1_1SimulationWorkload.xhtml#ae838b35257293e428d5c8d64006e8607', 1, 'gmx::SimulationWorkload']]], │ │ │ │ ['haveppdomaindecomposition_5f_137', ['havePpDomainDecomposition_', ['../classgmx_1_1DeviceStreamManager_1_1Impl.xhtml#ac5838ece3cc4aa5534d85d0d59f31d39', 1, 'gmx::DeviceStreamManager::Impl']]], │ │ │ │ ['haverestraints_138', ['haveRestraints', ['../classListedForces.xhtml#a56ae47b0b9044b2c489298ea1578f15c', 1, 'ListedForces']]], │ │ │ │ ['havescrewpbc_139', ['haveScrewPBC', ['../structUnitCellInfo.xhtml#ab5bba3c375df6499381d7020eb2449bb', 1, 'UnitCellInfo']]], │ │ │ │ ['havesecondupdatetask_140', ['haveSecondUpdateTask', ['../classgmx_1_1Lincs.xhtml#a556346e605d7c18a225864f73ab21d3d', 1, 'gmx::Lincs']]], │ │ │ │ ['haveseparatepmerank_141', ['haveSeparatePmeRank', ['../classgmx_1_1SimulationWorkload.xhtml#ab6ef46d7f69a25aa972254019686dccc', 1, 'gmx::SimulationWorkload']]], │ │ │ │ ['havesoftcore_142', ['haveSoftCore', ['../namespacegmx_1_1anonymous__namespace_02freeenergydispatch_8cpp_03.xhtml#a01bfead00417e4b79b79ebb4689da981', 1, 'gmx::anonymous_namespace{freeenergydispatch.cpp}']]], │ │ │ │ - ['havespecialforces_143', ['havespecialforces', ['../classgmx_1_1DomainLifetimeWorkload.xhtml#a488c257ad510afcf326eb547c203db9c', 1, 'gmx::DomainLifetimeWorkload::haveSpecialForces'], │ │ │ │ - ['../namespacegmx.xhtml#a07f20c896237b9d81d54c391c0a79573', 1, 'gmx::haveSpecialForces()'] │ │ │ │ + ['havespecialforces_143', ['havespecialforces', ['../namespacegmx.xhtml#a07f20c896237b9d81d54c391c0a79573', 1, 'gmx::haveSpecialForces()'], │ │ │ │ + ['../classgmx_1_1DomainLifetimeWorkload.xhtml#a488c257ad510afcf326eb547c203db9c', 1, 'gmx::DomainLifetimeWorkload::haveSpecialForces'] │ │ │ │ ]], │ │ │ │ ['havespreadvsiteforces_144', ['haveSpreadVsiteForces', ['../classgmx_1_1ForceWithShiftForces.xhtml#a0797be6859a3e138c94eb6b4388c2de0', 1, 'gmx::ForceWithShiftForces']]], │ │ │ │ ['havestreamtaskscompleted_145', ['haveStreamTasksCompleted', ['../oclutils_8h.xhtml#aa88a1dbdaeaeccfae95990dc6cd5bdc7', 1, 'oclutils.h']]], │ │ │ │ ['havesubscribers_146', ['haveSubscribers', ['../classgmx_1_1MDModulesNotifier.xhtml#a9fe2eaf34ecce424aed585cd6101b1c3', 1, 'gmx::MDModulesNotifier']]], │ │ │ │ ['havetype_147', ['haveType', ['../classSimulationParticle.xhtml#ad945ae525cf340063d00bf48bdb990da', 1, 'SimulationParticle']]], │ │ │ │ ['havevalidmtssetup_148', ['haveValidMtsSetup', ['../namespacegmx.xhtml#aa7f6a95d43d5e8db2b95967553c93432', 1, 'gmx']]], │ │ │ │ ['havework_149', ['havework', ['../structgmx_1_1NbnxmGpu.xhtml#a9dcea3095a20935487ecc9134b404ee0', 1, 'gmx::NbnxmGpu::haveWork'], │ │ │ │ @@ -221,16 +221,16 @@ │ │ │ │ ['heffte_5fsycl_5frocfft_164', ['HeFFTe_Sycl_Rocfft', ['../namespacegmx.xhtml#aad56f475765c1a78ee7f33e143e717bbae4dc8a36b2a94b284bdb29a5fc6c0af7', 1, 'gmx']]], │ │ │ │ ['helix_5f3_165', ['Helix_3', ['../namespacegmx_1_1analysismodules_1_1anonymous__namespace_02dssp_8cpp_03.xhtml#a8ec2371446161e824ba0e6fb1edbba0ca01a6e532ebbbfb4481e0794370bf04c8', 1, 'gmx::analysismodules::anonymous_namespace{dssp.cpp}']]], │ │ │ │ ['helix_5f4_166', ['Helix_4', ['../namespacegmx_1_1analysismodules_1_1anonymous__namespace_02dssp_8cpp_03.xhtml#a8ec2371446161e824ba0e6fb1edbba0caf0f421db295b9f5cbee24ea4fe7b202e', 1, 'gmx::analysismodules::anonymous_namespace{dssp.cpp}']]], │ │ │ │ ['helix_5f5_167', ['Helix_5', ['../namespacegmx_1_1analysismodules_1_1anonymous__namespace_02dssp_8cpp_03.xhtml#a8ec2371446161e824ba0e6fb1edbba0ca2196e9a842c0e57906d5e242eb8df770', 1, 'gmx::analysismodules::anonymous_namespace{dssp.cpp}']]], │ │ │ │ ['helix_5fpp_168', ['Helix_PP', ['../namespacegmx_1_1analysismodules_1_1anonymous__namespace_02dssp_8cpp_03.xhtml#a8ec2371446161e824ba0e6fb1edbba0ca77e4b5d7ba41232f4d3d01f8860ffb41', 1, 'gmx::analysismodules::anonymous_namespace{dssp.cpp}']]], │ │ │ │ ['helixpositions_169', ['HelixPositions', ['../namespacegmx_1_1analysismodules_1_1anonymous__namespace_02dssp_8cpp_03.xhtml#a869b266ce47ab7979503e4447d09f37a', 1, 'gmx::analysismodules::anonymous_namespace{dssp.cpp}']]], │ │ │ │ ['help_170', ['help', ['../page_wrapperbinary.xhtml#autotoc_md73', 1, 'Command line help'], │ │ │ │ - ['../structgmx__ana__selmethod__t.xhtml#ae7d6f1b14964a172d4d9ed38e50426a4', 1, 'gmx_ana_selmethod_t::help'], │ │ │ │ - ['../structgmx__ana__selmethod__help__t.xhtml#ac0d1505d6da8c1912a5a3aab37927e7f', 1, 'gmx_ana_selmethod_help_t::help'] │ │ │ │ + ['../structgmx__ana__selmethod__help__t.xhtml#ac0d1505d6da8c1912a5a3aab37927e7f', 1, 'gmx_ana_selmethod_help_t::help'], │ │ │ │ + ['../structgmx__ana__selmethod__t.xhtml#ae7d6f1b14964a172d4d9ed38e50426a4', 1, 'gmx_ana_selmethod_t::help'] │ │ │ │ ]], │ │ │ │ ['help_20formatting_171', ['Help formatting', ['../page_onlinehelp.xhtml', 1, 'index']]], │ │ │ │ ['help_20formatting_20for_20online_20help_20onlinehelp_172', ['Help Formatting for Online Help (onlinehelp)', ['../group__module__onlinehelp.xhtml', 1, '']]], │ │ │ │ ['help_20in_20other_20formats_173', ['Help in other formats', ['../page_wrapperbinary.xhtml#autotoc_md74', 1, '']]], │ │ │ │ ['help_5fatomname_174', ['help_atomname', ['../sm__simple_8cpp.xhtml#a29a0e2cf7b47229a76d97109c02345ae', 1, 'sm_simple.cpp']]], │ │ │ │ ['help_5fdistance_175', ['help_distance', ['../sm__distance_8cpp.xhtml#adfcf38060537bda993410d562cb09dea', 1, 'sm_distance.cpp']]], │ │ │ │ ['help_5finsolidangle_176', ['help_insolidangle', ['../sm__insolidangle_8cpp.xhtml#a8d1b673a4ecad9ac2f2b7b50495aa773', 1, 'sm_insolidangle.cpp']]], │ │ │ │ @@ -241,16 +241,16 @@ │ │ │ │ ['helpers_181', ['C++ standard library compatibility helpers.', ['../group__group__compatibility.xhtml', 1, '']]], │ │ │ │ ['helpexportcompletion_182', ['helpexportcompletion', ['../classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportCompletion.xhtml', 1, 'gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportCompletion'], │ │ │ │ ['../classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportCompletion.xhtml#ad83b694e2124de02d6db4b8248c83831', 1, 'gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportCompletion::HelpExportCompletion()'] │ │ │ │ ]], │ │ │ │ ['helpexportrestructuredtext_183', ['helpexportrestructuredtext', ['../classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportReStructuredText.xhtml#a7beb511be591b985e3b0ead22dfbe66d', 1, 'gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportReStructuredText::HelpExportReStructuredText()'], │ │ │ │ ['../classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1HelpExportReStructuredText.xhtml', 1, 'gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportReStructuredText'] │ │ │ │ ]], │ │ │ │ - ['helpformat_2ecpp_184', ['helpformat.cpp', ['../helpformat_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2helpformat_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['helpformat_2ecpp_184', ['helpformat.cpp', ['../tests_2helpformat_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../helpformat_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['helpformat_2eh_185', ['helpformat.h', ['../helpformat_8h.xhtml', 1, '']]], │ │ │ │ ['helplinks_186', ['helplinks', ['../classgmx_1_1HelpLinks.xhtml', 1, 'gmx::HelpLinks'], │ │ │ │ ['../classgmx_1_1HelpLinks.xhtml#a8be2854c046e14440fc5da7ebfb04767', 1, 'gmx::HelpLinks::HelpLinks()'] │ │ │ │ ]], │ │ │ │ ['helpmanager_187', ['helpmanager', ['../classgmx_1_1HelpManager.xhtml', 1, 'gmx::HelpManager'], │ │ │ │ ['../classgmx_1_1HelpManager.xhtml#a0578951cf2928a59819c0589065c4a5c', 1, 'gmx::HelpManager::HelpManager()'] │ │ │ │ @@ -258,41 +258,41 @@ │ │ │ │ ['helpmanager_2ecpp_188', ['helpmanager.cpp', ['../tests_2helpmanager_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../helpmanager_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['helpmanager_2eh_189', ['helpmanager.h', ['../helpmanager_8h.xhtml', 1, '']]], │ │ │ │ ['helpmanagertest_190', ['HelpManagerTest', ['../namespacegmx_1_1test_1_1anonymous__namespace_02helpmanager_8cpp_03.xhtml#af3f158bf9b2db55ac1e2a2a60f6ee995', 1, 'gmx::test::anonymous_namespace{helpmanager.cpp}']]], │ │ │ │ ['helpmodule_5f_191', ['helpModule_', ['../classgmx_1_1CommandLineModuleManager_1_1Impl.xhtml#a8b5a1258815add1b14dca4d8ff8998c4', 1, 'gmx::CommandLineModuleManager::Impl']]], │ │ │ │ ['helpoutputformat_192', ['HelpOutputFormat', ['../namespacegmx.xhtml#adc6936f6090da8e4cf7801c8e71ee37f', 1, 'gmx']]], │ │ │ │ - ['helptext_193', ['helptext', ['../classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordDetailsHelpTopic.xhtml#aa3cfab4bcc96ceda1c81456f1f6cbc3f', 1, 'gmx::anonymous_namespace{selhelp.cpp}::KeywordDetailsHelpTopic::helpText()'], │ │ │ │ - ['../classgmx_1_1AbstractSimpleHelpTopic.xhtml#ac8df9bdad0655b933a63d4fcb84c3c90', 1, 'gmx::AbstractSimpleHelpTopic::helpText()'], │ │ │ │ + ['helptext_193', ['helptext', ['../classgmx_1_1AbstractSimpleHelpTopic.xhtml#ac8df9bdad0655b933a63d4fcb84c3c90', 1, 'gmx::AbstractSimpleHelpTopic::helpText()'], │ │ │ │ ['../classgmx_1_1AbstractCompositeHelpTopic.xhtml#ab94bb5f1964de89ddb4da358aae48116', 1, 'gmx::AbstractCompositeHelpTopic::helpText()'], │ │ │ │ ['../classgmx_1_1SimpleHelpTopic.xhtml#a044e07745db4f94d13c1c99a7cfa7e31', 1, 'gmx::SimpleHelpTopic::helpText()'], │ │ │ │ - ['../classgmx_1_1CompositeHelpTopic.xhtml#a7452b0c48cc5fed19150f672bebf1646', 1, 'gmx::CompositeHelpTopic::helpText()'] │ │ │ │ + ['../classgmx_1_1CompositeHelpTopic.xhtml#a7452b0c48cc5fed19150f672bebf1646', 1, 'gmx::CompositeHelpTopic::helpText()'], │ │ │ │ + ['../classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordDetailsHelpTopic.xhtml#aa3cfab4bcc96ceda1c81456f1f6cbc3f', 1, 'gmx::anonymous_namespace{selhelp.cpp}::KeywordDetailsHelpTopic::helpText()'] │ │ │ │ ]], │ │ │ │ ['helptext_5f_194', ['helpText_', ['../classgmx_1_1CommandLineHelpWriter_1_1Impl.xhtml#a111543ff6be5909585275501b8c1a041', 1, 'gmx::CommandLineHelpWriter::Impl']]], │ │ │ │ ['helptitle_195', ['helpTitle', ['../structgmx__ana__selmethod__help__t.xhtml#a881ec7c346661f63a0f24ad1f543b671', 1, 'gmx_ana_selmethod_help_t']]], │ │ │ │ ['helptitle_5fatomname_196', ['helptitle_atomname', ['../sm__simple_8cpp.xhtml#a72cbdfb8b248a4378d1a3ff247dfcf2a', 1, 'sm_simple.cpp']]], │ │ │ │ ['helptitle_5fdistance_197', ['helptitle_distance', ['../sm__distance_8cpp.xhtml#ae4dcf55ca7cd7f92b81e9a57f8efb0c1', 1, 'sm_distance.cpp']]], │ │ │ │ ['helptitle_5fmerge_198', ['helptitle_merge', ['../sm__merge_8cpp.xhtml#afffcc8309d2f125d594d806812208277', 1, 'sm_merge.cpp']]], │ │ │ │ ['helptitle_5fresindex_199', ['helptitle_resindex', ['../sm__simple_8cpp.xhtml#a7af03298cdb6413820026fb020a77100', 1, 'sm_simple.cpp']]], │ │ │ │ ['helptopic_2ecpp_200', ['helptopic.cpp', ['../helptopic_8cpp.xhtml', 1, '']]], │ │ │ │ ['helptopic_2eh_201', ['helptopic.h', ['../helptopic_8h.xhtml', 1, '']]], │ │ │ │ ['helptopicpointer_202', ['HelpTopicPointer', ['../namespacegmx.xhtml#abb455c7711ece592606e70a093ff80b4', 1, 'gmx']]], │ │ │ │ - ['helpwritercontext_203', ['helpwritercontext', ['../classgmx_1_1HelpWriterContext.xhtml', 1, 'gmx::HelpWriterContext'], │ │ │ │ - ['../classgmx_1_1HelpWriterContext.xhtml#ae1e18511b3fea03259da87cceb160ef0', 1, 'gmx::HelpWriterContext::HelpWriterContext(const HelpWriterContext &other)'], │ │ │ │ - ['../classgmx_1_1HelpWriterContext.xhtml#a9cc36f78e38c772e52c4cdc73cf18d7c', 1, 'gmx::HelpWriterContext::HelpWriterContext(TextWriter *writer, HelpOutputFormat format, const HelpLinks *links)'], │ │ │ │ + ['helpwritercontext_203', ['helpwritercontext', ['../classgmx_1_1HelpLinks.xhtml#a734bf51c01e151da043a218f686b5114', 1, 'gmx::HelpLinks::HelpWriterContext'], │ │ │ │ ['../classgmx_1_1HelpWriterContext.xhtml#ab17b32ad5802855990bd79ae6ada94b4', 1, 'gmx::HelpWriterContext::HelpWriterContext(TextWriter *writer, HelpOutputFormat format)'], │ │ │ │ - ['../classgmx_1_1HelpLinks.xhtml#a734bf51c01e151da043a218f686b5114', 1, 'gmx::HelpLinks::HelpWriterContext'] │ │ │ │ + ['../classgmx_1_1HelpWriterContext.xhtml#a9cc36f78e38c772e52c4cdc73cf18d7c', 1, 'gmx::HelpWriterContext::HelpWriterContext(TextWriter *writer, HelpOutputFormat format, const HelpLinks *links)'], │ │ │ │ + ['../classgmx_1_1HelpWriterContext.xhtml#ae1e18511b3fea03259da87cceb160ef0', 1, 'gmx::HelpWriterContext::HelpWriterContext(const HelpWriterContext &other)'], │ │ │ │ + ['../classgmx_1_1HelpWriterContext.xhtml', 1, 'gmx::HelpWriterContext'] │ │ │ │ ]], │ │ │ │ ['helpwritercontext_2ecpp_204', ['helpwritercontext.cpp', ['../helpwritercontext_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../tests_2helpwritercontext_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['helpwritercontext_2eh_205', ['helpwritercontext.h', ['../helpwritercontext_8h.xhtml', 1, '']]], │ │ │ │ - ['helpwriting_2ecpp_206', ['helpwriting.cpp', ['../programs_2mdrun_2tests_2helpwriting_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../gromacs_2tools_2tests_2helpwriting_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['helpwriting_2ecpp_206', ['helpwriting.cpp', ['../gromacs_2tools_2tests_2helpwriting_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../programs_2mdrun_2tests_2helpwriting_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['hidden_207', ['hidden', ['../classgmx_1_1OptionTemplate.xhtml#a8a3e6c99bb3d8cae0318f6f3d96376b7', 1, 'gmx::OptionTemplate']]], │ │ │ │ ['hide_5ffrom_5fopencl_5fcompiler_208', ['HIDE_FROM_OPENCL_COMPILER', ['../pme__gpu__types_8h.xhtml#a683fdff44eefc1064e0e0e2ecba75fbe', 1, 'pme_gpu_types.h']]], │ │ │ │ ['high_209', ['High', ['../device__stream_8h.xhtml#a745c3a25d092600ae45b68d7e73d8319a655d20c1ca69519ca647684edbb2db35', 1, 'device_stream.h']]], │ │ │ │ ['high_20level_20framework_210', ['high level framework', ['../page_trajectoryanalysisframework.xhtml#autotoc_md98', 1, 'High-level framework'], │ │ │ │ ['../page_energyanalysisframework.xhtml#autotoc_md89', 1, 'High-level framework'] │ │ │ │ ]], │ │ │ │ @@ -309,27 +309,27 @@ │ │ │ │ ['../tests_2histogram_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['histogram_2eh_221', ['histogram.h', ['../histogram_8h.xhtml', 1, '']]], │ │ │ │ ['histogramfrombins_222', ['histogramFromBins', ['../group__group__publicapi.xhtml#ga73a2213cd82e2f915b9f9d65a4b85212', 1, 'gmx']]], │ │ │ │ ['histogramfromrange_223', ['histogramFromRange', ['../group__group__publicapi.xhtml#gaaf9a9e69ad91172d5f4fba7148280762', 1, 'gmx']]], │ │ │ │ ['histogramisequilibrated_224', ['histogramIsEquilibrated', ['../namespacegmx_1_1anonymous__namespace_02histogramsize_8cpp_03.xhtml#aa21d0e550b2eada448c1e14b657f1ca1', 1, 'gmx::anonymous_namespace{histogramsize.cpp}']]], │ │ │ │ ['histogramsize_225', ['histogramsize', ['../classgmx_1_1HistogramSize.xhtml', 1, 'gmx::HistogramSize'], │ │ │ │ + ['../classgmx_1_1HistogramSize.xhtml#ac1c0ea80231544919c124024db5b2203', 1, 'gmx::HistogramSize::HistogramSize()'], │ │ │ │ ['../classgmx_1_1BiasState.xhtml#aa9f45bf3772811b41c2263d8d7985c72', 1, 'gmx::BiasState::histogramSize()'], │ │ │ │ - ['../classgmx_1_1HistogramSize.xhtml#a114eca6ee210c4f957fb5f1850b4ae3f', 1, 'gmx::HistogramSize::histogramSize() const'], │ │ │ │ - ['../classgmx_1_1HistogramSize.xhtml#ac1c0ea80231544919c124024db5b2203', 1, 'gmx::HistogramSize::HistogramSize(const AwhBiasParams &awhBiasParams, double histogramSizeInitial)'] │ │ │ │ + ['../classgmx_1_1HistogramSize.xhtml#a114eca6ee210c4f957fb5f1850b4ae3f', 1, 'gmx::HistogramSize::histogramSize()'] │ │ │ │ ]], │ │ │ │ ['histogramsize_2ecpp_226', ['histogramsize.cpp', ['../histogramsize_8cpp.xhtml', 1, '']]], │ │ │ │ ['histogramsize_2eh_227', ['histogramsize.h', ['../histogramsize_8h.xhtml', 1, '']]], │ │ │ │ ['history_5ft_228', ['history_t', ['../classhistory__t.xhtml', 1, '']]], │ │ │ │ ['hostallocationpolicy_229', ['hostallocationpolicy', ['../classgmx_1_1HostAllocationPolicy.xhtml#ae21acc5cb9c70ea92fce07cb0d6e2947', 1, 'gmx::HostAllocationPolicy::HostAllocationPolicy()'], │ │ │ │ ['../classgmx_1_1HostAllocationPolicy.xhtml', 1, 'gmx::HostAllocationPolicy'] │ │ │ │ ]], │ │ │ │ ['hostallocator_230', ['HostAllocator', ['../namespacegmx.xhtml#aae347fd6abaab2e4d8278bf17973b664', 1, 'gmx']]], │ │ │ │ - ['hostallocator_2ecpp_231', ['hostallocator.cpp', ['../tests_2hostallocator_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../hostallocator_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['hostallocator_2ecpp_231', ['hostallocator.cpp', ['../hostallocator_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2hostallocator_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['hostallocator_2eh_232', ['hostallocator.h', ['../hostallocator_8h.xhtml', 1, '']]], │ │ │ │ ['hostallocatortest_233', ['HostAllocatorTest', ['../structgmx_1_1test_1_1HostAllocatorTest.xhtml', 1, 'gmx::test']]], │ │ │ │ ['hostallocatortestcopyable_234', ['HostAllocatorTestCopyable', ['../namespacegmx_1_1test.xhtml#af4467ed419f6f86b5167681787e399a2', 1, 'gmx::test']]], │ │ │ │ ['hostallocatortestnomem_235', ['HostAllocatorTestNoMem', ['../structgmx_1_1test_1_1HostAllocatorTestNoMem.xhtml', 1, 'gmx::test']]], │ │ │ │ ['hostallocatortestnomemcopyable_236', ['HostAllocatorTestNoMemCopyable', ['../structgmx_1_1test_1_1HostAllocatorTestNoMemCopyable.xhtml', 1, 'gmx::test']]], │ │ │ │ ['hostinteractionlist_237', ['HostInteractionList', ['../structgmx_1_1HostInteractionList.xhtml', 1, 'gmx']]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_1.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -30,26 +30,26 @@ │ │ │ │ ['bitmask_2eh_28', ['bitmask.h', ['../include_2gromacs_2utility_2bitmask_8h.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../tests_2bitmask_8h.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['bonded_2ecpp_29', ['bonded.cpp', ['../tests_2bonded_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../bonded_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['bonded_2eh_30', ['bonded.h', ['../bonded_8h.xhtml', 1, '']]], │ │ │ │ - ['booltype_2ecpp_31', ['booltype.cpp', ['../tests_2booltype_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../booltype_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['booltype_2ecpp_31', ['booltype.cpp', ['../booltype_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2booltype_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['booltype_2eh_32', ['booltype.h', ['../booltype_8h.xhtml', 1, '']]], │ │ │ │ ['bootstrap_5floadstore_2ecpp_33', ['bootstrap_loadstore.cpp', ['../bootstrap__loadstore_8cpp.xhtml', 1, '']]], │ │ │ │ ['boundingbox_2eh_34', ['boundingbox.h', ['../boundingbox_8h.xhtml', 1, '']]], │ │ │ │ ['boundingbox_5fsimd_2eh_35', ['boundingbox_simd.h', ['../boundingbox__simd_8h.xhtml', 1, '']]], │ │ │ │ ['boundingboxdistance_2eh_36', ['boundingboxdistance.h', ['../boundingboxdistance_8h.xhtml', 1, '']]], │ │ │ │ ['box_2ecpp_37', ['box.cpp', ['../box_8cpp.xhtml', 1, '']]], │ │ │ │ ['box_2eh_38', ['box.h', ['../box_8h.xhtml', 1, '']]], │ │ │ │ - ['boxdeformation_2ecpp_39', ['boxdeformation.cpp', ['../programs_2mdrun_2tests_2boxdeformation_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../gromacs_2mdlib_2boxdeformation_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['boxdeformation_2ecpp_39', ['boxdeformation.cpp', ['../gromacs_2mdlib_2boxdeformation_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../programs_2mdrun_2tests_2boxdeformation_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['boxdeformation_2eh_40', ['boxdeformation.h', ['../boxdeformation_8h.xhtml', 1, '']]], │ │ │ │ ['boxmatrix_2ecpp_41', ['boxmatrix.cpp', ['../boxmatrix_8cpp.xhtml', 1, '']]], │ │ │ │ ['boxmatrix_2eh_42', ['boxmatrix.h', ['../boxmatrix_8h.xhtml', 1, '']]], │ │ │ │ ['boxutilities_2ecpp_43', ['boxutilities.cpp', ['../boxutilities_8cpp.xhtml', 1, '']]], │ │ │ │ ['broadcaststructs_2eh_44', ['broadcaststructs.h', ['../broadcaststructs_8h.xhtml', 1, '']]], │ │ │ │ ['builder_2ecpp_45', ['builder.cpp', ['../builder_8cpp.xhtml', 1, '']]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_10.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -15,30 +15,30 @@ │ │ │ │ ['refdata_5fcheckers_2eh_11', ['refdata_checkers.h', ['../refdata__checkers_8h.xhtml', 1, '']]], │ │ │ │ ['refdata_5fimpl_2eh_12', ['refdata_impl.h', ['../refdata__impl_8h.xhtml', 1, '']]], │ │ │ │ ['refdata_5ftests_2ecpp_13', ['refdata_tests.cpp', ['../refdata__tests_8cpp.xhtml', 1, '']]], │ │ │ │ ['refdata_5fxml_2ecpp_14', ['refdata_xml.cpp', ['../refdata__xml_8cpp.xhtml', 1, '']]], │ │ │ │ ['refdata_5fxml_2eh_15', ['refdata_xml.h', ['../refdata__xml_8h.xhtml', 1, '']]], │ │ │ │ ['referencetemperaturemanager_2ecpp_16', ['referencetemperaturemanager.cpp', ['../referencetemperaturemanager_8cpp.xhtml', 1, '']]], │ │ │ │ ['referencetemperaturemanager_2eh_17', ['referencetemperaturemanager.h', ['../referencetemperaturemanager_8h.xhtml', 1, '']]], │ │ │ │ - ['register_2ecpp_18', ['register.cpp', ['../frameconverters_2register_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2register_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['register_2ecpp_18', ['register.cpp', ['../tests_2register_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../frameconverters_2register_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['register_2eh_19', ['register.h', ['../register_8h.xhtml', 1, '']]], │ │ │ │ ['repeatingsection_2ecpp_20', ['repeatingsection.cpp', ['../repeatingsection_8cpp.xhtml', 1, '']]], │ │ │ │ ['repeatingsection_2eh_21', ['repeatingsection.h', ['../repeatingsection_8h.xhtml', 1, '']]], │ │ │ │ - ['replicaexchange_2ecpp_22', ['replicaexchange.cpp', ['../gromacs_2mdrun_2replicaexchange_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../programs_2mdrun_2tests_2replicaexchange_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['replicaexchange_2ecpp_22', ['replicaexchange.cpp', ['../programs_2mdrun_2tests_2replicaexchange_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../gromacs_2mdrun_2replicaexchange_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['replicaexchange_2eh_23', ['replicaexchange.h', ['../replicaexchange_8h.xhtml', 1, '']]], │ │ │ │ ['replicaexchange_5fequivalence_2ecpp_24', ['replicaexchange_equivalence.cpp', ['../replicaexchange__equivalence_8cpp.xhtml', 1, '']]], │ │ │ │ ['report_5fmethods_2ecpp_25', ['report_methods.cpp', ['../tests_2report__methods_8cpp.xhtml', 1, '']]], │ │ │ │ ['reportgpuusage_2ecpp_26', ['reportgpuusage.cpp', ['../reportgpuusage_8cpp.xhtml', 1, '']]], │ │ │ │ ['reportgpuusage_2eh_27', ['reportgpuusage.h', ['../reportgpuusage_8h.xhtml', 1, '']]], │ │ │ │ - ['requirements_2ecpp_28', ['requirements.cpp', ['../requirements_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2requirements_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['requirements_2ecpp_28', ['requirements.cpp', ['../tests_2requirements_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../requirements_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['requirements_2eh_29', ['requirements.h', ['../tests_2requirements_8h.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../requirements_8h.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['rerun_2ecpp_30', ['rerun.cpp', ['../programs_2mdrun_2tests_2rerun_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../gromacs_2mdrun_2rerun_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_11.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -150,16 +150,16 @@ │ │ │ │ ['statepropagatordata_2ecpp_126', ['statepropagatordata.cpp', ['../statepropagatordata_8cpp.xhtml', 1, '']]], │ │ │ │ ['statepropagatordata_2eh_127', ['statepropagatordata.h', ['../statepropagatordata_8h.xhtml', 1, '']]], │ │ │ │ ['statistics_2eh_128', ['statistics.h', ['../statistics_8h.xhtml', 1, '']]], │ │ │ │ ['stdiohelper_2ecpp_129', ['stdiohelper.cpp', ['../stdiohelper_8cpp.xhtml', 1, '']]], │ │ │ │ ['stdiohelper_2eh_130', ['stdiohelper.h', ['../stdiohelper_8h.xhtml', 1, '']]], │ │ │ │ ['stophandler_2ecpp_131', ['stophandler.cpp', ['../stophandler_8cpp.xhtml', 1, '']]], │ │ │ │ ['stophandler_2eh_132', ['stophandler.h', ['../stophandler_8h.xhtml', 1, '']]], │ │ │ │ - ['strconvert_2ecpp_133', ['strconvert.cpp', ['../tests_2strconvert_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../strconvert_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['strconvert_2ecpp_133', ['strconvert.cpp', ['../strconvert_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2strconvert_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['strconvert_2eh_134', ['strconvert.h', ['../strconvert_8h.xhtml', 1, '']]], │ │ │ │ ['strdb_2eh_135', ['strdb.h', ['../strdb_8h.xhtml', 1, '']]], │ │ │ │ ['stringcompare_2eh_136', ['stringcompare.h', ['../stringcompare_8h.xhtml', 1, '']]], │ │ │ │ ['stringstream_2ecpp_137', ['stringstream.cpp', ['../stringstream_8cpp.xhtml', 1, '']]], │ │ │ │ ['stringstream_2eh_138', ['stringstream.h', ['../stringstream_8h.xhtml', 1, '']]], │ │ │ │ ['stringtest_2ecpp_139', ['stringtest.cpp', ['../stringtest_8cpp.xhtml', 1, '']]], │ │ │ │ @@ -167,16 +167,16 @@ │ │ │ │ ['stringtoenumvalueconverter_2ecpp_141', ['stringtoenumvalueconverter.cpp', ['../stringtoenumvalueconverter_8cpp.xhtml', 1, '']]], │ │ │ │ ['stringtoenumvalueconverter_2eh_142', ['stringtoenumvalueconverter.h', ['../stringtoenumvalueconverter_8h.xhtml', 1, '']]], │ │ │ │ ['stringutil_2ecpp_143', ['stringutil.cpp', ['../stringutil_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../tests_2stringutil_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['stringutil_2eh_144', ['stringutil.h', ['../stringutil_8h.xhtml', 1, '']]], │ │ │ │ ['surfacearea_2ecpp_145', ['surfacearea.cpp', ['../tests_2surfacearea_8cpp.xhtml', 1, '']]], │ │ │ │ - ['swapcoords_2ecpp_146', ['swapcoords.cpp', ['../programs_2mdrun_2tests_2swapcoords_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../gromacs_2swap_2swapcoords_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['swapcoords_2ecpp_146', ['swapcoords.cpp', ['../gromacs_2swap_2swapcoords_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../programs_2mdrun_2tests_2swapcoords_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['swapcoords_2eh_147', ['swapcoords.h', ['../swapcoords_8h.xhtml', 1, '']]], │ │ │ │ ['sycl_5fkernel_5futils_2eh_148', ['sycl_kernel_utils.h', ['../sycl__kernel__utils_8h.xhtml', 1, '']]], │ │ │ │ ['syclutils_2eh_149', ['syclutils.h', ['../syclutils_8h.xhtml', 1, '']]], │ │ │ │ ['symrec_2ecpp_150', ['symrec.cpp', ['../symrec_8cpp.xhtml', 1, '']]], │ │ │ │ ['symrec_2eh_151', ['symrec.h', ['../symrec_8h.xhtml', 1, '']]], │ │ │ │ ['symtab_2ecpp_152', ['symtab.cpp', ['../tests_2symtab_8cpp.xhtml', 1, '(Global Namespace)'], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_12.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -33,32 +33,32 @@ │ │ │ │ ['testoptions_2ecpp_31', ['testoptions.cpp', ['../testoptions_8cpp.xhtml', 1, '']]], │ │ │ │ ['testoptions_2eh_32', ['testoptions.h', ['../testoptions_8h.xhtml', 1, '']]], │ │ │ │ ['testsystem_2ecpp_33', ['testsystem.cpp', ['../testsystem_8cpp.xhtml', 1, '']]], │ │ │ │ ['testsystem_2eh_34', ['testsystem.h', ['../testsystem_8h.xhtml', 1, '']]], │ │ │ │ ['testutils_5fdoc_2eh_35', ['testutils_doc.h', ['../testutils__doc_8h.xhtml', 1, '']]], │ │ │ │ ['textblockmatchers_2ecpp_36', ['textblockmatchers.cpp', ['../textblockmatchers_8cpp.xhtml', 1, '']]], │ │ │ │ ['textblockmatchers_2eh_37', ['textblockmatchers.h', ['../textblockmatchers_8h.xhtml', 1, '']]], │ │ │ │ - ['textreader_2ecpp_38', ['textreader.cpp', ['../textreader_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2textreader_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['textreader_2ecpp_38', ['textreader.cpp', ['../tests_2textreader_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../textreader_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['textreader_2eh_39', ['textreader.h', ['../textreader_8h.xhtml', 1, '']]], │ │ │ │ ['textstream_2eh_40', ['textstream.h', ['../textstream_8h.xhtml', 1, '']]], │ │ │ │ ['textwriter_2ecpp_41', ['textwriter.cpp', ['../textwriter_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../tests_2textwriter_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['textwriter_2eh_42', ['textwriter.h', ['../textwriter_8h.xhtml', 1, '']]], │ │ │ │ ['thermochemistry_2eh_43', ['thermochemistry.h', ['../thermochemistry_8h.xhtml', 1, '']]], │ │ │ │ ['threadaffinity_2eh_44', ['threadaffinity.h', ['../threadaffinity_8h.xhtml', 1, '']]], │ │ │ │ ['threaded_5fforce_5fbuffer_2ecpp_45', ['threaded_force_buffer.cpp', ['../threaded__force__buffer_8cpp.xhtml', 1, '']]], │ │ │ │ ['threaded_5fforce_5fbuffer_2eh_46', ['threaded_force_buffer.h', ['../threaded__force__buffer_8h.xhtml', 1, '']]], │ │ │ │ ['threefry_2ecpp_47', ['threefry.cpp', ['../threefry_8cpp.xhtml', 1, '']]], │ │ │ │ ['threefry_2eh_48', ['threefry.h', ['../threefry_8h.xhtml', 1, '']]], │ │ │ │ ['timecontrol_2ecpp_49', ['timecontrol.cpp', ['../tests_2timecontrol_8cpp.xhtml', 1, '']]], │ │ │ │ - ['timeunitmanager_2ecpp_50', ['timeunitmanager.cpp', ['../timeunitmanager_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2timeunitmanager_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['timeunitmanager_2ecpp_50', ['timeunitmanager.cpp', ['../tests_2timeunitmanager_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../timeunitmanager_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['timeunitmanager_2eh_51', ['timeunitmanager.h', ['../timeunitmanager_8h.xhtml', 1, '']]], │ │ │ │ ['timing_2ecpp_52', ['timing.cpp', ['../timing_8cpp.xhtml', 1, '']]], │ │ │ │ ['tngio_2ecpp_53', ['tngio.cpp', ['../tests_2tngio_8cpp.xhtml', 1, '']]], │ │ │ │ ['topdirs_2ecpp_54', ['topdirs.cpp', ['../tests_2topdirs_8cpp.xhtml', 1, '']]], │ │ │ │ ['topologyhelpers_2ecpp_55', ['topologyhelpers.cpp', ['../topologyhelpers_8cpp.xhtml', 1, '']]], │ │ │ │ ['topologyhelpers_2eh_56', ['topologyhelpers.h', ['../topologyhelpers_8h.xhtml', 1, '']]], │ │ │ │ @@ -85,16 +85,16 @@ │ │ │ │ ['trajectorycomparison_2ecpp_73', ['trajectorycomparison.cpp', ['../trajectorycomparison_8cpp.xhtml', 1, '']]], │ │ │ │ ['trajectorycomparison_2eh_74', ['trajectorycomparison.h', ['../trajectorycomparison_8h.xhtml', 1, '']]], │ │ │ │ ['trajectoryelement_2ecpp_75', ['trajectoryelement.cpp', ['../trajectoryelement_8cpp.xhtml', 1, '']]], │ │ │ │ ['trajectoryelement_2eh_76', ['trajectoryelement.h', ['../trajectoryelement_8h.xhtml', 1, '']]], │ │ │ │ ['trajectoryreader_2ecpp_77', ['trajectoryreader.cpp', ['../trajectoryreader_8cpp.xhtml', 1, '']]], │ │ │ │ ['trajectoryreader_2eh_78', ['trajectoryreader.h', ['../trajectoryreader_8h.xhtml', 1, '']]], │ │ │ │ ['transformationcoordinate_2eh_79', ['transformationcoordinate.h', ['../transformationcoordinate_8h.xhtml', 1, '']]], │ │ │ │ - ['treesupport_2ecpp_80', ['treesupport.cpp', ['../treesupport_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2treesupport_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['treesupport_2ecpp_80', ['treesupport.cpp', ['../tests_2treesupport_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../treesupport_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['treesupport_2eh_81', ['treesupport.h', ['../treesupport_8h.xhtml', 1, '']]], │ │ │ │ ['trjconv_2ecpp_82', ['trjconv.cpp', ['../tests_2trjconv_8cpp.xhtml', 1, '']]], │ │ │ │ ['trotterhelperfunctions_2eh_83', ['trotterhelperfunctions.h', ['../trotterhelperfunctions_8h.xhtml', 1, '']]], │ │ │ │ ['txtdump_2eh_84', ['txtdump.h', ['../txtdump_8h.xhtml', 1, '']]], │ │ │ │ ['typecasts_2ecpp_85', ['typecasts.cpp', ['../typecasts_8cpp.xhtml', 1, '']]], │ │ │ │ ['typecasts_5fcuda_5fhip_2eh_86', ['typecasts_cuda_hip.h', ['../typecasts__cuda__hip_8h.xhtml', 1, '']]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_13.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -20,11 +20,11 @@ │ │ │ │ ['../usergpuids_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['usergpuids_2eh_18', ['usergpuids.h', ['../usergpuids_8h.xhtml', 1, '']]], │ │ │ │ ['utilities_2eh_19', ['utilities.h', ['../src_2gromacs_2mimic_2utilities_8h.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../src_2gromacs_2listed__forces_2utilities_8h.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['utility_2ecpp_20', ['utility.cpp', ['../utility_8cpp.xhtml', 1, '']]], │ │ │ │ - ['utility_2eh_21', ['utility.h', ['../domdec_2utility_8h.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../utility_8h.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['utility_2eh_21', ['utility.h', ['../utility_8h.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../domdec_2utility_8h.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]] │ │ │ │ ]; │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_2.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -10,36 +10,36 @@ │ │ │ │ ['checkpointdata_2ecpp_6', ['checkpointdata.cpp', ['../checkpointdata_8cpp.xhtml', 1, '']]], │ │ │ │ ['checkpointdata_2eh_7', ['checkpointdata.h', ['../checkpointdata_8h.xhtml', 1, '']]], │ │ │ │ ['checkpointhandler_2ecpp_8', ['checkpointhandler.cpp', ['../checkpointhandler_8cpp.xhtml', 1, '']]], │ │ │ │ ['checkpointhandler_2eh_9', ['checkpointhandler.h', ['../checkpointhandler_8h.xhtml', 1, '']]], │ │ │ │ ['checkpointhelper_2ecpp_10', ['checkpointhelper.cpp', ['../checkpointhelper_8cpp.xhtml', 1, '']]], │ │ │ │ ['checkpointhelper_2eh_11', ['checkpointhelper.h', ['../checkpointhelper_8h.xhtml', 1, '']]], │ │ │ │ ['classhelpers_2eh_12', ['classhelpers.h', ['../classhelpers_8h.xhtml', 1, '']]], │ │ │ │ - ['clfftinitializer_2ecpp_13', ['clfftinitializer.cpp', ['../tests_2clfftinitializer_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../clfftinitializer_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['clfftinitializer_2ecpp_13', ['clfftinitializer.cpp', ['../clfftinitializer_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2clfftinitializer_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['clfftinitializer_2eh_14', ['clfftinitializer.h', ['../clfftinitializer_8h.xhtml', 1, '']]], │ │ │ │ ['clusterdistancekerneltype_2eh_15', ['clusterdistancekerneltype.h', ['../clusterdistancekerneltype_8h.xhtml', 1, '']]], │ │ │ │ ['clustsize_2ecpp_16', ['clustsize.cpp', ['../clustsize_8cpp.xhtml', 1, '']]], │ │ │ │ ['cmdlinehelpcontext_2ecpp_17', ['cmdlinehelpcontext.cpp', ['../cmdlinehelpcontext_8cpp.xhtml', 1, '']]], │ │ │ │ ['cmdlinehelpcontext_2eh_18', ['cmdlinehelpcontext.h', ['../cmdlinehelpcontext_8h.xhtml', 1, '']]], │ │ │ │ ['cmdlinehelpmodule_2ecpp_19', ['cmdlinehelpmodule.cpp', ['../tests_2cmdlinehelpmodule_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../cmdlinehelpmodule_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['cmdlinehelpmodule_2eh_20', ['cmdlinehelpmodule.h', ['../cmdlinehelpmodule_8h.xhtml', 1, '']]], │ │ │ │ - ['cmdlinehelpwriter_2ecpp_21', ['cmdlinehelpwriter.cpp', ['../tests_2cmdlinehelpwriter_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../cmdlinehelpwriter_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['cmdlinehelpwriter_2ecpp_21', ['cmdlinehelpwriter.cpp', ['../cmdlinehelpwriter_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2cmdlinehelpwriter_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['cmdlinehelpwriter_2eh_22', ['cmdlinehelpwriter.h', ['../cmdlinehelpwriter_8h.xhtml', 1, '']]], │ │ │ │ ['cmdlineinit_2ecpp_23', ['cmdlineinit.cpp', ['../cmdlineinit_8cpp.xhtml', 1, '']]], │ │ │ │ ['cmdlineinit_2eh_24', ['cmdlineinit.h', ['../cmdlineinit_8h.xhtml', 1, '']]], │ │ │ │ ['cmdlinemodule_2ecpp_25', ['cmdlinemodule.cpp', ['../cmdlinemodule_8cpp.xhtml', 1, '']]], │ │ │ │ ['cmdlinemodule_2eh_26', ['cmdlinemodule.h', ['../cmdlinemodule_8h.xhtml', 1, '']]], │ │ │ │ - ['cmdlinemodulemanager_2ecpp_27', ['cmdlinemodulemanager.cpp', ['../tests_2cmdlinemodulemanager_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../cmdlinemodulemanager_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['cmdlinemodulemanager_2ecpp_27', ['cmdlinemodulemanager.cpp', ['../cmdlinemodulemanager_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2cmdlinemodulemanager_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['cmdlinemodulemanager_2eh_28', ['cmdlinemodulemanager.h', ['../cmdlinemodulemanager_8h.xhtml', 1, '']]], │ │ │ │ ['cmdlinemodulemanager_5fimpl_2eh_29', ['cmdlinemodulemanager_impl.h', ['../cmdlinemodulemanager__impl_8h.xhtml', 1, '']]], │ │ │ │ ['cmdlinemodulemanagertest_2ecpp_30', ['cmdlinemodulemanagertest.cpp', ['../cmdlinemodulemanagertest_8cpp.xhtml', 1, '']]], │ │ │ │ ['cmdlinemodulemanagertest_2eh_31', ['cmdlinemodulemanagertest.h', ['../cmdlinemodulemanagertest_8h.xhtml', 1, '']]], │ │ │ │ ['cmdlineoptionsmodule_2ecpp_32', ['cmdlineoptionsmodule.cpp', ['../cmdlineoptionsmodule_8cpp.xhtml', 1, '']]], │ │ │ │ ['cmdlineoptionsmodule_2eh_33', ['cmdlineoptionsmodule.h', ['../cmdlineoptionsmodule_8h.xhtml', 1, '']]], │ │ │ │ @@ -95,16 +95,16 @@ │ │ │ │ ['computeglobalselement_2eh_69', ['computeglobalselement.h', ['../computeglobalselement_8h.xhtml', 1, '']]], │ │ │ │ ['computemultibodycutoffs_2ecpp_70', ['computemultibodycutoffs.cpp', ['../computemultibodycutoffs_8cpp.xhtml', 1, '']]], │ │ │ │ ['computemultibodycutoffs_2eh_71', ['computemultibodycutoffs.h', ['../computemultibodycutoffs_8h.xhtml', 1, '']]], │ │ │ │ ['confio_2ecpp_72', ['confio.cpp', ['../tests_2confio_8cpp.xhtml', 1, '']]], │ │ │ │ ['conftest_2ecpp_73', ['conftest.cpp', ['../conftest_8cpp.xhtml', 1, '']]], │ │ │ │ ['conftest_2eh_74', ['conftest.h', ['../conftest_8h.xhtml', 1, '']]], │ │ │ │ ['constantacceleration_2ecpp_75', ['constantacceleration.cpp', ['../constantacceleration_8cpp.xhtml', 1, '']]], │ │ │ │ - ['constr_2ecpp_76', ['constr.cpp', ['../constr_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2constr_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['constr_2ecpp_76', ['constr.cpp', ['../tests_2constr_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../constr_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['constr_2eh_77', ['constr.h', ['../constr_8h.xhtml', 1, '']]], │ │ │ │ ['constraintelement_2ecpp_78', ['constraintelement.cpp', ['../constraintelement_8cpp.xhtml', 1, '']]], │ │ │ │ ['constraintelement_2eh_79', ['constraintelement.h', ['../constraintelement_8h.xhtml', 1, '']]], │ │ │ │ ['constrtestdata_2ecpp_80', ['constrtestdata.cpp', ['../constrtestdata_8cpp.xhtml', 1, '']]], │ │ │ │ ['constrtestdata_2eh_81', ['constrtestdata.h', ['../constrtestdata_8h.xhtml', 1, '']]], │ │ │ │ ['constrtestrunners_2ecpp_82', ['constrtestrunners.cpp', ['../constrtestrunners_8cpp.xhtml', 1, '']]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_5.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -27,29 +27,29 @@ │ │ │ │ ['findallgputasks_2ecpp_21', ['findallgputasks.cpp', ['../findallgputasks_8cpp.xhtml', 1, '']]], │ │ │ │ ['findallgputasks_2eh_22', ['findallgputasks.h', ['../findallgputasks_8h.xhtml', 1, '']]], │ │ │ │ ['firstorderpressurecoupling_2ecpp_23', ['firstorderpressurecoupling.cpp', ['../firstorderpressurecoupling_8cpp.xhtml', 1, '']]], │ │ │ │ ['firstorderpressurecoupling_2eh_24', ['firstorderpressurecoupling.h', ['../firstorderpressurecoupling_8h.xhtml', 1, '']]], │ │ │ │ ['fixedcapacityvector_2ecpp_25', ['fixedcapacityvector.cpp', ['../fixedcapacityvector_8cpp.xhtml', 1, '']]], │ │ │ │ ['fixedcapacityvector_2eh_26', ['fixedcapacityvector.h', ['../fixedcapacityvector_8h.xhtml', 1, '']]], │ │ │ │ ['flags_2eh_27', ['flags.h', ['../flags_8h.xhtml', 1, '']]], │ │ │ │ - ['forcebuffers_2ecpp_28', ['forcebuffers.cpp', ['../tests_2forcebuffers_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../forcebuffers_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['forcebuffers_2ecpp_28', ['forcebuffers.cpp', ['../forcebuffers_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2forcebuffers_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['forcebuffers_2eh_29', ['forcebuffers.h', ['../forcebuffers_8h.xhtml', 1, '']]], │ │ │ │ ['forceelement_2ecpp_30', ['forceelement.cpp', ['../forceelement_8cpp.xhtml', 1, '']]], │ │ │ │ ['forceelement_2eh_31', ['forceelement.h', ['../forceelement_8h.xhtml', 1, '']]], │ │ │ │ ['forceoutput_2eh_32', ['forceoutput.h', ['../forceoutput_8h.xhtml', 1, '']]], │ │ │ │ ['forcetable_2eh_33', ['forcetable.h', ['../forcetable_8h.xhtml', 1, '']]], │ │ │ │ ['frameaverager_2ecpp_34', ['frameaverager.cpp', ['../frameaverager_8cpp.xhtml', 1, '']]], │ │ │ │ ['frameaverager_2eh_35', ['frameaverager.h', ['../frameaverager_8h.xhtml', 1, '']]], │ │ │ │ ['frameconverter_2eh_36', ['frameconverter.h', ['../frameconverter_8h.xhtml', 1, '']]], │ │ │ │ ['frameconverterenums_2eh_37', ['frameconverterenums.h', ['../frameconverterenums_8h.xhtml', 1, '']]], │ │ │ │ ['framelocaldata_2eh_38', ['framelocaldata.h', ['../framelocaldata_8h.xhtml', 1, '']]], │ │ │ │ - ['freeenergy_2ecpp_39', ['freeenergy.cpp', ['../programs_2mdrun_2tests_2freeenergy_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../gromacs_2mdrunutility_2freeenergy_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['freeenergy_2ecpp_39', ['freeenergy.cpp', ['../gromacs_2mdrunutility_2freeenergy_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../programs_2mdrun_2tests_2freeenergy_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['freeenergy_2eh_40', ['freeenergy.h', ['../freeenergy_8h.xhtml', 1, '']]], │ │ │ │ ['freeenergydispatch_2eh_41', ['freeenergydispatch.h', ['../freeenergydispatch_8h.xhtml', 1, '']]], │ │ │ │ ['freeenergyparameters_2ecpp_42', ['freeenergyparameters.cpp', ['../tests_2freeenergyparameters_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../freeenergyparameters_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['freeenergyparameters_2eh_43', ['freeenergyparameters.h', ['../freeenergyparameters_8h.xhtml', 1, '']]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_7.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -3,48 +3,48 @@ │ │ │ │ ['hackblock_2eh_1', ['hackblock.h', ['../hackblock_8h.xhtml', 1, '']]], │ │ │ │ ['haloexchange_2ecpp_2', ['haloexchange.cpp', ['../haloexchange_8cpp.xhtml', 1, '']]], │ │ │ │ ['haloexchange_2eh_3', ['haloexchange.h', ['../haloexchange_8h.xhtml', 1, '']]], │ │ │ │ ['haloexchange_5fmpi_2ecpp_4', ['haloexchange_mpi.cpp', ['../haloexchange__mpi_8cpp.xhtml', 1, '']]], │ │ │ │ ['haloexchangesetup_2ecpp_5', ['haloexchangesetup.cpp', ['../haloexchangesetup_8cpp.xhtml', 1, '']]], │ │ │ │ ['handlerestart_2ecpp_6', ['handlerestart.cpp', ['../handlerestart_8cpp.xhtml', 1, '']]], │ │ │ │ ['handlerestart_2eh_7', ['handlerestart.h', ['../handlerestart_8h.xhtml', 1, '']]], │ │ │ │ - ['hardwaretopology_2ecpp_8', ['hardwaretopology.cpp', ['../tests_2hardwaretopology_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../hardwaretopology_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['hardwaretopology_2ecpp_8', ['hardwaretopology.cpp', ['../hardwaretopology_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2hardwaretopology_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['hardwaretopology_2eh_9', ['hardwaretopology.h', ['../hardwaretopology_8h.xhtml', 1, '']]], │ │ │ │ ['hashedmap_2ecpp_10', ['hashedmap.cpp', ['../hashedmap_8cpp.xhtml', 1, '']]], │ │ │ │ ['hashedmap_2eh_11', ['hashedmap.h', ['../hashedmap_8h.xhtml', 1, '']]], │ │ │ │ - ['hbond_2ecpp_12', ['hbond.cpp', ['../tests_2hbond_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../modules_2hbond_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['hbond_2ecpp_12', ['hbond.cpp', ['../modules_2hbond_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2hbond_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['hbond_2eh_13', ['hbond.h', ['../hbond_8h.xhtml', 1, '']]], │ │ │ │ - ['helpformat_2ecpp_14', ['helpformat.cpp', ['../tests_2helpformat_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../helpformat_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['helpformat_2ecpp_14', ['helpformat.cpp', ['../helpformat_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2helpformat_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['helpformat_2eh_15', ['helpformat.h', ['../helpformat_8h.xhtml', 1, '']]], │ │ │ │ - ['helpmanager_2ecpp_16', ['helpmanager.cpp', ['../tests_2helpmanager_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../helpmanager_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['helpmanager_2ecpp_16', ['helpmanager.cpp', ['../helpmanager_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2helpmanager_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['helpmanager_2eh_17', ['helpmanager.h', ['../helpmanager_8h.xhtml', 1, '']]], │ │ │ │ ['helptopic_2ecpp_18', ['helptopic.cpp', ['../helptopic_8cpp.xhtml', 1, '']]], │ │ │ │ ['helptopic_2eh_19', ['helptopic.h', ['../helptopic_8h.xhtml', 1, '']]], │ │ │ │ - ['helpwritercontext_2ecpp_20', ['helpwritercontext.cpp', ['../helpwritercontext_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2helpwritercontext_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['helpwritercontext_2ecpp_20', ['helpwritercontext.cpp', ['../tests_2helpwritercontext_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../helpwritercontext_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['helpwritercontext_2eh_21', ['helpwritercontext.h', ['../helpwritercontext_8h.xhtml', 1, '']]], │ │ │ │ ['helpwriting_2ecpp_22', ['helpwriting.cpp', ['../programs_2mdrun_2tests_2helpwriting_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../gromacs_2tools_2tests_2helpwriting_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['hip_5fkernel_5futils_2eh_23', ['hip_kernel_utils.h', ['../hip__kernel__utils_8h.xhtml', 1, '']]], │ │ │ │ ['hip_5fsycl_5fkernel_5futils_2eh_24', ['hip_sycl_kernel_utils.h', ['../hip__sycl__kernel__utils_8h.xhtml', 1, '']]], │ │ │ │ ['histogram_2ecpp_25', ['histogram.cpp', ['../tests_2histogram_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../modules_2histogram_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['histogram_2eh_26', ['histogram.h', ['../histogram_8h.xhtml', 1, '']]], │ │ │ │ ['histogramsize_2ecpp_27', ['histogramsize.cpp', ['../histogramsize_8cpp.xhtml', 1, '']]], │ │ │ │ ['histogramsize_2eh_28', ['histogramsize.h', ['../histogramsize_8h.xhtml', 1, '']]], │ │ │ │ - ['hostallocator_2ecpp_29', ['hostallocator.cpp', ['../hostallocator_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2hostallocator_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['hostallocator_2ecpp_29', ['hostallocator.cpp', ['../tests_2hostallocator_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../hostallocator_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['hostallocator_2eh_30', ['hostallocator.h', ['../hostallocator_8h.xhtml', 1, '']]], │ │ │ │ ['hsimd_5fdeclarations_2eh_31', ['hsimd_declarations.h', ['../hsimd__declarations_8h.xhtml', 1, '']]] │ │ │ │ ]; │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_b.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -36,45 +36,45 @@ │ │ │ │ ['mdspan_2eh_30', ['mdspan.h', ['../mdspan_8h.xhtml', 1, '']]], │ │ │ │ ['mempool_2ecpp_31', ['mempool.cpp', ['../mempool_8cpp.xhtml', 1, '']]], │ │ │ │ ['mempool_2eh_32', ['mempool.h', ['../mempool_8h.xhtml', 1, '']]], │ │ │ │ ['message_5fstring_5fcollector_2ecpp_33', ['message_string_collector.cpp', ['../tests_2message__string__collector_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../message__string__collector_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['message_5fstring_5fcollector_2eh_34', ['message_string_collector.h', ['../message__string__collector_8h.xhtml', 1, '']]], │ │ │ │ - ['mimic_2ecpp_35', ['mimic.cpp', ['../gromacs_2mdrun_2mimic_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../programs_2mdrun_2tests_2mimic_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['mimic_2ecpp_35', ['mimic.cpp', ['../programs_2mdrun_2tests_2mimic_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../gromacs_2mdrun_2mimic_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ - ['minimize_2ecpp_36', ['minimize.cpp', ['../gromacs_2mdrun_2minimize_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../programs_2mdrun_2tests_2minimize_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['minimize_2ecpp_36', ['minimize.cpp', ['../programs_2mdrun_2tests_2minimize_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../gromacs_2mdrun_2minimize_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['misc_2ecpp_37', ['misc.cpp', ['../misc_8cpp.xhtml', 1, '']]], │ │ │ │ ['mock_5fdatamodule_2ecpp_38', ['mock_datamodule.cpp', ['../mock__datamodule_8cpp.xhtml', 1, '']]], │ │ │ │ ['mock_5fdatamodule_2eh_39', ['mock_datamodule.h', ['../mock__datamodule_8h.xhtml', 1, '']]], │ │ │ │ ['mock_5fhelptopic_2ecpp_40', ['mock_helptopic.cpp', ['../mock__helptopic_8cpp.xhtml', 1, '']]], │ │ │ │ ['mock_5fhelptopic_2eh_41', ['mock_helptopic.h', ['../mock__helptopic_8h.xhtml', 1, '']]], │ │ │ │ ['mockhardwaretopology_2ecpp_42', ['mockhardwaretopology.cpp', ['../mockhardwaretopology_8cpp.xhtml', 1, '']]], │ │ │ │ ['modularsimulator_2ecpp_43', ['modularsimulator.cpp', ['../modularsimulator_8cpp.xhtml', 1, '']]], │ │ │ │ ['modularsimulator_2eh_44', ['modularsimulator.h', ['../modularsimulator_8h.xhtml', 1, '']]], │ │ │ │ ['modularsimulatorinterfaces_2eh_45', ['modularsimulatorinterfaces.h', ['../modularsimulatorinterfaces_8h.xhtml', 1, '']]], │ │ │ │ ['modules_2ecpp_46', ['modules.cpp', ['../modules_8cpp.xhtml', 1, '']]], │ │ │ │ ['modules_2eh_47', ['modules.h', ['../modules_8h.xhtml', 1, '']]], │ │ │ │ - ['moduletest_2ecpp_48', ['moduletest.cpp', ['../gromacs_2trajectoryanalysis_2tests_2moduletest_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../programs_2mdrun_2tests_2moduletest_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['moduletest_2ecpp_48', ['moduletest.cpp', ['../programs_2mdrun_2tests_2moduletest_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../gromacs_2trajectoryanalysis_2tests_2moduletest_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['moduletest_2eh_49', ['moduletest.h', ['../gromacs_2trajectoryanalysis_2tests_2moduletest_8h.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../programs_2mdrun_2tests_2moduletest_8h.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['mp11_2eh_50', ['mp11.h', ['../mp11_8h.xhtml', 1, '']]], │ │ │ │ ['mpi_5fprinter_2eh_51', ['mpi_printer.h', ['../mpi__printer_8h.xhtml', 1, '']]], │ │ │ │ - ['mpitest_2ecpp_52', ['mpitest.cpp', ['../mpitest_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2mpitest_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['mpitest_2ecpp_52', ['mpitest.cpp', ['../tests_2mpitest_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../mpitest_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['mpitest_2eh_53', ['mpitest.h', ['../mpitest_8h.xhtml', 1, '']]], │ │ │ │ - ['mrcdensitymap_2ecpp_54', ['mrcdensitymap.cpp', ['../mrcdensitymap_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2mrcdensitymap_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['mrcdensitymap_2ecpp_54', ['mrcdensitymap.cpp', ['../tests_2mrcdensitymap_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../mrcdensitymap_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['mrcdensitymap_2eh_55', ['mrcdensitymap.h', ['../mrcdensitymap_8h.xhtml', 1, '']]], │ │ │ │ ['mrcdensitymapheader_2ecpp_56', ['mrcdensitymapheader.cpp', ['../tests_2mrcdensitymapheader_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../mrcdensitymapheader_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['mrcdensitymapheader_2eh_57', ['mrcdensitymapheader.h', ['../mrcdensitymapheader_8h.xhtml', 1, '']]], │ │ │ │ ['mrcserializer_2ecpp_58', ['mrcserializer.cpp', ['../mrcserializer_8cpp.xhtml', 1, '(Global Namespace)'], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_c.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -63,31 +63,31 @@ │ │ │ │ ['neldermead_2eh_57', ['neldermead.h', ['../neldermead_8h.xhtml', 1, '']]], │ │ │ │ ['niceheader_2ecpp_58', ['niceheader.cpp', ['../niceheader_8cpp.xhtml', 1, '']]], │ │ │ │ ['niceheader_2eh_59', ['niceheader.h', ['../niceheader_8h.xhtml', 1, '']]], │ │ │ │ ['nnpot_2ecpp_60', ['nnpot.cpp', ['../nnpot_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../tests_2nnpot_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['nnpot_2eh_61', ['nnpot.h', ['../nnpot_8h.xhtml', 1, '']]], │ │ │ │ - ['nnpotforceprovider_2ecpp_62', ['nnpotforceprovider.cpp', ['../tests_2nnpotforceprovider_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../nnpotforceprovider_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['nnpotforceprovider_2ecpp_62', ['nnpotforceprovider.cpp', ['../nnpotforceprovider_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2nnpotforceprovider_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['nnpotforceprovider_2eh_63', ['nnpotforceprovider.h', ['../nnpotforceprovider_8h.xhtml', 1, '']]], │ │ │ │ ['nnpotforceprovider_5fstub_2ecpp_64', ['nnpotforceprovider_stub.cpp', ['../nnpotforceprovider__stub_8cpp.xhtml', 1, '']]], │ │ │ │ ['nnpotmodel_2eh_65', ['nnpotmodel.h', ['../nnpotmodel_8h.xhtml', 1, '']]], │ │ │ │ - ['nnpotoptions_2ecpp_66', ['nnpotoptions.cpp', ['../tests_2nnpotoptions_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../nnpotoptions_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['nnpotoptions_2ecpp_66', ['nnpotoptions.cpp', ['../nnpotoptions_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2nnpotoptions_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['nnpotoptions_2eh_67', ['nnpotoptions.h', ['../nnpotoptions_8h.xhtml', 1, '']]], │ │ │ │ ['nnpottopologypreprocessor_2ecpp_68', ['nnpottopologypreprocessor.cpp', ['../tests_2nnpottopologypreprocessor_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../nnpottopologypreprocessor_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['nnpottopologypreprocessor_2eh_69', ['nnpottopologypreprocessor.h', ['../nnpottopologypreprocessor_8h.xhtml', 1, '']]], │ │ │ │ ['nodelete_2eh_70', ['nodelete.h', ['../nodelete_8h.xhtml', 1, '']]], │ │ │ │ - ['nonbonded_5fbench_2ecpp_71', ['nonbonded_bench.cpp', ['../nonbonded__bench_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2nonbonded__bench_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['nonbonded_5fbench_2ecpp_71', ['nonbonded_bench.cpp', ['../tests_2nonbonded__bench_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../nonbonded__bench_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['nonbonded_5fbench_2eh_72', ['nonbonded_bench.h', ['../nonbonded__bench_8h.xhtml', 1, '']]], │ │ │ │ ['normaldistribution_2ecpp_73', ['normaldistribution.cpp', ['../normaldistribution_8cpp.xhtml', 1, '']]], │ │ │ │ ['normaldistribution_2eh_74', ['normaldistribution.h', ['../normaldistribution_8h.xhtml', 1, '']]], │ │ │ │ ['normalmodes_2ecpp_75', ['normalmodes.cpp', ['../normalmodes_8cpp.xhtml', 1, '']]], │ │ │ │ ['nosehooverchains_2ecpp_76', ['nosehooverchains.cpp', ['../nosehooverchains_8cpp.xhtml', 1, '']]], │ │ │ │ ['nosehooverchains_2eh_77', ['nosehooverchains.h', ['../nosehooverchains_8h.xhtml', 1, '']]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-full/search/files_e.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -1,12 +1,12 @@ │ │ │ │ var searchData = [ │ │ │ │ ['paddedvector_2ecpp_0', ['paddedvector.cpp', ['../paddedvector_8cpp.xhtml', 1, '']]], │ │ │ │ ['paddedvector_2eh_1', ['paddedvector.h', ['../paddedvector_8h.xhtml', 1, '']]], │ │ │ │ - ['pairdist_2ecpp_2', ['pairdist.cpp', ['../modules_2pairdist_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2pairdist_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['pairdist_2ecpp_2', ['pairdist.cpp', ['../tests_2pairdist_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../modules_2pairdist_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['pairdist_2eh_3', ['pairdist.h', ['../pairdist_8h.xhtml', 1, '']]], │ │ │ │ ['pairlist_2ecpp_4', ['pairlist.cpp', ['../tests_2pairlist_8cpp.xhtml', 1, '']]], │ │ │ │ ['pairlist_5fimask_2eh_5', ['pairlist_imask.h', ['../pairlist__imask_8h.xhtml', 1, '']]], │ │ │ │ ['pairlist_5fsimd_5fkernel_2ecpp_6', ['pairlist_simd_kernel.cpp', ['../pairlist__simd__kernel_8cpp.xhtml', 1, '']]], │ │ │ │ ['pairlist_5fsimd_5fkernel_2eh_7', ['pairlist_simd_kernel.h', ['../pairlist__simd__kernel_8h.xhtml', 1, '']]], │ │ │ │ ['pairlist_5ftuning_2ecpp_8', ['pairlist_tuning.cpp', ['../pairlist__tuning_8cpp.xhtml', 1, '']]], │ │ │ │ @@ -31,27 +31,27 @@ │ │ │ │ ['parrinellorahmanbarostat_2ecpp_25', ['parrinellorahmanbarostat.cpp', ['../parrinellorahmanbarostat_8cpp.xhtml', 1, '']]], │ │ │ │ ['parrinellorahmanbarostat_2eh_26', ['parrinellorahmanbarostat.h', ['../parrinellorahmanbarostat_8h.xhtml', 1, '']]], │ │ │ │ ['parser_5finternal_2eh_27', ['parser_internal.h', ['../parser__internal_8h.xhtml', 1, '']]], │ │ │ │ ['parsetree_2ecpp_28', ['parsetree.cpp', ['../parsetree_8cpp.xhtml', 1, '']]], │ │ │ │ ['parsetree_2eh_29', ['parsetree.h', ['../parsetree_8h.xhtml', 1, '']]], │ │ │ │ ['partition_2ecpp_30', ['partition.cpp', ['../partition_8cpp.xhtml', 1, '']]], │ │ │ │ ['partition_2eh_31', ['partition.h', ['../partition_8h.xhtml', 1, '']]], │ │ │ │ - ['path_2ecpp_32', ['path.cpp', ['../path_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../tests_2path_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['path_2ecpp_32', ['path.cpp', ['../tests_2path_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../path_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['path_2eh_33', ['path.h', ['../path_8h.xhtml', 1, '']]], │ │ │ │ ['pbc_2ecpp_34', ['pbc.cpp', ['../tests_2pbc_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ ['../pbc_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['pbc_5faiuc_2eh_35', ['pbc_aiuc.h', ['../pbc__aiuc_8h.xhtml', 1, '']]], │ │ │ │ ['pbc_5faiuc_5fsycl_2eh_36', ['pbc_aiuc_sycl.h', ['../pbc__aiuc__sycl_8h.xhtml', 1, '']]], │ │ │ │ ['pbc_5fsimd_2ecpp_37', ['pbc_simd.cpp', ['../pbc__simd_8cpp.xhtml', 1, '']]], │ │ │ │ ['pbc_5fsimd_2eh_38', ['pbc_simd.h', ['../pbc__simd_8h.xhtml', 1, '']]], │ │ │ │ - ['pbcenums_2ecpp_39', ['pbcenums.cpp', ['../tests_2pbcenums_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../pbcenums_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['pbcenums_2ecpp_39', ['pbcenums.cpp', ['../pbcenums_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2pbcenums_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['pbcenums_2eh_40', ['pbcenums.h', ['../pbcenums_8h.xhtml', 1, '']]], │ │ │ │ ['pdb2gmx_2ecpp_41', ['pdb2gmx.cpp', ['../tests_2pdb2gmx_8cpp.xhtml', 1, '']]], │ │ │ │ ['periodicactions_2ecpp_42', ['periodicactions.cpp', ['../periodicactions_8cpp.xhtml', 1, '']]], │ │ │ │ ['periodicactions_2eh_43', ['periodicactions.h', ['../periodicactions_8h.xhtml', 1, '']]], │ │ │ │ ['periodicactions_5fbasic_2ecpp_44', ['periodicactions_basic.cpp', ['../periodicactions__basic_8cpp.xhtml', 1, '']]], │ │ │ │ ['periodicactions_5fconstraints_2ecpp_45', ['periodicactions_constraints.cpp', ['../periodicactions__constraints_8cpp.xhtml', 1, '']]], │ │ │ │ @@ -147,31 +147,31 @@ │ │ │ │ ['pmetestcommon_2eh_131', ['pmetestcommon.h', ['../pmetestcommon_8h.xhtml', 1, '']]], │ │ │ │ ['pointers_2ecpp_132', ['pointers.cpp', ['../pointers_8cpp.xhtml', 1, '']]], │ │ │ │ ['pointers_2eh_133', ['pointers.h', ['../pointers_8h.xhtml', 1, '']]], │ │ │ │ ['pointstate_2ecpp_134', ['pointstate.cpp', ['../pointstate_8cpp.xhtml', 1, '']]], │ │ │ │ ['pointstate_2eh_135', ['pointstate.h', ['../pointstate_8h.xhtml', 1, '']]], │ │ │ │ ['polynomials_2ecpp_136', ['polynomials.cpp', ['../polynomials_8cpp.xhtml', 1, '']]], │ │ │ │ ['polynomials_2eh_137', ['polynomials.h', ['../polynomials_8h.xhtml', 1, '']]], │ │ │ │ - ['poscalc_2ecpp_138', ['poscalc.cpp', ['../tests_2poscalc_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../poscalc_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['poscalc_2ecpp_138', ['poscalc.cpp', ['../poscalc_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2poscalc_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['poscalc_2eh_139', ['poscalc.h', ['../poscalc_8h.xhtml', 1, '']]], │ │ │ │ ['position_2ecpp_140', ['position.cpp', ['../position_8cpp.xhtml', 1, '']]], │ │ │ │ ['position_2eh_141', ['position.h', ['../position_8h.xhtml', 1, '']]], │ │ │ │ - ['position_5frestraints_2ecpp_142', ['position_restraints.cpp', ['../tests_2position__restraints_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../position__restraints_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['position_5frestraints_2ecpp_142', ['position_restraints.cpp', ['../position__restraints_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../tests_2position__restraints_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['position_5frestraints_2eh_143', ['position_restraints.h', ['../position__restraints_8h.xhtml', 1, '']]], │ │ │ │ ['printtime_2eh_144', ['printtime.h', ['../printtime_8h.xhtml', 1, '']]], │ │ │ │ ['programcontext_2ecpp_145', ['programcontext.cpp', ['../programcontext_8cpp.xhtml', 1, '']]], │ │ │ │ ['programcontext_2eh_146', ['programcontext.h', ['../programcontext_8h.xhtml', 1, '']]], │ │ │ │ ['propagator_2ecpp_147', ['propagator.cpp', ['../propagator_8cpp.xhtml', 1, '']]], │ │ │ │ ['propagator_2eh_148', ['propagator.h', ['../propagator_8h.xhtml', 1, '']]], │ │ │ │ - ['pull_2ecpp_149', ['pull.cpp', ['../gromacs_2pulling_2tests_2pull_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ - ['../programs_2mdrun_2tests_2pull_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ + ['pull_2ecpp_149', ['pull.cpp', ['../programs_2mdrun_2tests_2pull_8cpp.xhtml', 1, '(Global Namespace)'], │ │ │ │ + ['../gromacs_2pulling_2tests_2pull_8cpp.xhtml', 1, '(Global Namespace)'] │ │ │ │ ]], │ │ │ │ ['pull_2eh_150', ['pull.h', ['../pull_8h.xhtml', 1, '']]], │ │ │ │ ['pull_5finternal_2eh_151', ['pull_internal.h', ['../pull__internal_8h.xhtml', 1, '']]], │ │ │ │ ['pull_5fparams_2eh_152', ['pull_params.h', ['../pull__params_8h.xhtml', 1, '']]], │ │ │ │ ['pull_5frotation_2ecpp_153', ['pull_rotation.cpp', ['../programs_2mdrun_2tests_2pull__rotation_8cpp.xhtml', 1, '']]], │ │ │ │ ['pull_5frotation_2eh_154', ['pull_rotation.h', ['../pull__rotation_8h.xhtml', 1, '']]], │ │ │ │ ['pullcoordexpressionparser_2eh_155', ['pullcoordexpressionparser.h', ['../pullcoordexpressionparser_8h.xhtml', 1, '']]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_17.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -22,16 +22,16 @@ │ │ │ │ ['uniquedeviceid_14', ['uniqueDeviceId', ['../device__management_8h.xhtml#ab7595ed839026b4d41d8eb72701a80eb', 1, 'device_management_common.cpp']]], │ │ │ │ ['unit_15', ['unit', ['../classgmx_1_1EnergyTerm.xhtml#aef5ad0000c2fbbc74c57f0b5e0ddb409', 1, 'gmx::EnergyTerm']]], │ │ │ │ ['unitcelliscompact_16', ['UnitCellIsCompact', ['../group__module__coordinateio.xhtml#ggae520b2721d9d5166e7c015b2654bd1d9ad4d785ddf0c77e7b697efd2b5ec376e1', 1, 'gmx']]], │ │ │ │ ['unitcellisrectangular_17', ['UnitCellIsRectangular', ['../group__module__coordinateio.xhtml#ggae520b2721d9d5166e7c015b2654bd1d9a8e7bda81ce54b8cf90c3b856c83e7d9f', 1, 'gmx']]], │ │ │ │ ['unitcellistriclinic_18', ['UnitCellIsTriclinic', ['../group__module__coordinateio.xhtml#ggae520b2721d9d5166e7c015b2654bd1d9a99285c8187fb87e756f127435045dc3f', 1, 'gmx']]], │ │ │ │ ['unitcelltype_19', ['UnitCellType', ['../namespacegmx.xhtml#af897bff42be729e6eaf3c4dc6e199722', 1, 'gmx']]], │ │ │ │ ['unitcelltypenames_20', ['unitCellTypeNames', ['../namespacegmx.xhtml#ae81efb97e81499b750d906d26a29ce18', 1, 'gmx']]], │ │ │ │ - ['unitvector_21', ['unitvector', ['../classgmx_1_1BasicVector.xhtml#a2fc805de143df5ecfe38f2cb50d84e6c', 1, 'gmx::BasicVector::unitVector()'], │ │ │ │ - ['../namespacegmx.xhtml#a53215047e2f488dfbf48164090c07b40', 1, 'gmx::unitVector(const VectorType &v)'] │ │ │ │ + ['unitvector_21', ['unitvector', ['../namespacegmx.xhtml#a53215047e2f488dfbf48164090c07b40', 1, 'gmx::unitVector()'], │ │ │ │ + ['../classgmx_1_1BasicVector.xhtml#a2fc805de143df5ecfe38f2cb50d84e6c', 1, 'gmx::BasicVector::unitVector()'] │ │ │ │ ]], │ │ │ │ ['unity_22', ['Unity', ['../namespacegmx.xhtml#ab0ad78613a262a1d4fcce5d18525099fa82dd98f1d663acc318e6a8ec4ab69b7a', 1, 'gmx']]], │ │ │ │ ['unknown_23', ['unknown', ['../classgmx_1_1CpuInfo.xhtml#acd7ff27553f3ff9fd1037c30c21a24f1a88183b946cc5f0e8c96b2e66e1c74a7e', 1, 'gmx::CpuInfo::Unknown'], │ │ │ │ ['../namespacegmx.xhtml#a20e189e3f31f5f1e8581a5cc84063453a88183b946cc5f0e8c96b2e66e1c74a7e', 1, 'gmx::Unknown'], │ │ │ │ ['../device__information_8h.xhtml#a5514710e3c78d4816da9e8d2e3cd508ca88183b946cc5f0e8c96b2e66e1c74a7e', 1, 'Unknown: device_information.h'] │ │ │ │ ]], │ │ │ │ ['unpackrecvbufkernel_24', ['unpackRecvBufKernel', ['../namespacegmx.xhtml#a704128fa72f8ce7dcf08d0063a166036', 1, 'gmx']]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-lib/search/all_8.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -34,16 +34,16 @@ │ │ │ │ ['../structFEPStateValue.xhtml', 1, 'FEPStateValue< T >'] │ │ │ │ ]], │ │ │ │ ['fepstatevalue_3c_20nameholder_20_3e_23', ['FEPStateValue< NameHolder >', ['../structFEPStateValue.xhtml', 1, '']]], │ │ │ │ ['fepstatevalue_3c_20real_20_3e_24', ['FEPStateValue< real >', ['../structFEPStateValue.xhtml', 1, '']]], │ │ │ │ ['fepstatevalue_3c_20unsigned_20short_20_3e_25', ['FEPStateValue< unsigned short >', ['../structFEPStateValue.xhtml', 1, '']]], │ │ │ │ ['fetchcoulombforcer_26', ['fetchCoulombForceR', ['../namespacegmx.xhtml#af4358df7df7ec8c2d2ad3014049c9ff0', 1, 'gmx']]], │ │ │ │ ['fetchfromparamlookuptable_27', ['fetchFromParamLookupTable', ['../hip__kernel__utils_8h.xhtml#a7ad14d6bc00ea67ddd8c5435c07a8881', 1, 'hip_kernel_utils.h']]], │ │ │ │ - ['fetchnextevent_28', ['fetchnextevent', ['../classGpuRegionTimerWrapper.xhtml#ae595ce381d09845166643647caf6b539', 1, 'GpuRegionTimerWrapper::fetchNextEvent()'], │ │ │ │ - ['../classGpuRegionTimerImpl.xhtml#ace9b9965e5b0dec64d5d74af36035a63', 1, 'GpuRegionTimerImpl::fetchNextEvent()'] │ │ │ │ + ['fetchnextevent_28', ['fetchnextevent', ['../classGpuRegionTimerImpl.xhtml#ace9b9965e5b0dec64d5d74af36035a63', 1, 'GpuRegionTimerImpl::fetchNextEvent()'], │ │ │ │ + ['../classGpuRegionTimerWrapper.xhtml#ae595ce381d09845166643647caf6b539', 1, 'GpuRegionTimerWrapper::fetchNextEvent()'] │ │ │ │ ]], │ │ │ │ ['ffallow_5fmissing_29', ['ffALLOW_MISSING', ['../group__module__commandline.xhtml#gaae8f2f42809cc00c087b4359507abb81', 1, 'filenm.h']]], │ │ │ │ ['fflib_30', ['ffLIB', ['../group__module__commandline.xhtml#gabcfe164407bc1fff8164f4779f0fe3ce', 1, 'filenm.h']]], │ │ │ │ ['ffliboptrd_31', ['ffLIBOPTRD', ['../group__module__commandline.xhtml#gaa168a891bb48ca53f62f04697add97f4', 1, 'filenm.h']]], │ │ │ │ ['fflibrd_32', ['ffLIBRD', ['../group__module__commandline.xhtml#ga70443d67e488b39409b37d98b9d2f8b8', 1, 'filenm.h']]], │ │ │ │ ['ffmult_33', ['ffMULT', ['../group__module__commandline.xhtml#ga50cb2de9aec8429fb44074a1bfdb19b2', 1, 'filenm.h']]], │ │ │ │ ['ffopt_34', ['ffOPT', ['../group__module__commandline.xhtml#ga070f4190c2bc4a6af08333851ddf42ac', 1, 'filenm.h']]], │ │ │ │ @@ -348,19 +348,19 @@ │ │ │ │ ['../classForceHelperBuffers.xhtml', 1, 'ForceHelperBuffers'] │ │ │ │ ]], │ │ │ │ ['forcemtscombined_201', ['forcemtscombined', ['../classgmx_1_1ForceBuffersView.xhtml#a166f7af032d4e40035ffec7b665ed572', 1, 'gmx::ForceBuffersView::forceMtsCombined() const'], │ │ │ │ ['../classgmx_1_1ForceBuffersView.xhtml#a6c291c3c289aecea56104b7e79325558', 1, 'gmx::ForceBuffersView::forceMtsCombined()'] │ │ │ │ ]], │ │ │ │ ['forcemtscombinedwithpadding_202', ['forceMtsCombinedWithPadding', ['../classgmx_1_1ForceBuffersView.xhtml#a297d8a01836b387a5ab1be510aed44fa', 1, 'gmx::ForceBuffersView']]], │ │ │ │ ['forceoutput_2eh_203', ['forceoutput.h', ['../forceoutput_8h.xhtml', 1, '']]], │ │ │ │ - ['forceoutputs_204', ['forceoutputs', ['../classgmx_1_1ForceOutputs.xhtml#abd589c42af0e81e787dd76f03d020187', 1, 'gmx::ForceOutputs::ForceOutputs()'], │ │ │ │ - ['../classgmx_1_1ForceOutputs.xhtml', 1, 'gmx::ForceOutputs'] │ │ │ │ + ['forceoutputs_204', ['forceoutputs', ['../classgmx_1_1ForceOutputs.xhtml', 1, 'gmx::ForceOutputs'], │ │ │ │ + ['../classgmx_1_1ForceOutputs.xhtml#abd589c42af0e81e787dd76f03d020187', 1, 'gmx::ForceOutputs::ForceOutputs()'] │ │ │ │ ]], │ │ │ │ - ['forceparam_205', ['forceparam', ['../classInteractionOfType.xhtml#a9377381fa12dd22697c3e1b256cd8cf3', 1, 'InteractionOfType::forceParam() const'], │ │ │ │ - ['../classInteractionOfType.xhtml#a6baea034eb73978879f0a9d1fe80d938', 1, 'InteractionOfType::forceParam()'] │ │ │ │ + ['forceparam_205', ['forceparam', ['../classInteractionOfType.xhtml#a6baea034eb73978879f0a9d1fe80d938', 1, 'InteractionOfType::forceParam()'], │ │ │ │ + ['../classInteractionOfType.xhtml#a9377381fa12dd22697c3e1b256cd8cf3', 1, 'InteractionOfType::forceParam() const'] │ │ │ │ ]], │ │ │ │ ['forceproviderinput_206', ['forceproviderinput', ['../classgmx_1_1ForceProviderInput.xhtml#a2f7907d0aae391014935b848ac4f3561', 1, 'gmx::ForceProviderInput::ForceProviderInput()'], │ │ │ │ ['../classgmx_1_1ForceProviderInput.xhtml', 1, 'gmx::ForceProviderInput'] │ │ │ │ ]], │ │ │ │ ['forceprovideroutput_207', ['forceprovideroutput', ['../classgmx_1_1ForceProviderOutput.xhtml#a462f088782c665aa46acd9a7492853df', 1, 'gmx::ForceProviderOutput::ForceProviderOutput()'], │ │ │ │ ['../classgmx_1_1ForceProviderOutput.xhtml', 1, 'gmx::ForceProviderOutput'] │ │ │ │ ]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/html-user/search/all_17.js │ │ │ ├── js-beautify {} │ │ │ │ @@ -2,29 +2,29 @@ │ │ │ │ ['u_0', ['u', ['../structt__pargs.xhtml#a9896c617087886506822e9a67795e651', 1, 't_pargs']]], │ │ │ │ ['uint8_1', ['uInt8', ['../namespacegmx.xhtml#a4355a7e0f393d42cbb5b2a47aefea966ab0cffa75aa037e628ccfdf46bcc086ac', 1, 'gmx']]], │ │ │ │ ['uniformintdistribution_2', ['uniformintdistribution', ['../classgmx_1_1UniformIntDistribution.xhtml#a09808fada94acf89dc12c30310afaeda', 1, 'gmx::UniformIntDistribution::UniformIntDistribution(const param_type &param)'], │ │ │ │ ['../classgmx_1_1UniformIntDistribution.xhtml#a790697adc208c8ecf2e9164ea00cf24b', 1, 'gmx::UniformIntDistribution::UniformIntDistribution(result_type a=0, result_type b=std::numeric_limits< result_type >::max())'], │ │ │ │ ['../classgmx_1_1UniformIntDistribution.xhtml', 1, 'gmx::UniformIntDistribution< IntType >'] │ │ │ │ ]], │ │ │ │ ['uniformintdistribution_2eh_3', ['uniformintdistribution.h', ['../uniformintdistribution_8h.xhtml', 1, '']]], │ │ │ │ - ['uniformrealdistribution_4', ['uniformrealdistribution', ['../classgmx_1_1UniformRealDistribution.xhtml', 1, 'gmx::UniformRealDistribution< RealType >'], │ │ │ │ - ['../classgmx_1_1UniformRealDistribution.xhtml#a8a58a25b5bc17882dfc3671530d1aad3', 1, 'gmx::UniformRealDistribution::UniformRealDistribution(const param_type &param)'], │ │ │ │ - ['../classgmx_1_1UniformRealDistribution.xhtml#abf980964b1ce2f1fade69a0578b25e33', 1, 'gmx::UniformRealDistribution::UniformRealDistribution(result_type a=0.0, result_type b=1.0)'] │ │ │ │ + ['uniformrealdistribution_4', ['uniformrealdistribution', ['../classgmx_1_1UniformRealDistribution.xhtml#a8a58a25b5bc17882dfc3671530d1aad3', 1, 'gmx::UniformRealDistribution::UniformRealDistribution()'], │ │ │ │ + ['../classgmx_1_1UniformRealDistribution.xhtml', 1, 'gmx::UniformRealDistribution< RealType >'], │ │ │ │ + ['../classgmx_1_1UniformRealDistribution.xhtml#abf980964b1ce2f1fade69a0578b25e33', 1, 'gmx::UniformRealDistribution::UniformRealDistribution()'] │ │ │ │ ]], │ │ │ │ ['uniformrealdistribution_2eh_5', ['uniformrealdistribution.h', ['../uniformrealdistribution_8h.xhtml', 1, '']]], │ │ │ │ ['uniformrealdistribution_3c_20real_20_3e_6', ['UniformRealDistribution< real >', ['../classgmx_1_1UniformRealDistribution.xhtml', 1, 'gmx']]], │ │ │ │ ['unique_5fcptr_7', ['unique_cptr', ['../namespacegmx.xhtml#a89d1da25b1e1f9331f1fe99b15072eac', 1, 'gmx']]], │ │ │ │ ['unique_5fcptr_2eh_8', ['unique_cptr.h', ['../unique__cptr_8h.xhtml', 1, '']]], │ │ │ │ ['unitcelliscompact_9', ['UnitCellIsCompact', ['../namespacegmx.xhtml#ae520b2721d9d5166e7c015b2654bd1d9ad4d785ddf0c77e7b697efd2b5ec376e1', 1, 'gmx']]], │ │ │ │ ['unitcellisrectangular_10', ['UnitCellIsRectangular', ['../namespacegmx.xhtml#ae520b2721d9d5166e7c015b2654bd1d9a8e7bda81ce54b8cf90c3b856c83e7d9f', 1, 'gmx']]], │ │ │ │ ['unitcellistriclinic_11', ['UnitCellIsTriclinic', ['../namespacegmx.xhtml#ae520b2721d9d5166e7c015b2654bd1d9a99285c8187fb87e756f127435045dc3f', 1, 'gmx']]], │ │ │ │ ['unitcelltype_12', ['UnitCellType', ['../namespacegmx.xhtml#af897bff42be729e6eaf3c4dc6e199722', 1, 'gmx']]], │ │ │ │ ['unitcelltypenames_13', ['unitCellTypeNames', ['../namespacegmx.xhtml#ae81efb97e81499b750d906d26a29ce18', 1, 'gmx']]], │ │ │ │ - ['unitvector_14', ['unitvector', ['../namespacegmx.xhtml#a53215047e2f488dfbf48164090c07b40', 1, 'gmx::unitVector()'], │ │ │ │ - ['../classgmx_1_1BasicVector.xhtml#a2fc805de143df5ecfe38f2cb50d84e6c', 1, 'gmx::BasicVector::unitVector()'] │ │ │ │ + ['unitvector_14', ['unitvector', ['../classgmx_1_1BasicVector.xhtml#a2fc805de143df5ecfe38f2cb50d84e6c', 1, 'gmx::BasicVector::unitVector()'], │ │ │ │ + ['../namespacegmx.xhtml#a53215047e2f488dfbf48164090c07b40', 1, 'gmx::unitVector(const VectorType &v)'] │ │ │ │ ]], │ │ │ │ ['unity_15', ['Unity', ['../namespacegmx.xhtml#ab0ad78613a262a1d4fcce5d18525099fa82dd98f1d663acc318e6a8ec4ab69b7a', 1, 'gmx']]], │ │ │ │ ['unknown_16', ['Unknown', ['../namespacegmx.xhtml#a20e189e3f31f5f1e8581a5cc84063453a88183b946cc5f0e8c96b2e66e1c74a7e', 1, 'gmx']]], │ │ │ │ ['unpackrecvbufkernel_17', ['unpackRecvBufKernel', ['../namespacegmx.xhtml#a704128fa72f8ce7dcf08d0063a166036', 1, 'gmx']]], │ │ │ │ ['unpaddedarrayref_18', ['unpaddedArrayRef', ['../classgmx_1_1ArrayRefWithPadding.xhtml#ad5b878ca7749f5b8f52e006269fbfc2f', 1, 'gmx::ArrayRefWithPadding']]], │ │ │ │ ['unpaddedconstarrayref_19', ['unpaddedConstArrayRef', ['../classgmx_1_1ArrayRefWithPadding.xhtml#a2c3f73497c6bc71264ae1af84b6522ae', 1, 'gmx::ArrayRefWithPadding']]], │ │ │ │ ['unset_20', ['Unset', ['../md__enums_8h.xhtml#a1df3eedfba9424ae3e518284a453d95cac9f88e098f6fe4e4e112eeb05ccb9671', 1, 'md_enums.h']]], │ │ ├── ./usr/share/doc/gromacs/html/doxygen/xml/index.xml.gz │ │ │ ├── index.xml │ │ │ │ ├── index.xml │ │ │ │ │┄ Ordering differences only │ │ │ │ │ @@ -76607,32 +76607,32 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ densityfittingparameters.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ densityfittingparameters.h │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + electricfield.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + electricfield.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ electricfield.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ nnpot.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ nnpot.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ nnpot.h │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - nnpotforceprovider.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - nnpotforceprovider.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ nnpotforceprovider.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ nnpotforceprovider_stub.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -76652,14 +76652,20 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ nnpottopologypreprocessor.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ nnpottopologypreprocessor.h │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + nnpotforceprovider.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + nnpotforceprovider.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ torchmodel.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ torchmodel.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -76790,20 +76796,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ qmmmtopologypreprocessor.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ qmmmtypes.h │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - electricfield.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - electricfield.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ cmdlinehelpcontext.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ cmdlinehelpcontext.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -79100,14 +79100,50 @@ │ │ │ │ │ │ │ │ │ │ check_screw_box │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ dd_resize_atominfo_and_state │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + utility.h │ │ │ │ │ + │ │ │ │ │ + isDlbOn │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + isDlbDisabled │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + dim2char │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + make_tric_corr_matrix │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_screw_box │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + ddGetAtomInfo │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + dd_load_count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + dd_resize_atominfo_and_state │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + atomToAtomIntoDomainToDomainCutoff │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + domainToDomainIntoAtomToDomainCutoff │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + utility.h │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ analysismodule.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ analysismodule.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -81563,482 +81599,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ rocfft_common_utils.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ fft_mpi.cpp │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - checkpoint.cpp │ │ │ │ │ - │ │ │ │ │ - CPT_MAGIC1 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - CPT_MAGIC2 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - StateKineticEntry │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - EkinNumber │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - EkinHalfStep │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DEkinDLambda │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Mvcos │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - EkinFullStep │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - EkinHalfStepOld │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - EkinNoseHooverScaleFullStep │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - EkinNoseHooverScaleHalfStep │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - VelocityScale │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - EkinTotal │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - StateEnergyEntry │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - N │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Aver │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Sum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumSum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - SumSim │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumSumSim │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumSteps │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumStepsSim │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DeltaHNN │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DeltaHList │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DeltaHStartTime │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DeltaHStartLambda │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - StatePullEntry │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumCoordinates │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumGroups │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumValuesInXSum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumValuesInFSum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - StatePullCoordEntry │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - ValueReferenceSum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - ValueSum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DR01Sum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DR23Sum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DR45Sum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - FScalarSum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DynaxSum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - StatePullGroupEntry │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - XSum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - StateFepEntry │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - IsEquilibrated │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumAtLambdaStats │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumAtLambdaEquil │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - WangLandauHistogram │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - WangLandauDelta │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - SumWeights │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - SumDG │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - SumMinVar │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - SumVar │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Accump │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Accumm │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Accump2 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Accumm2 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Tij │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - TijEmp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - StateAwhEntry │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - InInitial │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - EquilibrateHistogram │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - HistogramSize │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumPoints │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - CoordPoint │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - UmbrellaGridPoint │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - UpdateList │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - LogScaledSampleWeight │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - NumUpdates │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - ForceCorrelationGrid │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - StatePullCommunicationEntry │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - PreviousStepCom │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - CptElementType │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - integer │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - realnum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - real3 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - matrix3x3 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - cpt_version │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - enumValueToString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - enumValueToString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - enumValueToString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - enumValueToString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - enumValueToString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - enumValueToString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - enumValueToString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - enumValueToString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - cp_warning │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - cp_error │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_string_err │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_int │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_u_chars │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_enum_as_int │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_n_enum_as_int │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_int_err │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_bool_err │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_step_err │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_double_err │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_real_err │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_n_rvecs_err │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - sizeOfXdrType │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - xdrProc │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - listXdrVector │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - convertArrayRealPrecision │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - convertArrayRealPrecision │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - convertArrayRealPrecision │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - doVectorLow │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - doVector │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - doRealArrayRef │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - realArrayRefFromRVecArrayRef │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - doRvecVector │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_reals │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_real │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_ints │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_int │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_bool │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_doubles │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_double │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_matrix │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_nmatrix │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpte_matrices │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_header │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_footer │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_state │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_ekinstate │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_swapstate │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_enerhist │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - doCptPullCoordHist │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - doCptPullGroupHist │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - doCptPullHist │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_df_hist │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_EDstate │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_correlation_grid │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_awh_bias │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_awh │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_mdmodules │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_cpt_files │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - write_checkpoint_data │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_int │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_string │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_match │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - read_checkpoint │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - load_checkpoint │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - read_checkpoint_part_and_step │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - read_checkpoint_data │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - read_checkpoint_trxframe │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - list_checkpoint │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - read_checkpoint_simulation_part_and_filenames │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - checkpoint.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - checkpoint.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ checkpoint.h │ │ │ │ │ │ │ │ │ │ GMX_IGNORE_FSYNC_FAILURE_ENV │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ CPTSTRLEN │ │ │ │ │ @@ -90710,125 +90278,14 @@ │ │ │ │ │ │ │ │ │ │ gen_nnb │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ generate_excl │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - grompp.cpp │ │ │ │ │ - │ │ │ │ │ - NFILE │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - rm_interactions │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_atom_names │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_bonds_timestep │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_vel │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_shells_inputrec │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - nint_ftype │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - renumber_moltypes │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - molinfo2mtop │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - new_status │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - copy_state │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - cont_status │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - read_posres │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - sumComForRestraints │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - subComFromRestraints │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calcPosresCom │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gen_posres │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - set_wall_atomtype │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - nrdf_internal │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - spline1d │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - interpolate1d │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - setup_cmap │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_cmap_grid │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - count_constraints │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calc_temp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_max_reference_temp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - checkForUnboundAtoms │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - checkForUnboundAtoms │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - haveDecoupledModeInMol │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - checkDecoupledModeAccuracy │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - set_verlet_buffer │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - maxNonPerturbedExclusionDistance │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - checkExclusionDistances │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - deformInitFlow │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_grompp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - grompp.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ grompp.h │ │ │ │ │ │ │ │ │ │ gmx_grompp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -93386,14 +92843,20 @@ │ │ │ │ │ │ │ │ │ │ GMX_IS_X86_32 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ GMX_IS_X86_64 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + cpuinfo.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + cpuinfo.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ cpuinfo.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ detecthardware.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -93956,20 +93419,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ simd_support.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ simd_support.h │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - cpuinfo.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - cpuinfo.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ mockhardwaretopology.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ imd.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -94313,35 +93770,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ manage_threading.h │ │ │ │ │ │ │ │ │ │ setup_bonded_threading │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - orires.cpp │ │ │ │ │ - │ │ │ │ │ - extendStateWithOriresHistory │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - diagonalize_orires_tensors │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - print_orires_log │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calc_orires_dev │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - orires │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - orires.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ orires.h │ │ │ │ │ │ │ │ │ │ extendStateWithOriresHistory │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ calc_orires_dev │ │ │ │ │ @@ -94436,14 +93872,59 @@ │ │ │ │ │ │ │ │ │ │ compute_factors_restrdihs │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ compute_factors_cbtdihs │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + utilities.h │ │ │ │ │ + │ │ │ │ │ + MathOptimization │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Safe │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Unsafe │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_within_tol │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_numzero │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_int_multiply_for_overflow │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_feenableexcept │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_fedisableexcept │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmxShouldEnableFPExceptions │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + utilities.h │ │ │ │ │ + │ │ │ │ │ + ftypeIsListedPotential │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + ftype_is_bonded_potential │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + utilities.h │ │ │ │ │ + │ │ │ │ │ + genQmmmIndices │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ 3dtransforms.cpp │ │ │ │ │ │ │ │ │ │ N │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ gmx_mat4_copy │ │ │ │ │ @@ -94805,14 +94286,41 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ testarrayrefs.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ vectypes.cpp │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + utilities.cpp │ │ │ │ │ + │ │ │ │ │ + gmx_within_tol │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_numzero │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_int_multiply_for_overflow │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_feenableexcept │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_fedisableexcept │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmxShouldEnableFPExceptions │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + utilities.cpp │ │ │ │ │ + │ │ │ │ │ + genQmmmIndices │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ veccompare.cpp │ │ │ │ │ │ │ │ │ │ cmp_rvec │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ cmp_ivec │ │ │ │ │ @@ -94853,20 +94361,14 @@ │ │ │ │ │ │ │ │ │ │ pr_rvecs │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ prRVecs │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - boxdeformation.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - boxdeformation.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ boxdeformation.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ broadcaststructs.cpp │ │ │ │ │ │ │ │ │ │ bcastPaddedRVecVector │ │ │ │ │ @@ -95789,14 +95291,62 @@ │ │ │ │ │ │ │ │ │ │ cutoff_inf │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ init_forcerec │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + forcerec.h │ │ │ │ │ + │ │ │ │ │ + makeNonBondedParameterLists │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + makeLJPmeC6GridCorrectionParameters │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + forcerec_set_ranges │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_interaction_const_tables │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_forcerec │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + forcerec.h │ │ │ │ │ + │ │ │ │ │ + GMX_CUTOFF_INF │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + C6 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + C12 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + BHAMC │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + BHAMA │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + BHAMB │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + cutoff_inf │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + freeenergyparameters.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + freeenergyparameters.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ freeenergyparameters.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ gmx_omp_nthreads.cpp │ │ │ │ │ │ │ │ │ │ modth │ │ │ │ │ @@ -96737,20 +96287,14 @@ │ │ │ │ │ │ │ │ │ │ GPU_CONSTRAINTS_SUPPORTED │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ constrtestrunners_gpu.cpp │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - freeenergyparameters.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - freeenergyparameters.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ langevin.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ langevintestdata.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -96803,14 +96347,20 @@ │ │ │ │ │ │ │ │ │ │ GPU_SETTLE_SUPPORTED │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ settletestrunners_gpu.cpp │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + updategroupscog.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + updategroupscog.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ watersystem.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ tgroup.cpp │ │ │ │ │ │ │ │ │ │ sum_ekin │ │ │ │ │ @@ -96818,23 +96368,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ tgroup.h │ │ │ │ │ │ │ │ │ │ sum_ekin │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - trajectory_writing.cpp │ │ │ │ │ - │ │ │ │ │ - do_md_trajectory_writing │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - trajectory_writing.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ trajectory_writing.h │ │ │ │ │ │ │ │ │ │ EkindataState │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ NotUsed │ │ │ │ │ @@ -97040,20 +96581,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ updategroups.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ updategroups.h │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - updategroupscog.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - updategroupscog.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ updategroupscog.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ vcm.cpp │ │ │ │ │ │ │ │ │ │ enumValueToString │ │ │ │ │ @@ -97163,110 +96698,17 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ membedholder.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ membedholder.h │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - mimic.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - mimic.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - minimize.cpp │ │ │ │ │ - │ │ │ │ │ - em_state_t │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - print_em_start │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - em_time_end │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - sp_header │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - warn_step │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - print_converged │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_f_norm_max │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_state_f_norm_max │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_em │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - finish_em │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - swap_em_state │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - write_em_traj │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_em_step │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - em_dd_partition_system │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - reorder_partsum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pr_beta │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - minimize.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ minimize.h │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - replicaexchange.cpp │ │ │ │ │ - │ │ │ │ │ - MSRANK │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - ReplicaExchangeType │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Temperature │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Lambda │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - EndSingle │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - TemperatureLambda │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - c_probabilityCutoff │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - enumValueToString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - replicaexchange.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ replicaexchange.h │ │ │ │ │ │ │ │ │ │ gmx_repl_ex_t │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ init_replica_exchange │ │ │ │ │ @@ -97274,23 +96716,14 @@ │ │ │ │ │ │ │ │ │ │ replica_exchange │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ print_replica_exchange_statistics │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - rerun.cpp │ │ │ │ │ - │ │ │ │ │ - prepareRerunState │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - rerun.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ runner.cpp │ │ │ │ │ │ │ │ │ │ prepare_verlet_scheme │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ override_nsteps_cmdline │ │ │ │ │ @@ -97385,20 +96818,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ simulatorbuilder.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ tpi.cpp │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - freeenergy.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - freeenergy.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ freeenergy.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ handlerestart.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -97415,59 +96842,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ mdmodulesnotifiers.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ mdmodulesnotifiers.h │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - multisim.cpp │ │ │ │ │ - │ │ │ │ │ - buildMultiSimulation │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_sumd_sim │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_sumf_sim │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_sumi_sim │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_sumli_sim │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gatherIntFromMultiSimulation │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_multi_int │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_multi_int64 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - findIsSimulationMainRank │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - isMainSim │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - isMainSimMainRank │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - multisim_int_all_are_equal │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - logInitialMultisimStatus │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - multisim.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ multisim.h │ │ │ │ │ │ │ │ │ │ gmx_sum_sim │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ buildMultiSimulation │ │ │ │ │ @@ -97772,56 +97154,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ forcebuffers.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ forceoutput.h │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - forcerec.h │ │ │ │ │ - │ │ │ │ │ - makeNonBondedParameterLists │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - makeLJPmeC6GridCorrectionParameters │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - forcerec_set_ranges │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_interaction_const_tables │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_forcerec │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - forcerec.h │ │ │ │ │ - │ │ │ │ │ - GMX_CUTOFF_INF │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - C6 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - C12 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - BHAMC │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - BHAMA │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - BHAMB │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - cutoff_inf │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ group.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ group.h │ │ │ │ │ │ │ │ │ │ GID │ │ │ │ │ @@ -98480,86 +97820,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ communicator.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ communicator_stub.cpp │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - utilities.cpp │ │ │ │ │ - │ │ │ │ │ - gmx_within_tol │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_numzero │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_int_multiply_for_overflow │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_feenableexcept │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_fedisableexcept │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmxShouldEnableFPExceptions │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - utilities.cpp │ │ │ │ │ - │ │ │ │ │ - genQmmmIndices │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - utilities.h │ │ │ │ │ - │ │ │ │ │ - MathOptimization │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Safe │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Unsafe │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_within_tol │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_numzero │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_int_multiply_for_overflow │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_feenableexcept │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmx_fedisableexcept │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gmxShouldEnableFPExceptions │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - utilities.h │ │ │ │ │ - │ │ │ │ │ - ftypeIsListedPotential │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - ftype_is_bonded_potential │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - utilities.h │ │ │ │ │ - │ │ │ │ │ - genQmmmIndices │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ andersentemperaturecoupling.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ andersentemperaturecoupling.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -100004,14 +99272,20 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ helpformat.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ helpformat.h │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + helpmanager.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + helpmanager.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ helpmanager.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ helptopic.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -100031,20 +99305,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ rstparser.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ rstparser.h │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - helpmanager.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - helpmanager.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ mock_helptopic.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ mock_helptopic.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -100751,164 +100019,14 @@ │ │ │ │ │ │ │ │ │ │ pull_print_output │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ initPullHistory │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - pull.cpp │ │ │ │ │ - │ │ │ │ │ - Lock │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - sc_isAngleType │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - registrationMutex │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - groupPbcFromParams │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_coordinate_is_directional │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_coordinate_units │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_conversion_factor_userinput2internal │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_conversion_factor_internal2userinput │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - apply_forces_grp_part │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - apply_forces_grp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - apply_forces_cyl_grp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - apply_forces_vec_torque │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - apply_forces_coord │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - max_pull_distance2 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - low_get_pull_coord_dr │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_pull_coord_dr │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - make_periodic_2pi │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - sanitizePullCoordReferenceValue │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - updatePullCoordReferenceValue │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_dihedral_angle_coord │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_pull_coord_distance │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_pull_coord_deviation │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_pull_coord_value │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_pull_coord_value │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - clear_pull_forces │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_constraint │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - add_virial_coord_dr │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - add_virial_coord │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calc_pull_coord_scalar_force_and_potential │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calculateVectorForces │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - register_external_pull_potential │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_external_potential_registration │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - apply_external_pull_coord_force │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_pull_pot_coord │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_potential │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_apply_forces │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_constraint │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - dd_make_local_pull_groups │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_pull_group_index │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_pull │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - destroy_pull │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - preparePrevStepPullComNewSimulation │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - preparePrevStepPullCom │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - finish_pull │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_have_potential │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_have_constraint │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_have_constraint │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ pull_internal.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ epgrppbcNONE │ │ │ │ │ @@ -100934,236 +100052,14 @@ │ │ │ │ │ │ │ │ │ │ setPrevStepPullComFromState │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ allocStatePrevStepPullCom │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - pull_rotation.cpp │ │ │ │ │ - │ │ │ │ │ - WEIGHT_MIN │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - PRINT_FORCE_J │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - PRINT_POT_TAU │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - ISFLEX │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - ISCOLL │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - GAUSS_NORM │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - SLAB_MIN_ATOMS │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - RotStr │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - HaveFlexibleGroups │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - HavePotFitGroups │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - allocate_square_matrix │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - free_square_matrix │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_fitangle │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - bPotAngle │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - bSlabTau │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - reduce_output │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - add_rot_forces │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calc_beta_max │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calc_beta │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - gaussian_weight │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_slab_weight │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_slab_centers │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calc_rotmat │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - torque │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - print_aligned │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - print_aligned_short │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - open_output_file │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - open_slab_out │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - add_to_string │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - add_to_string_aligned │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - open_rot_out │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - open_angles_out │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - open_torque_out │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - swap_val │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - swap_col │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - diagonalize_symmetric │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - align_with_z │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calc_correl_matrix │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - weigh_coords │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - opt_angle_analytic │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - flex_fit_angle │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - flex_fit_angle_perslab │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - shift_single_coord │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_homeslab │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_single_atom_gaussians │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - flex2_precalc_inner_sum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - flex_precalc_inner_sum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_flex2_lowlevel │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_flex_lowlevel │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - sort_collective_coordinates │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_firstlast_atom_per_slab │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_first_slab │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_last_slab │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_firstlast_slab_check │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_flexible │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - angle │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - project_onto_plane │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_fixed │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_radial_motion │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_radial_motion_pf │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - radial_motion2_precalc_inner_sum │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_radial_motion2 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_firstlast_atom_ref │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - allocate_slabs │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_firstlast_slab_ref │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - copy_correct_pbc_image │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_rot_group │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - calc_mpi_bufsize │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_rot │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - rotate_local_reference │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - choose_pbc_image │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_rotation │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - pull_rotation.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ pullcoordexpressionparser.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ pullcoordexpressionparser.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -103985,164 +102881,14 @@ │ │ │ │ │ │ │ │ │ │ lsq_y_ax_b_xdouble │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ lsq_y_ax_b_error │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - swapcoords.cpp │ │ │ │ │ - │ │ │ │ │ - ChannelHistory │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - None │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Ch0 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Ch1 │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Domain │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Notset │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - A │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - B │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - Count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - t_compartment │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - t_swapgrp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - SwS │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - SwSEmpty │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - CompStr │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - SwapStr │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DimStr │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - ChannelString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - DomainString │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - is_in_channel │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - print_ionlist │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_molecule_center │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - compartment_contains_atom │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - update_time_window │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - add_to_list │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_compartment_boundaries │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - detect_flux_per_channel │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - sortMoleculesIntoCompartments │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_initial_ioncounts │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_initial_ioncounts_from_cpt │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - bc_initial_concentrations │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_swap_groups │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_group_apm_check │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - print_ionlist_legend │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - detect_flux_per_channel_init │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - outputStartStructureIfWanted │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_swapstate │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - getRequestedChargeImbalance │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - copyIndicesToGroup │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - convertOldToNewGroupFormat │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - bConvertFromOldTpr │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - init_swapcoords │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - finish_swapcoords │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - need_swap │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - get_index_of_distant_atom │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - translate_positions │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - apply_modified_positions │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - do_swapcoords │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - swapcoords.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ swapcoords.h │ │ │ │ │ │ │ │ │ │ init_swapcoords │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ finish_swapcoords │ │ │ │ │ @@ -105524,20 +104270,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ convert-tpr-with-leaks.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ convert-tpr.cpp │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - helpwriting.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - helpwriting.cpp │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ trjcat.cpp │ │ │ │ │ │ │ │ │ │ TIME_EXPLICIT │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ TIME_CONTINUE │ │ │ │ │ @@ -106856,26 +105596,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ runnercommon.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ clustsize.cpp │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - moduletest.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - moduletest.cpp │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - moduletest.h │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - moduletest.h │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ test_selection.cpp │ │ │ │ │ │ │ │ │ │ main │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -106883,50 +105611,14 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ topologyinformation.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ topologyinformation.cpp │ │ │ │ │ │ │ │ │ │ - │ │ │ │ │ - utility.h │ │ │ │ │ - │ │ │ │ │ - isDlbOn │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - isDlbDisabled │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - dim2char │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - make_tric_corr_matrix │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - check_screw_box │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - ddGetAtomInfo │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - dd_load_count │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - dd_resize_atominfo_and_state │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - atomToAtomIntoDomainToDomainCutoff │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - domainToDomainIntoAtomToDomainCutoff │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - │ │ │ │ │ - utility.h │ │ │ │ │ - │ │ │ │ │ │ │ │ │ │ alignedallocator.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ alignedallocator.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -108191,14 +106883,488 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ nonbonded_bench.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ nonbonded_bench.h │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + boxdeformation.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + boxdeformation.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + checkpoint.cpp │ │ │ │ │ + │ │ │ │ │ + CPT_MAGIC1 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + CPT_MAGIC2 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + StateKineticEntry │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + EkinNumber │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + EkinHalfStep │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DEkinDLambda │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Mvcos │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + EkinFullStep │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + EkinHalfStepOld │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + EkinNoseHooverScaleFullStep │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + EkinNoseHooverScaleHalfStep │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + VelocityScale │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + EkinTotal │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + StateEnergyEntry │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + N │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Aver │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Sum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumSum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + SumSim │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumSumSim │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumSteps │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumStepsSim │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DeltaHNN │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DeltaHList │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DeltaHStartTime │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DeltaHStartLambda │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + StatePullEntry │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumCoordinates │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumGroups │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumValuesInXSum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumValuesInFSum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + StatePullCoordEntry │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + ValueReferenceSum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + ValueSum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DR01Sum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DR23Sum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DR45Sum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + FScalarSum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DynaxSum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + StatePullGroupEntry │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + XSum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + StateFepEntry │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + IsEquilibrated │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumAtLambdaStats │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumAtLambdaEquil │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + WangLandauHistogram │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + WangLandauDelta │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + SumWeights │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + SumDG │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + SumMinVar │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + SumVar │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Accump │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Accumm │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Accump2 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Accumm2 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Tij │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + TijEmp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + StateAwhEntry │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + InInitial │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + EquilibrateHistogram │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + HistogramSize │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumPoints │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + CoordPoint │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + UmbrellaGridPoint │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + UpdateList │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + LogScaledSampleWeight │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + NumUpdates │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + ForceCorrelationGrid │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + StatePullCommunicationEntry │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + PreviousStepCom │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + CptElementType │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + integer │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + realnum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + real3 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + matrix3x3 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + cpt_version │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + enumValueToString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + enumValueToString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + enumValueToString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + enumValueToString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + enumValueToString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + enumValueToString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + enumValueToString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + enumValueToString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + cp_warning │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + cp_error │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_string_err │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_int │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_u_chars │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_enum_as_int │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_n_enum_as_int │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_int_err │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_bool_err │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_step_err │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_double_err │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_real_err │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_n_rvecs_err │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + sizeOfXdrType │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + xdrProc │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + listXdrVector │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + convertArrayRealPrecision │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + convertArrayRealPrecision │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + convertArrayRealPrecision │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + doVectorLow │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + doVector │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + doRealArrayRef │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + realArrayRefFromRVecArrayRef │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + doRvecVector │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_reals │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_real │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_ints │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_int │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_bool │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_doubles │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_double │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_matrix │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_nmatrix │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpte_matrices │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_header │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_footer │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_state │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_ekinstate │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_swapstate │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_enerhist │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + doCptPullCoordHist │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + doCptPullGroupHist │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + doCptPullHist │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_df_hist │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_EDstate │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_correlation_grid │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_awh_bias │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_awh │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_mdmodules │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_cpt_files │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + write_checkpoint_data │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_int │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_string │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_match │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + read_checkpoint │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + load_checkpoint │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + read_checkpoint_part_and_step │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + read_checkpoint_data │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + read_checkpoint_trxframe │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + list_checkpoint │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + read_checkpoint_simulation_part_and_filenames │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + checkpoint.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + checkpoint.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ comparison_helpers.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ compressed_x_output.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -108230,38 +107396,299 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ exactcontinuation.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ expandedensemble.cpp │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + freeenergy.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + freeenergy.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ freezegroups.cpp │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + grompp.cpp │ │ │ │ │ + │ │ │ │ │ + NFILE │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + rm_interactions │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_atom_names │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_bonds_timestep │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_vel │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_shells_inputrec │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + nint_ftype │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + renumber_moltypes │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + molinfo2mtop │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + new_status │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + copy_state │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + cont_status │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + read_posres │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + sumComForRestraints │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + subComFromRestraints │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calcPosresCom │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gen_posres │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + set_wall_atomtype │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + nrdf_internal │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + spline1d │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + interpolate1d │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + setup_cmap │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_cmap_grid │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + count_constraints │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calc_temp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_max_reference_temp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + checkForUnboundAtoms │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + checkForUnboundAtoms │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + haveDecoupledModeInMol │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + checkDecoupledModeAccuracy │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + set_verlet_buffer │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + maxNonPerturbedExclusionDistance │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + checkExclusionDistances │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + deformInitFlow │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_grompp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + grompp.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + helpwriting.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + helpwriting.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ initialconstraints.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ interactiveMD.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ mdruncomparison.h │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + mimic.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + mimic.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + minimize.cpp │ │ │ │ │ + │ │ │ │ │ + em_state_t │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + print_em_start │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + em_time_end │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + sp_header │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + warn_step │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + print_converged │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_f_norm_max │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_state_f_norm_max │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_em │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + finish_em │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + swap_em_state │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + write_em_traj │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_em_step │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + em_dd_partition_system │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + reorder_partsum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pr_beta │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + minimize.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + moduletest.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + moduletest.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + moduletest.h │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + moduletest.h │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ multiple_time_stepping.cpp │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + multisim.cpp │ │ │ │ │ + │ │ │ │ │ + buildMultiSimulation │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_sumd_sim │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_sumf_sim │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_sumi_sim │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gmx_sumli_sim │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gatherIntFromMultiSimulation │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_multi_int │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_multi_int64 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + findIsSimulationMainRank │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + isMainSim │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + isMainSimMainRank │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + multisim_int_all_are_equal │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + logInitialMultisimStatus │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + multisim.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ multisimtest.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ multisimtest.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ normalmodes.cpp │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + orires.cpp │ │ │ │ │ + │ │ │ │ │ + extendStateWithOriresHistory │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + diagonalize_orires_tensors │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + print_orires_log │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calc_orires_dev │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + orires │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + orires.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ outputfiles.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ periodicactions.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -108275,29 +107702,593 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ periodicactions_coupling.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ pmetest.cpp │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + pull.cpp │ │ │ │ │ + │ │ │ │ │ + Lock │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + sc_isAngleType │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + registrationMutex │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + groupPbcFromParams │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_coordinate_is_directional │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_coordinate_units │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_conversion_factor_userinput2internal │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_conversion_factor_internal2userinput │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + apply_forces_grp_part │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + apply_forces_grp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + apply_forces_cyl_grp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + apply_forces_vec_torque │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + apply_forces_coord │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + max_pull_distance2 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + low_get_pull_coord_dr │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_pull_coord_dr │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + make_periodic_2pi │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + sanitizePullCoordReferenceValue │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + updatePullCoordReferenceValue │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_dihedral_angle_coord │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_pull_coord_distance │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_pull_coord_deviation │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_pull_coord_value │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_pull_coord_value │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + clear_pull_forces │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_constraint │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + add_virial_coord_dr │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + add_virial_coord │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calc_pull_coord_scalar_force_and_potential │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calculateVectorForces │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + register_external_pull_potential │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_external_potential_registration │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + apply_external_pull_coord_force │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_pull_pot_coord │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_potential │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_apply_forces │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_constraint │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + dd_make_local_pull_groups │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_pull_group_index │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_pull │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + destroy_pull │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + preparePrevStepPullComNewSimulation │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + preparePrevStepPullCom │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + finish_pull │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_have_potential │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_have_constraint │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_have_constraint │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_rotation.cpp │ │ │ │ │ + │ │ │ │ │ + WEIGHT_MIN │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + PRINT_FORCE_J │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + PRINT_POT_TAU │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + ISFLEX │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + ISCOLL │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + GAUSS_NORM │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + SLAB_MIN_ATOMS │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + RotStr │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + HaveFlexibleGroups │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + HavePotFitGroups │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + allocate_square_matrix │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + free_square_matrix │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_fitangle │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + bPotAngle │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + bSlabTau │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + reduce_output │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + add_rot_forces │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calc_beta_max │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calc_beta │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + gaussian_weight │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_slab_weight │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_slab_centers │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calc_rotmat │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + torque │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + print_aligned │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + print_aligned_short │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + open_output_file │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + open_slab_out │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + add_to_string │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + add_to_string_aligned │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + open_rot_out │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + open_angles_out │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + open_torque_out │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + swap_val │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + swap_col │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + diagonalize_symmetric │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + align_with_z │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calc_correl_matrix │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + weigh_coords │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + opt_angle_analytic │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + flex_fit_angle │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + flex_fit_angle_perslab │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + shift_single_coord │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_homeslab │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_single_atom_gaussians │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + flex2_precalc_inner_sum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + flex_precalc_inner_sum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_flex2_lowlevel │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_flex_lowlevel │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + sort_collective_coordinates │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_firstlast_atom_per_slab │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_first_slab │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_last_slab │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_firstlast_slab_check │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_flexible │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + angle │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + project_onto_plane │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_fixed │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_radial_motion │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_radial_motion_pf │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + radial_motion2_precalc_inner_sum │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_radial_motion2 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_firstlast_atom_ref │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + allocate_slabs │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_firstlast_slab_ref │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + copy_correct_pbc_image │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_rot_group │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + calc_mpi_bufsize │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_rot │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + rotate_local_reference │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + choose_pbc_image │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_rotation │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + pull_rotation.cpp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + replicaexchange.cpp │ │ │ │ │ + │ │ │ │ │ + MSRANK │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + ReplicaExchangeType │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Temperature │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Lambda │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + EndSingle │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + TemperatureLambda │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + c_probabilityCutoff │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + enumValueToString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + replicaexchange.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ replicaexchange_equivalence.cpp │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + rerun.cpp │ │ │ │ │ + │ │ │ │ │ + prepareRerunState │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + rerun.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ simple_mdrun.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ simulator.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ simulatorcomparison.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ simulatorcomparison.h │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + swapcoords.cpp │ │ │ │ │ + │ │ │ │ │ + ChannelHistory │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + None │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Ch0 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Ch1 │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Domain │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Notset │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + A │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + B │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + Count │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + t_compartment │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + t_swapgrp │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + SwS │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + SwSEmpty │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + CompStr │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + SwapStr │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DimStr │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + ChannelString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + DomainString │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + is_in_channel │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + print_ionlist │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_molecule_center │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + compartment_contains_atom │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + update_time_window │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + add_to_list │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_compartment_boundaries │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + detect_flux_per_channel │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + sortMoleculesIntoCompartments │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_initial_ioncounts │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_initial_ioncounts_from_cpt │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + bc_initial_concentrations │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + check_swap_groups │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_group_apm_check │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + print_ionlist_legend │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + detect_flux_per_channel_init │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + outputStartStructureIfWanted │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_swapstate │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + getRequestedChargeImbalance │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + copyIndicesToGroup │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + convertOldToNewGroupFormat │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + bConvertFromOldTpr │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + init_swapcoords │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + finish_swapcoords │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + need_swap │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + get_index_of_distant_atom │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + translate_positions │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + apply_modified_positions │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + do_swapcoords │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + swapcoords.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ tabulated_bonded_interactions.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ termination.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ @@ -108305,14 +108296,23 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ terminationhelper.h │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ tpitest.cpp │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ + trajectory_writing.cpp │ │ │ │ │ + │ │ │ │ │ + do_md_trajectory_writing │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + │ │ │ │ │ + trajectory_writing.cpp │ │ │ │ │ + │ │ │ │ │ │ │ │ │ │ trajectorycomparison.cpp │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ trajectorycomparison.h │ │ │ │ │ │ │ │ │ │ │ │ ├── ./usr/share/doc/gromacs/html/manual-2025.4-Debian_2025.4_1.pdf │ │ │ ├── dumppdf -at {} │ │ │ │ @@ -158630,15 +158630,15 @@ │ │ │ │ 1040 │ │ │ │ Length │ │ │ │ 2843 │ │ │ │ Filter │ │ │ │ FlateDecode │ │ │ │ │ │ │ │ │ │ │ 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<< /D [23331 0 R /XYZ 71 807.752 null] >> << /D [23331 0 R /XYZ 72 356.341 null] >> << /D [23331 0 R /XYZ 72 234.417 null] >> << /Font << /F65 12664 0 R /F81 12717 0 R /F84 12967 0 R /F85 13188 0 R /F92 13214 0 R >> /ProcSet [ /PDF /Text ] >> << /Type /Page /Contents 23338 0 R /Resources 23336 0 R /MediaBox [0 0 595.276 841.89] /Parent 23279 0 R /Annots [ 23334 0 R 23335 0 R ] >> << /Type /Annot /Subtype /Link /Border[0 0 0]/H/I/C[1 0 0] /Rect [309.836 584.527 401.95 595.431] /A << /S /GoTo /D (chapter.8) >> >> << /Type /Annot /Subtype /Link /Border[0 0 0]/H/I/C[1 0 0] /Rect [460.252 528.292 524.272 539.196] /A << /S /GoTo /D (subsection.8.8.1) >> >> << /D [23337 0 R /XYZ 71 807.752 null] >> << /D [23337 0 R /XYZ 72 737.855 null] >> << /D [23337 0 R /XYZ 72 663.687 null] >> << /D [23337 0 R /XYZ 72 577.564 null] >> << /D [23337 0 R /XYZ 72 199.524 null] >> << /Font << /F65 12664 0 R /F92 13214 0 R /F81 12717 0 R /F85 13188 0 R /F84 12967 0 R /F80 12716 0 R >> /ProcSet [ /PDF /Text ] >> << /Type /Page /Contents 23347 0 R /Resources 23345 0 R /MediaBox [0 0 595.276 841.89] /Parent 23349 0 R /Annots [ 23340 0 R 23341 0 R 23342 0 R 23343 0 R 23344 0 R ] >> << /Type /Annot /Subtype /Link /Border[0 0 0]/H/I/C[1 0 0] /Rect [159.531 339.891 206.624 350.795] /A << /S /GoTo /D (subsection.3.11.54) >> >> │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ Font │ │ │ │ │ │ │ │ @@ -438817,15 +438817,15 @@ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ Producer │ │ │ │ cairo 1.18.4 (https://cairographics.org) │ │ │ │ CreationDate │ │ │ │ -D:20251123021942Z │ │ │ │ +D:20251123104835Z │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ Type │ │ │ │ Font