diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html
index 6b64b64b967de41e692195965bde0d68a40abcf2..8d0d30a2739ef6c93369f79eec0b568857d3466c 100644
--- a/doc/html/fix_nve_manifold_rattle.html
+++ b/doc/html/fix_nve_manifold_rattle.html
@@ -156,25 +156,32 @@ keyword = <em>every</em>
 <div class="section" id="description">
 <h2>Description</h2>
 <p>Perform constant NVE integration to update position and velocity for
-atoms constrained to a curved surface (manifold) in the group each timestep. The constraint
-is handled by RATTLE <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> written out for the special case of
-single-particle constraints as explained in <a class="reference internal" href="fix_nvt_manifold_rattle.html#paquay"><span class="std std-ref">(Paquay)</span></a>.
-V is volume; E is energy. This way, the dynamics of particles constrained to
-curved surfaces can be studied. If combined with <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this generates
-Brownian motion of particles constrained to a curved surface. For a list of currently supported
-manifolds and their parameters, see <a class="reference internal" href="manifolds.html"><span class="doc">manifolds</span></a>.</p>
-<p>Note that the particles must initially be close to the manifold in question. If not, RATTLE will
-not be able to iterate until the constraint is satisfied, and an error is generated. For simple
-manifolds this can be achieved with <em>region</em> and <em>create_atoms</em> commands, but for more complex
-surfaces it might be more useful to write a script.</p>
+atoms constrained to a curved surface (manifold) in the group each
+timestep. The constraint is handled by RATTLE <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a>
+written out for the special case of single-particle constraints as
+explained in <a class="reference internal" href="fix_nvt_manifold_rattle.html#paquay"><span class="std std-ref">(Paquay)</span></a>.  V is volume; E is energy. This way,
+the dynamics of particles constrained to curved surfaces can be
+studied. If combined with <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this
+generates Brownian motion of particles constrained to a curved
+surface. For a list of currently supported manifolds and their
+parameters, see <a class="reference internal" href="manifolds.html"><span class="doc">manifolds</span></a>.</p>
+<p>Note that the particles must initially be close to the manifold in
+question. If not, RATTLE will not be able to iterate until the
+constraint is satisfied, and an error is generated. For simple
+manifolds this can be achieved with <em>region</em> and <em>create_atoms</em>
+commands, but for more complex surfaces it might be more useful to
+write a script.</p>
 <p>The manifold args may be equal-style variables, like so:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">R</span> <span class="n">equal</span> <span class="s2">&quot;ramp(5.0,3.0)&quot;</span>
 <span class="n">fix</span> <span class="n">shrink_sphere</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">manifold</span><span class="o">/</span><span class="n">rattle</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">4</span> <span class="mi">10</span> <span class="n">sphere</span> <span class="n">v_R</span>
 </pre></div>
 </div>
-<p>In this case, the manifold parameter will change in time according to the variable.
-This is not a problem for the time integrator as long as the change of the manifold is slow with respect to the dynamics of the particles.
-Note that if the manifold has to exert work on the particles because of these changes, the total energy might not be conserved.</p>
+<p>In this case, the manifold parameter will change in time according to
+the variable.  This is not a problem for the time integrator as long
+as the change of the manifold is slow with respect to the dynamics of
+the particles.  Note that if the manifold has to exert work on the
+particles because of these changes, the total energy might not be
+conserved.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
@@ -188,12 +195,8 @@ This fix is not invoked during <a class="reference internal" href="minimize.html
 <hr class="docutils" />
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
-<p>This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
-was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
-section for more info.</p>
-<p>Only use this with <em>min_style hftn</em> or <em>min_style quickmin</em>. If not, the constraints
-will not be satisfied very well at all. A warning is generated if the <em>min_style</em> is
-incompatible but no error.</p>
+<p>This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="related-commands">
@@ -202,7 +205,7 @@ incompatible but no error.</p>
 <p><strong>Default:</strong> every = 0, tchain = 3</p>
 <hr class="docutils" />
 <p id="andersen"><strong>(Andersen)</strong> Andersen, J. Comp. Phys. 52, 24, (1983).</p>
-<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
+<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).
 preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
 </div>
 </div>
diff --git a/doc/html/fix_nvt_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html
index b27135b6fb5d9f4a07fa65b3eea85bab3dcd3035..35e6ea6135f9aef00e8fa8a88a462bef8daf4af5 100644
--- a/doc/html/fix_nvt_manifold_rattle.html
+++ b/doc/html/fix_nvt_manifold_rattle.html
@@ -176,9 +176,6 @@ This fix is not invoked during <a class="reference internal" href="minimize.html
 <p>This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
 was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
 section for more info.</p>
-<p>Only use this with <em>min_style hftn</em> or <em>min_style quickmin</em>. If not, the constraints
-will not be satisfied very well at all. A warning is generated if the <em>min_style</em> is
-incompatible but no error.</p>
 </div>
 <hr class="docutils" />
 <div class="section" id="related-commands">
@@ -187,7 +184,7 @@ incompatible but no error.</p>
 <strong>Default:</strong> every = 0</p>
 <hr class="docutils" />
 <p id="andersen"><strong>(Andersen)</strong> Andersen, J. Comp. Phys. 52, 24, (1983).</p>
-<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
+<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).
 preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
 </div>
 </div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 22518f84adbe968c3473ff67ff1be57af65967b7..8ab032e71c17af31883898fefeddba362fe384e2 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:[19,40,43,60,64,71,72,78,79,83,93,134],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:[0,1,2,3,11,48,58,62,63,64,66,69,71,72,77,82,83,84,93,107,124,147,155,157,159],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:[0,1,2,3,4,6,19,21,22,28,29,35,37,39,40,43,44,47,58,60,61,63,66,67,68,69,73,74,75,78,79,80,81,82,85,93,94,95,96,98,99,100,101,103,106,107,113,115,116,117,120,121,123,124,128,133,134,136,138,139,142,143,144,146,149,150,155,156,157,158,159,160,163,164],fischer:[2,5,46,103],fit:[2,76,96,99,136,142,143,158,164],five:[30,75,99,137],fix:[0,1],fix_flux:59,fix_heat:64,fix_id:[62,69,70,75],fix_manifoldforc:164,fix_modifi:2,fix_nv:164,fix_rattl:78,fix_shak:78,fixedpoint:[62,69],fixid:[58,59],fji:110,flag:[3,4,33,34,38,41,44,58,61,96,122,123,136,139,155,164],flag_buck:102,flag_coul:[102,110,128],flag_lj:[110,128],flagfld:[133,134],flaghi:[133,134],flaglog:[133,134],flagvf:[133,134],flat:[2,4,82,83],fld:[83,133,134],flexibl:[2,58,115,158],flip:[2,69],fluctuat:[2,32,62,67,68,69,70,73,81,82,91,112],fluid:[2,38,62],flux:2,flv:58,fly:[19,58,59,78,99,139],fmass:74,fmax:93,fmsec:69,fno:4,fnorm:93,fnve:64,focu:78,foil:[42,73,150],fold:[4,79],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,39,42,43,45,46,48,49,50,51,52,53,54,55,56,58,59,60,63,65,66,67,68,69,70,74,75,76,77,78,80,81,82,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],foo:[3,58,77],foo_species:77,foot:2,forc:[0,1],forcefield:[76,122],forcegroup:68,ford:110,forgiv:69,fork:164,form:[2,28,32,33,34,36,38,42,43,63,67,76,77,82,83,84,85,88,91,94,96,99,112,113,115,118,122,123,135,136,138,139,142,143,144,145,146,147,149,150,151,157,158,159,162],formal:[2,35,67,69,74,149],format:[2,19,58,60,66,77,82,94,95,96,99,113,116,117,123,136,138,142,143,148,150,160],formation:66,former:[2,19,60,82,99],formul:[1,2,43,69,76,78,96,99,113,115,119,136],formula:[2,6,28,29,30,32,33,34,35,38,40,41,43,44,47,57,63,73,79,83,85,87,96,98,99,103,104,105,110,111,113,114,119,120,121,122,123,124,126,127,128,130,131,133,134,136,140,141,147,148,151,156,157,158,159,160,161,162],forth:[1,2,3],fortran:[2,3,113,136],forward:[32,94],foster:[99,146],found:[2,30,61,64,68,107,110],four:[2,3,28,42,63,82,91,94,139],fourier:2,fourth:[2,4,37,76,103,117,144,149],fox:[2,41,46,154],fqq:110,fraction:[1,2,4,19,43,58,61,62,75,77,94,99,117,120,133,134],frame:[42,59,75,119],framer:58,framework:[95,150],frattl:64,free:[2,13,29,32,73,80,81,82,94,115,132,139,141,146,162],freedom:[2,40,61,69,70,74,78,81,93,110],freeli:[0,2,58],freez:2,frenkel:[2,64,81],frequenc:[2,4,74,75,77,111,115,149],frequent:[29,30,36,39,42,64],fri:75,friction:[2,75,82,120],from:[0,1],front:75,frontend:58,frozen:[2,40,67,118],fs2:[2,35],ftol:[93,94],fuction:107,fudg:78,fulfil:2,full:[1,2,4,35,58,64,68,73,77,99,113,115,116,119],fuller:93,fulli:[2,73,93,94,107,146,164],fulton:113,fumi:100,funcfl:113,fund:0,funrol:139,further:[2,37,58,68,74,82,93,94,95,98,106,139,149],furthermor:[11,48,64,77,112,115],futur:[0,2,60,67,94,137,138],g_jik:146,g_p:82,ga3:44,gaa:99,gai:119,gain:[4,63],galindo:140,gamma0:13,gamma:[2,13,68,75,111,112,114,119,136,140,152,153,154,156,157,159,160],gamma_:82,gamma_ijk:157,gamma_n:120,gamma_p:82,gamma_t:120,gammaa:140,gammafactor:68,gammar:140,gan:[146,156,157,159,160],gan_sw:146,gan_tersoff:146,gao:[2,5,46,103],gap:[133,134,150],gather:3,gather_atom:3,gathert_atom:3,gauch:51,gauss:108,gaussian:[2,35,37,67,74,76,111,115,118],gavhan:4,gaybern:[2,4,93],gd3:44,gdot:134,ge4:44,gec:[157,159],gen:69,gener:0,gentler:83,gentli:114,geom:2,geometr:[2,45,60,69,84,94,98,104,105,107,110,115,117,119,121,124,125,126,127,128,129,130,131,132,133,134,135,140,143,147,151,161,162],geometri:[2,9,19,45,60,62],gerber:132,germann:[70,126],germano:119,get:[0,1,2,3,4,19,35,42,45,58,60,62,84,94,107,160,164],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[107,124],ghost:[2,4,30,62,69,111,112,115,120,123],gif:58,gifsicl:58,gillan:150,gingold:[152,153],git:164,give:[0,1,2,3,4,28,36,39,45,62,69,73,93,96,99,115,122,136,139,147,157,158,159],given:[2,3,4,11,39,42,43,48,57,62,64,67,68,69,70,73,74,75,76,77,78,79,82,83,84,95,96,99,100,101,102,104,105,106,107,108,111,112,113,115,116,117,119,120,122,124,125,126,128,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,163],glosli:139,glotzer:111,glue:3,gnu:0,gnuplot:3,goal:63,goddard:[2,9,92,115,122],goe:[28,42,45,64,93,110,114,121,126,129,151,163],gold:29,goldman:75,good:[1,2,4,19,30,41,44,60,63,69,78,94,95,105,113,139,160,164],gordan:42,gordon:2,got:164,gould:[2,46],gov:[0,95,113,116],govern:68,gpa:96,gpl:0,gpt:139,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,40,46,47,48,49,50,51,52,53,54,55,69,70,78,85,86,87,89,90,91,92,95,96],grab:2,grad:2,gradient:[2,62,64,82,94,134,142,143],graft:61,grain:[2,13,18,28,45,51,66,73,77,117,121,139,143,148],gram:113,gran:[2,83,84],granular:0,graph:3,graphic:3,graviti:2,grdient:59,great:[75,164],greater:[1,62,67,69,73,98,100,101,102],greatli:[41,64],green:[2,35,58,74,99,164],green_kubo:2,grest:[21,22,61,102,120,128],grid:[19,41,44,60,68,82],grigera:2,gromac:93,gromacs:[2,93,121],groot:111,ground:[2,31,65,115],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,58,59,60,61,62,63,64,65,66,67,6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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 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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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,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 tutorial"],titleterms:{"default":[29,32,36,37,39,41,42,44,45,57,58,59,62,67,68,69,70,74,75,80,81,83,99,115,133,134,139,155],"long":[100,101,102,103,104,107,109,110,124,128,132,145,148],acceler:1,adiabat:2,adp:95,airebo:96,alloi:113,amber:2,angle_styl:[5,6,7,8,9,10,11,12,13,14,15,16,17,18],arrai:2,aspher:2,atc:59,atom:[2,29,30,36,39,42,43],aug:0,balanc:[19,60],barostat:2,bcc:73,beck:97,between:2,bodi:[2,98],bond:61,bond_styl:[20,21,22,23,24,25,26,27,28],bop:99,born:[100,109],box:[2,62],buck:[101,102,109,135],build:3,calcul:2,centro:29,charmm:[2,5,46,103,132],chunk:[2,34,38],class2:[6,20,47,85,104],cna:30,code:2,coeffici:2,colloid:[83,105,162],comb3:106,comb:106,command:[2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],comparison:1,compos:2,comput:[2,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44],conduct:2,constant:2,control:63,core:2,cosin:[7,8,9,10,11,12,48],cossq:86,coul:[100,101,102,103,104,107,108,109,121,124,128,132,145,148],coupl:2,create_atom:45,cubic:126,cut:[25,101,104,107,110,115,118,124,125,132,140,145],cvff:87,data:2,deby:[107,124],delta:8,descript:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],diel:108,diffus:2,dihedral_styl:[46,47,48,49,50,51,52,53,54,55,56,57],dipol:[2,13,110],discuss:2,disp:2,distanc:88,document:0,dpd:[31,111,112],dreid:122,dreiding:2,drude:2,dsf:[107,124],dump:[2,58],eam:113,edip:114,eff:115,ehex:64,eim:116,elastic:2,energi:112,exampl:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],exp6:117,exp:[11,48],expand:[22,127],extend:3,fcc:73,fdt:112,fene:[21,22],fep:32,field:2,file:2,finit:2,fix:[2,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84],fix_modifi:[59,60,62,63,64,68,69,70,71,72,73,75,76,78,79,80,81,82,83,84],flow:2,fluid:68,flux:35,forc:2,fourier:[14,15,49,89],from:[2,3],gauss:118,gaybern:119,gener:[1,2],github:164,gld:67,global:2,gpu:[97,100,101,103,104,105,107,110,111,113,118,119,121,124,125,126,127,140,141,147,148,151,156,157,158,159,161,162,163],gran:120,granular:2,gromac:121,gyrat:[33,34],harmon:[16,23,24,25,50,52,83,90,144],hbond:122,heat:35,helix:51,hertz:120,hexord:36,histori:120,hook:120,how:2,idealga:152,imag:58,implicit:103,improper_styl:[85,86,87,88,89,90,91,92],indice:0,induc:2,info:[0,59,60,62,63,64,68,69,70,71,72,73,75,76,78,79,80,81,82,83,84],input:2,install:3,integr:2,intel:[4,5,16,21,23,46,50,54,69,87,90,101,103,119,124,156,157],interfac:[2,3],kspace_styl:2,lammps:[0,1,2,3,164],lennard:135,librari:[2,3],linear:[131,141],list:123,lj1043:83,lj126:83,lj93:83,lj96:125,local:2,lubric:133,lubricateu:134,luci:[142,143],manifold:[71,72],mdf:135,meam:[136,137,138],measur:1,mgpt:139,mie:140,minim:[59,60,62,63,64,68,69,70,71,72,73,75,76,78,79,80,81,82,83,84,93],mod:[82,158],model:2,morri:154,mors:[26,96,122,141],movi:58,mpi:3,msd:37,msm:[100,101,103,107,124],multi:[2,52,142,143],multipl:2,nb3b:144,neb:94,nemd:2,nharmon:53,non:2,nongauss:37,nonlinear:27,nph:69,nphug:70,npt:69,nve:71,nvt:[69,72],omega:38,omp:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,46,47,48,49,50,51,52,53,54,55,69,70,85,86,87,89,90,91,92,95,96,97,100,101,102,103,104,105,106,107,108,110,111,113,116,118,119,120,121,122,124,125,126,127,128,129,130,131,132,133,137,138,141,144,145,147,148,151,156,157,158,159,160,161,162,163],opl:54,opt:[103,113,124,128,141],optim:1,option:2,orient:73,orientord:39,orthogon:2,other:2,output:[2,59,60,62,63,64,68,69,70,71,72,73,75,76,78,79,80,81,82,83,84],overview:3,packag:[1,4],pair:2,pair_styl:[95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],parallel:3,paramet:2,particl:2,per:2,perform:1,period:9,pimd:74,polariz:2,poli:[133,134],polymorph:146,potenti:2,pppm:2,pressur:40,process:2,properti:2,python:3,qbmsst:75,quadrat:55,quantiti:2,quartic:[17,28],rattl:[71,72,78],rebo:96,region:84,relat:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,75,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163],relax:62,replica:2,resquar:147,restart:[2,59,60,62,63,64,68,69,70,71,72,73,75,76,78,79,80,81,82,83,84],restrain:76,restrict:[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163],rigid:2,ring:91,run:[2,3,59,60,62,63,64,68,69,70,71,72,73,75,76,78,79,80,81,82,83,84],scalar:2,script:[2,3],sdk:[18,148],serial:3,set:2,shake:78,share:3,shell:2,shift:[10,11,24,25,48],simpl:15,simul:2,size:2,smooth:[130,131,141],smtbq:149,sna:42,snad:42,snap:150,snapshot:2,snav:42,soft:[132,141,151],spc:2,sph:[152,153,154],spheric:[2,56],spline:[137,138],spring:[79,81],squar:12,srp:155,start:[59,60,62,63,64,68,69,70,71,72,73,75,76,78,79,80,81,82,83,84],stop:[59,60,62,63,64,68,69,70,71,72,73,75,76,78,79,80,81,82,83,84],strategi:1,streitz:107,stress:43,style:[1,2],summari:2,swap:61,syntax:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],system:2,tabl:[0,2,66,157],taitwat:[153,154],temperatur:2,tersoff:[157,158,159],test:3,thermal:2,thermo:2,thermodynam:2,thermostat:2,time:2,tip3p:2,tip4p:[2,107,124,128,132],triclin:2,tstat:111,ttm:82,tutori:164,umbrella:92,user:4,using:[2,3],valu:2,variabl:2,variou:1,vashishta:160,vector:2,version:0,viscos:2,visual:2,wall:[2,83,84],water:2,wolf:[100,107],wrapper:3,write:2,xrd:44,yukawa:[161,162],zbl:[159,163]}})
\ No newline at end of file
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt
index a35c234e636e1595be0f71c97f32dada9dd3d241..7bc2a78553c46379aa1685f17a6f72b876a7ee72 100644
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/doc/src/fix_nve_manifold_rattle.txt
@@ -22,7 +22,6 @@ one or more keyword/value pairs may be appended :l
 keyword = {every}
   {every} values = N
     N = print info about iteration every N steps. N = 0 means no output :pre
-
 :ule
 
 [Examples:]
@@ -33,28 +32,34 @@ fix step all nve/manifold/rattle 1e-8 100 ellipsoid 2.5 2.5 5.0 every 25 :pre
 [Description:]
 
 Perform constant NVE integration to update position and velocity for
-atoms constrained to a curved surface (manifold) in the group each timestep. The constraint
-is handled by RATTLE "(Andersen)"_#Andersen written out for the special case of
-single-particle constraints as explained in "(Paquay)"_#Paquay.
-V is volume; E is energy. This way, the dynamics of particles constrained to
-curved surfaces can be studied. If combined with "fix langevin"_fix_langevin.html, this generates
-Brownian motion of particles constrained to a curved surface. For a list of currently supported
-manifolds and their parameters, see "manifolds"_manifolds.html.
-
-Note that the particles must initially be close to the manifold in question. If not, RATTLE will
-not be able to iterate until the constraint is satisfied, and an error is generated. For simple
-manifolds this can be achieved with {region} and {create_atoms} commands, but for more complex
-surfaces it might be more useful to write a script.
+atoms constrained to a curved surface (manifold) in the group each
+timestep. The constraint is handled by RATTLE "(Andersen)"_#Andersen
+written out for the special case of single-particle constraints as
+explained in "(Paquay)"_#Paquay.  V is volume; E is energy. This way,
+the dynamics of particles constrained to curved surfaces can be
+studied. If combined with "fix langevin"_fix_langevin.html, this
+generates Brownian motion of particles constrained to a curved
+surface. For a list of currently supported manifolds and their
+parameters, see "manifolds"_manifolds.html.
+
+Note that the particles must initially be close to the manifold in
+question. If not, RATTLE will not be able to iterate until the
+constraint is satisfied, and an error is generated. For simple
+manifolds this can be achieved with {region} and {create_atoms}
+commands, but for more complex surfaces it might be more useful to
+write a script.
 
 The manifold args may be equal-style variables, like so:
 
 variable R equal "ramp(5.0,3.0)"
 fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R :pre
 
-In this case, the manifold parameter will change in time according to the variable.
-This is not a problem for the time integrator as long as the change of the manifold is slow with respect to the dynamics of the particles.
-Note that if the manifold has to exert work on the particles because of these changes, the total energy might not be conserved.
-
+In this case, the manifold parameter will change in time according to
+the variable.  This is not a problem for the time integrator as long
+as the change of the manifold is slow with respect to the dynamics of
+the particles.  Note that if the manifold has to exert work on the
+particles because of these changes, the total energy might not be
+conserved.
 
 :line
 
@@ -72,15 +77,16 @@ This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
 
-This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
-was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
 
 :line
 
 [Related commands:]
 
-"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html
+"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix
+manifoldforce"_fix_manifoldforce.html
 
 [Default:] every = 0, tchain = 3
 
diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp
index 602888af8f0e51363bdecce632cba262de271892..ca4af7931f1f913924714ebd5e6a5f4c2b8c201d 100644
--- a/src/compute_omega_chunk.cpp
+++ b/src/compute_omega_chunk.cpp
@@ -86,7 +86,7 @@ void ComputeOmegaChunk::init()
 
 void ComputeOmegaChunk::compute_array()
 {
-  int i,j,index;
+  int i,j,m,index;
   double dx,dy,dz,massone;
   double unwrap[3];