From f94bbc0de05ea9ea595a8edcbb0cfa6f697d90f8 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 31 Aug 2016 22:21:11 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15532
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/html/Section_start.html | 8 ++++++++
 doc/html/searchindex.js     | 2 +-
 doc/src/Section_start.txt   | 9 +++++++++
 python/lammps.py            | 5 +++++
 4 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/doc/html/Section_start.html b/doc/html/Section_start.html
index c6462223d3..b31c4631b5 100644
--- a/doc/html/Section_start.html
+++ b/doc/html/Section_start.html
@@ -389,6 +389,7 @@ within the LAMMPS code.  The options that are currently recogized are:</p>
 <li>-DLAMMPS_BIGBIG</li>
 <li>-DLAMMPS_SMALLSMALL</li>
 <li>-DLAMMPS_LONGLONG_TO_LONG</li>
+<li>-DLAMMPS_EXCEPTIONS</li>
 <li>-DPACK_ARRAY</li>
 <li>-DPACK_POINTER</li>
 <li>-DPACK_MEMCPY</li>
@@ -457,6 +458,13 @@ be compiled with the same setting, or the link will fail.</p>
 MPI version does not recognize &#8220;long long&#8221; data types.  In this case a
 &#8220;long&#8221; data type is likely already 64-bits, in which case this setting
 will convert to that data type.</p>
+<p>The -DLAMMPS_EXCEPTIONS setting can be used to activate alternative
+versions of error handling inside of LAMMPS.  This is useful when
+external codes drive LAMMPS as a library.  Using this option, LAMMPS
+errors do not kill the caller.  Instead, the call stack is unwound and
+control returns to the caller.  The library interface provides the
+lammps_has_error() and lammps_get_last_error_message() functions to
+detect and find out more about a LAMMPS error.</p>
 <p>Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
 options can make for faster parallel FFTs (in the PPPM solver) on some
 platforms.  The -DPACK_ARRAY setting is the default.  See the
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 8ab032e71c..4c867b7219 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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,82,96,118,122],colvar:0,com:[2,37,64,98,164],comand:61,combiant:108,combin:[2,3,18,32,56,58,59,64,69,71,72,74,84,85,105,107,108,112,115,116,117,131,132,150,156,157,159,160,162],come:[0,2,13,62,63,69,80,81,156,157,159,160,164],comit:164,comm:[0,3,30,94,111],comm_modifi:[2,99,105,111,115,120],comm_styl:[19,60],comm_world:3,command:[0,1],comment:[3,46,66,77,82,94,95,113,114,116,117,123,136,142,143,144,149,150,156,157,158,159,160,164],commit:164,commmand:2,common:[0,1,2,3,4,30,62,74,84,85,120,122,156,157,159],commonli:[2,9,37,39,58,92,121,126,150,157,159],commun:[1,2,3,4,19,58,60,62,68,69,82,112],comp:[71,72,78,94,115,147,154,158],compar:[1,2,4,41,44,57,93,94,136,149],comparison:0,compass:[6,20,47,57,85,104],compat:[3,19,50,60,63,64,83,139],compens:[2,115],compil:[4,58,139],complain:3,complement:136,complementari:[107,124],complet:[2,3,19,60,74,94,116],complex:[2,3,9,36,39,42,45,68,71,84,94,115,139],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,40,42,43,58,61,62,63,64,68,69,70,74,78,84,93,94,111,115,120,133,134,149,150],componenet:2,composit:[2,68,113],compound:[106,115,116,160],compress:[2,58,70,75],compris:[84,117,147],compton:[41,44],comput:[0,1],computation:[2,82,99],compute_modifi:[61,62,69,70],compute_sa:41,compute_xrd:44,concav:84,concentr:[66,77,113,117,143],concept:2,conceptu:[2,62,94,107,136],concern:[2,30,32,67],concis:3,concurr:4,conden:[82,157,159],condens:[2,82,96,109,113,124,160],condit:[2,40,41,43,44,58,59,68,70,73,75,78,79,82,112,115,121],conducit:2,conduct:0,confer:[4,139],configur:[1,2,4,58,62,74,93,94,96,99,114,136,139,156,157,159,160,164],conflict:164,conform:[2,61,62,76,91,94,115],confus:160,conjuct:111,conjug:115,conjunct:[2,32,45,68,94,100,101,107,111,115,122,124,145,148],connect:[2,32,61,78,94,108,120,155,159],conner:96,connor:96,consecut:[3,45,107,124,128],consequ:[1,2,82,123],conserv:[13,61,67,68,69,71,77,78,94,110,111,112,120,130,149],consid:[2,29,32,60,61,82,115,147,149,155],consider:2,consist:[2,3,40,45,51,63,67,69,70,75,76,77,94,96,99,105,107,115,119,133,134,136,139,142,143,147,149],consistent_fe_initi:59,constant:0,constantli:64,constitu:[2,83,84,105,147],constrain:[2,64,67,71,72,78,79,93,115],constraint:[19,40,43,60,64,71,78,79,83,93,134],construct:[2,28,29,30,36,39,41,42,44,62,69,76,77,84,110,139,155,156],constructor:3,consult:4,consum:1,contact:[0,108,114,116,119,120,147],contain:[0,1,2,3,19,32,35,41,42,44,45,46,57,58,59,60,63,66,68,73,75,77,82,84,94,95,96,99,106,107,110,113,114,115,117,136,139,142,143,144,146,150,156,157,158,159,160,164],context:[2,4,162],contibut:29,contin:4,continu:[0,2,19,60,61,62,63,64,67,69,70,75,80,81,82,84,99,111,126,129,147,158],continuum:[2,59,82],contour_integr:59,contract:[62,69],contrain:78,contrast:[1,2,162],contrib:82,contribut:[2,29,32,33,34,35,38,40,42,43,62,68,78,93,94,111,113,115,133,134,139,149,164],control:[2,3,4,11,13,19,32,35,42,48,58,59,60,62],control_typ:59,convect:35,conveni:[2,13,150,164],convent:[13,50,55,57,76,113,115],converg:[2,19,58,60,61,62,70,71,72,75,76,78,93,94,106,107,124,149],convers:[42,58,107,108,109,115,124,128,132,145],convert:[2,5,6,8,12,16,17,18,35,45,47,58,85,86,90,91,94,95,113,139,157,159,163],convex:84,cool:64,coord:[2,3,36,39,73,83,94],coordb:149,coordbb:149,coordiat:93,coordin:[1,2,3,19,32,33,34,38,42,45,58,60,61,62,64,69,73,78,79,81,82,93,94,95,96,98,114,149],coords:149,copi:[0,3,58,82,94,164],copper:163,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,101,107,109],cornel:[2,46],corner:[2,58,84,164],corpor:4,corr:106,correct:[2,3,32,46,58,64,69,75,83,84,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],correction_max_iter:59,correctli:[3,69,78,84,94,109,134,139,164],correl:[2,35,36,42,67,74],correpond:66,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,40,41,42,44,46,47,48,49,50,51,52,53,54,55,56,58,62,63,64,66,68,69,70,73,74,77,78,83,84,85,86,87,89,90,91,92,94,95,96,97,100,101,102,103,104,105,106,107,110,111,113,114,115,116,117,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,136,137,139,141,143,144,145,146,147,148,149,150,151,156,157,158,159,160,161,162,163],correspondingli:[133,134],cosin:2,cosineshift:11,cost:[1,2,3,19,41,43,44,58,60,69,77,82,107,124,128,139,156],costheta0:[156,157,159,160],costheta:146,costli:[3,4],coul:[2,4,18,21,22,32,46,93],could:[2,3,19,32,34,35,38,40,58,60,63,75,82,83,84,93,96,118,122],coulomb:[2,43,93,100,101,102,103,104,106,107,108,109,110,115,120,121,124,128,132,135,145,148,149,159,160,162],coulommb:2,count:[1,2,3,19,35,46,60,62,69,78,84,93,94,118,122],counteract:63,counterbal:64,counterbalanc:13,counterclockwis:46,coupl:0,couple:[2,3],cours:[4,67,76,83,133,151],cov:149,coval:[2,13,115,136,149],cover:[2,59,68,115],cpp:[1,2,3,32,78],cpu:[1,4],cpuinfo:4,cr2:44,cr3:44,creat:[0,1,2,3,19,35,40,41,45,58,59,60,61,62,66,69,70,73,74,76,82,94,96,99,106,113,114,132,141,142,143,146,149,156,157,158,159,160,164],create_atom:[2,19,35],create_box:[2,19,35,45,62,69,155],create_elementset:59,create_faceset:59,create_nodeset:59,createatom:0,creation:45,criteria:[58,61,93],criterion:[19,45,60,61,93,94,106,115,120,149],critic:[2,24,25,82,93],cross:[4,33,58,94,103,111,113,121,122,124,126,128,146,148,157,159,163],crossov:1,crozier:0,crucial:75,crystal:[2,4,29,30,39,73,81],crystallin:[2,158],crystallogr:[41,44],crystallographi:[41,44],cs1:44,cs_chunk:2,csanyi:[42,150],cscl:136,csequ:2,csh:[3,4],cshrc:3,csic:[114,156,157,159,160],csinfo:2,csisi:[114,156,157,159,160],cst:113,cstherm:2,csvr:2,ctcm:[95,113],ctype:3,cu1:44,cu2:44,cu3au:136,cube:[2,84],cubes:[19,60],cubic:[39,68,73,113],cuda:1,cuh:99,cummul:[2,61,122],cumul:[2,69,70,94],currenlti:63,current:[0,1,2,3,4,19,30,32,43,58,59,60,61,62,63,64,69,71,72,76,77,78,79,82,83,93,94,99,106,110,113,115,116,120,123,133,134,136,137,138,146,151,157,159,164],curv:[2,45,71,72],curvatur:[119,147,163],custom:[0,2,3,33,34,35,38,43,58,61,62,69,70,75,93,96,118,122],cut:[1,2,4,19],cuthi:73,cutinn:[133,134],cutlo:73,cutmax:146,cutoff1:[104,110,124,128,132,135,145,148],cutoff2:[100,101,102,104,109,110,124,128,132,135,145,148],cutoff:[2,4,21,22,28,29,30,32,36,39,42,61,66,73,75,83,84,93,95,96,97,98,99,100,101,102,103,104,105,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],cutoffa:114,cutoffc:114,cuu3:113,cval:44,cvar:63,cvff:4,cwiggl:83,cyan:58,cycl:[69,70],cyclic:46,cylind:[58,72,84],cylindr:2,cyrot:99,d3q15:68,d3q19:68,d_e:82,daan:81,damp:[2,69,70,72,75,93,94,100,101,103,107,110,115,120,124,132,145,148],dampflag:120,danger:111,darden:110,darken:58,dash:120,dat:[2,35,59],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:135,davi:83,david:[157,159],daw:[113,146],dcd:[2,58,74],deactiv:132,debug:[2,3,41,44,45,74],decai:[36,107,163],decid:[2,4,164],decod:58,decompos:[32,150],decomposit:[59,74],decoupl:2,decreas:[4,61,64],dedic:4,defect:[2,29,139],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,68,69,70,73,74,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,96,97,98,100,101,102,103,104,105,107,108,110,111,112,114,115,117,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,134,135,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163],definit:[2,42,63,65,70,83,99,105,112,115,146,150],deform:[2,43,62,69,133,134],deg2theta:44,degre:[2,5,6,8,12,13,16,17,18,36,39,40,44,45,46,47,49,50,55,56,58,61,69,70,74,76,78,81,85,86,90,91,92,93,110,113,122],delai:2,delet:[28,61,69,155,164],delete_atom:45,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:59,delimit:77,dellago:[2,64],deloc:[115,149],delr:136,delta_1:99,delta_3:99,delta_7:99,delta_ij:[136,146],delta_pi:99,delta_r:146,delta_sigma:99,deltah_f:66,demo:3,demonstr:[75,136],dendrim:122,denniston:68,denot:[41,64,107,121],dens:[61,77,115],densiti:[2,19,42,45,59,60,68,82,83,95,96,99,113,136,137,138,142,143,146,147,149,152,153,154],depart:0,departur:75,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,40,42,45,46,47,48,49,50,51,52,53,54,55,57,58,60,62,66,68,69,70,73,77,78,80,82,83,84,85,86,87,89,90,91,92,93,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,113,114,115,116,117,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,156,157,158,159,160,161,162,163],dependend:2,deposit:[69,78],depth:[26,58,82,117,119,147],der:[32,105,106,132,162],deriv:[2,32,42,62,63,64,69,70,73,80,81,82,83,84,96,99,105,110,115,116,121,126,130,131,136,139,162],derjagin:162,derlet:73,descib:58,describ:[0,1,2,3,4,19,29,30,41,42,43,44,45,51,54,60,61,62,63,66,67,68,69,70,73,74,75,77,80,81,83,93,94,96,98,100,101,103,104,105,106,107,110,113,115,116,117,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,139,140,142,143,146,147,148,149,150,151,155,156,157,158,159,160,161,162,163,164],descript:[2,3],descriptor:42,design:[0,2,3,41,44,59,61,69,73,82,97,98,103,107,109,115,132,133,134,137,138,146],desir:[2,3,4,35,40,43,45,62,63,67,69,78,93,94,111,113,122,133,134,156,157,159],desktop:[2,58],destabil:99,destre:91,destroi:3,detail:[1,2,3,4,19,34,35,38,40,42,43,45,57,58,59,60,61,62,63,64,67,68,69,70,75,78,81,82,93,95,96,98,99,102,103,104,105,106,107,110,111,115,116,119,120,121,122,124,125,126,127,128,129,130,131,132,133,134,135,136,140,142,143,147,149,150,151,161,162,164],detect:[36,94,106,122,123],determin:[1,2,4,26,32,40,41,43,44,45,58,60,62,66,69,73,74,75,76,77,83,84,96,102,106,110,113,117,118,120,128,136,139,143,147,149,155,162],devan:148,devanathan:159,develop:[0,2,3,4,63,70,75,96,99,115,138,139,149,160],deviat:[70,73,118],devic:1,devin:106,devis:138,dfactor:58,dft:139,dhug:75,dhugoniot:75,dia:136,diag:77,diagnost:[4,61,77],diagon:[2,42,43,62,69],diagonalstyl:150,diagram:[19,41,44,57,60,74],diallo:122,diam:58,diamet:[2,45,58,105,119,120,126,147,162],diamond:[115,136],dick:2,dicken:63,did:[93,111,113,120,157,159],dielectr:[103,107,108,109,124,128,132,145],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,42,45,57,58,60,61,62,63,64,67,68,69,73,74,75,78,79,80,81,82,83,84,85,94,95,96,99,102,103,105,106,111,112,113,115,117,119,120,121,124,125,127,128,135,136,137,138,140,141,142,143,144,146,147,148,149,150,151,156,157,159,160,162],differenti:[1,2,13,77,107,146,158],difficult:[62,63,74,122],difficulti:[36,39,78],diffract:[41,44],diffraction:[41,44],diffus:0,diffuse:2,digit:139,dihedr:[0,4,28,36,39,40,42,43,45,46,47,48,49,50,51,52,53,54,55,56,57,61,76,86,87,88,90,93,96,99,103],dihedral_coeff:[46,47,48,49,50,51,52,53,54,55,56,57],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,43],dihydrid:115,dij:78,dilat:[62,69,70],dim:[45,136],dimens:[1,2,19,35,43,45,58,60,62,68,69,70,75,83,94],dimension:[36,40,41,42,44,82,94,146],dimensionless:[37,42,63,82,150,162],dimer:[2,136],dimstr:[19,60],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:110,dir:[1,3,73,75,146],dirac:42,direc:146,direct:[2,4,13,29,39,41,42,44,45,46,58,68,70,73,75,80,81,82,83,84,93,94,111,112,120,134],directli:[2,3,32,42,45,58,63,68,77,84,95,96,100,101,102,107,110,113,115,124,128,145,148,155],directori:[0,1,2,3,4,63,80,81,94,95,96,99,106,107,113,114,116,132,136,137,138,139,144,146,149,150,156,157,158,159,160],disabl:[4,82,123],disadvantag:[2,60],disallow:69,discard:[19,60,84],discontinu:[93,130],discourag:136,discret:[2,58,63,68,72],discuss:[0,1],disk:[2,36],disloc:[29,139],disord:[29,139],disp:0,dispar:147,disperion:[110,128],dispers:[2,102,110,128,133,160],displac:[2,37,62,69,73,120],displai:[3,57,58],disregard:139,dissip:[2,31,65,67,80,81,111,112,120,133,134],dist:[2,35,74,76,155],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,39,41,42,45,47,58,61,62,64,68,69,70,73,75,76,78,79,81,82,83,84,85],distinct:[2,147],distinguish:[2,42,115],distort:95,distrbut:95,distribut:[0,2,3,19,32,42,57,60,67,68,69,95,99,107,113,114,116,136,137,138,144,146,147,156,157,158,159,160],distro:146,ditto:163,div:4,diverg:[81,96],divid:[2,4,19,35,40,43,57,60,73,93,94,116,149,160],divis:[2,56,68,99,132],dl_poly:2,dlammps_ffmpeg:58,dlammps_gzip:58,dlammps_jpeg:58,dlammps_memalign:4,dlammps_png:58,dlm:69,dlmp_intel_offload:4,dlopen:2,dlvo:[105,162],dm_lb:68,doc:[0,1,2,3,32,34,37,38,40,43,45,57,58,63,69,84,93,94,95,96,98,106,107,113,114,116,122,136,137,138,144,146,150,156,157,159,160,164],docuement:147,doe:[0,1,2,3,19,28,29,32,35,41,44,45,46,57,58,59,60,61,62,63,64,66,67,68,69,72,82,83,84,86,87,88,90,91,94,95,96,97,98,99,102,103,104,105,106,107,108,110,111,113,114,115,117,118,119,120,121,123,126,127,129,130,131,133,134,136,137,138,139,142,143,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],doesn:[45,96,106,114,156,157,158,159,160],dof:40,doi:[2,73],domain:[2,19,41,44,58,60,62,68,69,74,82,83,94],domin:[1,115],don:[0,4,84,136,149,164],done:[1,2,19,45,56,58,59,60,61,62,63,66,69,74,78,80,81,93,94,96,102,113,128,134,135,136,142,143,155,164],donor:122,dot:43,doti:[99,146],doubl:[1,2,3,4,32,46,62,84,99,116,121,139],dover:59,down:[2,3,62,115,149],download:3,downsid:2,dpd:2,dpdtheta:[31,112],dpdtheta_i:[65,66],dr_ewald:41,drag:[2,35,69,70,79],dragforc:68,drai:[58,75],drain:93,dramat:[61,62,69,149],drautz:99,draw:58,drawn:[58,67],drayleigh:75,dreid:2,dreiding:0,drfourth:37,drho:[95,113,142,143],drift:[2,37,64,67],drive:[3,62,69,73,94],driven:[2,51],driver:2,drop:111,drsquar:37,drude:0,dt_collis:68,dt_lb:68,dt_md:68,dtqm:75,dudarev:44,due:[1,2,4,28,29,33,34,37,38,41,42,43,44,45,58,61,62,67,68,69,70,73,76,80,81,82,83,84,93,94,108,111,112,113,118,119,133,134,146,147,148,155,157,159,162,163],duffi:82,dullweb:69,dummi:[13,158],dump:[0,1],dump_modifi:[2,58],dunbrack:[2,5,46,103],duplic:[19,60,73],durat:[57,82,120],dure:[2,4,19,32,46,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,93,94,111,132,139,141,142,143],dvlo:162,dvx:2,dx_lb:68,dy3:44,dyanam:2,dynam:[0,2,3,4,19,31,37,45,58,59,60,61,63,65,67,69,70,71,74,75,76,80,81,82,93,94,111,112,115,133,134,154],dynamo:[95,113,136],dyre:129,e28637:13,e_1:99,e_2:99,e_a:77,e_b:116,e_ee:115,e_hbond:122,e_i:[2,99,116],e_j:[2,99],e_k:99,e_ke:115,e_kl:2,e_lj:[96,110],e_n:[63,99],e_ne:115,e_nn:115,e_pr:115,e_rebo:96,e_torsion:96,e_tot:139,e_vol:139,eaa:85,eaat:47,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,66,67,68,69,70,71,73,74,77,78,79,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,159,160,161,162,163],eacn:[19,60],eam:[0,95,107],earli:[19,60],earlier:[94,120,136],earth:115,easi:[2,3,32,43,83],easier:[4,58],easili:[3,58,94],eat:47,eaxmpl:2,eba:6,ebb13:47,ebb:6,ebt:47,ec_ii:136,ec_ij:136,ec_jj:136,echo:[3,41,44],ecp:115,edg:[2,19,41,44,58,83,84],edge:83,edit:[4,164],edition:4,edu:[3,113,133],eebt:47,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,38,40,43,46,47,48,49,50,51,52,53,54,55,57,58,59,61,62,64,67,69,70,73,74,75,76,78,81,82,83,84,85,86,87,89,90,91,92,93,94,95,96,97,99,100,101,102,103,104,105,106,107,110,111,113,114,115,116,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,137,139,141,142,143,144,145,147,148,149,151,156,157,158,159,160,161,162,163],effici:[0,1,2,4,40,56,58,62,69,74,78,99,105,107,124,128,139,142,143,147],efficienc:4,efield:[78,93],eggebrecht:[107,149],ehex:2,eigenvalu:74,einstein:[2,81],either:[1,2,3,4,19,29,41,42,43,44,45,58,60,61,62,63,64,68,69,70,73,77,78,84,93,99,105,113,117,120,133,134,136,139,143,146,155,157,159],ejtehadi:[105,119,147],elaps:[83,151],elast:[2,21,22,94,120,158],elastic:0,elba:13,electr:[2,59,116,163],electric:4,electrolyt:162,electron:[2,41,59,82,95,106,110,113,115,116,136,139,146,149,159,160,163],electron_integr:59,electron_temperatur:59,electron_unit:115,electroneg:[2,106,116,149],electroneg_compon:149,electrostat:[2,4,105,110,115,124,132,134,149,162],elem1:[116,136,150],elem2:[116,136,150],elem:149,element1:[95,113,149],element2:[95,113,149],element:[2,33,37,40,42,43,58,59,95,96,99,106,113,114,115,116,136,137,138,139,144,146,149,150,156,157,158,159,160],elementn:[95,113],elementset:59,elif:42,elig:122,elimin:[2,67,78,80,81],elj:110,ellips:2,ellipsoid:[2,45,71,93,119,134,147],els:[58,63,69,82],elsewher:136,elt:136,emac:0,email:[0,3,116],emb:84,emb_lin_neg:136,embed:[3,13,82,95,113,116,132,136,137,138,146],embt:47,emin:62,emphas:120,empir:[59,115],empiric:96,emploi:[64,158],empti:123,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,40,41,42,44,46,47,48,49,50,51,52,53,54,55,57,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,80,81,82,83,84,85,86,87,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,138,139,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],enclos:[2,136,149],encod:58,encompass:2,encount:39,encourag:[77,79],end:[1,2,3,4,19,47,58,61,62,64,67,69,72,76,77,82,94,111,113,119,135,139,147,150,151],endbondtors:47,energet:[61,96],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,40,43,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111],energy_compon:149,enforc:[2,58,61,69,78,124],enforce2d:[2,93],eng:[3,106,138],engineer:[59,80,113],enginer:137,enhanc:[59,64],enlarg:58,enough:[45,60,75,83,84,107],enpub:113,ensembl:[2,32,35,69,72,74,75,111,149],ensight:2,ensur:[2,42,62,67,69,99,132,156,160],enter:[116,139,160],enthalpi:[77,113],entir:[0,2,3,19,31,40,41,43,44,45,60,61,64,67,69,70,73,74,77,79,82,110,128],entiti:2,entri:[41,66,75,99,114,136,142,143,144,150,156,157,158,159,160],entry1:[142,143],enumuer:2,environ:[1,2,3,4,58,73,95,99,106,114,115,146,157],eos:66,epair:[96,118,122],epp:110,epq:110,eps0:162,eps14:132,epsilon0:159,epsilon:[2,18,21,22,27,28,32,46,83,84,93,98,103,104,105,107,108,109,110,117,119,121,122,123,124,125,126,127,128,129,130,131,132,135,140,145,147,148,156,161,162],epsilon_0:163,epsilon_14:103,epsilon_:147,epsilon_d:108,epsilon_i:[119,147],epsilon_i_:147,epsilon_i_a:[119,147],epsilon_i_b:[119,147],epsilon_i_c:[119,147],epsilon_j:[119,147],epsilon_j_:147,epsilon_j_a:[119,147],epsilon_j_b:[119,147],epsilon_j_c:[119,147],epsilon_lj:147,eqp:110,eqq:110,equal:[2,3,19,28,32,35,43,45,58,60,62,63,67,68,70,71,73,74,75,76,77,80,81,82,83,93,94,96,106,111,112,118,119,122,133,139,140,146,147,149,150,151,160,163],equat:[2,35,39,40,41,44,57,62,63,64,65,66,68,69,70,73,74,75,77,78,82,83,105,110,111,112,115,116,117,120,133,134,136,143,147,152,153,154,163],equation:[73,91],equilibr:[2,35,45,61,62,69,75,80,81,106,107],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,47,48,62,67,68,69,70,75,76,78,81,85,86,90,91,106,136,144,149],equilibrium_start:59,equival:[2,13,62,69,76,96,111,115,149,157,159],equlibrium:2,er3:44,eradiu:115,eras:80,erat:134,erc:107,erfc:[107,124],erhart:[113,157,159],eros:136,erose_form:136,erot:2,errata:[157,159],erratum:83,error:[0,1,2,3,11,48,58,62,63,64,66,69,71,77,82,83,84,93,107,124,147,155,157,159],erta:120,especi:[4,45,60,75,76],essenti:[3,11,48,96,107,124,159],essential:70,essex:13,establish:32,estim:[1,2,19,29,35,43,59,60,77],esub:136,eta:[2,68,69,75,114,116,119,146,158,160],eta_dot:69,eta_ij:146,eta_ji:116,etap:69,etap_dot:69,etc:[1,2,3,4,28,33,34,35,43,45,58,59,67,69,82,84,93,94,113,114,132,134,139,156,157,159,160],etol:[93,94],etot0:75,etot:[2,43,75],eu2:44,eu3:44,euler:[77,93,94],eulerian:59,europhi:68,evalu:[3,32,35,42,45,46,58,59,63,67,77,83,93,139,142,143,146,149],evanseck:[2,5,46,103],evaul:93,even:[2,4,19,29,56,60,62,64,69,82,83,84,93,94,98,115,116,120,147,160],evenli:[19,43,60,68],event:[2,69,82],eventu:2,ever:28,everaer:[105,119,147],everi:[0,1,2,3,4,19,35,58,59,60,61,62,63,64,68,69,70,71,72,73,75,77,78,82,94,111,132,149,164],everyth:164,everywher:126,eviri:115,evolut:[64,68,74],evolv:[68,74],ewald:[2,41,43,93,100,101,102,107,110,115,124,128,145,148],ewald_disp:110,exact:[19,60,61,67,82],exactli:[2,19,35,45,60,67,75,111,113,120,133,142,143],examin:[2,61,77],exampl:[0,1],exce:[2,4,19,60,62,69,93],exceed:[19,60,69],excel:115,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,40,43,45,46,47,48,49,50,51,52,53,54,55,57,60,62,69,70,74,78,82,85,86,87,89,90,91,92,94,95,96,97,100,101,102,103,104,105,106,107,109,110,111,113,114,115,116,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,134,137,141,144,145,147,148,151,156,157,158,159,160,161,162,163],excess:115,exchang:[2,59,64,82,115],excit:115,excite:115,exclud:[2,4,40,42,93,120,133,134,155],exclus:[1,4,32,46,106,139],excurs:69,execut:[1,2,3,58],exempl:149,exemplari:67,exemplifi:115,exert:[2,71,84],exhaust:59,exhibit:[36,64,69,115],exist:[2,3,29,45,57,58,62,85,86,87,88,90,112,155,164],exit:[3,19,60],expans:[42,56],expect:[1,4,19,60,73,75,136,139],expens:[2,73,82],experi:[2,76,94,111],experienc:[2,4],explain:[1,2,3,19,30,58,60,62,69,71,73,94,98,113,149,151,164],explan:[2,42,73],explic:140,explicit:[2,3,32,77,96,99,103,113,115,123,133,164],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,40,45,46,47,48,49,50,51,52,53,54,55,62,67,69,70,75,78,82,85,86,87,89,90,91,92,95,96,97,100,101,102,103,104,105,106,107,108,110,111,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,137,139,141,142,143,144,145,147,148,151,152,153,154,156,157,158,159,160,161,162,163,164],explictli:4,exploit:74,explor:[41,44],expon:[77,113,117,119,122,132,140,148],exponenti:[32,77,117,146,156,160,163],expos:3,exposit:[59,111],express:[2,42,45,62,73,77,82,99,113,115,126,136,149,150],expressiont:99,extend:[0,2],extens:[2,4,21,22,27,32,35,63,64,69,70,73,76,80,81,82,83,84,119,136,139,147,150],extent:[1,19,21,60,96],exterior:[2,84],extern:[32,58,62,67,68,69,70,72,82,93,137,138],extra:[2,3,4,19,22,40,41,43,44,45,60,69,75,93,110,120,136],extract:[2,3,18,32,94,107,116,136,150],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,58,62,69,81,115,158],extrema:132,extreme:115,extrins:59,f_1:[2,62],f_a:[157,158,159],f_c:158,f_f:159,f_fix_id:75,f_harm:81,f_i:[13,146],f_id:[2,63],f_ij:146,f_int:80,f_j:13,f_jj:35,f_k:146,f_langevin:82,f_max:75,f_r:[157,158,159],f_sigma:99,f_solid:81,f_ss:2,face:[2,83,84,119,136,147],facil:0,facilit:2,fact:[2,4,81,120,149],factor:[1,2,8,12,16,17,18,19,22,23,32,35,41,42,44,46,54,58,60,62,64,68,69,70,74,76,77,78,83,84,90,96,99,100,101,103,107,108,109,111,112,115,120,123,124,136,139,142,143,144,145,148,151,156],fail:[3,62,93,94,109],fairli:[3,164],faken:30,fall:2,fals:149,famili:160,familiar:[0,3,164],fan:146,far:[2,60,62,69,73,76,83,86,90,94],farrel:[157,159],fashion:[2,19,45,60,63,69,70,75,81,82,83,94,133],fast:[2,4,63,75,77,133,134,139],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,40,46,47,48,49,50,51,52,53,54,55,60,69,70,78,80,82,85,86,87,89,90,91,92,95,96,97,99,100,101,102,103,104,105,106,107,110,111,113,114,116,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,137,141,144,145,147,148,151,156,157,158,159,160,161,162,163],fastest:[1,2,82],fault:29,fava:119,favor:61,fcc:[2,29,30,35,39],fcold:64,fdt:[65,66,77],fdti:32,fe2:44,fe3:44,fe_md_boundari:59,featur:[0,2,3,42,58,61,67,74,84,93,164],fecr:113,feedback:63,feel:[73,84,94],fehlberg:77,felling:138,felt:84,fene:[2,4],fennel:[107,124],fep:0,ferguson:[2,46],fermi:[1,159],fermion:115,fernando:135,few:[1,2,3,64,69,78,93,94,96,149],fewer:[1,3,4],feynman:74,ffield:[106,116,149],fflag1:58,fflag2:58,ffmpeg:58,ffplai:58,fft:[1,3,43],fhot:64,ficiti:155,fictiti:[2,74,76,107,124,128,155],field:0,fifth:[2,117,144],figshar:73,figur:[1,4,75,164],fij:110,file0:73,file1:[3,66,73],file2:[3,66],file:[0,1],filenam:[4,19,58,59,60,66,73,77,82,94,95,96,99,107,113,114,116,117,136,137,138,142,143,144,146,149,150,156,157,158,159,160],fill:[45,58,82,99,139,164],filter:59,finchham:[2,109],find:[0,2,3,4,30,32,61,62,63,66,73,76,93,94,107,124,128,136,142,143,149,164],fine:[4,81,164],finer:[42,45],finger:45,finish:[2,3,19,60],finit:0,finni:113,fire:[93,94],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,39,40,43,44,47,58,60,61,63,66,67,68,69,73,74,75,78,79,80,81,82,85,93,94,95,96,98,99,100,101,103,106,107,113,115,116,117,120,121,123,124,128,133,134,136,138,139,142,143,144,146,149,150,155,156,157,158,159,160,1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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix nve/manifold/rattle command","fix nvt/manifold/rattle command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub 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anch:[3,162],branicio2009:158,branicio:[31,158],breakdown:[1,4,94],brennan:[32,65,110,140,141,153],brenner:94,brick:[20,60],brief:[1,2,4,69,94,97],briefli:[2,72,104,147,162],brilliantov:118,broadwel:5,broken:[29,30,69,97],brook:2,brown:[5,41,43],brownian:[2,38,131,132],brows:0,browser:58,bryantsev:120,bsd:4,btype:[105,122,126,130,153],buc:99,buck:[2,5,33,98],buckingham:[98,99,100,107,133],buckplusattr:147,buffer:58,bufi:58,bug:[0,4],bui:58,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,24,25,26,27,28,29,32,33,38,40,41,42,44,46,47,48,49,50,51,52,53,54,55,56,57,61,64,65,66,67,68,69,70,71,72,73,75,76,78,79,80,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],bulatov:[135,136],bulk:[2,30,68,71,106,134,137,147],bundl:[58,162],button:162,bypass:2,c11:134,c_0:[80,94,151,152],c_1:[41,44,67],c_2:[41,44],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:80,c_flux:36,c_gauss:116,c_hb:120,c_i:66,c_id:[2,33,63],c_ij:2,c_ijkl:2,c_k:67,c_mychunk:[2,35],c_n_k:67,c_p:43,c_peratom:43,c_pi:97,c_prop:2,c_sigma:97,c_size:2,c_thermo_temp:63,ca2:44,cach:5,cacul:76,calcforc:68,calclat:36,calcluat:[38,40,43,105],calcualt:36,calcul:[0,1],caldwel:[2,46],calhoun:72,call:[1,2,3],callabl:3,callback:3,caller:4,caltech:[2,113],calucl:2,calul:[3,4,30],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cannot:[1,2,3,4,5,20,29,58,60,61,62,67,69,73,80,81,82,91,92,99,100,102,111,117,119,122,126,128,130,143,145,146,153],canon:[69,72,79,137],cao1:72,cao2:72,cao:72,capabl:[3,5,94,102],capac:[65,80,150],capolungo:[41,44],captur:[2,94,100,113,118,126,134],carbid:105,carbon:[58,89,94,104,134],card:[4,5,33,120],care:[2,45,56,68,69,96],carefulli:[3,4,29],carlo:[2,61],caro:111,carri:[5,80,118],carrillo:5,cartesian:[2,93],cascad:80,cat:[5,58],cate:68,categori:[0,4,94],cation:[114,147],caus:[1,2,4,5,45,62,69,71,75,76,81,82,91,92,120,122,128,131,132],caution:1,cautious:94,caveat:94,cbecker:[93,111],cc1:[2,35],ccc:[112,154,155,157,158],ccflag:5,ccflags:5,ccm6:111,ccsi:[112,154,155,157,158],ccu:97,cd2:44,cdeam:111,cdll:3,cdof:2,cdte:97,cdte_bop:97,cdtese:97,cdzn:97,cdznte:97,ce3:44,ce4:44,cell:[2,41,44,45,62,69,70,73,80,113,137],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,10,34,35,38,41,45,58,62,67,69,77,79,81,82,83,96,112,113,117,118,131,132,134,135,136,154,155,156,157,158],centr:64,central:[30,37,39,42,71,76,77,86,137,142,158],centro:2,centroid:72,centrosymmetri:30,certain:[1,2,4,58,61,63],cfg:[2,58],cg_type:146,ch2:76,ch2lmp:[0,2],ch3:76,chain:[0,2,14,29,61,69,70,72,76,79,89,108,109,153],challeng:2,champaign:131,chan:137,chandler:[93,111],chandrasekhar:[2,122],chang:[1,2,3,4,5,20,23,33,45,58,59,60,61,62,63,68,69,70,71,73,74,75,76,78,79,80,82,91,92,109,113,118,131,132,134,137,147,153,162],change_box:2,chapter:72,charact:[2,4,20,58,60,66,75,113,115,121,140,141,144,147],character:[2,30,39,42,148],characterist:78,charg:[1,2,3,33,41,44,45,98,99,104,105,107,108,111,113,114,122,126,130,143,147,157,158,160,161],charl:63,charmm:0,cheaper:[117,145],check:[2,3,4,20,36,60,74,76,79,91,92,121],checkout:162,chem:[2,6,7,10,21,22,23,33,39,40,43,46,47,54,64,67,68,69,72,73,78,79,81,83,89,90,92,94,98,101,102,104,105,106,108,109,110,113,116,117,119,120,122,126,127,130,134,138,140,141,143,147,153],chemic:[32,41,44,59,115,141],chemistri:[73,94,97,113],chen:80,cheng:104,chi:[71,114,117],chiral:89,chmod:[3,4],cho:134,choic:[2,4,5,20,29,30,33,43,56,60,61,68,69,72,92,130],choos:[1,2,4,14,29,33,58,61,62,63,68,69,70],chose:[155,157],chosen:[2,4,42,45,51,58,62,63,67,68,69,70,72,110,113,118,121,124,146,155],chunk:0,chunkid:35,ciccotti:76,cieplak:[2,46],circular:2,circumv:[37,39],citat:[0,4,68],cite:[4,147],cl1:44,clarendon:[14,108],clarifi:[155,157],clark:143,classic:[0,2,5,72,73,80,90,113],classifi:158,clean:[2,4],clear:[2,3,63],clebsch:42,click:[3,45,57,58,92,162],climb:92,clock:4,clockwis:46,clone:162,close:[2,3,4,20,43,61,62,68,69,76,82,92,94,97,105,106,134,140,141,157,162],closer:[20,60,62,78,92],closest:[71,117,145,153],cloud:147,cluster:[2,4,5,43,64,76],cmax:134,cmd:[3,4,72],cmdarg:3,cmin:134,cmm:[19,146],cna:30,co2:[44,75,76,115],coars:[14,19,29,51,66,75,115,119,141,146],coarsest:42,code:[0,1],coeff:[4,7,46,47,56,83,121,149],coeffici:0,coefficienct:109,coefficient0:111,coefficient1:111,coeffieci:[2,95],coeffincientn:111,coexist:113,cohes:[2,114,134],coincid:[82,101,131,132],cold:2,coleman:[41,44],collect:[2,35,45,103],colliex:44,collis:[68,118,161],colloid:[2,4],color:[20,58,60,67,73],column:[2,4,30,35,37,39,42,43,44,73,80,94,116,120],colvar:[0,4],colvarmodul:4,com:[2,38,64,96,162],comand:61,combiant:106,combin:[2,3,19,33,56,58,59,64,69,72,82,83,103,105,106,110,113,114,115,129,130,148,154,155,157,158,160],come:[0,2,14,62,63,69,78,79,154,155,157,158,162],comfort:4,comit:162,comm:[0,3,4,31,92,109],comm_modifi:[2,97,103,109,113,118],comm_styl:[20,60],comm_world:3,command:[0,1],comment:[3,4,46,66,75,80,92,93,111,112,114,115,121,134,140,141,142,147,148,154,155,156,157,158,162],commit:162,commmand:[2,4],common:[0,1,2,3,4,5,31,62,72,82,83,118,120,154,155,157],commonli:[2,4,10,38,39,58,90,119,124,148,155,157],commun:[1,2,3,4,5,20,58,60,62,68,69,80,110],comp:[76,92,113,145,152,156],compar:[1,2,4,5,41,44,57,91,92,134,147],comparison:0,compass:[7,21,47,57,83,102],compat:[3,4,20,50,60,63,64,81,137],compens:[2,113],compil:[4,5,58,137],complain:[3,4],complement:134,complementari:[105,122],complet:[2,3,4,20,60,72,92,114],complex:[2,3,4,10,37,39,42,45,68,82,92,113,137],complic:[2,4],complier:4,compon:[2,4,30,31,34,35,36,37,38,39,40,42,43,58,61,62,63,64,68,69,70,72,76,82,91,92,109,113,118,131,132,147,148],componenet:2,composit:[2,68,111],compound:[104,113,114,158],compress:[2,4,58,70,73],compris:[82,115,145],compton:[41,44],comput:[0,1],computation:[2,80,97],compute_modifi:[61,62,69,70],compute_sa:41,compute_xrd:44,concav:82,concentr:[66,75,111,115,141],concept:2,conceptu:[2,62,92,105,134],concern:[2,31,33,67],concis:3,conclud:4,concurr:5,conden:[80,155,157],condens:[2,80,94,107,111,122,158],condit:[2,40,41,43,44,58,59,68,70,71,73,76,77,80,110,113,119],conducit:2,conduct:0,confer:[5,137],config:4,configur:[1,2,4,5,58,62,72,91,92,94,97,112,134,137,154,155,157,158,162],conflict:[4,162],conform:[2,61,62,74,89,92,113],confus:158,conjuct:109,conjug:113,conjunct:[2,33,45,68,92,98,99,105,109,113,120,122,143,146],connect:[2,33,61,76,92,106,118,153,157],conner:94,connor:94,consecut:[3,4,45,105,122,126],consequ:[1,2,80,121],conserv:[14,61,67,68,69,75,76,92,108,109,110,118,128,147],consid:[2,30,33,60,61,80,113,145,147,153],consider:2,consist:[2,3,4,40,45,51,63,67,69,70,73,74,75,92,94,97,103,105,113,117,131,132,134,137,140,141,145,147],consistent_fe_initi:59,constant:0,constantli:64,constitu:[2,81,82,103,145],constrain:[2,64,67,76,77,91,113],constraint:[20,40,43,60,64,76,77,81,91,132],construct:[2,4,29,30,31,37,39,41,42,44,62,69,74,75,82,108,137,153,154],constructor:3,consult:5,consum:1,contact:[0,4,106,112,114,117,118,145],contain:[0,1,2,3,4,20,33,36,41,42,44,45,46,57,58,59,60,63,66,68,71,73,75,80,82,92,93,94,97,104,105,108,111,112,113,115,134,137,140,141,142,144,148,154,155,156,157,158,162],content:4,context:[2,4,5,160],contibut:30,contin:5,continu:[0,2,4,20,60,61,62,63,64,67,69,70,73,78,79,80,82,97,109,124,127,145,156],continuum:[2,59,80],contour_integr:59,contract:[62,69],contrain:76,contrast:[1,2,160],contrib:80,contribut:[2,4,30,33,34,35,36,40,42,43,62,68,76,91,92,109,111,113,131,132,137,147,162],contributor:4,control:[2,3,4,5,12,14,20,33,36,42,48,58,59,60,62],control_typ:59,convect:36,conveni:[2,4,14,148,162],convent:[14,50,55,57,74,111,113],converg:[2,20,58,60,61,62,70,73,74,76,91,92,104,105,122,147],convers:[42,58,105,106,107,113,122,126,130,143],convert:[2,4,6,7,9,13,17,18,19,36,45,47,58,83,84,88,89,92,93,111,137,155,157,161],convex:82,convinc:4,cool:64,coord:[2,3,37,39,71,81,92],coordb:147,coordbb:147,coordiat:91,coordin:[1,2,3,20,33,34,35,42,45,58,60,61,62,64,69,71,76,77,79,80,91,92,93,94,96,112,147],coords:147,copi:[0,3,4,58,80,92,162],copper:161,coprocessor:[1,5],core:[0,1],coreshel:2,coreshell:[2,99,105,107],cornel:[2,46],corner:[2,58,82,162],corpor:5,corr:104,correct:[2,3,4,33,46,58,64,69,73,81,82,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],correction_max_iter:59,correctli:[3,69,76,82,92,107,132,137,162],correl:[2,36,37,42,67,72],correpond:66,correspond:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,33,40,41,42,44,46,47,48,49,50,51,52,53,54,55,56,58,62,63,64,66,68,69,70,71,72,75,76,81,82,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],correspondingli:[131,132],cosin:2,cosineshift:12,cost:[1,2,3,4,20,41,43,44,58,60,69,75,80,105,122,126,137,154],costheta0:[154,155,157,158],costheta:144,costli:[3,5],coul:[2,5,19,22,23,33,46,91],could:[2,3,4,20,33,35,36,40,58,60,63,73,80,81,82,91,94,116,120],coulomb:[2,4,43,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,143,146,147,157,158,160],coulommb:2,count:[1,2,3,4,20,36,46,60,62,69,76,82,91,92,116,120],counteract:63,counterbal:64,counterbalanc:14,counterclockwis:46,coupl:0,couple:[2,3,4],cours:[5,67,74,81,131,149],cov:147,coval:[2,14,113,134,147],cover:[2,4,59,68,113],cpp:[1,2,3,4,33,76],cpu:[1,4,5],cpuinfo:5,cpus:4,cr2:44,cr3:44,crash:4,creat:[0,1,2,3,4,20,36,40,41,45,58,59,60,61,62,66,69,70,71,72,74,80,92,94,97,104,111,112,130,139,140,141,144,147,154,155,156,157,158,162],create_atom:[2,20,36],create_box:[2,20,36,45,62,69,153],create_elementset:59,create_faceset:59,create_nodeset:59,createatom:0,creation:[4,45],criteria:[58,61,91],criterion:[4,20,45,60,61,91,92,104,113,118,147],critic:[2,25,26,80,91],cross:[4,5,34,58,92,101,109,111,119,120,122,124,126,144,146,155,157,161],crossov:1,crozier:0,crucial:73,crystal:[2,5,30,31,39,71,79],crystallin:[2,156],crystallogr:[41,44],crystallographi:[41,44],cs1:44,cs_chunk:2,csanyi:[42,148],cscl:134,csequ:2,csh:[3,4,5],cshrc:[3,4],csic:[112,154,155,157,158],csinfo:2,csisi:[112,154,155,157,158],cst:111,cstherm:2,csvr:2,ctcm:[93,111],ctype:3,cu1:44,cu2:44,cu3au:134,cube:[2,82],cubes:[20,60],cubic:[39,68,71,111],cuda:[1,4],cuh:97,cummul:[2,61,120],cumul:[2,69,70,92],currenlti:63,current:[0,1,2,3,4,5,20,31,33,43,58,59,60,61,62,63,64,69,74,75,76,77,80,81,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,144,149,155,157,162],curv:[2,45],curvatur:[117,145,161],custom:[0,2,3,4,34,35,36,43,58,61,62,69,70,73,91,94,116,120],cut:[1,2,4,5,20],cuthi:71,cutinn:[131,132],cutlo:71,cutmax:144,cutoff1:[102,108,122,126,130,133,143,146],cutoff2:[98,99,100,102,107,108,122,126,130,133,143,146],cutoff:[2,5,22,23,29,30,31,33,37,39,42,61,66,71,73,81,82,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cutoffa:112,cutoffc:112,cuu3:111,cval:44,cvar:63,cvff:5,cwiggl:81,cyan:58,cycl:[69,70],cyclic:46,cygwin:4,cylind:[58,82],cylindr:2,cyrot:97,d3q15:68,d3q19:68,d_e:80,daan:79,dai:4,daili:4,damp:[2,69,70,73,91,92,98,99,101,105,108,113,118,122,130,143,146],dampflag:118,danger:[4,109],darden:108,darken:58,dash:118,dat:[2,36,59],data2xmovi:0,data:1,databas:0,datafil:4,date:[0,2,4],datum:2,davenport:133,davi:81,david:[155,157],daw:[111,144],dcd:[2,58,72],deactiv:130,debug:[2,3,4,41,44,45,72],decai:[37,105,161],decid:[2,4,5,162],decod:58,decompos:[33,148],decomposit:[59,72],decoupl:2,decreas:[5,61,64],dedic:5,def:4,defect:[2,30,137],defin:[2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,68,69,70,71,72,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],definit:[2,4,42,63,65,70,81,97,103,110,113,144,148],deform:[2,43,62,69,131,132],deg2theta:44,degre:[2,6,7,9,13,14,17,18,19,37,39,40,44,45,46,47,49,50,55,56,58,61,69,70,72,74,76,79,83,84,88,89,90,91,108,111,120],delai:[2,4],delet:[4,29,61,69,153,162],delete_atom:45,delete_bond:[21,22,23,24,25,26,27,28,29],delete_el:59,delimit:75,dellago:[2,64],deloc:[113,147],delr:134,delta_1:97,delta_3:97,delta_7:97,delta_ij:[134,144],delta_pi:97,delta_r:144,delta_sigma:97,deltah_f:66,demo:3,demonstr:[73,134],dendrim:120,denniston:68,denot:[41,64,105,119],dens:[61,75,113],densiti:[2,20,42,45,59,60,68,80,81,93,94,97,111,134,135,136,140,141,144,145,147,150,151,152],depart:0,departur:73,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,37,40,42,45,46,47,48,49,50,51,52,53,54,55,57,58,60,62,66,68,69,70,71,75,76,78,80,81,82,83,84,85,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],dependend:2,depflags:4,deposit:[69,76],depth:[27,58,80,115,117,145],der:[33,103,104,130,160],deriv:[2,33,42,62,63,64,69,70,71,78,79,80,81,82,94,97,103,108,113,114,119,124,128,129,134,137,160],derjagin:160,derlet:71,descib:58,describ:[0,1,2,3,4,5,20,30,31,41,42,43,44,45,51,54,60,61,62,63,66,67,68,69,70,71,72,73,75,78,79,81,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,140,141,144,145,146,147,148,149,153,154,155,156,157,158,159,160,161,162],descript:[2,3,4],descriptor:42,design:[0,2,3,41,44,59,61,69,71,80,95,96,101,105,107,113,130,131,132,135,136,144],desir:[2,3,4,5,36,40,43,45,62,63,67,69,76,91,92,109,111,120,131,132,154,155,157],desktop:[2,4,58],destabil:97,destre:89,destroi:3,detail:[1,2,3,4,5,20,35,36,40,42,43,45,57,58,59,60,61,62,63,64,67,68,69,70,73,76,79,80,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,140,141,145,147,148,149,159,160,162],detect:[4,37,92,104,120,121],determin:[1,2,4,5,27,33,40,41,43,44,45,58,60,62,66,69,71,72,73,74,75,81,82,94,100,104,108,111,115,116,118,126,134,137,141,145,147,153,160],devan:146,devanathan:157,develop:[0,2,3,4,5,63,70,73,94,97,113,136,137,147,158],deviat:[70,71,116],devic:[1,4],devin:104,devis:136,dfactor:58,dfft_fftw2:4,dfft_fftw3:4,dfft_fftw:4,dfft_none:4,dfft_single:4,dfft_xxx:4,dfftw:4,dfftw_size:4,dft:137,dhug:73,dhugoniot:73,dia:134,diag:75,diagnost:[4,5,61,75],diagon:[2,42,43,62,69],diagonalstyl:148,diagram:[20,41,44,57,60,72],diallo:120,diam:58,diamet:[2,45,58,103,117,118,124,145,160],diamond:[113,134],dick:2,dicken:63,did:[4,91,109,111,118,155,157],dielectr:[101,105,106,107,122,126,130,143],diff:[2,4,5],differ:[1,2,3,4,5,20,29,30,33,37,42,45,57,58,60,61,62,63,64,67,68,69,71,72,73,76,77,78,79,80,81,82,83,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,144,145,146,147,148,149,154,155,157,158,160],differenti:[1,2,14,75,105,144,156],difficult:[62,63,72,120],difficulti:[37,39,76],diffract:[41,44],diffraction:[41,44],diffus:0,diffuse:2,digit:137,dihedr:[0,4,5,29,37,39,40,42,43,45,46,47,48,49,50,51,52,53,54,55,56,57,61,74,84,85,86,88,91,94,97,101],dihedral_coeff:[46,47,48,49,50,51,52,53,54,55,56,57],dihedral_cosine_shift_exp:12,dihedral_styl:[0,2,43],dihydrid:113,dij:76,dilat:[62,69,70],dim:[45,134],dimens:[1,2,4,20,36,43,45,58,60,62,68,69,70,73,81,92],dimension:[37,40,41,42,44,80,92,144],dimensionless:[38,42,63,80,148,160],dimer:[2,134],dimstr:[20,60],dintel_offload_noaffinity:5,dipol:0,dipolar:14,dipole:108,dir:[1,3,4,71,73,144],dirac:42,direc:144,direct:[2,4,5,14,30,39,41,42,44,45,46,58,68,70,71,73,78,79,80,81,82,91,92,109,110,118,132],directli:[2,3,4,33,42,45,58,63,68,75,82,93,94,98,99,100,105,108,111,113,122,126,143,146,153],directori:[0,1,2,3,4,5,63,78,79,92,93,94,97,104,105,111,112,114,130,134,135,136,137,142,144,147,148,154,155,156,157,158],disabl:[4,5,80,121],disadvantag:[2,60],disallow:69,discard:[20,60,82],discontinu:[91,128],discourag:134,discret:[2,58,63,68],discuss:[0,1],disk:[2,37],disloc:[30,137],disord:[30,137],disp:0,dispar:145,disperion:[108,126],dispers:[2,100,108,126,131,158],displac:[2,4,38,62,69,71,118],displai:[3,57,58],disregard:137,dissip:[2,32,65,67,78,79,109,110,118,131,132],dist:[2,36,72,74,153],distanc:[2,4,6,7,21,22,23,24,25,26,27,28,29,31,34,35,37,38,39,41,42,45,47,58,61,62,64,68,69,70,71,73,74,76,77,79,80,81,82,83],distinct:[2,145],distinguish:[2,42,113],distort:93,distrbut:93,distribut:[0,2,3],distro:144,ditto:[4,161],div:5,diverg:[4,79,94],divid:[2,5,20,36,40,43,57,60,71,91,92,114,147,158],divis:[2,56,68,97,130],dl_poly:2,dlammps_bigbig:4,dlammps_exceptions:4,dlammps_ffmpeg:[4,58],dlammps_gzip:[4,58],dlammps_jpeg:[4,58],dlammps_longlong_to_long:4,dlammps_memalign:[4,5],dlammps_png:[4,58],dlammps_smallbig:4,dlammps_smallsmall:4,dlammps_xdr:4,dlm:69,dlmp_intel_offload:5,dlopen:2,dlvo:[103,160],dm_lb:68,doc:[0,1,2,3,4,33,35,38,40,43,45,57,58,63,69,82,91,92,93,94,96,104,105,111,112,114,120,134,135,136,142,144,148,154,155,157,158,162],docuement:145,doe:[0,1,2,3,4,20,29,30,33,36,41,44,45,46,57,58,59,60,61,62,63,64,66,67,68,69,80,81,82,84,85,86,88,89,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,140,141,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],doesn:[4,45,94,104,112,154,155,156,157,158],dof:40,doi:[2,71],domain:[2,4,20,41,44,58,60,62,68,69,72,80,81,92],domin:[1,113],don:[0,4,5,82,134,147,162],done:[1,2,4,20,45,56,58,59,60,61,62,63,66,69,72,76,78,79,91,92,94,100,111,126,132,133,134,140,141,153,162],donor:120,dot:43,doti:[97,144],doubl:[1,2,3,4,5,33,46,62,82,97,114,119,137],dover:59,down:[2,3,62,113,147],download:[3,4],downsid:2,dozen:4,dpack_array:4,dpack_memcpy:4,dpack_pointer:4,dpd:2,dpdtheta:[32,110],dpdtheta_i:[65,66],dr_ewald:41,drag:[2,36,69,70,77],dragforc:68,drai:[58,73],drain:91,dramat:[61,62,69,147],drautz:97,draw:58,drawn:[58,67],drayleigh:73,dreid:2,dreiding:0,drfourth:38,drho:[93,111,140,141],drift:[2,38,64,67],drive:[3,4,62,69,71,92],driven:[2,51],driver:[2,4],drop:109,drsquar:38,drude:0,dt_collis:68,dt_lb:68,dt_md:68,dtqm:73,dudarev:44,due:[1,2,4,5,29,30,34,35,38,41,42,43,44,45,58,61,62,67,68,69,70,71,74,78,79,80,81,82,91,92,106,109,110,111,116,117,131,132,144,145,146,153,155,157,160,161],duffi:80,dullweb:69,dummi:[4,14,156],dump:[0,1],dump_modifi:[2,58],dunbrack:[2,6,46,101],duplic:[20,60,71],durat:[57,80,118],dure:[2,4,5,20,33,46,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,76,77,78,79,80,81,82,91,92,109,130,137,139,140,141],dvlo:160,dvx:2,dx_lb:68,dy3:44,dyamic:4,dyanam:2,dynam:[0,2,3,4,5,20,32,38,45,58,59,60,61,63,65,67,69,70,72,73,74,78,79,80,91,92,109,110,113,131,132,152],dynamo:[93,111,134],dyre:127,e28637:14,e_1:97,e_2:97,e_a:75,e_b:114,e_ee:113,e_hbond:120,e_i:[2,97,114],e_j:[2,97],e_k:97,e_ke:113,e_kl:2,e_lj:[94,108],e_n:[63,97],e_ne:113,e_nn:113,e_pr:113,e_rebo:94,e_torsion:94,e_tot:137,e_vol:137,eaa:83,eaat:47,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,33,34,35,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,66,67,68,69,70,71,72,75,76,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,157,158,159,160,161],eacn:[20,60],eam:[0,4,93,105],earli:[20,60],earlier:[4,92,118,134],earth:113,easi:[2,3,33,43,81],easier:[5,58],easili:[3,58,92],eat:47,eaxmpl:2,eba:7,ebb13:47,ebb:7,ebt:47,ec_ii:134,ec_ij:134,ec_jj:134,echo:[3,4,41,44],ecp:113,edg:[2,20,41,44,58,81,82],edge:81,edit:[4,5,162],edition:5,edu:[3,111,131],eebt:47,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,34,35,38,40,43,46,47,48,49,50,51,52,53,54,55,57,58,59,61,62,64,67,69,70,71,72,73,74,76,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,147,149,154,155,156,157,158,159,160,161],effici:[0,1,2,4,5,40,56,58,62,69,72,76,97,103,105,122,126,137,140,141,145],efficienc:5,efield:[76,91],eggebrecht:[105,147],ehex:2,eigenvalu:72,einstein:[2,79],either:[1,2,3,4,5,20,30,41,42,43,44,45,58,60,61,62,63,64,68,69,70,71,75,76,82,91,97,103,111,115,118,131,132,134,137,141,144,153,155,157],ejtehadi:[103,117,145],elaps:[81,149],elast:[2,22,23,92,118,156],elastic:0,elba:14,electr:[2,59,114,161],electric:5,electrolyt:160,electron:[2,41,59,80,93,104,108,111,113,114,134,137,144,147,157,158,161],electron_integr:59,electron_temperatur:59,electron_unit:113,electroneg:[2,104,114,147],electroneg_compon:147,electrostat:[2,5,103,108,113,122,130,132,147,160],elem1:[114,134,148],elem2:[114,134,148],elem:147,element1:[93,111,147],element2:[93,111,147],element:[2,4,34,38,40,42,43,58,59,93,94,97,104,111,112,113,114,134,135,136,137,142,144,147,148,154,155,156,157,158],elementn:[93,111],elementset:59,elif:42,elig:120,elimin:[2,67,76,78,79],elj:108,ellips:2,ellipsoid:[2,45,91,117,132,145],els:[4,58,63,69,80],elsewher:134,elt:134,emac:0,email:[0,3,114],emb:82,emb_lin_neg:134,embed:[3,4,14,80,93,111,114,130,134,135,136,144],embt:47,emin:62,emphas:118,empir:[59,113],empiric:94,emploi:[64,156],empti:121,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,32,33,38,40,41,42,44,46,47,48,49,50,51,52,53,54,55,57,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],enclos:[2,4,134,147],encod:58,encompass:2,encount:[4,39],encourag:[75,77],end:[1,2,3,4,5,20,47,58,61,62,64,67,69,74,75,80,92,109,111,117,133,137,145,148,149],endbondtors:47,energet:[61,94],energi:[0,1,2,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,24,25,26,27,28,29,32,33,36,40,43,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,62,63,64,65,66,67,68,69,70,71,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109],energy_compon:147,enforc:[2,58,61,69,76,122],enforce2d:[2,91],eng:[3,104,136],engineer:[59,78,111],enginer:135,enhanc:[59,64],enlarg:58,enough:[45,60,73,81,82,105],enpub:111,ensembl:[2,33,36,69,72,73,109,147],ensight:2,ensur:[2,42,62,67,69,97,130,154,158],enter:[114,137,158],enthalpi:[75,111],entir:[0,2,3,20,32,40,41,43,44,45,60,61,64,67,69,70,71,72,75,77,80,108,126],entiti:2,entri:[4,41,66,73,97,112,134,140,141,142,148,154,155,156,157,158],entry1:[140,141],enumuer:2,environ:[1,2,3,4,5,58,71,93,97,104,112,113,144,155],eos:66,epair:[94,116,120],epp:108,epq:108,eps0:160,eps14:130,epsilon0:157,epsilon:[2,19,22,23,28,29,33,46,81,82,91,96,101,102,103,105,106,107,108,115,117,119,120,121,122,123,124,125,126,127,128,129,130,133,138,143,145,146,154,159,160],epsilon_0:161,epsilon_14:101,epsilon_:145,epsilon_d:106,epsilon_i:[117,145],epsilon_i_:145,epsilon_i_a:[117,145],epsilon_i_b:[117,145],epsilon_i_c:[117,145],epsilon_j:[117,145],epsilon_j_:145,epsilon_j_a:[117,145],epsilon_j_b:[117,145],epsilon_j_c:[117,145],epsilon_lj:145,eqp:108,eqq:108,equal:[2,3,4,20,29,33,36,43,45,58,60,62,63,67,68,70,71,72,73,74,75,78,79,80,81,91,92,94,104,109,110,116,117,120,131,137,138,144,145,147,148,149,158,161],equat:[2,36,39,40,41,44,57,62,63,64,65,66,68,69,70,71,72,73,75,76,80,81,103,108,109,110,113,114,115,118,131,132,134,141,145,150,151,152,161],equation:[71,89],equilibr:[2,36,45,61,62,69,73,78,79,104,105],equilibrium:[1,2,7,9,11,12,13,14,17,18,19,21,24,25,26,27,28,47,48,62,67,68,69,70,73,74,76,79,83,84,88,89,104,134,142,147],equilibrium_start:59,equival:[2,4,14,62,69,74,94,109,113,147,155,157],equlibrium:2,er3:44,eradiu:113,eras:78,erat:132,erc:105,erfc:[105,122],erhart:[111,155,157],eros:134,erose_form:134,erot:2,errata:[155,157],erratum:81,error:[0,1,2,3,4,12,48,58,62,63,64,66,69,75,80,81,82,91,105,122,145,153,155,157],erta:118,especi:[5,45,60,73,74],essenti:[3,4,12,48,94,105,122,157],essential:70,essex:14,establish:33,estim:[1,2,4,20,30,36,43,59,60,75],esub:134,eta:[2,68,69,73,112,114,117,144,156,158],eta_dot:69,eta_ij:144,eta_ji:114,etap:69,etap_dot:69,etc:[1,2,3,4,5,29,34,35,36,43,45,58,59,67,69,80,82,91,92,111,112,130,132,137,154,155,157,158],etol:[91,92],etot0:73,etot:[2,43,73],eu2:44,eu3:44,euler:[75,91,92],eulerian:59,europhi:68,evalu:[3,4,33,36,42,45,46,58,59,63,67,75,81,91,137,140,141,144,147],evanseck:[2,6,46,101],evaul:91,even:[2,4,5,20,30,56,60,62,64,69,80,81,82,91,92,96,113,114,118,145,158],evenli:[20,43,60,68],event:[2,69,80],eventu:[2,4],ever:29,everaer:[103,117,145],everi:[0,1,2,3,4,5,20,36,58,59,60,61,62,63,64,68,69,70,71,73,75,76,80,92,109,130,147,162],everyth:162,everywher:124,eviri:113,evolut:[64,68,72],evolv:[68,72],ewald:[2,4,41,43,91,98,99,100,105,108,113,122,126,143,146],ewald_disp:108,exact:[20,60,61,67,80],exactli:[2,4,20,36,45,60,67,73,109,111,118,131,140,141],examin:[2,61,75],exampl:[0,1],exce:[2,5,20,60,62,69,91],exceed:[20,60,69],excel:113,except:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,34,35,40,43,45,46,47,48,49,50,51,52,53,54,55,57,60,62,69,70,72,76,80,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],excess:113,exchang:[2,59,64,80,113],excit:113,excite:113,exclud:[2,4,5,40,42,91,118,131,132,153],exclus:[1,4,5,33,46,104,137],excurs:69,exectubl:4,execut:[1,2,3,4,58],exempl:147,exemplari:67,exemplifi:113,exert:[2,82],exhaust:59,exhibit:[37,64,69,113],exist:[2,3,4,30,45,57,58,62,83,84,85,86,88,110,153,162],exit:[3,4,20,60],expans:[4,42,56],expect:[1,4,5,20,60,71,73,134,137],expens:[2,71,80],experi:[2,74,92,109],experienc:[2,4,5],expert:4,explain:[1,2,3,4,20,31,58,60,62,69,71,92,96,111,147,149,162],explan:[2,42,71],explic:138,explicit:[2,3,33,75,94,97,101,111,113,121,131,162],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,40,45,46,47,48,49,50,51,52,53,54,55,62,67,69,70,73,76,80,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,149,150,151,152,154,155,156,157,158,159,160,161,162],explictli:5,exploit:72,explor:[41,44],expon:[75,111,115,117,120,130,138,146],exponenti:[33,75,115,144,154,158,161],expos:3,exposit:[59,109],express:[2,42,45,62,71,75,80,97,111,113,124,134,147,148],expressiont:97,extend:[0,2],extens:[2,5,22,23,28,33,36,63,64,69,70,71,74,78,79,80,81,82,117,134,137,145,148],extent:[1,20,22,60,94],exterior:[2,82],extern:[4,33,58,62,67,68,69,70,80,91,135,136],extra:[2,3,4,5,20,23,40,41,43,44,45,60,69,73,91,108,118,134],extract:[2,3,19,33,92,105,114,134,148],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extramake:4,extrapol:1,extrem:[1,2,58,62,69,79,113,156],extrema:130,extreme:113,extrins:59,f77:4,f90:4,f_1:[2,62],f_a:[155,156,157],f_c:156,f_f:157,f_fix_id:73,f_harm:79,f_i:[14,144],f_id:[2,63],f_ij:144,f_int:78,f_j:14,f_jj:36,f_k:144,f_langevin:80,f_max:73,f_r:[155,156,157],f_sigma:97,f_solid:79,f_ss:2,face:[2,81,82,117,134,145],facil:[0,4],facilit:2,fact:[2,5,79,118,147],factor:[1,2,4,9,13,17,18,19,20,23,24,33,36,41,42,44,46,54,58,60,62,64,68,69,70,72,74,75,76,81,82,88,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,140,141,142,143,146,149,154],fail:[3,4,62,91,92,107],fairli:[3,162],faken:31,fall:2,fals:147,famili:158,familiar:[0,3,162],fan:144,far:[2,4,60,62,69,71,74,81,84,88,92],farrel:[155,157],fashion:[2,20,45,60,63,69,70,73,79,80,81,92,131],fast:[2,4,5,63,73,75,131,132,137],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,38,40,46,47,48,49,50,51,52,53,54,55,60,69,70,76,78,80,83,84,85,87,88,89,90,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],fastest:[1,2,80],fault:30,faulti:4,fava:117,favor:61,fcc:[2,30,31,36,39],fcold:64,fdt:[65,66,75],fdti:33,fe2:44,fe3:44,fe_md_boundari:59,featur:[0,2,3,4,42,58,61,67,72,82,91,162],fecr:111,feedback:63,feel:[71,82,92],fehlberg:75,felling:136,felt:82,fene:[2,5],fennel:[105,122],fep:0,ferguson:[2,46],fermi:[1,4,157],fermion:113,fernando:133,few:[1,2,3,4,64,69,76,91,92,94,147],fewer:[1,3,5],feynman:72,ffield:[104,114,147],fflag1:58,fflag2:58,ffmpeg:[4,58],ffplai: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0],reset:[2,3,4,34,35,45,62,69,70,76,80,91,132],reset_atomic_reference_posit:59,reset_tim:59,reset_timestep:[2,36],resist:2,resolut:147,resolv:[62,72,132,162],resourc:[93,111],respa:[5,69,71,74,77,81,82,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],respecifi:137,respect:[1,2,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,33,34,40,41,44,46,47,48,49,50,51,52,53,54,55,58,61,62,64,68,69,70,76,80,81,83,84,85,87,88,89,90,91,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,142,143,145,146,147,148,149,154,155,156,157,158,159,160,161],respond:[2,63,113],respons:[2,63],resquar:[2,117],rest:[2,4,74,97,132,134],restart1:72,restart2:72,restart2data:[0,4],restart:[0,1],restartfil:4,restrain:14,restraint:[74,121],restratin:74,restrict:[1,2,4],result:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,33,35,36,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,58,60,61,62,63,64,67,68,69,70,72,75,76,78,79,80,81,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,134,135,137,139,140,141,142,143,145,146,149,154,155,156,157,158,159,160,161],retain:[94,97,137],retriev:[2,135,136],rev:[2,30,37,39,42,43,69,70,78,79,97,103,104,105,108,111,112,113,117,118,124,131,132,133,134,136,140,141,144,145,148,154,155,156,157,158],revers:[2,33,50,61,69,71,78,92,130],review:[42,137,148,162],rewrit:4,rfac0:[42,148],rg0:77,rh3:44,rh4:44,rheolog:2,rhi:[140,141],rho0:[134,151,152],rho0_meam:134,rho:[68,93,98,99,100,111,133,134,135,136,140,141,145,150],rho_0:[151,152],rho_alpha_beta:111,rho_bkgd:134,rho_colloid:81,rho_e:80,rho_i:[135,136],rho_ref_meam:134,rho_wal:81,rhodopsin:[1,5],rhosum:[150,151,152],rhot:64,rhs:75,rick:[104,147],right:[2,3,4,20,30,45,55,57,60,61,68,71,75,105,162],rightmost:[20,60],rii:[34,35],rij:[37,39,71,109,110,140,141,153],rin:[120,127,128],ring:[2,46,72],rino:[31,158],rirj:118,risi:[42,148],risk:74,rix:[34,35],rk4:75,rkf45:75,rlo:[140,141],rmin0:[42,148],rmin:124,rms:75,rnemd:2,robust:91,rock:134,rockett:144,rodata:4,role:2,roll:4,ronchetti:39,root:[3,33,34,35,111],rose:134,ross:134,rosski:72,rot:[2,36,72,74],rotat:[2,42,45,82,91,108,117,145],rotation:39,rough:[2,45,58],roughli:[4,20,58,69,92],round:[1,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,40,46,47,48,49,50,51,52,53,54,55,69,70,76,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,140,141,142,143,145,146,149,154,155,156,157,158,159,160,161],rous:67,rout:[33,120,130],routin:[2,3,5,68,137],roux:2,row:[2,35,44,80,113],rozero:134,rpm:4,rrespa:[1,5,69,93,94,95,96,98,99,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rsq:[140,141],rsurfac:80,ru3:44,ru4:44,rub:6,rubia:[135,136],rule:[0,2,4,14,30,45,61,69,82,93,95,96,102,103,108,120,125,134,138,149,153,154,155,157,161],run1:2,run2:2,run3:2,run4:2,run5:2,run6:2,run7:2,run8:2,run:[0,1],run_styl:[4,5,69,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rung:75,runtim:[4,58],rutherford:80,rutuparna:[155,157],rxn:75,ryckaert:[76,89],rydberg:137,s0st:2,s2050:1,s2629:111,s319:59,s_i:[2,113],s_ij:2,saddl:92,sadigh:[111,135,136],saed_vtk:41,safe:[4,58,162],safran:160,sagui:108,sai:[1,4,162],said:91,sakai:156,sall:147,salt:[106,116,134],salter:147,same:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,33,34,35,36,37,38,39,40,42,43,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,62,63,64,67,68,69,70,71,72,73,74,76,78,79,80,82,83,84,85,87,88,89,90,92,93,94,95,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,138,139,142,143,144,145,146,147,149,153,154,155,156,157,158,159,160,161,162],sampl:[1,2,3,4,36,58,69,72,77,79,97],sample_frequ:59,sandia:[0,30,114,134],saniti:74,satellit:2,satisfi:[4,31,41,42,44,62,64,68,70,76,91,118],satur:106,save:[2,4,58,61,67,75,80,97],sb3:44,sb5:44,sc3:44,scalabl:[0,1,5],scale:[0,1,2,5,36,42,46,58,59,62,68,69,70,72,73,78,79,80,93,94,106,113,115,118,131,132,134,137],scalegamma:68,scalexi:[62,69,70],scalexz:[62,69,70],scaleyz:[62,69,70],scatter:[3,41,44],scatter_atom:3,scatter_coord:3,scenario:[2,61,82],schaik:130,schell:156,schemat:61,scheme:[2,63,67,69,72,76,80],schmid:109,schroding:113,schroeder:39,sci:[31,1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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","2. Getting Started","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub tutorial"],titleterms:{"default":[30,33,37,38,39,41,42,44,45,57,58,59,62,67,68,69,70,72,73,78,79,81,97,113,131,132,137,153],"long":[98,99,100,101,102,105,107,108,122,126,130,143,146],"static":4,acceler:1,addition:4,adiabat:2,adp:93,airebo:94,alloi:111,amber:2,angle_styl:[6,7,8,9,10,11,12,13,14,15,16,17,18,19],arrai:2,aspher:2,atc:59,atom:[2,30,31,37,39,42,43],aug:0,balanc:[20,60],barostat:2,bcc:71,beck:95,between:2,bodi:[2,96],bond:61,bond_styl:[21,22,23,24,25,26,27,28,29],bop:97,born:[98,107],box:[2,62],buck:[99,100,107,133],build:[3,4],calcul:2,call:4,centro:30,charmm:[2,6,46,101,130],chunk:[2,35],class2:[7,21,47,83,102],cna:31,code:2,coeffici:2,colloid:[81,103,160],comb3:104,comb:104,command:[2,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],comparison:1,compos:2,comput:[2,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44],conduct:2,constant:2,control:63,core:2,cosin:[8,9,10,11,12,13,48],cossq:84,coul:[98,99,100,101,102,105,106,107,119,122,126,130,143,146],coupl:2,create_atom:45,cubic:124,cut:[26,99,102,105,108,113,116,122,123,130,138,143],cvff:85,data:2,deby:[105,122],delta:9,descript:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],diel:106,diffus:2,dihedral_styl:[46,47,48,49,50,51,52,53,54,55,56,57],dipol:[2,14,108],discuss:2,disp:2,distanc:86,distribut:4,document:0,dpd:[32,109,110],dreid:120,dreiding:2,drude:2,dsf:[105,122],dump:[2,58],eam:111,edip:112,eff:113,ehex:64,eim:114,elastic:2,energi:110,exampl:[2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],exp6:115,exp:[12,48],expand:[23,125],extend:3,fcc:71,fdt:110,fene:[22,23],fep:33,field:2,file:2,finit:2,fix:[2,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82],fix_modifi:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],flow:2,fluid:68,flux:36,forc:2,fourier:[15,16,49,87],from:[2,3],gauss:116,gaybern:117,gener:[1,2],get:4,github:162,gld:67,global:2,gpu:[95,98,99,101,102,103,105,108,109,111,116,117,119,122,123,124,125,138,139,145,146,149,154,155,156,157,159,160,161],gran:118,granular:2,gromac:119,gyrat:[34,35],harmon:[17,24,25,26,50,52,81,88,142],hbond:120,heat:36,helix:51,hertz:118,hexord:37,histori:118,hook:118,how:2,idealga:150,imag:58,implicit:101,improper_styl:[83,84,85,86,87,88,89,90],indice:0,induc:2,info:[0,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],input:2,install:3,integr:2,intel:[5,6,17,22,24,46,50,54,69,85,88,99,101,117,122,154,155],interfac:[2,3],kspace_styl:2,lammps:[0,1,2,3,4,162],lennard:133,librari:[2,3,4],line:4,linear:[129,139],list:121,lj1043:81,lj126:81,lj93:81,lj96:123,local:2,lubric:131,lubricateu:132,luci:[140,141],make:4,mdf:133,meam:[134,135,136],measur:1,mgpt:137,mie:138,minim:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82,91],mod:[80,156],model:2,morri:152,mors:[27,94,120,139],movi:58,mpi:3,msd:38,msm:[98,99,101,105,122],multi:[2,52,140,141],multipl:2,nb3b:142,neb:92,nemd:2,nharmon:53,non:2,nongauss:38,nonlinear:28,nph:69,nphug:70,npt:69,nvt:69,omp:[6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,46,47,48,49,50,51,52,53,54,55,69,70,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,136,139,142,143,145,146,149,154,155,156,157,158,159,160,161],opl:54,opt:[101,111,122,126,139],optim:1,option:[2,4],orient:71,orientord:39,orthogon:2,other:2,output:[2,4,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],overview:3,packag:[1,4,5],pair:2,pair_styl:[93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],parallel:3,paramet:2,particl:2,per:2,perform:1,period:10,pimd:72,polariz:2,poli:[131,132],polymorph:144,potenti:2,pppm:2,pressur:40,previou:4,process:2,properti:2,python:3,qbmsst:73,quadrat:55,quantiti:2,quartic:[18,29],rattl:76,rebo:94,region:82,relat:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],relax:62,replica:2,requir:4,resquar:145,restart:[2,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],restrain:74,restrict:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rigid:2,ring:89,run:[2,3,4,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],scalar:2,screen:4,script:[2,3],sdk:[19,146],serial:3,set:2,shake:76,share:[3,4],shell:2,shift:[11,12,25,26,48],simpl:16,simul:2,size:2,smooth:[128,129,139],smtbq:147,sna:42,snad:42,snap:148,snapshot:2,snav:42,soft:[130,139,149],spc:2,sph:[150,151,152],spheric:[2,56],spline:[135,136],spring:[77,79],squar:13,srp:153,start:[4,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],stop:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],strategi:1,streitz:105,stress:43,style:[1,2],summari:2,swap:61,syntax:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],system:2,tabl:[0,2,66,155],taitwat:[151,152],temperatur:2,tersoff:[155,156,157],test:3,thermal:2,thermo:2,thermodynam:2,thermostat:2,time:2,tip3p:2,tip4p:[2,105,122,126,130],tip:4,tool:4,triclin:2,tstat:109,ttm:80,tutori:162,umbrella:90,user:[4,5],using:[2,3],valu:2,variabl:2,variou:1,vashishta:158,vector:2,version:[0,4],via:4,viscos:2,visual:2,wall:[2,81,82],water:2,what:4,wolf:[98,105],wrapper:3,write:2,xrd:44,yukawa:[159,160],zbl:[157,161]}})
\ No newline at end of file
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index 94850da0d8..c1b0e796b6 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -262,6 +262,7 @@ within the LAMMPS code.  The options that are currently recogized are:
 -DLAMMPS_BIGBIG
 -DLAMMPS_SMALLSMALL
 -DLAMMPS_LONGLONG_TO_LONG
+-DLAMMPS_EXCEPTIONS
 -DPACK_ARRAY
 -DPACK_POINTER
 -DPACK_MEMCPY :ul
@@ -334,6 +335,14 @@ MPI version does not recognize "long long" data types.  In this case a
 "long" data type is likely already 64-bits, in which case this setting
 will convert to that data type.
 
+The -DLAMMPS_EXCEPTIONS setting can be used to activate alternative
+versions of error handling inside of LAMMPS.  This is useful when
+external codes drive LAMMPS as a library.  Using this option, LAMMPS
+errors do not kill the caller.  Instead, the call stack is unwound and
+control returns to the caller.  The library interface provides the
+lammps_has_error() and lammps_get_last_error_message() functions to
+detect and find out more about a LAMMPS error.
+
 Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
 options can make for faster parallel FFTs (in the PPPM solver) on some
 platforms.  The -DPACK_ARRAY setting is the default.  See the
diff --git a/python/lammps.py b/python/lammps.py
index 0a996d0235..e1c25cb840 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -150,6 +150,11 @@ class lammps(object):
     if cmd: cmd = cmd.encode()
     self.lib.lammps_command(self.lmp,cmd)
 
+    if self.lib.lammps_has_error(self.lmp):
+      sb = create_string_buffer(100)
+      self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
+      raise Exception(sb.value.decode().strip())
+
   def extract_global(self,name,type):
     if name: name = name.encode()
     if type == 0:
-- 
GitLab