--- /srv/rebuilderd/tmp/rebuilderdUr2Vuy/inputs/lammps-doc_20250204+dfsg.1-2_all.deb +++ /srv/rebuilderd/tmp/rebuilderdUr2Vuy/out/lammps-doc_20250204+dfsg.1-2_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2025-03-03 05:03:37.000000 debian-binary │ --rw-r--r-- 0 0 0 30344 2025-03-03 05:03:37.000000 control.tar.xz │ --rw-r--r-- 0 0 0 57460964 2025-03-03 05:03:37.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 30348 2025-03-03 05:03:37.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 57460992 2025-03-03 05:03:37.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -80,15 +80,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 32600 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_chunk.html │ │ │ -rw-r--r-- 0 root (0) root (0) 52080 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_cmake.html │ │ │ -rw-r--r-- 0 root (0) root (0) 34375 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_coreshell.html │ │ │ -rw-r--r-- 0 root (0) root (0) 14973 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_couple.html │ │ │ -rw-r--r-- 0 root (0) root (0) 12486 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_diffusion.html │ │ │ -rw-r--r-- 0 root (0) root (0) 16378 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_dispersion.html │ │ │ -rw-r--r-- 0 root (0) root (0) 15614 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_drude.html │ │ │ --rw-r--r-- 0 root (0) root (0) 65285 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_drude2.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 65304 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_drude2.html │ │ │ -rw-r--r-- 0 root (0) root (0) 15424 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_elastic.html │ │ │ -rw-r--r-- 0 root (0) root (0) 35109 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_github.html │ │ │ -rw-r--r-- 0 root (0) root (0) 15379 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_granular.html │ │ │ -rw-r--r-- 0 root (0) root (0) 17083 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_grid.html │ │ │ -rw-r--r-- 0 root (0) root (0) 16201 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_kappa.html │ │ │ -rw-r--r-- 0 root (0) root (0) 70350 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_lammps_gui.html │ │ │ -rw-r--r-- 0 root (0) root (0) 13465 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/Howto_library.html │ │ │ @@ -944,15 +944,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 45552 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_store_force.html │ │ │ -rw-r--r-- 0 root (0) root (0) 49873 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_store_state.html │ │ │ -rw-r--r-- 0 root (0) root (0) 53502 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_temp_berendsen.html │ │ │ -rw-r--r-- 0 root (0) root (0) 55220 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_temp_csvr.html │ │ │ -rw-r--r-- 0 root (0) root (0) 53834 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_temp_rescale.html │ │ │ -rw-r--r-- 0 root (0) root (0) 46104 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_temp_rescale_eff.html │ │ │ -rw-r--r-- 0 root (0) root (0) 51130 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_tfmc.html │ │ │ --rw-r--r-- 0 root (0) root (0) 65933 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_tgnh_drude.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 65916 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_tgnh_drude.html │ │ │ -rw-r--r-- 0 root (0) root (0) 52689 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_thermal_conductivity.html │ │ │ -rw-r--r-- 0 root (0) root (0) 51739 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_ti_spring.html │ │ │ -rw-r--r-- 0 root (0) root (0) 48518 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_tmd.html │ │ │ -rw-r--r-- 0 root (0) root (0) 69084 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_ttm.html │ │ │ -rw-r--r-- 0 root (0) root (0) 46437 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_tune_kspace.html │ │ │ -rw-r--r-- 0 root (0) root (0) 53958 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_vector.html │ │ │ -rw-r--r-- 0 root (0) root (0) 52835 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/fix_viscosity.html │ │ │ @@ -1016,15 +1016,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 55035 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/molecule.html │ │ │ -rw-r--r-- 0 root (0) root (0) 49614 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/neb.html │ │ │ -rw-r--r-- 0 root (0) root (0) 44879 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/neb_spin.html │ │ │ -rw-r--r-- 0 root (0) root (0) 40269 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/neigh_modify.html │ │ │ -rw-r--r-- 0 root (0) root (0) 29539 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/neighbor.html │ │ │ -rw-r--r-- 0 root (0) root (0) 25051 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/newton.html │ │ │ -rw-r--r-- 0 root (0) root (0) 32528 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/next.html │ │ │ --rw-r--r-- 0 root (0) root (0) 46557 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/objects.inv │ │ │ +-rw-r--r-- 0 root (0) root (0) 46561 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/objects.inv │ │ │ -rw-r--r-- 0 root (0) root (0) 71583 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/package.html │ │ │ -rw-r--r-- 0 root (0) root (0) 62544 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/pair_adp.html │ │ │ -rw-r--r-- 0 root (0) root (0) 57450 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/pair_agni.html │ │ │ -rw-r--r-- 0 root (0) root (0) 68537 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/pair_aip_water_2dm.html │ │ │ -rw-r--r-- 0 root (0) root (0) 67827 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/pair_airebo.html │ │ │ -rw-r--r-- 0 root (0) root (0) 66877 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/pair_amoeba.html │ │ │ -rw-r--r-- 0 root (0) root (0) 64878 2025-03-03 05:03:37.000000 ./usr/share/doc/lammps/html/pair_atm.html │ │ ├── ./usr/share/doc/lammps/html/Howto_drude2.html │ │ │ @@ -474,15 +474,15 @@ │ │ │ fix NPT ATOMS npt temp 300. 300. 100 iso 1. 1. 500 │ │ │ fix_modify NPT temp TATOMS press thermo_press │ │ │ fix NVT DRUDES nvt temp 1. 1. 20 │ │ │ fix INVERSE all drude/transform/inverse │ │ │ │ │ │ │ │ │

Another option for thermalizing the Drude model is to use the │ │ │ -temperature-grouped Nose-Hoover (TGNH) thermostat proposed by (Son). │ │ │ +temperature-grouped Nose-Hoover (TGNH) thermostat proposed by (Son). │ │ │ This is implemented as fix tgnvt/drude and fix tgnpt/drude. │ │ │ It separates the kinetic energy into three contributions: │ │ │ the molecular center of mass (COM) motion, the motion of atoms or atom-Drude pairs relative to molecular COMs, │ │ │ and the relative motion of atom-Drude pairs. │ │ │ An independent Nose-Hoover chain is applied to each type of motion. │ │ │ When TGNH is used, the temperatures of molecular, atomic and Drude motion can be printed out with thermo_style command command.

│ │ │

NVT simulation with TGNH thermostat

│ │ ├── ./usr/share/doc/lammps/html/fix_tgnh_drude.html │ │ │ @@ -452,15 +452,15 @@ │ │ │ │ │ │

Example input scripts available: examples/PACKAGES/drude

│ │ │ │ │ │
│ │ │

Description

│ │ │

These commands are variants of the Nose-Hoover fix styles fix nvt and fix npt for thermalized Drude polarizable │ │ │ models. They apply temperature-grouped Nose-Hoover thermostat (TGNH) │ │ │ -proposed by (Son). When there are fast vibrational │ │ │ +proposed by (Son). When there are fast vibrational │ │ │ modes with frequencies close to Drude oscillators (e.g. double bonds or │ │ │ out-of-plane torsions), this thermostat can provide better kinetic │ │ │ energy equipartitioning.

│ │ │

The difference between TGNH and the original Nose-Hoover thermostat is that, │ │ │ TGNH separates the kinetic energy of the group into three contributions: │ │ │ molecular center of mass (COM) motion, │ │ │ motion of COM of atom-Drude pairs or non-polarizable atoms relative to molecular COM, │ │ ├── ./usr/share/doc/lammps/html/objects.inv │ │ │ ├── Sphinx inventory │ │ │ │ @@ -159,26 +159,26 @@ │ │ │ │  h3.x"[=)G(/,,_=ai.?)t/E9I9RYAeDle<'q)H88aLIaO;|c QNbtX b1gyIA*Dq)ur0Z?%?FCgc!e%1hh=#.r)xp#0|3JZ.b5.@ì؍&Kx-. ME$`,`RЬHV%,hK@raQ+x t(*6x+K zqjLVHF1 }I ze VcYZYLS L_LP)KX{l>$i%JpshkE9]-'%O9E2C$)LY>LHZ„HH@3C_d} @}bN@$ <%BŘ`9.AdY zfJ spġ>Sv[-q=]޴dpk'?Ae({H l;L<dSL82ۧkA7\+sN#IXLepY=xc_ h q5]@о؊ԃG;`I{oӮ:Ħs)w㜎NU02ͨS3Qwj;?2|܂+.4O_p 0yMǵ†u ]%GSu"Nݯ~;ZJL &0U'Z3p`O9-9ԟR^Ƚ?Rn9.xRk&75[Ϧ.iYtPk>q/~>SBB}~CFِ*sQ&^]9 ~b3528@ 5!+7'֫b&bi+V=c Vfۃʣُz=NJsjLw˭߭~¾;\P0Uw1֦GU;%>Xc"LZx/ ܻqz!_ӣcJe#['gc(= ,h[`:V │ │ │ │ }'}(=uGmPHܓ$)5NE=hpqT?GSDLkmwg9ȵ^;@MEӵ8B)`Fz=ƏE50q'B&*grsINU.]i)j"0qi^ǽ-j*XQQ5u.;7O0Ehp 7֖p }$4tKf5`¤  D`_܋1@ KÝOޥv4JWP%H ~W!Ux>O蟏C `;Dy3Sg` │ │ │ │ ޭ^Oi̓6nH UiY-2ZiL@3sFR>췒N2,>q[4@`fV<8TH p+Xm³(/bx| >sQ_֋}G=1a^9\҂ onQw*FL""Z`J۬`)u=U>VE}yڭF bFh\v=t!lZwl] │ │ │ │ f9m7վ-:Pe`>Fҩ-wlNU[*Ҕx̤Qfhb#@]e^e48hSMЦX=tt- │ │ │ │ շ$zݳ^ךՄVY&[H*lmp O7ph)Ñ`[51i^n<_n׺'⠵:5A&7P_Kծ@WO4`Wj `/Bv| Tm`]~7zHj"|b1RjۇJKfQ)s`[>~g0tPEsD\&/WʩΙ2n,VR\ot$.+.o3 │ │ │ │ E:˓c1y.â߀wΙ#̞ZJQ:%8Г=9g_}5}L?+QG):%֙ΚH:*:iQ"Z"6>gHˤ}%E:!>B4}b}n]#v>.6n4ûSJ-νNUmE:X2mFZtvXok;БQ# ~h&Yo^)d&! /6b/~"6D?13NԺ │ │ │ │ -c~Vu n#j^7qf=nhA[9-fW_o_4n&tɰi蟁VfJ=]M:qO# pBnc/n $Ly\[؉9::Ɯz'g8{SP7 ,}6|5iA:\D │ │ │ │ -`^شbwgOU0L]7Mgy؁иwϭ}'w}uqIPi"CAr;9q'.wz;=q6w Σ:kmT:dө:<$.넾V-QG%W/>{y6k*ӨhQ8?h>1ϹYmḓh&l|JhӇNGí<,0(嗦~ZU]Uw}Z!ћ^p>vюQI}KH_rxgB -đ]vzhgN΋)(ٶ'^<,zT?,B.|GBs8YHTь[q?KFzq邑<;adTǮ ̭ yB$eaa"88/H NR"qr0,EYD:jL pYJ"Q2QgPde4Q^D8OEK\J? "aB │ │ │ │ -ey*2)i.sޠkT g.h _)VV cF 8I!0 "9#|qihIqJ'T%;E.eW "&jy3D8QB%6bA/VE^%EeKH2[f(È*•,Ғ,44}/c+fxYAr @Y72" lr{VVfXb=#1 │ │ │ │ -ONNi)$q+AS-S │ │ │ │ -"9Ze8JV\2zZ4x 5#4h │ │ │ │ -n}ķwۚmg;ϣ,n`VYA@wɖGz^׍岦2p#vM2`d JPg?գe&>o7`4b\Ȟ\j|n2t1cn;j͠6cNPc6P~a[K │ │ │ │ -{z${|޿v5aĂKX1r߂DsNZv ўV4ɛ}}7z+/gPTr8Eυ(3r`UBaŞŊ- IWs5c.>6 Qܫ&ݨ!enPSieShE8VƔ^ S!y@sgF │ │ │ │ -|o.~nO .a 8٩0|9s "b~AE"P5Xr? 4s]ƫ@bOWD0 : \\QggvB}lFUVh<_ɒ N^p VT@$we)QhDk28yqfRE]cs\G%BAUvJ a/WkR*{ُ5`EJALeJ0 │ │ │ │ +c~V^V}583zG4Kn渿]}Y}tCA2%kr[&x(rv^6,='/)OdgҔ" i43/tkc;1=I}q 5"vDS= w'r$EOEXݵAХo#HCh;kc)'At!eZgQ │ │ │ │ ++AUBÙL6e^mo<9U׷#7 T'qK>h}Ho=;s=]0z=} │ │ │ │ +;UUD29O 1U Ge)@QpL2 }KXIIQ │ │ │ │ +ٓ&Y[VAI3c 3'fLE@9yQhLdfʀB'HyTH"e #c.S8O`fy.V Jaعxq2RhUD+fx0Fy 6rԫR([ј尲SEʦ)( ^|bd(R91AW YiFd@|Εc$% A!TtAA,/"(`*X. {Dx*A0A2L`/G4/, 7YAd1+AWY1{L,wQN@4(.WB -cy`s-cT9#+W>W"f bHp │ │ │ │ +9Q+fl4oB'ƒSel / 02Qx!#0Hn Ye │ │ │ │ +9"$SX"]kޚP*Jxi& │ │ │ │ +dC$D^ │ │ │ │ +DO\(@q5C5*%bPKYU3F`X l-Hc"Q AbW 8Q 1YQMt51ŨP:;"D+d:&ZKXm9 Ŋi@~Bm[`0/f&,"a1-5m$Έ $@ eƜJaz>"#ERbFM~A8-xYzG8E\Ē)Ҥ.e1 │ │ │ │ +g%gAIXK0V$#PRj0'FFDаMY"Txo Tg1Fa))9eD3s"tJe*GAYD4SLPGɊK^&"+0%:_0Ao~>"|J=?gqZ$j @]a+I : %SAn&6WH3%i@Űa\0=Q ,@NAzB%@2Zӏ%0lH0Jƹ@3,_QDf30=@Zs@]@G%s~kL]S │ │ │ │ +^{OBo{:Xt:Xp `+F[hi"@>ڳ*&yoCϴkF]o │ │ │ │ +_ ]sJl·QTQ9^;سXQ4!4jfe?ǦA70{5 |*59Cs*M(IҪ0ݨ+`RP#(^vHͅo=pE ';uwߞOQ{}0$YDߕwsPﶕ9ObHD<!궆}Rn<^vf.xHl&A~0s~pk@>Y(ÍȺ │ │ │ │ +q4Y2f ~7ي │ │ │ │ +1C:" │ │ │ │ +v6bMF'!Nڌ_Kwl4\(>=N!TjM]e/_@qTLHI5ɰL 1