diff --git a/doc/README.md b/doc/README.md
index 26a51c13ab..b843b7eabe 100644
--- a/doc/README.md
+++ b/doc/README.md
@@ -14,8 +14,8 @@ make clean-all    # remove entire build folder and any cached data
 
 ## Installing prerequisites
 
-To run the documention build toolchain Python 3 and virtualenv have to be
-installed. Here are instructions for common setups:
+To run the documention build toolchain, Python 3 and virtualenv have
+to be installed. Here are instructions for common setups:
 
 ### Ubuntu
 
@@ -23,10 +23,16 @@ installed. Here are instructions for common setups:
 sudo apt-get install python-virtualenv
 ```
 
-### Fedora
+### Fedora (up to version 21), Red Hat Enterprise Linux or CentOS (up to version 7.x)
 
+```bash
+sudo yum install python3-virtualenv
 ```
-sudo yum install python-virtualenv
+
+### Fedora (since version 22)
+
+```bash
+sudo dnf install python3-virtualenv
 ```
 
 ### MacOS X
diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html
index 307539d233..903441ecd2 100644
--- a/doc/html/Section_howto.html
+++ b/doc/html/Section_howto.html
@@ -2339,14 +2339,14 @@ velocity:</p>
 <ol class="arabic simple" start="4">
 <li>Total force on each molecule and ave/max across all molecules:</li>
 </ol>
-<pre class="literal-block">
-compute cc1 all chunk/atom molecule
-fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
-variable xave equal ave(f_1<strong>2</strong>)
-variable xmax equal max(f_1<strong>2</strong>)
-thermo 1000
-thermo_style custom step temp v_xave v_xmax
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">1000</span> <span class="mi">1</span> <span class="mi">1000</span> <span class="n">cc1</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span>
+<span class="n">variable</span> <span class="n">xave</span> <span class="n">equal</span> <span class="n">ave</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+<span class="n">variable</span> <span class="n">xmax</span> <span class="n">equal</span> <span class="nb">max</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+<span class="n">thermo</span> <span class="mi">1000</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">v_xave</span> <span class="n">v_xmax</span>
+</pre></div>
+</div>
 <ol class="arabic simple" start="5">
 <li>Histogram of cluster sizes:</li>
 </ol>
diff --git a/doc/html/compute_omega_chunk.html b/doc/html/compute_omega_chunk.html
index 80f35b0737..47b39d5623 100644
--- a/doc/html/compute_omega_chunk.html
+++ b/doc/html/compute_omega_chunk.html
@@ -178,11 +178,11 @@ how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute omega/chunk
 calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
 command, for example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">omega</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute cc1 all chunk/atom molecule
+compute myChunk all omega/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk<strong>*</strong> file tmp.out mode vector
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =
diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html
index dbcf0a2488..6b64b64b96 100644
--- a/doc/html/fix_nve_manifold_rattle.html
+++ b/doc/html/fix_nve_manifold_rattle.html
@@ -158,7 +158,7 @@ keyword = <em>every</em>
 <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="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a>.
+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
diff --git a/doc/html/fix_nvt_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html
index 98dd612247..b27135b6fb 100644
--- a/doc/html/fix_nvt_manifold_rattle.html
+++ b/doc/html/fix_nvt_manifold_rattle.html
@@ -157,7 +157,7 @@ keyword = <em>temp</em> or <em>tchain</em> or <em>every</em>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
-<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the
+<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the
 canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
 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>
 </div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 655458bf7d..22518f84ad 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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,133],brows:0,browser:57,bryantsev:121,btype:[106,123,127,131,154],buc:100,buck:[2,4,32,99],buckingham:[99,100,101,108,134],buckplusattr:148,buffer:57,bufi:57,bug:0,bui:57,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,73,74,76,77,79,80,81,84,85,86,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],bulatov:[136,137],bulk:[2,29,67,72,107,135,138,148],bundl:[57,163],button:163,bypass:2,c11:135,c_0:[81,95,152,153],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:81,c_flux:35,c_gauss:117,c_hb:121,c_i:65,c_id:[2,32,62],c_ij:2,c_ijkl:2,c_k:66,c_mychunk:[2,34],c_n_k:66,c_p:42,c_peratom:42,c_pi:98,c_prop:2,c_sigma:98,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:77,calcforc:67,calclat:35,calcluat:[37,39,42,106],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:73,call:[1,2,3,4,73,95,104,161,163],callabl:3,callback:3,caltech:[2,114],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,74,81,82,83,92,93,100,101,103,112,118,120,123,127,129,131,144,146,147,154],canon:[68,71,73,80,138],cao1:73,cao2:73,cao:73,capabl:[3,4,95,103],capac:[64,81,151],capolungo:[40,43],captur:[2,95,101,114,119,127,135],carbid:106,carbon:[57,90,95,105,135],card:[4,32,121],care:[2,44,55,67,68,97],carefulli:[3,28],carlo:[2,60],caro:112,carri:[4,81,119],carrillo:4,cartesian:[2,94],cascad:81,cat:[4,57],cate:67,categori:[0,95],cation:[115,148],caus:[1,2,4,44,61,68,72,76,77,82,83,92,93,121,123,129,132,133],caution:1,cautious:95,caveat:95,cbecker:[94,112],cc1:[2,34],ccc:[113,155,156,158,159],ccflag:4,ccflags:4,ccm6:112,ccsi:[113,155,156,158,159],ccu:98,cd2:43,cdeam:112,cdll:3,cdof:2,cdte:98,cdte_bop:98,cdtese:98,cdzn:98,cdznte:98,ce3:43,ce4:43,cell:[2,40,43,44,61,68,69,74,81,114,138],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,78,80,82,83,84,97,113,114,118,119,132,133,135,136,137,155,156,157,158,159],centr:63,central:[29,36,38,41,72,77,78,87,138,143,159],centro:2,centroid:73,centrosymmetri:29,certain:[1,2,57,60,62],cfg:[2,57],cg_type:147,ch2:77,ch2lmp:[0,2],ch3:77,chain:[0,2,13,28,60,68,69,71,73,77,80,90,109,110,154],challeng:2,champaign:132,chan:138,chandler:[94,112],chandrasekhar:[2,123],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,74,75,76,77,79,80,81,83,92,93,110,114,119,132,133,135,138,148,154,163],change_box:2,chapter:73,charact:[2,19,57,59,65,76,114,116,122,141,142,145,148],character:[2,29,38,41,149],characterist:79,charg:[1,2,3,32,40,43,44,99,100,105,106,108,109,112,114,115,123,127,131,144,148,158,159,161,162],charl:62,charmm:0,cheaper:[118,146],check:[2,3,19,35,59,75,77,80,92,93,122],checkout:163,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,73,74,79,80,82,84,90,91,93,95,99,102,103,105,106,107,109,110,111,114,117,118,120,121,123,127,128,131,135,139,141,142,144,148,154],chemic:[31,40,43,58,116,142],chemistri:[74,95,98,114],chen:81,cheng:105,chi:[72,115,118],chiral:90,chmod:3,cho:135,choic:[2,4,19,28,29,32,42,55,59,60,67,68,73,93,131],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[156,158],chosen:[2,41,44,50,57,61,62,66,67,68,69,73,111,114,119,122,125,147,156],chunk:0,chunkid:34,ciccotti:77,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:148,cl1:43,clarendon:[13,109],clarifi:[156,158],clark:144,classic:[0,2,4,73,74,81,91,114],classifi:159,clean:2,clear:[2,3,62],clebsch:41,click:[3,44,56,57,93,163],climb:93,clockwis:45,clone:163,close:[2,3,19,42,60,61,67,68,70,77,83,93,95,98,106,107,135,141,142,158,163],closer:[19,59,61,79,93],closest:[72,118,146,154],cloud:148,cluster:[2,4,42,63,77],cmax:135,cmd:[3,73],cmdarg:3,cmin:135,cmm:[18,147],cna:29,co2:[43,76,77,116],coars:[13,18,28,50,65,76,116,120,142,147],coarsest:41,code:[0,1],coeff:[6,45,46,55,84,122,150],coeffici:0,coefficienct:110,coefficient0:112,coefficient1:112,coeffieci:[2,96],coeffincientn:112,coexist:114,cohes:[2,115,135],coincid:[83,102,132,133],cold:2,coleman:[40,43],collect:[2,34,44,104],colliex:43,collis:[67,119,162],colloid:2,color:[19,57,59,66,74],column:[2,29,34,36,38,41,42,43,74,81,95,117,121],colvar:0,com:[2,37,63,97,163],comand:60,combiant:107,combin:[2,3,18,32,55,57,58,63,68,70,71,73,83,84,104,106,107,111,114,115,116,130,131,149,155,156,158,159,161],come:[0,2,13,61,62,68,79,80,155,156,158,159,163],comit:163,comm:[0,3,30,93,110],comm_modifi:[2,98,104,110,114,119],comm_styl:[19,59],comm_world:3,command:[0,1],comment:[3,45,65,76,81,93,94,112,113,115,116,122,135,141,142,143,148,149,155,156,157,158,159,163],commit:163,commmand:2,common:[0,1,2,3,4,30,61,73,83,84,119,121,155,156,158],commonli:[2,9,37,38,57,91,120,125,149,156,158],commun:[1,2,3,4,19,57,59,61,67,68,81,111],comp:[70,71,77,93,114,146,153,157],compar:[1,2,4,40,43,56,92,93,135,148],comparison:0,compass:[6,20,46,56,84,103],compat:[3,19,49,59,62,63,82,138],compens:[2,114],compil:[4,57,138],complain:3,complement:135,complementari:[106,123],complet:[2,3,19,59,73,93,115],complex:[2,3,9,36,38,41,44,67,70,83,93,114,138],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,73,77,83,92,93,110,114,119,132,133,148,149],componenet:2,composit:[2,67,112],compound:[105,114,115,159],compress:[2,57,69,74],compris:[83,116,146],compton:[40,43],comput:[0,1],computation:[2,81,98],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:83,concentr:[65,76,112,116,142],concept:2,conceptu:[2,61,93,106,135],concern:[2,30,32,66],concis:3,concurr:4,conden:[81,156,158],condens:[2,81,95,108,112,123,159],condit:[2,39,40,42,43,57,58,67,69,72,74,77,78,81,111,114,120],conducit:2,conduct:0,confer:[4,138],configur:[1,2,4,57,61,73,92,93,95,98,113,135,138,155,156,158,159,163],conflict:163,conform:[2,60,61,75,90,93,114],confus:159,conjuct:110,conjug:114,conjunct:[2,32,44,67,93,99,100,106,110,114,121,123,144,147],connect:[2,32,60,77,93,107,119,154,158],conner:95,connor:95,consecut:[3,44,106,123,127],consequ:[1,2,81,122],conserv:[13,60,66,67,68,70,76,77,93,109,110,111,119,129,148],consid:[2,29,32,59,60,81,114,146,148,154],consider:2,consist:[2,3,39,44,50,62,66,68,69,74,75,76,93,95,98,104,106,114,118,132,133,135,138,141,142,146,148],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,82,83,104,146],constrain:[2,63,66,70,71,77,78,92,114],constraint:[19,39,42,59,63,70,77,78,82,92,133],construct:[2,28,29,30,36,38,40,41,43,61,68,75,76,83,109,138,154,155],constructor:3,consult:4,consum:1,contact:[0,107,113,115,118,119,146],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,72,74,76,81,83,93,94,95,98,105,106,109,112,113,114,116,135,138,141,142,143,145,149,155,156,157,158,159,163],context:[2,4,161],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,74,79,80,81,83,98,110,125,128,146,157],continuum:[2,58,81],contour_integr:58,contract:[61,68],contrain:77,contrast:[1,2,161],contrib:81,contribut:[2,29,32,33,34,35,39,41,42,61,67,77,92,93,110,112,114,132,133,138,148,163],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,149,163],convent:[13,49,54,56,75,112,114],converg:[2,19,57,59,60,61,69,70,71,74,75,77,92,93,105,106,123,148],convers:[41,57,106,107,108,114,123,127,131,144],convert:[2,5,6,8,12,16,17,18,35,44,46,57,84,85,89,90,93,94,112,138,156,158,162],convex:83,cool:63,coord:[2,3,36,38,72,82,93],coordb:148,coordbb:148,coordiat:92,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,72,77,78,80,81,92,93,94,95,97,113,148],coords:148,copi:[0,3,57,81,93,163],copper:162,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,100,106,108],cornel:[2,45],corner:[2,57,83,163],corpor:4,corr:105,correct:[2,3,32,45,57,63,68,74,82,83,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],correction_max_iter:58,correctli:[3,68,77,83,93,108,133,138,163],correl:[2,35,36,41,66,73],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,72,73,76,77,82,83,84,85,86,88,89,90,91,93,94,95,96,99,100,101,102,103,104,105,106,109,110,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,135,136,138,140,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],correspondingli:[132,133],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,76,81,106,123,127,138,155],costheta0:[155,156,158,159],costheta:145,costli:[3,4],coul:[2,4,18,21,22,32,45,92],could:[2,3,19,32,34,35,39,57,59,62,74,81,82,83,92,95,117,121],coulomb:[2,42,92,99,100,101,102,103,105,106,107,108,109,114,119,120,123,127,131,134,144,147,148,158,159,161],coulommb:2,count:[1,2,3,19,35,45,59,61,68,77,83,92,93,117,121],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,75,82,132,150],cov:148,coval:[2,13,114,135,148],cover:[2,58,67,114],cpp:[1,2,3,32,77],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,72,73,75,81,93,95,98,105,112,113,131,140,141,142,145,148,155,156,157,158,159,163],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,154],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,92],criterion:[19,44,59,60,92,93,105,114,119,148],critic:[2,24,25,81,92],cross:[4,33,57,93,102,110,112,120,121,123,125,127,145,147,156,158,162],crossov:1,crozier:0,crucial:74,crystal:[2,4,29,30,38,72,80],crystallin:[2,157],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,149],cscl:135,csequ:2,csh:[3,4],cshrc:3,csic:[113,155,156,158,159],csinfo:2,csisi:[113,155,156,158,159],cst:112,cstherm:2,csvr:2,ctcm:[94,112],ctype:3,cu1:43,cu2:43,cu3au:135,cube:[2,83],cubes:[19,59],cubic:[38,67,72,112],cuda:1,cuh:98,cummul:[2,60,121],cumul:[2,68,69,93],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,70,71,75,76,77,78,81,82,92,93,98,105,109,112,114,115,119,122,132,133,135,136,137,145,150,156,158,163],curv:[2,44,70,71],curvatur:[118,146,162],custom:[0,2,3,33,34,35,42,57,60,61,68,69,74,92,95,117,121],cut:[1,2,4,19],cuthi:72,cutinn:[132,133],cutlo:72,cutmax:145,cutoff1:[103,109,123,127,131,134,144,147],cutoff2:[99,100,101,103,108,109,123,127,131,134,144,147],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,72,74,82,83,92,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cutoffa:113,cutoffc:113,cuu3:112,cval:43,cvar:62,cvff:4,cwiggl:82,cyan:57,cycl:[68,69],cyclic:45,cylind:[57,71,83],cylindr:2,cyrot:98,d3q15:67,d3q19:67,d_e:81,daan:80,damp:[2,68,69,71,74,92,93,99,100,102,106,109,114,119,123,131,144,147],dampflag:119,danger:110,darden:109,darken:57,dash:119,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:134,davi:82,david:[156,158],daw:[112,145],dcd:[2,57,73],deactiv:131,debug:[2,3,40,43,44,73],decai:[36,106,162],decid:[2,4,163],decod:57,decompos:[32,149],decomposit:[58,73],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,138],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,72,73,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,95,96,97,99,100,101,102,103,104,106,107,109,110,111,113,114,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],definit:[2,41,62,64,69,82,98,104,111,114,145,149],deform:[2,42,61,68,132,133],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,73,75,77,80,84,85,89,90,91,92,109,112,121],delai:2,delet:[28,60,68,154,163],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:76,dellago:[2,63],deloc:[114,148],delr:135,delta_1:98,delta_3:98,delta_7:98,delta_ij:[135,145],delta_pi:98,delta_r:145,delta_sigma:98,deltah_f:65,demo:3,demonstr:[74,135],dendrim:121,denniston:67,denot:[40,63,106,120],dens:[60,76,114],densiti:[2,19,41,44,58,59,67,81,82,94,95,98,112,135,136,137,141,142,145,146,148,151,152,153],depart:0,departur:74,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,72,76,77,79,81,82,83,84,85,86,88,89,90,91,92,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],dependend:2,deposit:[68,77],depth:[26,57,81,116,118,146],der:[32,104,105,131,161],deriv:[2,32,41,61,62,63,68,69,72,79,80,81,82,83,95,98,104,109,114,115,120,125,129,130,135,138,161],derjagin:161,derlet:72,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,72,73,74,76,79,80,82,92,93,95,97,99,100,102,103,104,105,106,109,112,114,115,116,118,119,120,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,141,142,145,146,147,148,149,150,154,155,156,157,158,159,160,161,162,163],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,72,81,96,97,102,106,108,114,131,132,133,136,137,145],desir:[2,3,4,35,39,42,44,61,62,66,68,77,92,93,110,112,121,132,133,155,156,158],desktop:[2,57],destabil:98,destre:90,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,74,77,80,81,92,94,95,97,98,101,102,103,104,105,106,109,110,114,115,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,135,139,141,142,146,148,149,150,160,161,163],detect:[36,93,105,121,122],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,72,73,74,75,76,82,83,95,101,105,109,112,116,117,119,127,135,138,142,146,148,154,161],devan:147,devanathan:158,develop:[0,2,3,4,62,69,74,95,98,114,137,138,148,159],deviat:[69,72,117],devic:1,devin:105,devis:137,dfactor:57,dft:138,dhug:74,dhugoniot:74,dia:135,diag:76,diagnost:[4,60,76],diagon:[2,41,42,61,68],diagonalstyl:149,diagram:[19,40,43,56,59,73],diallo:121,diam:57,diamet:[2,44,57,104,118,119,125,146,161],diamond:[114,135],dick:2,dicken:62,did:[92,110,112,119,156,158],dielectr:[102,106,107,108,123,127,131,144],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,68,72,73,74,77,78,79,80,81,82,83,84,93,94,95,98,101,102,104,105,110,111,112,114,116,118,119,120,123,124,126,127,134,135,136,137,139,140,141,142,143,145,146,147,148,149,150,155,156,158,159,161],differenti:[1,2,13,76,106,145,157],difficult:[61,62,73,121],difficulti:[36,38,77],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:138,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,75,85,86,87,89,92,95,98,102],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:114,dij:77,dilat:[61,68,69],dim:[44,135],dimens:[1,2,19,35,42,44,57,59,61,67,68,69,74,82,93],dimension:[36,39,40,41,43,81,93,145],dimensionless:[37,41,62,81,149,161],dimer:[2,135],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:109,dir:[1,3,72,74,145],dirac:41,direc:145,direct:[2,4,13,29,38,40,41,43,44,45,57,67,69,72,74,79,80,81,82,83,92,93,110,111,119,133],directli:[2,3,32,41,44,57,62,67,76,83,94,95,99,100,101,106,109,112,114,123,127,144,147,154],directori:[0,1,2,3,4,62,79,80,93,94,95,98,105,106,112,113,115,131,135,136,137,138,143,145,148,149,155,156,157,158,159],disabl:[4,81,122],disadvantag:[2,59],disallow:68,discard:[19,59,83],discontinu:[92,129],discourag:135,discret:[2,57,62,67,71],discuss:[0,1],disk:[2,36],disloc:[29,138],disord:[29,138],disp:0,dispar:146,disperion:[109,127],dispers:[2,101,109,127,132,159],displac:[2,37,61,68,72,119],displai:[3,56,57],disregard:138,dissip:[2,31,64,66,79,80,110,111,119,132,133],dist:[2,35,73,75,154],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,63,67,68,69,72,74,75,77,78,80,81,82,83,84],distinct:[2,146],distinguish:[2,41,114],distort:94,distrbut:94,distribut:[0,2,3,19,32,41,56,59,66,67,68,94,98,106,112,113,115,135,136,137,143,145,146,155,156,157,158,159],distro:145,ditto:162,div:4,diverg:[80,95],divid:[2,4,19,35,39,42,56,59,72,92,93,115,148,159],divis:[2,55,67,98,131],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[104,161],dm_lb:67,doc:[0,1,2,3,32,34,37,39,42,44,56,57,62,68,83,92,93,94,95,97,105,106,112,113,115,121,135,136,137,143,145,149,155,156,158,159,163],docuement:146,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,63,65,66,67,68,71,81,82,83,85,86,87,89,90,93,94,95,96,97,98,101,102,103,104,105,106,107,109,110,112,113,114,116,117,118,119,120,122,125,126,128,129,130,132,133,135,136,137,138,141,142,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],doesn:[44,95,105,113,155,156,157,158,159],dof:39,doi:[2,72],domain:[2,19,40,43,57,59,61,67,68,73,81,82,93],domin:[1,114],don:[0,4,83,135,148,163],done:[1,2,19,44,55,57,58,59,60,61,62,65,68,73,77,79,80,92,93,95,101,112,127,133,134,135,141,142,154,163],donor:121,dot:42,doti:[98,145],doubl:[1,2,3,4,32,45,61,83,98,115,120,138],dover:58,down:[2,3,61,114,148],download:3,downsid:2,dpd:2,dpdtheta:[31,111],dpdtheta_i:[64,65],dr_ewald:40,drag:[2,35,68,69,78],dragforc:67,drai:[57,74],drain:92,dramat:[60,61,68,148],drautz:98,draw:57,drawn:[57,66],drayleigh:74,dreid:2,dreiding:0,drfourth:37,drho:[94,112,141,142],drift:[2,37,63,66],drive:[3,61,68,72,93],driven:[2,50],driver:2,drop:110,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:74,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,66,67,68,69,72,75,79,80,81,82,83,92,93,107,110,111,112,117,118,132,133,145,146,147,154,156,158,161,162],duffi:81,dullweb:68,dummi:[13,157],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,102],duplic:[19,59,72],durat:[56,81,119],dure:[2,4,19,32,45,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,92,93,110,131,138,140,141,142],dvlo:161,dvx:2,dx_lb:67,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,64,66,68,69,70,73,74,75,79,80,81,92,93,110,111,114,132,133,153],dynamo:[94,112,135],dyre:128,e28637:13,e_1:98,e_2:98,e_a:76,e_b:115,e_ee:114,e_hbond:121,e_i:[2,98,115],e_j:[2,98],e_k:98,e_ke:114,e_kl:2,e_lj:[95,109],e_n:[62,98],e_ne:114,e_nn:114,e_pr:114,e_rebo:95,e_torsion:95,e_tot:138,e_vol:138,eaa:84,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,72,73,76,77,78,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,158,159,160,161,162],eacn:[19,59],eam:[0,94,106],earli:[19,59],earlier:[93,119,135],earth:114,easi:[2,3,32,42,82],easier:[4,57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lerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,76,82,92,138,141,142,145,148],evanseck:[2,5,45,102],evaul:92,even:[2,4,19,29,55,59,61,63,68,81,82,83,92,93,97,114,115,119,146,159],evenli:[19,42,59,67],event:[2,68,81],eventu:2,ever:28,everaer:[104,118,146],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,71,72,74,76,77,81,93,110,131,148,163],everyth:163,everywher:125,eviri:114,evolut:[63,67,73],evolv:[67,73],ewald:[2,40,42,92,99,100,101,106,109,114,123,127,144,147],ewald_disp:109,exact:[19,59,60,66,81],exactli:[2,19,35,44,59,66,74,110,112,119,132,141,142],examin:[2,60,76],exampl:[0,1],exce:[2,4,19,59,61,68,92],exceed:[19,59,68],excel:114,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,73,77,81,84,85,86,88,89,90,91,93,94,95,96,99,100,101,102,103,104,105,106,108,109,110,112,113,114,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,136,140,143,144,146,147,150,155,156,157,158,159,160,161,162],excess:114,exchang:[2,58,63,81,114],excit:114,excite:114,exclud:[2,4,39,41,92,119,132,133,154],exclus:[1,4,32,45,105,138],excurs:68,execut:[1,2,3,57],exempl:148,exemplari:66,exemplifi:114,exert:[2,70,83],exhaust:58,exhibit:[36,63,68,114],exist:[2,3,29,44,56,57,61,84,85,86,87,89,111,154,163],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,72,74,135,138],expens:[2,72,81],experi:[2,75,93,110],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,72,93,97,112,148,150,163],explan:[2,41,72],explic:139,explicit:[2,3,32,76,95,98,102,112,114,122,132,163],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,61,66,68,69,74,77,81,84,85,86,88,89,90,91,94,95,96,99,100,101,102,103,104,105,106,107,109,110,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,136,138,140,141,142,143,144,146,147,150,151,152,153,155,156,157,158,159,160,161,162,163],explictli:4,exploit:73,explor:[40,43],expon:[76,112,116,118,121,131,139,147],exponenti:[32,76,116,145,155,159,162],expos:3,exposit:[58,110],express:[2,41,44,61,72,76,81,98,112,114,125,135,148,149],expressiont:98,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,72,75,79,80,81,82,83,118,135,138,146,149],extent:[1,19,21,59,95],exterior:[2,83],extern:[32,57,61,66,67,68,69,71,81,92,136,137],extra:[2,3,4,19,22,39,40,42,43,44,59,68,74,92,109,119,135],extract:[2,3,18,32,93,106,115,135,149],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,80,114,157],extrema:131,extreme:114,extrins:58,f_1:[2,61],f_a:[156,157,158],f_c:157,f_f:158,f_fix_id:74,f_harm:80,f_i:[13,145],f_id:[2,62],f_ij:145,f_int:79,f_j:13,f_jj:35,f_k:145,f_langevin:81,f_max:74,f_r:[156,157,158],f_sigma:98,f_solid:80,f_ss:2,face:[2,82,83,118,135,146],facil:0,facilit:2,fact:[2,4,80,119,148],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,73,75,76,77,82,83,89,95,98,99,100,102,106,107,108,110,111,114,119,122,123,135,138,141,142,143,144,147,150,155],fail:[3,61,92,93,108],fairli:[3,163],faken:30,fall:2,fals:148,famili:159,familiar:[0,3,163],fan:145,far:[2,59,61,68,72,75,82,85,89,93],farrel:[156,158],fashion:[2,19,44,59,62,68,69,74,80,81,82,93,132],fast:[2,4,62,74,76,132,133,138],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,77,79,81,84,85,86,88,89,90,91,94,95,96,98,99,100,101,102,103,104,105,106,109,110,112,113,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,136,140,143,144,146,147,150,155,156,157,158,159,160,161,162],fastest:[1,2,81],fault:29,fava:118,favor:60,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,76],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,73,83,92,163],fecr:112,feedback:62,feel:[72,83,93],fehlberg:76,felling:137,felt:83,fene:[2,4],fennel:[106,123],fep:0,ferguson:[2,45],fermi:[1,158],fermion:114,fernando:134,few:[1,2,3,63,68,77,92,93,95,148],fewer:[1,3,4],feynman:73,ffield:[105,115,148],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:154,fictiti:[2,73,75,106,123,127,154],field:0,fifth:[2,116,143],figshar:72,figur:[1,4,74,163],fij:109,file0:72,file1:[3,65,72],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,72,76,81,93,94,95,98,106,112,113,115,116,135,136,137,141,142,143,145,148,149,155,156,157,158,159],fill:[44,57,81,98,138,163],filter:58,finchham:[2,108],find:[0,2,3,4,30,32,60,61,62,65,72,75,92,93,106,123,127,135,141,142,148,163],fine:[4,80,163],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:112,fire:[92,93],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,72,73,74,77,78,79,80,81,84,92,93,94,95,97,98,99,100,102,105,106,112,114,115,116,119,120,122,123,127,132,133,135,137,138,141,142,143,145,148,149,154,155,156,157,158,159,162,163],fischer:[2,5,45,102],fit:[2,75,95,98,135,141,142,157,163],five:[30,74,98,136],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,74],fix_manifoldforc:163,fix_modifi:2,fix_nv:163,fix_rattl:77,fix_shak:77,fixedpoint:[61,68],fixid:[57,58],fji:109,flag:[3,4,33,34,40,43,57,60,95,121,122,135,138,154,163],flag_buck:101,flag_coul:[101,109,127],flag_lj:[109,127],flagfld:[132,133],flaghi:[132,133],flaglog:[132,133],flagvf:[132,133],flat:[2,4,81,82],fld:[82,132,133],flexibl:[2,57,114,157],flip:[2,68],fluctuat:[2,32,61,66,67,68,69,72,80,81,90,111],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,77,98,138],fmass:73,fmax:92,fmsec:68,fno:4,fnorm:92,fnve:63,focu:77,foil:[41,72,149],fold:[4,78],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,73,74,75,76,77,79,80,81,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],foo:[3,57,76],foo_species:76,foot:2,forc:[0,1],forcefield:[75,121],forcegroup:67,ford:109,forgiv:68,fork:163,form:[2,28,32,33,34,36,41,42,62,66,75,76,81,82,83,84,87,90,93,95,98,111,112,114,117,121,122,134,135,137,138,141,142,143,144,145,146,148,149,150,156,157,158,161],formal:[2,35,66,68,73,148],format:[2,19,57,59,65,76,81,93,94,95,98,112,115,116,122,135,137,141,142,147,149,159],formation:65,former:[2,19,59,81,98],formul:[1,2,42,68,75,77,95,98,112,114,118,135],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,46,56,62,72,78,82,84,86,95,97,98,102,103,104,109,110,112,113,118,119,120,121,122,123,125,126,127,129,130,132,133,135,139,140,146,147,150,155,156,157,158,159,160,161],forth:[1,2,3],fortran:[2,3,112,135],forward:[32,93],foster:[98,145],found:[2,30,60,63,67,106,109],four:[2,3,28,41,62,81,90,93,138],fourier:2,fourth:[2,4,37,75,102,116,143,148],fox:[2,40,45,153],fqq:109,fraction:[1,2,4,19,42,57,60,61,74,76,93,98,116,119,132,133],frame:[41,58,74,118],framer:57,framework:[94,149],frattl:63,free:[2,13,29,32,72,79,80,81,93,114,131,138,140,145,161],freedom:[2,39,60,68,69,73,77,80,92,109],freeli:[0,2,57],freez:2,frenkel:[2,63,80],frequenc:[2,4,73,74,76,110,114,148],frequent:[29,30,36,38,41,63],fri:74,friction:[2,74,81,119],from:[0,1],front:74,frontend:57,frozen:[2,39,66,117],fs2:[2,35],ftol:[92,93],fuction:106,fudg:77,fulfil:2,full:[1,2,4,35,57,63,67,72,76,98,112,114,115,118],fuller:92,fulli:[2,72,92,93,106,145,163],fulton:112,fumi:99,funcfl:112,fund:0,funrol:138,further:[2,37,57,67,73,81,92,93,94,97,105,138,148],furthermor:[11,47,63,76,111,114],futur:[0,2,59,66,93,136,137],g_jik:145,g_p:81,ga3:43,gaa:98,gai:118,gain:[4,62],galindo:139,gamma0:13,gamma:[2,13,67,74,110,111,113,118,135,139,151,152,153,155,156,158,159],gamma_:81,gamma_ijk:156,gamma_n:119,gamma_p:81,gamma_t:119,gammaa:139,gammafactor:67,gammar:139,gan:[145,155,156,158,159],gan_sw:145,gan_tersoff:145,gao:[2,5,45,102],gap:[132,133,149],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:107,gaussian:[2,35,37,66,73,75,110,114,117],gavhan:4,gaybern:[2,4,92],gd3:43,gdot:133,ge4:43,gec:[156,158],gen:68,gener:0,gentler:82,gentli:113,geom:2,geometr:[2,44,59,68,83,93,97,103,104,106,109,114,116,118,120,123,124,125,126,127,128,129,130,131,132,133,134,139,142,146,150,160,161],geometri:[2,9,19,44,59,61],gerber:131,germann:[69,125],germano:118,get:[0,1,2,3,4,19,35,41,44,57,59,61,83,93,106,159,163],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[106,123],ghost:[2,4,30,61,68,110,111,114,119,122],gif:57,gifsicl:57,gillan:149,gingold:[151,152],git:163,give:[0,1,2,3,4,28,36,38,44,61,68,72,92,95,98,114,121,135,138,146,156,157,158],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,72,73,74,75,76,77,78,81,82,83,94,95,98,99,100,101,103,104,105,106,107,110,111,112,114,115,116,118,119,121,123,124,125,127,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,162],glosli:138,glotzer:110,glue:3,gnu:0,gnuplot:3,goal:62,goddard:[2,9,91,114,121],goe:[28,41,44,63,92,109,113,120,125,128,150,162],gold:29,goldman:74,good:[1,2,4,19,30,40,43,59,62,68,77,93,94,104,112,138,159,163],gordan:41,gordon:2,got:163,gould:[2,45],gov:[0,94,112,115],govern:67,gpa:95,gpl:0,gpt:138,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,77,84,85,86,88,89,90,91,94,95],grab:2,grad:2,gradient:[2,61,63,81,93,133,141,142],graft:60,grain:[2,13,18,28,44,50,65,72,76,116,120,138,142,147],gram:112,gran:[2,82,83],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[74,163],greater:[1,61,66,68,72,97,99,100,101],greatli:[40,63],green:[2,35,57,73,98,163],green_kubo:2,grest:[21,22,60,101,119,127],grid:[19,40,43,59,67,81],grigera:2,gromac:92,gromacs:[2,92,120],groot:110,ground:[2,31,64,114],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,93,148,159],group_id:3,grow:[2,68,72,76,119],growth:2,gsmooth_factor:135,guarante:44,guess:163,gui:[3,163],guid:[1,151,152,153],gu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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 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 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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:[19,40,43,60,64,71,72,78,79,83,93,134],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 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/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt
index f820f1cd72..c46184212f 100644
--- a/doc/src/compute_omega_chunk.txt
+++ b/doc/src/compute_omega_chunk.txt
@@ -64,7 +64,7 @@ command, for example:
 
 compute cc1 all chunk/atom molecule
 compute myChunk all omega/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector :pre
 
 [Output info:]
 
diff --git a/lib/meam/meam_setup_done.F b/lib/meam/meam_setup_done.F
index f33ac96f1e..0684fde70b 100755
--- a/lib/meam/meam_setup_done.F
+++ b/lib/meam/meam_setup_done.F
@@ -438,9 +438,17 @@ c     use precomputed values
           rho0_2 = rho0_meam(b)*Z2*G2
         endif
         Gam1 = (t11av*rho11+t21av*rho21+t31av*rho31)
-        Gam1 = Gam1/(rho01*rho01)
+        if (rho01 < 1.0d-14) then
+          Gam1 = 0.0d0
+        else
+          Gam1 = Gam1/(rho01*rho01)
+        endif
         Gam2 = (t12av*rho12+t22av*rho22+t32av*rho32)
-        Gam2 = Gam2/(rho02*rho02)
+        if (rho02 < 1.0d-14) then
+          Gam2 = 0.0d0
+        else
+          Gam2 = Gam2/(rho02*rho02)
+        endif
         call G_gam(Gam1,ibar_meam(a),gsmooth_factor,G1,errorflag)
         call G_gam(Gam2,ibar_meam(b),gsmooth_factor,G2,errorflag)
         if (mix_ref_t.eq.1) then
diff --git a/src/BODY/compute_body_local.h b/src/BODY/compute_body_local.h
index 5e9c036ff2..e2ff9a38bd 100644
--- a/src/BODY/compute_body_local.h
+++ b/src/BODY/compute_body_local.h
@@ -37,8 +37,6 @@ class ComputeBodyLocal : public Compute {
   int *which,*index;
 
   int nmax;
-  double *vector;
-  double **array;
 
   class AtomVecBody *avec;
   class Body *bptr;
diff --git a/src/RIGID/compute_rigid_local.h b/src/RIGID/compute_rigid_local.h
index 2e54a19ab5..d7d545d1fd 100644
--- a/src/RIGID/compute_rigid_local.h
+++ b/src/RIGID/compute_rigid_local.h
@@ -41,8 +41,6 @@ class ComputeRigidLocal : public Compute {
   class FixRigidSmall *fixrigid;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_rigid(int);
   void reallocate(int);
diff --git a/src/USER-REAXC/compute_spec_atom.h b/src/USER-REAXC/compute_spec_atom.h
index 107a2bd39f..4d5cb86d71 100644
--- a/src/USER-REAXC/compute_spec_atom.h
+++ b/src/USER-REAXC/compute_spec_atom.h
@@ -36,8 +36,6 @@ class ComputeSpecAtom : public Compute {
  private:
   int nvalues;
   int nmax;
-  double *vector;
-  double **array;
   double *buf;
   double *vbuf;
 
diff --git a/src/atom.cpp b/src/atom.cpp
index a6463259fd..86b1dea3d6 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1589,6 +1589,7 @@ void Atom::add_molecule(int narg, char **arg)
 
 int Atom::find_molecule(char *id)
 {
+  if(id == NULL) return -1;
   int imol;
   for (imol = 0; imol < nmolecule; imol++)
     if (strcmp(id,molecules[imol]->id) == 0) return imol;
@@ -1913,6 +1914,8 @@ void Atom::add_callback(int flag)
 
 void Atom::delete_callback(const char *id, int flag)
 {
+  if(id==NULL) return;
+
   int ifix;
   for (ifix = 0; ifix < modify->nfix; ifix++)
     if (strcmp(id,modify->fix[ifix]->id) == 0) break;
@@ -1968,6 +1971,8 @@ void Atom::update_callback(int ifix)
 
 int Atom::find_custom(const char *name, int &flag)
 {
+  if(name == NULL) return -1;
+
   for (int i = 0; i < nivector; i++)
     if (iname[i] && strcmp(iname[i],name) == 0) {
       flag = 0;
diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp
index 2ea78311a2..c9d4c00a67 100644
--- a/src/compute_angle_local.cpp
+++ b/src/compute_angle_local.cpp
@@ -33,8 +33,7 @@ using namespace MathConst;
 /* ---------------------------------------------------------------------- */
 
 ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
-  vector(NULL), array(NULL)
+  Compute(lmp, narg, arg)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute angle/local command");
 
diff --git a/src/compute_angle_local.h b/src/compute_angle_local.h
index c3248b242a..cf5d2fbe37 100644
--- a/src/compute_angle_local.h
+++ b/src/compute_angle_local.h
@@ -37,8 +37,6 @@ class ComputeAngleLocal : public Compute {
   int ncount;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_angles(int);
   void reallocate(int);
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index f7917acd2b..6fb1b689b6 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -34,7 +34,7 @@ enum{DIST,ENG,FORCE};
 
 ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  bstyle(NULL), vector(NULL), array(NULL)
+  bstyle(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute bond/local command");
 
diff --git a/src/compute_bond_local.h b/src/compute_bond_local.h
index a6639c2118..7d04515007 100644
--- a/src/compute_bond_local.h
+++ b/src/compute_bond_local.h
@@ -39,8 +39,6 @@ class ComputeBondLocal : public Compute {
   int singleflag;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_bonds(int);
   void reallocate(int);
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index 7b578611f0..fafcf7aee3 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -57,9 +57,10 @@ ComputeChunkAtom *ComputeChunkAtom::cptr;
 
 ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  id_fix(NULL), chunk(NULL), ichunk(NULL), exclude(NULL),
-  chunk_volume_vec(NULL), coord(NULL), chunkID(NULL), idregion(NULL), cfvid(NULL), 
-  hash(NULL), varatom(NULL)
+  chunk_volume_vec(NULL), coord(NULL), ichunk(NULL), chunkID(NULL),
+  cfvid(NULL), idregion(NULL), region(NULL), cchunk(NULL), fchunk(NULL),
+  varatom(NULL), id_fix(NULL), fixstore(NULL), lockfix(NULL), chunk(NULL),
+  exclude(NULL), hash(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute chunk/atom command");
 
diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp
index 024a95d9d1..9680921e5f 100644
--- a/src/compute_cna_atom.cpp
+++ b/src/compute_cna_atom.cpp
@@ -279,7 +279,7 @@ void ComputeCNAAtom::compute_peratom()
       for (n = 0; n < ncommon; n++) bonds[n] = 0;
 
       nbonds = 0;
-      for (jj = 0; jj < ncommon; jj++) {
+      for (jj = 0; jj < ncommon-1; jj++) {
         j = common[jj];
         xtmp = x[j][0];
         ytmp = x[j][1];
diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp
index f50f49fa11..d8fc1b792c 100644
--- a/src/compute_dihedral_local.cpp
+++ b/src/compute_dihedral_local.cpp
@@ -34,8 +34,7 @@ using namespace MathConst;
 /* ---------------------------------------------------------------------- */
 
 ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
-  vector(NULL), array(NULL)
+  Compute(lmp, narg, arg)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute dihedral/local command");
 
diff --git a/src/compute_dihedral_local.h b/src/compute_dihedral_local.h
index 095ed68df3..cc4c16ca79 100644
--- a/src/compute_dihedral_local.h
+++ b/src/compute_dihedral_local.h
@@ -37,8 +37,6 @@ class ComputeDihedralLocal : public Compute {
   int ncount;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_dihedrals(int);
   void reallocate(int);
diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp
index 03a56b2bc4..9b9e165699 100644
--- a/src/compute_displace_atom.cpp
+++ b/src/compute_displace_atom.cpp
@@ -30,7 +30,7 @@ using namespace LAMMPS_NS;
 
 ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  id_fix(NULL), displace(NULL)
+  displace(NULL), id_fix(NULL)
 {
   if (narg != 3) error->all(FLERR,"Illegal compute displace/atom command");
 
diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp
index b9d69dc5b8..05a0cb4291 100644
--- a/src/compute_improper_local.cpp
+++ b/src/compute_improper_local.cpp
@@ -35,8 +35,7 @@ using namespace MathConst;
 /* ---------------------------------------------------------------------- */
 
 ComputeImproperLocal::ComputeImproperLocal(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
-  vector(NULL), array(NULL)
+  Compute(lmp, narg, arg)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute improper/local command");
 
diff --git a/src/compute_improper_local.h b/src/compute_improper_local.h
index 9a3905e057..57f6b9dcf9 100644
--- a/src/compute_improper_local.h
+++ b/src/compute_improper_local.h
@@ -37,8 +37,6 @@ class ComputeImproperLocal : public Compute {
   int ncount;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_impropers(int);
   void reallocate(int);
diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp
index a924cef208..602888af8f 100644
--- a/src/compute_omega_chunk.cpp
+++ b/src/compute_omega_chunk.cpp
@@ -27,8 +27,8 @@ using namespace LAMMPS_NS;
 
 ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL), 
-  angmom(NULL), angmomall(NULL)
+  idchunk(NULL),massproc(NULL),masstotal(NULL),com(NULL),comall(NULL),
+  inertia(NULL),inertiaall(NULL),angmom(NULL),angmomall(NULL),omega(NULL)
 {
   if (narg != 4) error->all(FLERR,"Illegal compute omega/chunk command");
 
@@ -64,6 +64,9 @@ ComputeOmegaChunk::~ComputeOmegaChunk()
   memory->destroy(comall);
   memory->destroy(angmom);
   memory->destroy(angmomall);
+  memory->destroy(inertia);
+  memory->destroy(inertiaall);
+  memory->destroy(omega);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -83,7 +86,7 @@ void ComputeOmegaChunk::init()
 
 void ComputeOmegaChunk::compute_array()
 {
-  int i,j,m,index;
+  int i,j,index;
   double dx,dy,dz,massone;
   double unwrap[3];
 
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index 6ba4b75728..01a317f4a4 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -37,7 +37,7 @@ enum{TYPE,RADIUS};
 
 ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  pstyle(NULL), pindex(NULL), vector(NULL), array(NULL)
+  pstyle(NULL), pindex(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute pair/local command");
 
diff --git a/src/compute_pair_local.h b/src/compute_pair_local.h
index d6c2a12f22..2e01cba3ac 100644
--- a/src/compute_pair_local.h
+++ b/src/compute_pair_local.h
@@ -41,8 +41,6 @@ class ComputePairLocal : public Compute {
   int singleflag;
 
   int nmax;
-  double *vector;
-  double **array;
 
   class NeighList *list;
 
diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp
index 2ce10fdb68..5d454fef84 100644
--- a/src/compute_property_atom.cpp
+++ b/src/compute_property_atom.cpp
@@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
 
 ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  index(NULL), vector(NULL), array(NULL), pack_choice(NULL)
+  index(NULL), pack_choice(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute property/atom command");
 
diff --git a/src/compute_property_atom.h b/src/compute_property_atom.h
index 67fe83eeab..a81f39f6a9 100644
--- a/src/compute_property_atom.h
+++ b/src/compute_property_atom.h
@@ -36,8 +36,6 @@ class ComputePropertyAtom : public Compute {
   int nvalues;
   int nmax;
   int *index;
-  double *vector;
-  double **array;
   double *buf;
   class AtomVecEllipsoid *avec_ellipsoid;
   class AtomVecLine *avec_line;
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index b9472cb45b..d39f8825e3 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -35,7 +35,7 @@ enum{TYPE,RADIUS};
 
 ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  vector(NULL), array(NULL), indices(NULL), pack_choice(NULL)
+  indices(NULL), pack_choice(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute property/local command");
 
diff --git a/src/compute_property_local.h b/src/compute_property_local.h
index 9262bf163f..fb2c5d2d18 100644
--- a/src/compute_property_local.h
+++ b/src/compute_property_local.h
@@ -37,8 +37,6 @@ class ComputePropertyLocal : public Compute {
   int nvalues,kindflag,cutstyle;
 
   int nmax;
-  double *vector;
-  double **array;
   double *buf;
 
   class NeighList *list;
diff --git a/src/create_box.cpp b/src/create_box.cpp
index 94a11c1af8..c7fd98b2b2 100644
--- a/src/create_box.cpp
+++ b/src/create_box.cpp
@@ -158,7 +158,7 @@ void CreateBox::command(int narg, char **arg)
       iarg += 2;
     } else if (strcmp(arg[iarg],"extra/special/per/atom") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
-      atom->maxspecial = force->inumeric(FLERR,arg[iarg+1]);
+      force->special_extra = force->inumeric(FLERR,arg[iarg+1]);
       iarg += 2;
     } else error->all(FLERR,"Illegal create_box command");
   }
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 6c0951597f..0223636a77 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -40,7 +40,14 @@ enum{ONE,RUNNING,WINDOW};
 /* ---------------------------------------------------------------------- */
 
 FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
-  Fix(lmp, narg, arg)
+  Fix(lmp, narg, arg),
+  nvalues(0), nrepeat(0),
+  which(NULL), argindex(NULL), value2index(NULL), ids(NULL),
+  fp(NULL), idchunk(NULL), varatom(NULL),
+  count_one(NULL), count_many(NULL), count_sum(NULL),
+  values_one(NULL), values_many(NULL), values_sum(NULL),
+  count_total(NULL), count_list(NULL),
+  values_total(NULL), values_list(NULL)
 {
   if (narg < 7) error->all(FLERR,"Illegal fix ave/chunk command");
 
@@ -72,7 +79,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   argindex = new int[nargnew];
   ids = new char*[nargnew];
   value2index = new int[nargnew];
-  nvalues = 0;
 
   int iarg = 0;
   while (iarg < nargnew) {
@@ -149,7 +155,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   normflag = ALL;
   scaleflag = ATOM;
   ave = ONE;
-  fp = NULL;
   nwindow = 0;
   biasflag = 0;
   id_bias = NULL;
@@ -433,7 +438,6 @@ FixAveChunk::~FixAveChunk()
   if (fp && me == 0) fclose(fp);
 
   memory->destroy(varatom);
-
   memory->destroy(count_one);
   memory->destroy(count_many);
   memory->destroy(count_sum);
@@ -457,6 +461,24 @@ FixAveChunk::~FixAveChunk()
   }
 
   delete [] idchunk;
+  which = NULL;
+  argindex = NULL;
+  ids = NULL;
+  value2index = NULL;
+  fp = NULL;
+  varatom = NULL;
+  count_one = NULL;
+  count_many = NULL;
+  count_sum = NULL;
+  count_total = NULL;
+  count_list = NULL;
+  values_one = NULL;
+  values_many = NULL;
+  values_sum = NULL;
+  values_total = NULL;
+  values_list = NULL;
+  idchunk = NULL;
+  cchunk = NULL;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/modify.cpp b/src/modify.cpp
index 5c37aa5c56..219c233f2b 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -911,6 +911,7 @@ void Modify::delete_fix(const char *id)
 
 int Modify::find_fix(const char *id)
 {
+  if(id==NULL) return -1;
   int ifix;
   for (ifix = 0; ifix < nfix; ifix++)
     if (strcmp(id,fix[ifix]->id) == 0) break;
@@ -1040,6 +1041,7 @@ void Modify::delete_compute(const char *id)
 
 int Modify::find_compute(const char *id)
 {
+  if(id==NULL) return -1;
   int icompute;
   for (icompute = 0; icompute < ncompute; icompute++)
     if (strcmp(id,compute[icompute]->id) == 0) break;
diff --git a/src/variable.cpp b/src/variable.cpp
index 05c55ec7c6..63fcf1dfda 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -710,6 +710,7 @@ int Variable::next(int narg, char **arg)
 
 int Variable::find(char *name)
 {
+  if(name==NULL) return -1;
   for (int i = 0; i < nvar; i++)
     if (strcmp(name,names[i]) == 0) return i;
   return -1;