Here is a quick overview of how to use the GPU package:
+Here is a quick overview of how to enable and use the GPU package:
-+none
This compute is part of the RIGID package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info.
The fix_modify respa option is supported by +this fix. This allows to set at which level of the r-RESPA +integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various output commands. The scalar is the potential
energy discussed above. The vector is the total force on the group of
diff --git a/doc/html/fix_addtorque.html b/doc/html/fix_addtorque.html
index a746392bae..8926210c55 100644
--- a/doc/html/fix_addtorque.html
+++ b/doc/html/fix_addtorque.html
@@ -178,6 +178,9 @@ needed so that the
+ The fix_modify respa option is supported by
+this fix. This allows to set at which level of the r-RESPA
+integrator the fix is adding its torque. Default is the outermost level. This fix computes a global scalar and a global 3-vector, which can be
accessed by various output commands.
The scalar is the potential energy discussed above. The vector is the
diff --git a/doc/html/fix_aveforce.html b/doc/html/fix_aveforce.html
index 40d26663d8..a03272b7b1 100644
--- a/doc/html/fix_aveforce.html
+++ b/doc/html/fix_aveforce.html
@@ -201,8 +201,10 @@ more instructions on how to use the accelerated styles effectively. No information about this fix is written to binary restart files. None of the fix_modify options
-are relevant to this fix. No information about this fix is written to binary restart files. The fix_modify respa option is supported by this
+fix. This allows to set at which level of the r-RESPA
+integrator the fix is adding its forces. Default is the outermost level. This fix computes a global 3-vector of forces, which can be accessed
by various output commands. This is the
total force on the group of atoms before the forces on individual
diff --git a/doc/html/fix_drag.html b/doc/html/fix_drag.html
index f067ce4a9b..c464c735a2 100644
--- a/doc/html/fix_drag.html
+++ b/doc/html/fix_drag.html
@@ -159,8 +159,10 @@ in the simulation. No information about this fix is written to binary restart files. None of the fix_modify options
-are relevant to this fix. No information about this fix is written to binary restart files. The fix_modify respa option is supported by this
+fix. This allows to set at which level of the r-RESPA
+integrator the fix is adding its forces. Default is the outermost level. This fix computes a global 3-vector of forces, which can be accessed
by various output commands. This is the
total force on the group of atoms by the drag force. The vector
diff --git a/doc/html/fix_efield.html b/doc/html/fix_efield.html
index e68661400a..c724217123 100644
--- a/doc/html/fix_efield.html
+++ b/doc/html/fix_efield.html
@@ -231,6 +231,9 @@ quantity but is needed so that the fix_modify respa option is supported by this
+fix. This allows to set at which level of the r-RESPA
+integrator the fix adding its forces. Default is the outermost level. This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various output commands. The scalar is the potential
energy discussed above. The vector is the total force added to the
diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html
index f8cc9ef5c9..e770f8e7fe 100644
--- a/doc/html/fix_gravity.html
+++ b/doc/html/fix_gravity.html
@@ -228,6 +228,9 @@ more instructions on how to use the accelerated styles effectively. The fix_modify energy option is supported by this
fix to add the gravitational potential energy of the system to the
system’s potential energy as part of thermodynamic output. The fix_modify respa option is supported by this
+fix. This allows to set at which level of the r-RESPA
+integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar which can be accessed by various
output commands. This scalar is the
gravitational potential energy of the particles in the defined field,
diff --git a/doc/html/fix_indent.html b/doc/html/fix_indent.html
index c8a8ce8bb9..366694bd8a 100644
--- a/doc/html/fix_indent.html
+++ b/doc/html/fix_indent.html
@@ -283,6 +283,9 @@ fix 1 all indent $k sphere ...
fix to add the energy of interaction between atoms and the indenter to
the system’s potential energy as part of thermodynamic output. The energy of each particle interacting
with the indenter is K/3 (r - R)^3. The fix_modify respa option is supported by this
+fix. This allows to set at which level of the r-RESPA
+integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar energy and a global 3-vector of
forces (on the indenter), which can be accessed by various output commands. The scalar and vector values
calculated by this fix are “extensive”.
Restart, fix_modify, output, run start/stop, minimize info
-Restart, fix_modify, output, run start/stop, minimize info
-
temp value = compute ID that calculates a temperature
press value = compute ID that calculates a pressure
energy value = yes or no
+respa value = 1 to max respa level or 0 (= outmost level)
Examples
fix_modify 3 temp myTemp press myPress
fix_modify 1 energy yes
+fix_modify tether respa 2
For fixes that set or modify forces, it may be possible to select at +which r-RESPA level the fix operates via the respa +keyword. The RESPA level at which the fix is active can be selected. +This is a number ranging from 1 to the number of levels. If the RESPA +level is larger than the current maximum, the outermost level will be +used, which is also the default setting. This default can be restored +using a value of 0 for the RESPA level. The affected fix has to be +programmed to support this feature; if not, fix_modify will report +an error. Active fixes with a custom RESPA level setting are reported +with their specified level at the beginning of a r-RESPA run.
The option defaults are temp = ID defined by fix, press = ID defined -by fix, energy = no.
+by fix, energy = no, respa = 0.The fix_modify respa option is supported by these +fixes. This allows to set at which level of the r-RESPA +integrator a fix is adding its forces. Default is the outermost level.
This fix calculates a global scalar which can be accessed by various output commands. The scalar is the potential energy change due to this fix. The scalar value calculated diff --git a/doc/html/fix_qeq_comb.html b/doc/html/fix_qeq_comb.html index 52302b0950..c7382d021d 100644 --- a/doc/html/fix_qeq_comb.html +++ b/doc/html/fix_qeq_comb.html @@ -199,8 +199,11 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to binary restart files. None of the fix_modify options -are relevant to this fix.
+No information about this fix is written to binary restart files.
+The fix_modify respa option is supported by this +fix. This allows to set at which level of the r-RESPA +integrator the fix is performing charge equilibration. Default is +the outermost level.
This fix produces a per-atom vector which can be accessed by various output commands. The vector stores the gradient of the charge on each atom. The per-atom values be accessed diff --git a/doc/html/fix_restrain.html b/doc/html/fix_restrain.html index d48a6fa861..34228509c9 100644 --- a/doc/html/fix_restrain.html +++ b/doc/html/fix_restrain.html @@ -267,6 +267,9 @@ current dihedral angle phi is equal to phi0.
The fix_modify energy option is supported by this fix to add the potential energy associated with this fix to the system’s potential energy as part of thermodynamic output.
+The fix_modify respa option is supported by this +fix. This allows to set at which level of the r-RESPA +integrator the fix is adding its forces. Default is the outermost level.
Note
If you want the fictitious potential energy associated with the diff --git a/doc/html/fix_setforce.html b/doc/html/fix_setforce.html index 7c92b7dc69..35b7f76194 100644 --- a/doc/html/fix_setforce.html +++ b/doc/html/fix_setforce.html @@ -204,8 +204,13 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to binary restart files. None of the fix_modify options -are relevant to this fix.
+No information about this fix is written to binary restart files.
+The fix_modify respa option is supported by +this fix. This allows to set at which level of the r-RESPA +integrator the fix is setting the forces to the desired values; on all +other levels, the force is set to 0.0 for the atoms in the fix group, +so that setforce values are not counted multiple times. Default is to +to override forces at the outermost level.
This fix computes a global 3-vector of forces, which can be accessed
by various output commands. This is the
total force on the group of atoms before the forces on individual
diff --git a/doc/html/fix_shardlow.html b/doc/html/fix_shardlow.html
index e54353f7eb..3f9d81d749 100644
--- a/doc/html/fix_shardlow.html
+++ b/doc/html/fix_shardlow.html
@@ -180,6 +180,8 @@ integration, e.g.
+ This fix also requires atom_style dpd to be used
+due to shared data structures.
None of the fix_modify options are relevant to this -fix.
+The fix_modify respa option is supported by +this fix. This allows to set at which level of the r-RESPA +integrator the fix is adding its forces. Default is the outermost level.
This fix computes a vector list of 7 quantities, which can be accessed
by various output commands. The
quantities in the vector are in this order: the x-, y-, and
diff --git a/doc/html/fix_spring.html b/doc/html/fix_spring.html
index b02b7b0544..a1d40fbf68 100644
--- a/doc/html/fix_spring.html
+++ b/doc/html/fix_spring.html
@@ -222,6 +222,9 @@ way, as explained on the
The fix_modify respa option is supported by this +fix. This allows to set at which level of the r-RESPA +integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various output commands. The scalar is the spring energy = 0.5 * K * r^2.
diff --git a/doc/html/fix_spring_chunk.html b/doc/html/fix_spring_chunk.html index d48b7b6973..7373fd8e56 100644 --- a/doc/html/fix_spring_chunk.html +++ b/doc/html/fix_spring_chunk.html @@ -173,6 +173,9 @@ atom.The fix_modify energy option is supported by this fix to add the energy stored in all the springs to the system’s potential energy as part of thermodynamic output.
+The fix_modify respa option is supported by this +fix. This allows to set at which level of the r-RESPA +integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various output commands. The scalar is the energy of all the springs, i.e. 0.5 * K * r^2 per-spring.
diff --git a/doc/html/fix_spring_rg.html b/doc/html/fix_spring_rg.html index 47c35ddcb7..aeaa3bece4 100644 --- a/doc/html/fix_spring_rg.html +++ b/doc/html/fix_spring_rg.html @@ -174,6 +174,9 @@ are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization. +The fix_modify respa option is supported by this +fix. This allows to set at which level of the r-RESPA +integrator the fix is adding its forces. Default is the outermost level.
The fix_modify energy option is supported by this fix to add the energy stored in the per-atom springs to the system’s potential energy as part of thermodynamic output.
+The fix_modify respa option is supported by +this fix. This allows to set at which level of the r-RESPA +integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various output commands. The scalar is an energy which is the sum of the spring energy for each atom, where the diff --git a/doc/html/fix_viscous.html b/doc/html/fix_viscous.html index b097a4c1e6..5bf3e54e0a 100644 --- a/doc/html/fix_viscous.html +++ b/doc/html/fix_viscous.html @@ -202,6 +202,9 @@ easily be used as a thermostat.
are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. +The fix_modify respa option is supported by this +fix. This allows to set at which level of the r-RESPA +integrator the fix is modifying forces. Default is the outermost level.
The forces due to this fix are imposed during an energy minimization, invoked by the minimize command. This fix should only be used with damped dynamics minimizers that allow for diff --git a/doc/html/fix_wall.html b/doc/html/fix_wall.html index 2c601bc4a5..8f3ac46551 100644 --- a/doc/html/fix_wall.html +++ b/doc/html/fix_wall.html @@ -362,6 +362,9 @@ perturbation on the particles:
The fix_modify energy option is supported by this fix to add the energy of interaction between atoms and each wall to the system’s potential energy as part of thermodynamic output.
+The fix_modify respa option is supported by this +fix. This allows to set at which level of the r-RESPA +integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar energy and a global vector of forces, which can be accessed by various output commands. Note that the scalar energy is the sum of interactions with all defined walls. If you want the diff --git a/doc/html/fix_wall_region.html b/doc/html/fix_wall_region.html index 2ef30494f3..4f24bee99a 100644 --- a/doc/html/fix_wall_region.html +++ b/doc/html/fix_wall_region.html @@ -287,6 +287,9 @@ region surface (r > 0).
The fix_modify energy option is supported by this fix to add the energy of interaction between atoms and the wall to the system’s potential energy as part of thermodynamic output.
+The fix_modify respa option is supported by this +fix. This allows to set at which level of the r-RESPA +integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar energy and a global 3-length vector of forces, which can be accessed by various output commands. The scalar energy is the sum of energy interactions for all particles interacting with the wall diff --git a/doc/html/pair_dpd_fdt.html b/doc/html/pair_dpd_fdt.html index a06112c8fc..120496b3cd 100644 --- a/doc/html/pair_dpd_fdt.html +++ b/doc/html/pair_dpd_fdt.html @@ -235,6 +235,9 @@ stored by ghost atoms.
Pair style dpd/fdt/energy requires atom_style dpd to be used in order to properly account for the particle internal energies and temperatures.
+Pair style dpd/fdt currently also requires +atom_style dpd to be used in conjunction with +fix shardlow due to shared data structures.
-none
All the granular pair styles are part of the GRANULAR package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.
These pair styles require that atoms store torque and angular velocity diff --git a/doc/html/run_style.html b/doc/html/run_style.html index 8f5cc37612..9ef0e69f67 100644 --- a/doc/html/run_style.html +++ b/doc/html/run_style.html @@ -267,6 +267,8 @@ forces are computed where angle forces are, improper forces are computed where dihedral forces are, pair forces are computed at the outermost level, and kspace forces are computed where pair forces are. The inner, middle, outer forces have no defaults.
+For fixes that support it, the rRESPA level at which a given fix is +active, can be selected through the fix_modify command.
The inner and middle keywords take additional arguments for cutoffs that are used by the pairwise force computations. If the 2 cutoffs for inner are 5.0 and 6.0, this means that all pairs up to diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 392653b423..1809553926 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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40,441,443,444,445,458,459,477,480,481,482,484,485,500,507,518,524],centimet:523,centr:237,central:[3,63,74,80,81,100,117,127,134,152,176,259,297,298,321,333,365,387,446,452,458,459,485,497],centro:[],centroid:[3,300,484,507],cerda:377,ceriotti2:247,ceriotti:[13,247,252],certain:[1,2,3,6,8,12,16,39,75,124,128,131,182,202,203,205,217,218,219,221,222,227,243,244,317,320,336,349,360,368,376,389,426,448,459,483,499,503,518,524],certainli:251,cerutti:378,cfg:[3,6,7,9,13,202,204,205,206,207],cfile:459,cfl:[140,324],cfor:323,cg_type:461,cgiko:[],cgikot:[],cgkio:[],cgko:[],cgkot:[],cgo:[],cgot:[],ch2:321,ch2lmp:[],ch3:321,ch5md:204,chain3:389,chain:[],challeng:[6,323],chalopin:312,champaign:[250,377,378,440],chan:446,chandler:[394,416],chandrasekhar:[6,431],chang:[],change_box:[],changeabl:202,channel:[4,212],chapter:[300,378],charact:[2,3,6,12,37,41,56,65,198,202,203,205,206,207,209,224,240,241,306,314,318,360,387,392,418,420,430,450,451,456,458,459,466,478,479,494,495,499,504,505,524,527,528,529],character:[6,70,74,117,127,152,467,492,511],characterist:[254,335,344],charg:[1,3,4,5,6,7,9,11,14,40,86,95,96,124,130,177,178,202,203,207,209,210,211,216,231,236,245,306,308,309,310,314,337,350,377,378,387,400,402,408,409,411,412,416,418,419,426,431,435,439,453,458,459,466,476,482,483,485,486,488,489,497,498,502,507,509,518,523,524],charmm2lammp:13,charmm:[],chartreus:206,cheap:335,cheaper:[235,422,460],check:[3,6,8,9,11,12,14,16,38,39,41,58,75,99,198,199,216,224,225,226,231,242,245,251,252,303,316,321,335,343,345,350,358,360,373,376,386,387,388,389,390,393,415,427,430,448,459,490,492,494,495,497,505,511,514,515,524],checkf:198,checkout:519,checkqeq:459,checku:198,chem:[6,13,19,20,24,39,40,43,45,46,95,96,117,123,153,184,185,195,220,229,234,237,246,247,254,256,269,270,271,293,294,300,304,307,309,317,322,323,335,338,339,342,343,344,345,352,361,370,372,377,378,385,388,395,400,404,405,408,409,410,412,413,414,418,421,422,424,425,431,435,436,439,443,447,448,450,451,453,466,475,483,506,509,511,518],chemic:[9,40,88,89,130,172,177,202,203,215,216,245,308,313,314,342,378,420,451,458,459,471,479],chemistri:[307,308,310,395,399,418,458,459],chen:347,cheng:408,chenoweth:[458,459],chenoweth_2008:[458,459],chi:[102,167,201,297,298,308,310,373,419,422,525],chiefli:457,child:8,chip:[7,9,16,17,393,510],chipot:229,chiral:370,chmod:[11,12],cho:443,chocol:[7,206],choic:[3,6,9,12,14,15,17,40,41,54,95,153,156,157,171,182,198,218,224,227,230,231,247,253,256,268,270,300,304,308,317,342,371,378,384,385,388,390,393,426,439,448,454,497,506,507,510,511,517,518,523],choos:[1,3,6,7,8,9,12,15,16,17,28,39,54,95,128,168,169,205,225,226,227,228,231,242,253,256,268,270,272,273,274,275,276,277,278,303,304,322,335,339,353,377,378,385,486,492,494,506,512],chose:[480,482],chosen:[2,3,6,12,16,152,178,181,190,198,205,211,216,228,231,242,245,246,254,256,268,270,275,300,303,314,335,339,342,343,348,350,351,357,378,379,385,393,414,418,423,430,433,461,480,492,506,511,512,518],chri:176,christian:[7,9,16],christoph:7,chunk:[],chunkid:[69,79,86,98,103,114,116,125,158,173,175,218,332],chute:[4,9,10,248],ciccotti:321,cieplak:[6,184,509],cii:219,cij:219,ciko:[],circl:[42,75,330],circular:[3,6,156,200],circumst:17,circumv:[100,117,312],citat:[],cite:[3,7,8,12,253,466],civ:9,ckio:[],cko:[],cl1:177,clarendon:[28,412],clarifi:[7,480,482],clariti:360,clark:453,class2:[],classic:[0,3,5,6,7,8,9,243,300,307,312,347,372,418],classifi:[476,485],claus:495,clean:[6,12,14,16,505],cleanli:[496,528],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:501,click:[2,11,21,36,44,55,178,186,197,205,250,362,371,388,406,476,519],client:[250,252],climb:[269,388,511],clinic:[7,13],clo:[167,201,525],clock:[12,492,511],clockwis:[184,353],clone:519,close:[3,6,11,12,13,39,41,70,75,153,181,202,226,227,228,247,254,256,270,286,293,317,321,353,356,376,378,381,384,385,388,393,395,399,409,410,429,443,448,450,451,458,462,464,478,482,501,507,518,519,521],closer:[3,10,41,127,176,201,202,224,228,232,344,388],closest:[226,297,298,317,350,422,460,475,486],cloud:[466,518],clovertown:17,clsuter:76,clump1:[302,317],clump2:[302,317],clump3:[302,317],clump:317,cluster:[],clutter:3,cmap:497,cmatrix:247,cmax:443,cmd:[11,12,300,508],cmdarg:11,cmin:443,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:13,cnrs:9,cnt:[426,501],co2:[40,177,318,321,387,420],coars:[7,9,10,28,35,40,54,190,241,302,317,318,335,420,424,451,461,479,506,509],coarser:[378,524],coarsest:152,code:[],coeff:[3,7,8,12,20,21,32,44,50,184,185,186,191,361,362,368,406,426,430,448,463,465,468,497,526],coeffcient:497,coeffici:[],coefficienct:413,coefficient0:416,coefficient1:416,coeffieci:[6,397,429],coeffincientn:416,coexist:[245,418],cohes:[6,419,443],coincid:[134,356,404,440,441,492],colberg:204,cold:[6,163,245,249,389,518],coldest:343,coleman8:9,coleman:[9,130,177,319],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,158,166,173,175,178,202,203,206,218,229,259,266,302,312,315,317,358,377,387,389,407,497,504,510,516,529],collid:[235,335,357],colliex:177,collinear:[3,302],collis:[3,256,335,353,357,415,423,489],colllis:335,colloid:[],colombo:39,colon:[207,358,498],color1:206,color2:206,color:[3,9,41,202,205,206,224,246,307,312],column:[3,6,9,12,13,42,65,68,69,70,71,73,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,259,267,268,307,317,336,337,347,357,395,421,425,458,459,498,512,514,524],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:393,comb3:[],comb:[],comb_1:309,comb_2:309,combiant:410,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,202,205,215,221,237,245,250,259,262,270,286,292,300,306,322,339,348,356,359,361,377,378,380,385,393,407,409,410,414,418,419,420,426,438,439,467,477,480,482,483,485,488,500,505,510,518,524,526],come:[],comfort:[12,13],comid:332,comit:519,comm:[0,3,11,12,63,77,204,250,252,253,378,388,393,413,448,455,478,479,499],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,37,56,184,198,202,240,241,254,317,318,347,387,388,394,416,417,419,420,430,443,450,451,452,459,466,467,477,478,479,480,481,482,485,494,495,497,518,519,524],commerci:7,commit:[9,519],commmand:[3,6,12,61,118,294,429,491,492,494,511,528],common:[],commonli:[3,6,9,12,16,24,59,61,115,117,180,202,205,207,372,424,433,467,480,482,497,500,509],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,205,206,224,225,226,228,229,230,250,252,256,258,259,260,270,299,306,308,309,310,317,322,335,347,358,375,377,389,390,391,393,414,415,454,490,494,495,506,507,524,527,529],communc:377,comp:[7,204,252,253,286,292,321,378,388,418,448,455,460,474,478,479,481],compact:[65,209,406,476],compani:[5,7],compar:[1,3,4,6,8,12,16,39,94,121,130,161,177,186,197,206,234,308,358,360,377,378,386,388,443,466,492,511,512,518,523],comparison:[],comparison_of_nvidia_graphics_processing_unit:[],compart:382,compass:[7,9,20,21,36,43,44,55,185,186,197,361,362,371,405,476],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,202,207,211,217,218,219,221,222,224,237,299,311,339,342,349,352,355,377,393,427,446,448,478,494,495,524],compens:[6,225,226,315,389,418],compet:346,competit:378,compil:[3,7,8,9,12,13,14,15,16,17,18,176,202,204,205,207,250,346,378,393,446,497,498,502,518,524],compl:16,complain:[11,12,16],complement:443,complementari:[7,409,431],complet:[3,6,9,11,12,14,41,61,75,206,224,229,259,300,303,306,335,346,348,359,360,376,388,393,419,463,465,484,492,497,502,505,509,511,514,518,524],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,256,286,330,356,375,388,418,446,478,479,495,497,500,524],compli:[342,346],complic:[6,7,9,12,13,129,216,245,495],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,243,248,252,253,256,259,261,262,266,267,269,270,271,275,276,277,278,290,291,293,295,296,299,300,301,304,315,317,320,321,323,327,328,331,335,338,339,340,342,349,350,355,356,357,377,380,385,386,387,388,393,413,418,423,440,441,463,465,466,467,497,498,507,515,524,525],componenet:6,componennt:129,composit:[6,216,256,416],compound:[408,418,419,485],compres:[75,125,218],compress:[],compris:[40,356,420,460,484],compton:[130,177],comptu:3,compuat:378,comput:[],computation:[3,6,225,226,347,399],computational:518,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,319],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,528],concav:356,concentr:[75,241,318,416,420,451,479],concept:[6,158,168,218,506],conceptu:[3,6,75,166,228,230,388,409,426,443,502],concern:[6,77,95,204,246],concetr:75,concis:[11,346],conclud:12,concret:8,concurr:[15,378,524],conden:[347,480,482],condens:[6,160,347,395,411,416,431,485],condit:[],conducit:6,conduct:[],cone:500,confer:446,confid:[3,511],config:[12,202,494],configfil:229,configur:[1,2,6,12,14,16,37,61,134,180,198,201,202,205,209,228,229,230,231,235,245,252,253,284,300,308,346,375,386,388,395,399,417,443,446,477,480,482,485,492,497,499,500,511,519],confin:[497,511],conflict:[3,12,40,203,448,495,519],conform:[3,6,13,61,227,228,269,316,323,346,370,388,418,509],confus:[3,485],conjuct:[9,413],conjug:[7,8,253,385,418,458,459],conjunct:[6,7,75,94,95,125,161,166,172,178,182,206,210,211,253,256,260,284,303,304,308,309,310,312,317,322,335,343,350,355,377,378,388,400,402,406,409,413,418,425,431,448,453,461,483,497,500,504,518,529],connect:[3,6,9,95,163,181,227,250,302,317,321,331,382,388,410,423,458,459,475,482,494,495,497,501,518],conner:395,connor:395,conput:3,consecut:[3,11,12,39,75,178,206,210,211,231,250,251,409,431,435,492,498,500],consequ:[1,6,216,347,430,511],conserv:[3,9,28,209,216,227,234,235,246,249,253,255,256,260,266,268,270,284,286,317,321,322,338,339,343,350,351,355,388,412,413,414,423,437,466,506,511],consid:[6,74,75,82,95,126,129,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,257,271,299,317,342,343,346,347,350,378,406,418,426,459,460,466,475,492,493,495,498,499,500,502,505,507,515,518,524],consider:[6,8,253,254,338,339,340,393,506],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,201,207,212,213,218,230,231,234,236,243,246,253,254,255,267,270,272,273,274,275,276,277,278,279,280,282,283,284,285,288,289,290,291,293,294,295,304,307,312,314,315,316,317,318,338,339,340,341,351,377,378,380,382,387,388,393,395,399,401,407,409,418,422,426,429,440,441,443,446,448,450,451,460,463,465,466,478,479,486,495,497,498,499,500,501,502,509,518,524],consistent_fe_initi:215,consit:317,constant:[],constantli:237,constitu:[3,6,259,317,352,356,407,460],constitut:[463,465],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,245,246,251,259,262,264,286,292,302,303,315,317,321,333,343,350,386,387,418,502,509,518],constraint:[],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,228,270,299,316,318,356,389,393,412,446,448,475,477,478,479,500,501,516,524],constructor:[8,11],consult:459,consum:[1,312,454,524],consumpt:375,contact:[],contact_stiff:[462,464],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,241,247,251,252,253,256,268,284,297,298,299,302,303,305,306,307,310,314,317,318,319,324,335,342,346,347,356,357,360,376,378,387,388,391,392,394,395,396,399,408,409,412,416,417,418,420,426,427,443,446,450,451,452,456,457,458,459,467,477,478,479,480,481,482,483,485,492,493,494,495,497,498,499,500,502,504,506,509,511,512,514,515,518,519,524,527,529],content:[4,8,9,12,17,459,513,515],context:[3,6,8,12,16,127,128,206,225,226,231,302,314,351,385,488,497,504,513,523,524,525],contibut:74,contigu:494,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,245,246,247,249,250,251,253,254,255,261,267,268,270,272,273,274,275,276,277,278,290,291,293,294,295,301,303,306,307,317,319,323,334,335,337,344,345,347,353,356,360,376,392,393,399,413,415,433,436,458,459,460,463,465,481,492,495,497,499,500,505,511,512,514,515,524,527],continuum:[6,7,9,215,347,463,465],contour_integr:215,contract:[61,228,230,270,304,317],contradictori:3,contrain:321,contraint:284,contrari:[247,254],contrast:[1,6,42,55,66,160,163,203,230,358,463,465,488,528],contrib:347,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,245,253,256,259,260,265,271,293,294,302,303,311,314,317,319,321,349,377,386,388,396,413,415,416,418,426,440,441,446,448,458,459,466,509,515,518,519],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,202,203,205,209,215,216,224,228,229,230,249,250,253,254,270,272,273,274,275,276,277,278,304,309,317,318,325,326,338,339,340,347,351,375,377,390,418,422,446,458,459,462,464,477,482,492,494,506,512,513],control_typ:215,controlfil:459,convect:99,conveni:[6,12,28,202,207,222,319,380,467,483,519,524],convent:[3,8,28,189,196,197,203,206,316,331,359,416,418,524],converg:[3,6,41,96,202,203,205,207,212,224,227,228,236,243,275,286,292,307,309,312,316,321,384,385,386,388,408,409,431,466,492,504,511],convers:[3,8,152,205,206,216,219,304,377,409,410,411,418,431,435,439,453,495,511,523],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,202,205,206,219,222,268,303,306,358,361,363,367,370,380,388,394,416,446,480,482,489,495,497,498,499,504,514,518,523,524,527,529],convex:[42,356],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,249,315],cooordin:[202,203],cooper:[5,7],coord123:125,coord1:[3,125,218],coord2:[3,125,218],coord3:[3,125,218],coord:[],coordb:466,coordbb:466,coordiat:386,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,243,245,248,249,250,251,252,253,254,267,269,270,272,273,274,276,277,278,293,296,297,298,299,302,303,304,314,315,317,320,321,323,328,331,332,333,334,335,337,345,346,347,354,355,357,358,380,386,387,388,393,394,395,398,417,466,492,497,498,499,500,502,505,507,511,518,524,525],coordn:[125,218],coords:466,copi:[0,3,4,8,9,11,12,14,16,40,131,205,347,388,406,458,495,519],copper:489,coproccesor:15,coprocessor:[1,7,9,15,16,393,510],coproprocessor:16,copy_arrai:8,copyright:[7,8,302],coral:206,core:[],core_shel:160,cores:518,coreshel:[4,6,9],coreshell:[],cornel:[6,184,509],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,205,356,357,380,484,497,519],cornflowerblu:206,cornsilk:206,corp:9,corpor:15,corr:408,correct:[3,6,9,11,12,15,16,61,86,95,96,112,113,118,121,127,160,165,172,184,203,205,230,237,245,247,253,270,271,293,302,304,307,346,352,356,377,388,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,497,512,515,518,519],correction_max_iter:215,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,243,254,264,270,271,310,317,321,331,334,353,356,388,389,393,411,441,446,494,495,497,507,519,523,525],correl:[],correpond:[240,241],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,241,243,244,248,253,256,257,266,267,268,270,272,273,274,275,276,277,278,279,280,284,288,290,291,293,295,297,299,300,304,309,317,318,320,321,342,352,353,355,356,357,359,361,362,363,364,366,367,370,372,378,383,385,387,388,394,395,397,400,401,402,403,404,405,406,407,408,409,412,413,416,417,418,419,420,421,422,423,424,425,426,429,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,451,452,453,455,456,458,459,460,461,466,467,468,477,478,479,480,481,482,483,485,487,488,489,492,494,495,497,498,500,510,511,512,514,515,518,524],correspondingli:[440,441,506],corrupt:3,cosin:[],cosineshift:26,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,205,206,218,224,225,226,242,270,309,347,377,378,391,409,431,435,446,448,477,494,506],costheta0:[477,480,482,485],costheta:456,costli:[11,96,247,389],couett:4,coul:[],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,243,252,306,307,308,312,315,317,320,335,336,342,346,347,348,352,356,358,360,368,374,376,384,386,389,393,395,396,421,425,426,429,458,459,493,494,495,497,499,501,504,505,512,513,518,524,525],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,308,310,348,377,378,386,393,400,402,403,404,405,408,409,410,411,412,418,423,424,426,431,435,439,442,448,453,458,459,461,466,476,482,483,485,488,502,509,515,518,523],coulommb:6,cound:3,count:[1,3,6,8,11,12,15,41,65,71,81,99,125,127,128,166,176,182,184,212,213,216,218,221,223,224,231,236,242,245,251,270,284,303,321,338,339,356,378,386,387,388,390,393,421,425,448,515,524],counter:[3,353,492,503,505,511],counteract:245,counterbal:[237,249],counterbalanc:28,counterclockwis:184,counterpart:[202,492],counterproduct:17,coupl:[],couple:[4,6,11,12],courant:324,cours:[3,8,138,140,172,202,210,211,246,316,331,346,352,354,355,357,358,378,440,468,494,497,510,518,524,527],courtesi:380,cov:466,coval:[6,9,28,418,443,466,518],covari:247,cover:[6,12,75,198,206,215,256,418,484],coverag:75,cpc:252,cpp:[1,3,6,8,9,11,12,13,95,202,210,211,243,321],cpu:[1,3,9,10,12,14,15,16,17,65,75,206,220,234,254,348,375,378,393,406,476,492,510,511,514,515,516,524],cpuremain:515,cpus:12,cr2:177,cr3:177,crack:[4,389],crada:[5,7],crai:[5,7,13,17,202],crash:[3,12,389,518],craympi:393,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:302,criteria:[3,127,179,205,206,225,226,227,265,386,455,484,499,502,524],criterion:[12,41,133,178,181,216,224,227,245,284,309,324,353,358,386,388,408,418,423,466,502,511,512],criterioni:511,critic:[6,48,49,268,342,347,386],crmax:75,crmin:75,cross:[3,12,21,75,97,129,156,176,186,202,203,205,217,226,230,267,269,293,317,327,331,334,343,350,362,380,388,404,413,415,416,424,425,426,431,433,435,456,461,463,465,480,482,489,497,501,507,527],crossov:1,crossterm:497,crozier:[0,7,13],crucial:307,crystal:[3,4,6,13,77,117,297,298,299,345,380,389,497,501,515,518],crystallin:[6,113,299,380,481,518],crystallis:342,crystallogr:[130,177],crystallograph:[380,515],crystallographi:[130,177,380],cs1:177,cs_chunk:6,cs_im:[40,497],cs_re:[40,497],csanyi:[152,457,467],cscl:443,csequ:6,csh:[11,12,406],cshrc:[11,12],csic:[417,477,480,482,485],csinfo:6,csisi:[417,477,480,482,485],csld:[],cst:416,cstherm:6,cstyle:494,csvr:[],ctcm:[394,416],ctemp_core:234,cterm:323,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:443,cube:[6,176,181,234,356,380,518],cubes:[41,224],cubic:[],cuda:[],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cufft:[],cuh:399,cummul:[3,6,222,225,226,227,229,242,247,253,255,335,338,339,340,341,343,350,425,515],cumul:[6,216,218,221,235,245,253,268,270,275,284,317,319,388],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,112,113,119,127,128,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,243,245,247,250,251,253,259,267,270,271,276,277,278,284,286,290,291,292,293,295,302,303,308,309,311,314,315,316,317,318,321,322,323,324,325,326,327,328,330,332,333,334,335,338,339,340,346,347,350,351,352,353,354,355,357,358,360,375,376,377,378,381,382,383,385,386,387,388,393,399,406,408,412,416,418,419,423,426,427,430,440,441,443,444,445,448,456,458,459,462,463,464,465,468,480,482,483,486,492,493,494,495,497,498,499,500,501,503,504,505,507,509,511,512,514,515,519,524,525,526,527,528,529],curv:[6,178,245,286,292,299],curvatur:[422,460,489],custom:[],cut0:495,cut1:506,cut2:506,cut:[],cuthi:[297,298,310],cutinn:[401,440,441],cutlo:[297,298,310],cutmax:456,cutoff1:[405,412,431,435,439,442,453,461],cutoff2:[400,402,403,405,411,412,431,435,439,442,453,461,483],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,226,227,232,240,241,297,298,307,308,310,312,314,317,322,335,348,352,356,358,375,377,378,386,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,466,467,468,469,470,471,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,495,499,502,506,518,524],cutoffa:417,cutoffc:417,cuu3:416,cval:177,cvd:342,cvel:323,cvff:[],cwiggl:[3,267,352,355,357,524],cyan:[2,205,206],cycl:[3,245,268,270,271,275],cyclic:[3,184,198],cygwin:12,cylind:[3,4,75,205,218,251,292,303,353,356,382,500],cylinder_d:382,cylindr:[6,251,331,353],cypress:393,cyrot:399,cyrstal:299,d3q15:256,d3q19:256,d_double_double:14,d_e:347,d_flag2:306,d_flag:306,d_name:[124,202,306,337,507],d_single_double:14,d_single_single:14,d_sx:306,d_sy:306,d_sz:306,daan:345,dai:12,daili:12,daivi:293,damag:[],dammak:312,damp:[3,6,209,214,253,254,255,260,270,271,275,292,304,307,308,312,317,338,339,351,353,354,385,386,388,400,402,404,409,412,418,423,431,439,453,461,476,483,511,518],damp_com:254,damp_drud:254,dampen:[317,518],dampflag:[353,423],dan:16,danger:[3,12,245,358,413,515],dangl:181,daniel:9,darden:[378,412],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:308,dash:[423,514],dat:[6,99,198,215,493],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,319],dataset:319,datatyp:3,date:[0,4,6,12,13,201,458,459,524],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,42,68,71,73,84,102,119,126,202,219],davenport:442,davi:352,david:[9,18,377,378,480,482],daw:[416,456],dbg:[],dcd:[3,6,7,202,204,205,206,207,300,498,502],dcs:9,ddim:201,deactiv:439,dealt:252,debug:[6,7,11,12,13,16,57,130,134,177,178,300,305,375,377,427,448,486,495,496,504,507,514,524],deby:[],decai:[100,409,489],decid:[3,6,12,15,75,267,306,317,348,512,519],decipher:380,deck:306,declar:204,declin:335,decod:205,decompos:[95,467],decomposit:[3,5,7,17,64,215,300,322],decoupl:[6,518],decreas:[3,202,203,212,213,220,227,230,236,237,243,245,253,346,377],decrement:323,deepli:374,deeppink:206,deepskyblu:206,def:[12,13,495],defaul:63,defect:[6,74,176,446],defgrad:[],defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,241,243,244,245,248,251,252,253,254,255,256,265,267,269,270,271,272,273,274,275,276,277,278,280,281,282,285,288,289,290,291,293,294,295,297,298,299,300,302,303,304,306,308,310,315,317,318,319,320,321,324,328,332,333,335,337,338,339,340,341,343,344,345,347,349,350,352,353,354,355,356,357,358,360,361,362,363,364,365,366,367,370,371,372,373,375,377,378,380,383,385,386,387,388,389,390,391,392,393,395,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,417,418,420,421,422,423,424,425,426,427,429,431,432,433,434,435,436,437,438,439,440,441,442,446,447,448,449,450,451,452,453,455,456,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,497,498,500,501,502,503,506,507,508,509,511,512,514,515,518,520,521,522,523,524,525,526],definit:[2,3,6,8,12,13,82,85,127,152,206,218,219,220,221,222,230,239,251,275,319,337,349,352,355,357,359,371,375,387,396,399,407,414,418,429,456,463,465,467,484,495,497,499,506,508,523,524],defint:515,deform:[],deg2theta:177,deg:518,degener:[3,302],degrad:[8,17,299,378,506],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,245,247,248,253,254,259,270,271,275,276,277,278,290,291,293,295,300,302,316,317,321,338,339,340,345,361,363,367,370,372,386,412,416,425,507,515,518,525],degrees:198,degress:[158,218],del:511,delai:[3,6,12,389,415,515],deleg:426,delet:[2,3,7,8,12,54,59,62,65,176,181,182,209,218,219,221,222,225,227,242,245,270,319,338,339,358,360,376,387,389,392,448,475,497,498,499,500,508,509,514,519,520,522,524,525],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[318,495,524],dellago:[6,237],deloc:[271,418,466],delr:443,delt_lo:511,delta:[],delta_1:399,delta_3:399,delta_7:399,delta_conf:3,delta_ij:[443,456],delta_pi:399,delta_r:456,delta_sigma:399,deltah_f:241,delx:201,delz:201,demand:312,demo:11,demon:296,demonstr:[307,443],den:303,dendrim:425,dendtrit:382,denniston:[9,256,258,259,260,299],denomin:[7,183],denot:[130,234,237,254,299,310,312,409,424,426,459,463,465],dens:[75,227,418],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,210,211,215,218,224,230,243,256,259,263,264,299,303,304,306,308,347,352,380,383,387,394,395,399,416,443,444,445,450,451,456,460,466,470,472,473,474,497,506,507,515,523],density_continuity:465,density_summation:465,dent:382,depart:[0,7],departur:[268,307],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,241,244,247,248,249,251,253,254,256,258,259,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,297,298,309,312,314,317,318,320,321,322,328,335,338,339,340,342,344,346,347,349,352,355,356,357,358,360,361,362,363,364,366,367,370,372,378,380,386,387,389,390,391,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,416,417,418,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,447,449,450,451,452,453,455,456,458,459,460,461,466,467,468,476,477,478,480,481,482,483,485,487,488,489,492,494,497,499,500,503,507,509,511,514,515,517,524,525],dependend:6,depflags:12,dephas:[492,511],depos:231,deposit:[],deprec:[3,308,458],deprect:218,depth:[51,156,205,347,420,422,460],dequidt:9,der:[95,118,407,408,439,458,459,488],deriv:[6,7,8,9,37,56,65,95,152,172,198,219,228,230,237,245,253,267,270,272,273,274,275,276,277,278,297,298,304,308,312,344,345,347,352,353,356,385,387,395,399,407,412,418,419,424,433,437,438,443,446,458,459,476,478,479,488,518],derjagin:488,derlet:[297,298],descend:206,descent:[7,385],descib:[40,205,308],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,241,246,247,250,251,252,253,254,255,256,258,259,260,265,269,270,271,275,283,294,297,298,300,305,306,307,308,309,310,317,318,323,331,335,336,337,338,339,340,341,342,343,344,345,350,352,353,355,360,377,378,380,384,385,386,387,388,392,395,396,398,400,401,402,404,405,406,407,408,409,412,416,418,419,420,422,423,424,426,429,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,450,451,455,456,457,458,459,460,461,466,467,468,475,476,477,478,479,480,481,482,483,485,487,488,489,490,492,494,495,497,498,499,500,501,507,510,511,514,519,524,525,527],descript:[],descriptor:[152,202,427],deserno:378,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,215,227,233,234,270,271,297,298,299,319,342,347,396,397,398,401,404,409,411,418,439,440,441,444,445,456,459,478],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,201,218,222,228,230,243,245,246,253,254,255,259,270,293,302,303,304,305,308,312,317,321,335,338,339,340,341,346,353,368,374,377,378,380,384,386,387,388,413,416,425,440,441,477,480,482,493,494,495,497,501,506,511,512,514,515,524,525,527],desk:7,desktop:[4,6,7,10,12,205],despit:518,destabil:399,destre:370,destroi:[9,11,39,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,112,114,116,118,120,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,243,245,246,247,248,250,251,253,255,256,260,267,268,269,270,271,272,273,274,275,276,277,278,282,284,290,291,293,294,295,299,302,303,304,306,307,309,310,311,317,321,322,335,338,339,340,341,342,343,345,346,347,348,349,350,351,358,360,362,371,377,378,381,386,387,389,390,393,394,395,396,398,399,401,403,404,405,406,407,408,409,412,413,418,419,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,447,448,450,451,455,458,459,460,466,467,468,476,484,487,488,490,495,497,498,499,500,502,503,506,507,509,512,515,516,519,524,525,529],detect:[2,3,12,42,63,65,94,100,244,303,346,388,408,425,430,492,494,497,508,511,524],determ:[],determin:[1,3,6,8,9,12,14,39,40,42,51,59,60,61,63,64,71,75,95,112,118,120,123,129,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,241,245,248,249,251,253,254,259,265,267,268,270,276,277,278,290,291,293,295,297,298,300,303,304,307,314,315,316,317,318,319,320,324,326,328,335,338,339,340,342,348,349,352,353,354,355,356,357,358,371,377,378,380,387,389,390,393,395,396,403,408,412,415,416,420,421,423,426,427,435,443,446,448,451,459,460,466,475,478,479,483,488,494,497,498,500,502,504,507,511,513,514,516,523,524,525],determinist:322,detil:119,devan:[9,461],devanathan:482,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,250,275,302,307,308,311,395,399,418,445,446,466,485,499],devemi:9,deviat:[268,275,297,298,421],deviator:9,devic:[1,3,12,14,16,250,393],device_typ:393,devin:[309,408],devis:445,dfactor:205,dff:518,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,378],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,311,446],dhi:[61,201,230,303],dhug:[268,307],dhugoniot:[268,307],dia:443,diagnost:[],diagon:[3,6,91,129,152,153,154,228,270,304,317,350,463,465],diagonalstyl:467,diagram:[41,130,177,197,224,300],diallo:425,diam:[205,206,303,387],diamet:[3,6,40,42,124,178,202,203,205,206,210,211,253,303,306,317,335,337,351,353,387,407,422,423,433,460,484,488,497,498,507],diamond:[380,418,443],diamter:[40,303],dick:6,dicsuss:267,dictat:[216,268],did:[3,12,386,413,415,416,423,448,480,482,505],didn:3,die:17,diel:[],dielectr:[],diff:[3,6,12,174,349,377],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,244,245,246,247,248,249,250,253,254,256,267,270,271,272,273,274,276,277,278,280,282,285,288,289,290,291,295,297,298,300,302,304,307,308,309,312,315,317,321,323,331,333,335,338,339,340,343,344,345,347,350,351,352,353,356,360,361,371,374,376,377,378,380,381,384,385,387,388,390,391,392,393,394,395,399,403,404,406,407,408,413,414,416,418,420,422,423,424,426,429,431,432,434,435,442,443,444,445,447,448,449,450,451,452,456,458,459,460,461,462,463,465,466,467,468,476,477,478,479,480,482,484,485,488,491,492,494,495,497,499,500,501,502,505,506,507,509,511,512,514,515,516,518,523,524,525,527],differenti:[1,3,6,28,198,318,377,409,456,481],difficult:[228,300,393,425,506],difficulti:[100,117,321,458],diffract:[7,9,130,177,319],diffus:[],diffuse:[4,6],digit:[2,3,206,360,446,524],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:26,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:418,dij:321,dilat:[],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,201,230,251,353,380,443,500,523,524,525],dimdim:524,dimems:299,dimens:[],dimensinon:75,dimension:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,269,299,347,380,384,388,456,497,507],dimensionless:[115,133,134,136,139,141,143,148,152,347,378,467,488],dimensions:319,diment:3,dimentionless:147,dimer:[6,317,443],dimgrai:206,dimstr:[41,224],dinola:[304,338],dintel_offload_noaffinity:15,dipol:[],dipolar:[4,28,40,202,203,337,518],dir1:508,dir2:508,dir:[1,3,4,8,10,11,12,268,297,298,307,334,456,458,459,495,508,524],dirac:152,direc:456,direct:[],directli:[3,6,8,9,11,12,95,124,129,152,154,202,203,204,205,212,236,247,251,256,299,318,319,339,351,353,354,355,356,380,385,393,394,395,400,402,403,409,412,416,418,431,435,448,453,461,475,495,507,508,509,515,524],directoi:[],directori:[],disabl:[3,12,15,347,430,495,510,524],disadvantag:[6,224],disallow:[202,230,270],disappear:499,discard:[2,3,41,75,220,224,348,356,494,499,500],discontinu:[198,386,437],discourag:443,discov:[13,348],discret:[6,8,40,42,205,206,253,256,292],discuss:[],disk:[6,92,93,100,171,200,231,245,303,495],disloc:[74,446],disord:[39,74,446],disp:[],dispar:460,disperion:[412,435],dispers:[3,6,7,9,176,299,377,378,403,412,435,440,448,459,478,485],displac:[],displace_atom:[],displace_box:61,displacemet:500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12,180,202,305,360,443,466,493,495,505,524],encod:[13,39,42,202,205,206,306,426],encompass:[3,6,40,42,59,61,127,179,330,349,476,500],encount:[3,8,12,61,117,221,392,502,524],encourag:[7,8,311,333],end12i:124,end12x:124,end12z:124,end1i:124,end1x:124,end1z:124,end2i:124,end2x:124,end2z:124,end:[1,2,3,5,6,8,11,12,14,15,16,17,18,37,40,41,42,57,59,61,75,124,181,182,185,201,202,203,205,206,207,210,211,219,221,222,227,230,237,246,251,253,255,269,270,271,284,292,304,316,317,323,335,338,339,340,341,343,346,347,350,354,357,358,376,377,387,388,392,393,413,416,422,429,442,446,460,463,465,467,468,486,492,495,497,498,499,500,502,504,505,509,513,515,518,524,529],end_of_step:8,endbondtors:[3,185,191,497],endif:8,energet:[227,395,459],energi:[],energy_compon:466,energy_update_freq:459,enforc:[6,9,59,60,114,201,202,203,204,205,207,209,216,227,230,270,296,299,309,317,321,360,377,431,494,524,525],enforce2d:[],eng:[11,68,73,119,202,243,358,360,408,445],eng_previ:360,engiliti:9,engilitycorp:9,engin:230,engineer:[215,302,323,344,416],enginer:444,enhanc:[211,215,237,492],enlarg:[61,205],enough:[3,40,63,94,178,179,181,182,224,254,303,307,312,317,348,352,353,356,389,393,409,454,497,501,502],enpub:416,ensembl:[],ensight:6,ensur:[3,6,152,202,203,216,220,228,245,246,270,324,346,378,399,415,439,477,485],enter:[59,168,419,446,485,511],enthalpi:[135,272,273,274,318,416,514,515,524],entir:[0,2,3,6,11,14,41,42,65,88,89,96,120,121,123,127,129,130,153,158,177,178,206,209,210,211,218,224,227,229,237,242,245,246,249,253,254,266,270,272,273,274,275,276,277,278,297,298,300,302,315,317,318,333,347,349,360,393,412,435,448,478,479,497,505,506],entireti:484,entiti:[6,8,40,42,202,317],entri:[3,8,12,37,42,56,68,73,84,102,119,126,129,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,241,307,358,387,399,417,443,450,451,452,459,467,477,478,479,480,481,482,485,524],entries:206,entropi:511,entry1:[37,56,206,406,450,451,478,479],entry2:206,entryn:206,enumer:[179,202,490],enumuer:6,env:393,environ:[1,3,6,11,12,15,16,17,205,247,252,297,298,393,394,399,406,408,417,418,456,480,494,508,524],eos:[9,240,241],epair:[118,206,395,421,425,458,459,515],epen:[458,459],epfl:[247,252],epp:412,epq:412,eps0:488,eps14:439,eps:[455,476],epsilon0:482,epsilon:[3,6,35,45,46,50,53,54,95,184,210,211,245,317,335,352,356,384,386,398,404,405,407,409,410,411,412,420,422,424,425,426,429,430,431,432,433,434,435,436,437,438,439,442,447,453,460,461,471,477,483,484,487,488,506,518,523],epsilon_0:489,epsilon_14:404,epsilon_:460,epsilon_d:410,epsilon_i:[422,448,460],epsilon_i_:460,epsilon_i_a:[422,460],epsilon_i_b:[422,460],epsilon_i_c:[422,460],epsilon_ij:448,epsilon_j:[422,448,460],epsilon_j_:460,epsilon_j_a:[422,460],epsilon_j_b:[422,460],epsilon_j_c:[422,460],epsilon_lj:460,epton:455,eqch:173,eqeq:[458,459],eqp:412,eqq:412,equal:[2,3,6,8,11,12,16,39,41,54,65,68,71,73,75,80,84,94,95,99,102,119,121,126,128,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,245,246,248,249,251,253,254,256,259,260,267,268,275,286,287,297,298,300,303,305,307,308,309,312,314,316,317,318,320,323,328,330,338,339,340,343,344,345,347,349,350,352,355,357,358,360,376,380,386,388,389,390,392,393,395,408,413,414,421,422,425,429,440,446,447,456,458,459,460,462,463,464,466,467,468,478,479,484,485,489,493,494,495,497,499,500,504,505,508,511,513,515,524,525],equat:[3,6,7,8,9,99,117,123,130,177,186,197,209,228,234,235,237,239,240,241,247,253,254,256,259,268,269,270,271,275,293,297,298,300,307,308,312,318,321,322,335,343,347,350,352,353,355,357,377,378,382,407,412,413,414,418,419,420,423,428,440,441,443,448,451,460,463,465,470,471,473,474,479,489,518],equation:[247,297,298,370],equi:271,equidist:269,equil:[3,308,381,504,529],equilater:507,equilibr:[3,4,5,6,7,9,61,99,178,209,216,219,227,228,245,268,270,271,293,294,304,307,308,309,310,343,344,345,350,408,409,458,459,493,507],equilibria:350,equilibribum:[225,226],equilibrium:[1,3,4,6,7,20,23,25,26,27,28,31,34,35,37,38,43,47,48,49,51,53,56,58,61,161,162,185,187,228,230,245,246,247,254,256,270,275,293,307,308,312,316,321,323,331,335,342,343,345,350,361,363,367,370,408,443,452,466,518],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,28,61,63,136,137,145,150,176,180,206,221,222,228,230,245,253,270,293,304,316,317,355,395,413,418,466,480,482,483,497,500,505,506,515,518],equlibrium:6,equliibr:[308,310],er3:177,eradiu:[40,124,203,418,497],eras:[320,344],erat:[230,441],erc:409,erfc:[409,431,448],erforc:[124,203],erg:523,erhart:[216,416,480,482],ermscal:396,ernst:9,eror:3,eros:443,erose_form:443,erot:[],errata:[480,482],erratum:352,erron:3,error:[],erta:423,ervel:[124,203,497],escap:[231,518],especi:[8,15,166,178,209,216,224,245,307,312,315,316,393,494],espresso:[9,311],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,219,299,351,378,395,409,431,482,502,515],essential:[8,275],essex:28,establish:[95,249],estim:[1,3,6,10,12,37,41,56,99,153,215,224,235,268,335,342,377,378,384,448,459,478,479,511,515],estimat:3,esu:523,esub:443,eta:[6,256,270,307,308,310,351,417,419,422,456,481,485,523],eta_dot:270,eta_ij:456,eta_ji:419,etag:[40,497],etail:515,etap:270,etap_dot:270,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,243,245,246,253,270,303,314,319,347,348,356,360,376,377,386,387,388,389,391,416,417,426,439,441,446,454,458,459,477,480,482,485,492,495,497,498,499,504,506,507,511,512,513,514,515,516,518,523,524,527,529],ethernet:17,etol:[386,388,492,511],etot0:307,etot:[6,104,106,107,121,153,164,206,234,254,268,307,514,515],eu2:177,eu3:177,euler:[386,388],eulerian:215,euqat:469,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,246,248,249,251,252,253,254,299,305,308,320,324,328,338,339,340,349,352,355,357,358,360,384,386,446,448,450,451,456,462,464,466,478,479,492,493,495,499,500,502,504,505,506,507,511,513,515,524,525],evaluat:[377,378,524],evalut:[360,495],evan:[166,293],evanseck:[6,19,184,404,509],evapor:[],evaul:[8,386],evdwl:[118,154,458,459,515],even:[3,6,8,12,14,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,251,254,268,270,271,299,303,312,314,317,319,330,335,343,347,350,352,356,358,369,377,384,386,388,393,398,418,419,423,426,429,448,460,485,486,490,497,498,500,502,503,504,506,507,509,512,514,515,516,518,529],evenli:[3,41,57,153,198,224,256,429,486],event:[],eventu:[3,6,12,14,180,511],eventual:308,ever:[9,54,56,252,335],everaer:[407,422,460,476],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,242,243,245,247,249,250,251,256,257,266,270,271,275,286,292,296,297,298,299,303,304,305,306,307,308,309,310,312,314,315,317,318,319,321,323,332,335,337,338,339,340,341,342,343,346,347,348,349,350,358,360,376,378,388,389,390,393,413,415,426,439,458,459,466,472,491,492,493,497,499,501,502,504,505,506,511,512,513,515,519,524,529],everyth:[8,118,519],everywher:[127,433],eviri:418,evolut:[237,247,256,300,492],evolv:[256,300,348],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,348,377,378,386,400,402,403,409,412,418,431,435,453,461,476,478,483],ewald_disp:412,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,224,227,246,247,253,254,255,303,312,313,335,347,362,377,406,499,504,511,524,527,529],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,198,210,211,221,224,230,235,240,246,253,254,255,271,283,284,294,299,306,307,335,340,341,354,393,406,413,416,423,426,440,448,450,451,478,479,499,500,507,511,524],exager:518,examin:[6,8,16,227,299],examp:[495,524],exampl:[],exce:[3,6,15,16,17,41,60,75,180,217,218,221,222,224,228,230,235,242,270,299,314,319,325,326,335,386,393,497,524],exceed:[3,41,61,224,230,270,335,505],excel:418,except:[1,2,5,6,8,10,11,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,244,245,248,251,253,255,270,271,272,273,274,275,276,277,278,279,280,283,284,288,290,291,293,294,295,300,309,310,317,320,321,331,335,341,347,355,358,359,360,361,362,363,364,366,367,370,371,372,377,378,380,383,387,388,389,391,392,393,394,395,397,400,401,402,403,404,405,406,407,408,409,411,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,444,449,452,453,455,458,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,494,495,497,499,500,502,505,506,507,508,509,511,515,518,523,524,525,528],exception:495,excess:[220,418],exchang:[2,3,6,8,63,64,209,215,216,237,245,249,253,309,317,343,347,350,377,393,418,512],exchange:377,excit:418,excite:418,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,202,218,225,226,257,266,302,315,317,342,353,358,386,387,389,401,423,426,429,440,441,448,475,509],exclude:389,exclus:[1,3,12,15,95,184,408,446,448,506,516],excurs:[270,492],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,205,250,311,360,376,379,392,493,495,505,508,511,524],exempl:466,exemplari:246,exemplifi:418,exert:[6,251,254,286,312,354,355,356,378],exhaust:[215,392,524],exhibit:[100,237,249,270,385,418,506],exist:[3,6,7,8,11,12,13,15,36,55,57,61,71,74,134,178,179,197,204,205,206,209,214,223,226,228,231,245,302,303,305,306,358,359,361,363,364,365,367,371,381,387,414,426,458,475,486,493,495,497,498,499,508,509,510,519,524,525,527],exit:[2,3,11,12,41,59,202,224,376,392,495,496,505,514,524],exlanatori:3,exp6:[],exp:[],expand:[],expans:[12,152,202,508,524],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,198,224,236,245,247,267,297,298,304,306,307,312,317,358,378,389,406,443,446,448,492,495,497,499,502,506,511,524],expens:[6,75,206,297,298,302,317,347,358,377,378,389,393,495],experi:[6,13,14,223,231,250,259,269,304,316,317,384,388,413,448,506,511],experienc:[6,12,258,259],experiment:[16,245,377,393,511],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,15,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,270,286,297,298,306,317,331,358,360,376,377,380,387,388,392,398,416,429,466,468,484,495,498,499,502,504,507,518,519,524,529],explan:[3,6,61,124,129,152,202,203,218,269,297,298,426,491,494,495,497,506],explanatori:[3,8,128,202,203,217,218,221,317,387,494,524],explantori:[3,313],explic:447,explicit:[6,9,11,21,44,81,95,124,127,172,186,210,211,230,318,325,326,362,377,383,395,396,399,404,406,416,418,430,440,483,491,494,498,501,519],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,244,246,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,306,307,309,317,320,321,340,341,347,355,361,363,364,366,367,370,372,387,393,394,395,397,400,401,402,403,404,405,406,407,408,409,410,412,413,415,416,417,419,420,421,422,423,424,425,426,430,431,432,433,434,435,436,437,438,439,440,444,446,448,449,450,451,452,453,455,460,461,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,485,487,488,489,497,499,500,506,507,509,510,516,518,519],explictli:[15,510],exploit:[14,16,300],explor:[130,177],expon:[3,308,310,318,416,420,422,425,439,447,461],exponenti:[95,420,456,477,485,489,511,524],expos:11,exposit:[215,413,415],express:[6,152,164,178,210,211,228,267,297,298,308,318,347,353,360,399,416,418,433,443,466,467,476,524],expression:360,expressiont:399,extend:[],extens:[3,6,9,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,243,244,245,247,248,249,251,253,255,268,270,275,284,297,298,299,315,316,317,320,323,328,331,332,334,338,339,340,341,342,344,345,347,349,352,356,357,422,443,446,459,460,467,514,515,523],extensiv:[65,209,515],extent:[1,3,41,42,45,59,75,176,180,202,214,224,251,354,357,377,380,395,462,464,478,479,494,497,500],exterior:[3,6,176,356],extern:[],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,270,305,306,307,317,335,386,387,390,391,412,423,426,429,443,448,494,495,497,500,509,518,524],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,210,211,310,388,409,419,443,467,495,502,514],extract_atom:11,extract_comput:[11,495],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,205,220,228,230,270,345,418,481,518],extrema:439,extreme:418,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,349],f_a:[480,481,482],f_ave:128,f_c:481,f_f:482,f_fix_id:307,f_foo:524,f_harm:345,f_i:[28,456],f_id:[6,75,128,131,202,203,209,217,218,219,220,221,222,265,337,349,515,524],f_ij:456,f_indent:222,f_int:344,f_j:28,f_jj:99,f_k:456,f_langevin:347,f_max:[307,312],f_msst:268,f_r:[254,480,481,482],f_sigma:399,f_solid:345,f_ss:6,face:[3,6,59,61,75,166,176,180,214,352,354,355,356,357,380,422,443,460,497,500],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,247,303,335,345,423,458,466,509],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,245,250,253,255,256,268,270,271,275,300,304,308,316,318,321,324,326,335,339,343,350,351,352,356,367,378,380,387,393,395,396,399,400,402,404,409,410,411,413,414,418,423,426,430,431,443,446,448,450,451,452,453,459,461,468,477,483,494,497,500,501,506,509,511,512,515,518,523,524],factori:[3,495],factoriz:377,fail:[3,9,11,12,61,182,228,231,377,386,388,411,459,495],failur:[133,463,496,524],fairli:[11,448,506,511,519],faken:77,falcon:250,fall:[3,6,206,221,303,495,524],fals:[94,358,466,524],fame:8,famili:[485,494],familiar:[0,11,519],fan:456,far:[3,6,12,16,59,61,63,94,202,203,206,207,224,225,226,228,231,270,297,298,316,317,335,352,363,367,384,388,389,484,495,497,502,515],farago:253,farrel:[480,482],farther:202,fashion:[6,8,41,75,178,206,209,210,211,216,224,226,231,245,247,251,267,268,270,272,273,274,275,276,277,278,287,290,291,293,294,295,306,307,309,317,323,327,334,337,345,347,351,352,353,355,357,388,426,440,500,509,524,528],fasolino:428,fast:[6,7,9,12,13,16,39,202,203,281,307,348,377,378,401,440,441,446,476,478,479,499,504,506,515,525,529],faster:[1,6,9,11,12,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,244,248,252,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,304,308,309,317,320,321,335,342,344,347,351,355,361,363,364,366,367,370,372,377,378,390,391,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,500,506,510,518],fastest:[1,6,16,166,347,348,393,494],fatal:[3,514],fault:[74,459],faulti:12,fava:422,favor:227,favorit:7,fbmc:342,fcc:[],fcm:[287,524],fcold:237,fdirect:234,fdotr:427,fdt:[],fdti:95,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:416,feedback:[7,250],feel:[7,250,251,259,297,298,356,358,388,448],felling:445,felt:356,femtosecond:523,fene:[],fennel:[409,431],fep:[],ferguson:[6,184,509],fermi:[1,9,10,12,14,164,393,482],fermion:418,fernando:442,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,207,217,218,219,221,222,237,254,270,303,306,308,321,349,377,386,387,388,395,466,494,497,502,506,508,516,527],fewer:[1,3,11,14,15,63,259,506],fewest:3,fextern:243,feynman:300,fff:495,ffield:[408,419,458,459,466],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,96,120,121,153,299,377,378,506],fft_inc:[12,378],fft_lib:12,fft_path:12,fftbench:[377,516],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:475,fictiti:[6,212,213,236,243,247,300,316,409,431,435,475],field1:[498,502],field2:498,field:[],fifth:[6,331,420,452],figshar:297,figur:[1,3,8,12,307,494,495,519],fij:412,file0:[297,298],file1:[11,13,241,297,298,346,360,387,502,504,508],file2:[11,13,241,346,360,387,502,504,508],file:[],file_from:204,filen:387,filenam:[3,12,13,37,41,56,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,241,297,298,302,305,308,309,310,313,314,317,318,319,346,347,374,375,376,387,388,394,395,399,409,416,417,419,420,428,443,444,445,450,451,452,456,457,458,459,466,467,477,478,479,480,481,482,485,493,494,495,498,499,504,508,515,524,527,528,529],filennam:504,filep:[3,202,203,206,499,504,529],filepo:314,fill:[7,9,178,205,303,347,380,389,399,446,459,500,519],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,411],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,198,207,216,227,228,240,241,242,245,269,297,298,303,304,312,316,384,386,388,389,409,426,431,435,443,450,451,466,476,478,479,518,519,524],find_custom:8,fine:[15,16,182,212,236,345,389,393,519,524],finer:[152,178,524],finest:377,finger:[178,201,267,500],finish:[6,11,41,224,360,374,376,377,390,392,393,484,502,524,525],finit:[],finni:[7,416,476],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,241,245,246,251,256,267,268,269,270,297,298,300,305,306,307,309,314,317,321,323,331,332,333,335,336,337,344,345,346,347,349,353,358,360,361,368,380,386,387,388,389,392,393,394,395,398,399,400,402,404,406,408,409,416,418,419,420,423,424,426,427,428,429,430,431,435,440,441,443,445,446,448,450,451,452,456,458,459,466,467,475,477,478,479,480,481,482,485,489,492,493,494,495,497,498,499,502,504,506,509,510,511,514,515,518,519,524,525,526,527,529],fischer:[6,9,18,19,184,404,509],fit:[3,6,9,12,37,56,198,240,316,335,395,399,428,443,448,450,451,471,478,479,481,505,519,524],five:[77,164,307,387,399,444,497,511],fix:[],fix_deposit:3,fix_ehex07:[],fix_flux:215,fix_heat:237,fix_id:[3,228,268,270,272,273,274,275,276,277,278,304,307],fix_manifoldforc:519,fix_modifi:[],fix_nh:8,fix_nv:519,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:321,fix_reax_bond:458,fix_saed_vtk:319,fix_setforc:8,fix_shak:321,fix_srd:3,fixedpoint:[228,270],fixextern:243,fixid:215,fji:412,flag1:[233,391],flag2:[233,391],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,199,202,203,205,206,207,222,227,229,233,250,253,257,259,266,267,299,306,317,331,334,335,342,346,355,358,373,375,378,387,391,392,393,395,425,430,443,446,475,490,492,494,495,497,498,499,501,502,503,507,519,524],flag_buck:403,flag_coul:[403,412,435],flag_lj:[412,435],flagfld:[401,440,441],flaghi:[3,401,440,441],flaglog:[401,440,441],flagn:233,flagvf:[401,440,441],flat:[6,347,352,353,357],flavor:[2,7,12],fld:[352,440,441],flen:396,flex_press:396,flexibl:[3,6,8,179,205,218,229,247,271,343,350,418,481,515],flip:[3,6,230,270,354,355],floor:524,flop:12,floralwhit:206,flow:[],fluctuat:[6,66,95,228,245,246,253,256,270,275,297,298,299,304,322,345,347,370,414],fluid:[],fluid_veloc:260,flush:[3,206,514],flux:[],flv:205,fly:[7,9,12,41,205,209,215,220,231,234,317,321,348,399,446,515,518],fmackai:9,fmag:232,fmass:300,fmax:[386,515],fmomentum:234,fmsec:[2,206,253,254,267,270,304,317,338,339,506,517,523,525],fname:376,fno:[9,15],fnorm:[386,515],fnpt:234,fnve:237,fnvt:234,foce:426,fock:396,focu:321,fogarti:[9,310,459],foil:[152,297,298,467],fold:[333,506],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,241,243,245,246,247,250,252,253,254,256,259,268,270,275,276,277,278,290,291,293,295,299,300,302,305,306,307,308,310,312,314,316,317,318,319,321,337,338,339,340,343,344,345,346,347,349,350,358,359,363,364,365,366,367,370,372,375,380,383,386,387,388,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,451,452,453,455,456,457,458,459,460,461,463,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,494,495,497,498,500,502,504,505,506,509,511,512,513,518,519,524,525,528],foo:[4,8,11,12,202,205,243,318,495,508,524],foo_species:318,foot:6,footprint:[12,393],fopenmp:[9,15,17],forc:[],force_uvm:16,forceatom:259,forcefield:[316,425],forcegroup:256,forcezero:384,ford:412,forestgreen:206,forev:75,forget:[254,518],forgiv:270,fork:[],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,152,153,172,173,182,186,206,209,210,211,226,246,247,253,255,259,267,293,299,310,312,316,317,318,347,352,356,361,362,365,370,383,385,387,388,395,396,399,406,414,416,418,421,425,426,430,442,443,445,446,450,451,452,453,456,458,459,460,466,467,468,476,478,480,481,482,488,491,494,495,497,502,507,514,518,524],formal:[6,82,85,99,246,247,253,270,300,335,343,466],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,198,202,203,204,205,206,207,218,221,222,224,226,240,241,299,302,306,308,310,313,317,318,319,330,346,347,358,359,362,383,387,388,394,395,399,406,416,419,420,430,443,445,450,451,457,458,459,461,467,478,479,485,486,494,495,497,498,499,502,513,514,515,524,526,527],formation:241,former:[6,12,15,39,41,206,224,347,351,399,401,503,509,524],formerli:[7,13],formul:[1,6,9,40,66,153,212,236,253,270,293,308,310,316,321,346,377,395,399,416,418,422,443,455],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,222,223,230,236,248,249,251,253,254,267,297,298,299,305,314,320,328,333,335,338,339,340,349,352,355,357,358,360,361,362,364,371,380,387,395,396,398,399,404,405,406,407,412,413,416,417,422,423,424,425,427,430,431,433,434,435,437,438,440,441,443,447,448,449,460,461,468,476,477,478,480,481,482,485,487,488,493,497,500,507,514,515,523,524,525],forth:[1,6,11,12,13,14,392,495,500,504],fortran:[3,6,9,11,12,13,243,416,426,443,458,459],fortun:8,forward:[3,8,95,376,388,393],foster:[399,455,456],foul:181,found:[3,6,9,12,77,172,202,227,229,237,245,250,256,262,299,342,348,360,376,389,406,409,412,492,498,499,514],four:[6,11,54,87,113,114,152,174,268,347,370,387,388,446,492],fourier:[],fourth:[6,115,316,331,342,404,420,452,466],fox:[6,130,184,474,509],fphi:[37,56,478,479],fpic:12,fplo:[37,56,478,479],fprime:[478,479],fqdn:252,fqq:412,fraction:[1,3,6,8,12,15,39,41,85,120,153,181,201,205,206,216,225,226,227,228,268,303,307,314,315,335,340,341,380,388,393,399,401,420,423,440,441,502,507],fragment:[42,250,314],fraig:42,frame:[91,152,206,215,268,307,354,422],framer:[205,206],framework:[5,247,394,467],franc:9,frattl:237,fraunhof:9,free:[5,6,7,9,13,28,62,65,74,95,172,210,211,297,298,335,344,345,346,347,385,388,396,418,439,446,449,456,488,494],freedom:[3,6,8,104,106,107,109,111,112,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,227,234,245,247,253,254,259,270,271,275,276,277,278,290,291,293,295,300,302,317,321,338,339,340,345,386,412,515,518,525],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[6,237,245,345],freq:214,frequenc:[3,6,15,39,113,206,220,284,299,300,307,312,375,413,418,459,466,492,506,511,524,528],frequent:[3,66,70,74,76,77,81,96,100,117,152,206,225,226,237,242,343,350,448,483,504],fri:[268,307],friction:[4,5,6,9,10,42,209,247,253,307,312,317,347,351,353,423,507],friedrich:324,from:[],front:[268,307,354],frontend:[205,311],frozen:[6,123,182,244,246,254,389,421],fs2:[6,99],fscale:250,fstr:524,fstring:495,ftol:[386,388,492,511],fuchsia:206,fuction:409,fudg:321,fugac:245,fugacity_coeff:245,fulfil:6,full:[1,2,3,6,9,12,16,37,39,40,99,205,219,220,229,237,256,297,298,318,377,378,393,399,416,418,419,422,483,497,499,504,505,509,511,516,518,528],full_energi:[3,245],fuller:386,fulli:[3,6,82,247,252,297,298,386,388,409,456,457,497,519,526,527],fulton:416,fumi:400,func:[495,524],funcfl:416,functionaliri:229,fund:[0,7],fundament:[335,523],funnel_flow:330,funrol:446,further:[3,4,6,8,12,13,63,65,67,72,75,83,94,101,115,118,127,205,206,209,218,221,222,225,231,235,256,260,300,308,319,322,324,335,347,349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remain:[7,12,32,36,41,50,55,61,75,95,114,158,159,160,161,165,166,167,168,170,181,191,197,198,202,210,211,216,218,219,228,230,253,254,261,270,271,276,277,278,290,291,293,295,301,302,326,335,338,339,340,346,347,358,360,368,371,387,399,418,426,439,446,448,476,492,497,498,502,507,509,511,515,518,519,524,525],remaina:399,remaind:[9,178,202,231,303,335,348,482,497],remap:[3,6,12,61,63,75,161,178,201,230,251,267,293,377,497,498,499],remedi:[6,518],rememb:[2,519],remot:519,remov:[2,3,6,8,13,54,75,76,81,100,117,125,127,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,203,209,218,225,242,253,254,259,262,266,268,270,276,277,278,290,291,293,295,302,308,317,318,319,321,335,338,339,340,342,358,377,388,412,441,446,497,500,508,509,519,524,525],remove_bia:8,remove_bias_al:8,remove_molecul:215,remove_sourc:215,remove_speci:215,ren:177,renam:[12,359,508,519],render:[12,13,202,205,206],rendon:[270,271],reneighbor:[3,8,12,39,59,75,224,245,335,348,358,413,514,515],renssela:302,renumb:75,reorder:[3,12,39,494],rep:512,repeat:[2,6,205,206,227,228,245,327,380,399,480,482,484,492,511],repeatedli:2,repel:251,repes:202,replac:[2,3,6,11,12,41,65,97,98,128,155,156,157,158,159,160,161,164,165,166,167,168,170,171,202,203,205,206,207,218,219,221,222,224,227,231,253,275,305,306,312,314,395,409,433,450,451,478,498,499,504,505,515,524,525,527,529],replic:[],replica:[],replica_fil:12,report:[],repositori:[],reprens:347,repres:[1,3,6,8,9,12,14,40,41,42,61,70,75,98,124,127,129,190,198,202,203,205,218,219,220,221,222,228,234,241,246,248,253,256,270,300,302,304,312,317,318,319,323,331,332,347,349,356,378,388,394,399,422,429,439,440,441,443,444,445,453,456,458,459,483,484,492,494,497,507,509,512,518,524,527],represent:[3,6,8,9,59,61,146,180,202,246,247,300,347,399,418,422,446,460,497,500,518],reprocess:502,reproduc:[3,270,353,409,416,423],repul:443,repuls:[6,7,35,40,45,46,119,251,308,352,353,356,395,399,407,409,413,418,420,423,425,439,443,447,466,475,482,485,488,489,507],reqir:[308,310],request:[3,6,8,12,41,113,181,198,202,250,256,315,322,335,337,375,377,448,458,459,492,502,507,511,519,524,525,527],requir:[],rerun:[],rescal:[],research:[5,7,88,89,239,256,260,322,446,492,511],resembl:[312,519],resepct:6,reserv:[12,250,518],reservoir:[99,237,245,249,253,347],reset:[],reset_atomic_reference_posit:215,reset_dt:8,reset_target:8,reset_tim:215,reset_timestep:[],resid:13,residu:250,residue1:389,resist:[6,250],resolut:[220,466,478,479],resolv:[228,300,335,441,519],resort:3,resourc:[7,394,416],respa:[3,15,235,250,270,391,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,487,488,489,490,505,506,517,524],respecifi:446,respect:[1,6,9,13,14,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,42,43,45,46,47,48,49,51,53,54,56,61,74,75,95,97,106,107,123,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,198,203,205,206,221,226,227,228,230,237,248,251,253,254,256,270,272,273,274,275,276,277,278,279,280,286,288,290,291,293,295,308,309,317,319,323,331,334,347,352,355,361,363,364,366,367,370,372,375,377,378,383,386,387,392,393,394,395,397,399,400,401,402,403,404,405,407,408,409,412,413,416,417,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,452,453,455,460,461,465,466,467,468,477,478,480,481,482,483,485,487,488,489,494,498,507,510,518,524,526,527,529],respon:9,respond:[6,7,161,230,418,455],respons:[6,7,268,343,350],resquar:[],rest:[6,8,12,38,58,199,306,310,316,373,399,441,443,490,514,515,518],restart1:300,restart2:300,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,62,63,113,178,210,211,306,323,331,332,337,359,514,515],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,229,268,316,334,430],restratin:316,restrict:[],result:[1,2,3,6,7,9,10,11,12,13,14,15,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,45,46,47,48,49,51,53,54,56,65,66,69,70,75,79,86,95,98,99,103,113,114,116,121,123,125,126,127,128,130,131,153,155,158,161,165,172,173,175,177,178,181,184,185,187,188,189,190,192,193,195,196,198,201,202,203,205,206,209,212,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,234,237,238,240,244,245,246,248,253,254,256,260,268,270,272,273,274,275,276,277,278,279,280,288,290,291,293,294,295,299,300,308,309,314,315,317,318,320,321,335,343,344,345,347,348,349,352,353,355,357,360,361,363,364,366,367,370,372,377,378,388,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,443,444,446,448,449,450,451,452,453,455,459,460,461,468,477,478,479,480,481,482,483,485,487,488,489,492,494,497,499,500,501,502,506,507,508,509,511,523,524,525],resum:524,retain:[2,225,226,395,399,446,494],retart:[32,50,191,368],retir:[3,458],retreiv:8,retriev:[6,8,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff 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 hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff 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 hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute rigid/local command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian 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_coeff 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 dsmc 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 hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/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_modify 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 none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[36,39,40,55,59,60,61,63,64,75,95,96,100,112,113,115,117,118,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,242,245,246,251,253,254,255,256,257,259,265,268,270,271,275,293,294,299,300,303,304,305,306,307,309,312,314,315,317,319,335,337,342,343,344,345,348,350,352,354,358,371,375,377,378,380,381,384,385,387,389,390,391,393,396,399,401,418,440,441,446,448,458,459,475,476,492,493,494,497,498,500,502,504,505,506,509,511,513,514,515,516,517,523,525,527,528],"function":524,"long":[220,400,402,403,404,405,409,411,412,431,435,439,453,461,483],"new":8,"static":12,acceler:1,account:519,ackland:66,acknowledg:7,adapt:[210,211],addforc:212,adding:519,addition:[12,13,519],addtorqu:213,adiabat:6,adjust_dt:324,adp:394,after:519,airebo:395,alloi:416,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:214,arrai:6,aspher:[6,90,156,272,276,280,281,290],asphere:9,atc:[9,215],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,214,216,217,306,524],atom_modifi:39,atom_styl:40,attract:5,aveforc:223,awpmd:[9,396],axel:519,balanc:[41,224],barostat:6,basal:70,bcc:297,beck:397,berendsen:[304,338],between:6,binary2txt:13,bodi:[6,8,42,71,157,273,277,282,291,398],body:9,bond:[8,13,72,73,225,226,227,313],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:399,born:[400,411],boundari:[7,59],box:[6,60,228],branch:519,brownian:401,buck:[402,403,411,442],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:519,change_box:61,charmm:[6,19,184,404,439],chunk:[6,69,75,79,86,98,103,114,116,125,158,173,175,218,332],citat:7,class2:[9,20,43,185,361,405],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,352,407,488],colvar:[13,229],colvars:9,com:[78,79,159],comb3:408,comb:[309,408],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,524],compute_modifi:112,condit:7,conduct:[6,343],constant:[6,524],constraint:7,contact:[80,132],coord:81,core:6,coreshell:9,correl:[219,220],cosin:[22,23,24,25,26,27,187],cossq:363,coul:[400,402,403,404,405,409,410,411,424,431,435,439,453,461],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:339,csvr:339,cubic:433,cuda:[],custom:[8,202,203],cut:[49,396,402,405,409,412,418,421,431,432,439,447,453,483],cvff:364,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[409,431],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:23,deposit:231,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],diagnost:7,diel:410,dielectr:183,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:85,dimens:200,dipol:[6,28,86,412],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:201,distanc:365,distribut:[7,12],document:0,dpd:[9,88,89,413,414],drag:232,dreid:425,dreiding:6,drude:[6,9,163,233,234,254,518],dsf:[409,431],dsmc:415,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:308,eam:[13,416],echo:208,edip:417,eff:[9,13,106,107,162,164,169,255,271,283,294,341,418],efield:236,ehex:237,eim:419,elastic:6,emac:13,energi:[135,414],enforce2d:238,ensembl:7,erot:[90,91,92,93],error:[3,134],evapor:242,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],exp6:420,exp:[26,187],expand:[46,434],extend:[8,11],extern:243,fcc:[297,298],fdt:414,featur:[7,8,519,524],fene:[45,46],fep:[9,13,95,211],field:[6,7],file:6,finit:6,fire:308,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,2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6,125,158,166,173,175,178,202,203,206,218,229,259,266,302,312,315,317,358,377,387,389,407,497,504,510,516,529],collid:[235,335,357],colliex:177,collinear:[3,302],collis:[3,256,335,353,357,415,423,489],colllis:335,colloid:[],colombo:39,colon:[207,358,498,516],color1:206,color2:206,color:[3,9,41,202,205,206,224,246,307,312],column:[3,6,9,12,13,42,65,68,69,70,71,73,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,259,267,268,307,317,336,337,347,357,395,421,425,458,459,498,512,514,524],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:393,comb3:[],comb:[],comb_1:309,comb_2:309,combiant:410,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,202,205,215,221,237,245,250,259,262,270,286,292,300,306,322,339,348,356,359,361,377,378,380,385,393,407,409,410,414,418,419,420,426,438,439,467,477,480,482,483,485,488,500,505,510,518,524,526],come:[],comfort:[12,13],comid:332,comit:519,comm:[0,3,11,12,63,77,204,250,252,253,378,388,393,413,448,455,478,479,499],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,37,56,184,198,202,240,241,254,317,318,347,387,388,394,416,417,419,420,430,443,450,451,452,459,466,467,477,478,479,480,481,482,485,494,495,497,518,519,524],commerci:7,commit:[9,519],commmand:[3,6,12,61,118,294,429,491,492,494,511,528],common:[],commonli:[3,6,9,12,16,24,59,61,115,117,180,202,205,207,372,424,433,467,480,482,497,500,509],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,205,206,224,225,226,228,229,230,250,252,256,258,259,260,270,299,306,308,309,310,317,322,335,347,358,375,377,389,390,391,393,414,415,454,490,494,495,506,507,524,527,529],communc:377,comp:[7,204,252,253,286,292,321,378,388,418,448,455,460,474,478,479,481],compact:[65,209,406,476],compani:[5,7],compar:[1,3,4,6,8,12,16,39,94,121,130,161,177,186,197,206,234,308,358,360,377,378,386,388,443,466,492,511,512,518,523],comparison:[],comparison_of_nvidia_graphics_processing_unit:[],compart:382,compass:[7,9,20,21,36,43,44,55,185,186,197,361,362,371,405,476],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,202,207,211,217,218,219,221,222,224,237,299,311,339,342,349,352,355,377,393,427,446,448,478,494,495,524],compens:[6,225,226,315,389,418],compet:346,competit:378,compil:[3,7,8,9,12,13,14,15,16,17,18,176,202,204,205,207,250,346,378,393,446,497,498,502,518,524],compl:16,complain:[11,12,16],complement:443,complementari:[7,409,431],complet:[3,6,9,11,12,14,41,61,75,206,224,229,259,300,303,306,335,346,348,359,360,376,388,393,419,463,465,484,492,497,502,505,509,511,514,518,524],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,256,286,330,356,375,388,418,446,478,479,495,497,500,524],compli:[342,346],complic:[6,7,9,12,13,129,216,245,495],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,243,248,252,253,256,259,261,262,266,267,269,270,271,275,276,277,278,290,291,293,295,296,299,300,301,304,315,317,320,321,323,327,328,331,335,338,339,340,342,349,350,355,356,357,377,380,385,386,387,388,393,413,418,423,440,441,463,465,466,467,497,498,507,515,524,525],componenet:6,componennt:129,composit:[6,216,256,416],compound:[408,418,419,485],compres:[75,125,218],compress:[],compris:[40,356,420,460,484],compton:[130,177],comptu:3,compuat:378,comput:[],computation:[3,6,225,226,347,399],computational:518,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,319],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,528],concav:356,concentr:[75,241,318,416,420,451,479],concept:[6,158,168,218,506],conceptu:[3,6,75,166,228,230,388,409,426,443,502],concern:[6,77,95,204,246],concetr:75,concis:[11,346],conclud:12,concret:8,concurr:[15,378,524],conden:[347,480,482],condens:[6,160,347,395,411,416,431,485],condit:[],conducit:6,conduct:[],cone:500,confer:446,confid:[3,511],config:[12,202,494],configfil:229,configur:[1,2,6,12,14,16,37,61,134,180,198,201,202,205,209,228,229,230,231,235,245,252,253,284,300,308,346,375,386,388,395,399,417,443,446,477,480,482,485,492,497,499,500,511,519],confin:[497,511],conflict:[3,12,40,203,448,495,519],conform:[3,6,13,61,227,228,269,316,323,346,370,388,418,509],confus:[3,485],conjuct:[9,413],conjug:[7,8,253,385,418,458,459],conjunct:[6,7,75,94,95,125,161,166,172,178,182,206,210,211,253,256,260,284,303,304,308,309,310,312,317,322,335,343,350,355,377,378,388,400,402,406,409,413,414,418,425,431,448,453,461,483,497,500,504,518,529],connect:[3,6,9,95,163,181,227,250,302,317,321,331,382,388,410,423,458,459,475,482,494,495,497,501,518],conner:395,connor:395,conput:3,consecut:[3,11,12,39,75,178,206,210,211,231,250,251,409,431,435,492,498,500],consequ:[1,6,216,347,430,511],conserv:[3,9,28,209,216,227,234,235,246,249,253,255,256,260,266,268,270,284,286,317,321,322,338,339,343,350,351,355,388,412,413,414,423,437,466,506,511],consid:[6,74,75,82,95,126,129,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,257,271,299,317,342,343,346,347,350,378,406,418,426,459,460,466,475,492,493,495,498,499,500,502,505,507,515,518,524],consider:[6,8,253,254,338,339,340,393,506],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,201,207,212,213,218,230,231,234,236,243,246,253,254,255,267,270,272,273,274,275,276,277,278,279,280,282,283,284,285,288,289,290,291,293,294,295,304,307,312,314,315,316,317,318,338,339,340,341,351,377,378,380,382,387,388,393,395,399,401,407,409,418,422,426,429,440,441,443,446,448,450,451,460,463,465,466,478,479,486,495,497,498,499,500,501,502,509,518,524],consistent_fe_initi:215,consit:317,constant:[],constantli:237,constitu:[3,6,259,317,352,356,407,460],constitut:[463,465],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,245,246,251,259,262,264,286,292,302,303,315,317,321,333,343,350,386,387,418,502,509,518],constraint:[],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,228,270,299,316,318,356,389,393,412,446,448,475,477,478,479,500,501,516,524],constructor:[8,11],consult:459,consum:[1,312,454,524],consumpt:375,contact:[],contact_stiff:[462,464],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,241,247,251,252,253,256,268,284,297,298,299,302,303,305,306,307,310,314,317,318,319,324,335,342,346,347,356,357,360,376,378,387,388,391,392,394,395,396,399,408,409,412,416,417,418,420,426,427,443,446,450,451,452,456,457,458,459,467,477,478,479,480,481,482,483,485,492,493,494,495,497,498,499,500,502,504,506,509,511,512,514,515,518,519,524,527,529],content:[4,8,9,12,17,459,513,515],context:[3,6,8,12,16,127,128,206,225,226,231,302,314,351,385,488,497,504,513,523,524,525],contibut:74,contigu:494,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,245,246,247,249,250,251,253,254,255,261,267,268,270,272,273,274,275,276,277,278,290,291,293,294,295,301,303,306,307,317,319,323,334,335,337,344,345,347,353,356,360,376,392,393,399,413,415,433,436,458,459,460,463,465,481,492,495,497,499,500,505,511,512,514,515,524,527],continuum:[6,7,9,215,347,463,465],contour_integr:215,contract:[61,228,230,270,304,317],contradictori:3,contrain:321,contraint:284,contrari:[247,254],contrast:[1,6,42,55,66,160,163,203,230,358,463,465,488,528],contrib:347,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,245,253,256,259,260,265,271,293,294,302,303,311,314,317,319,321,349,377,386,388,396,413,415,416,418,426,440,441,446,448,458,459,466,509,515,518,519],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,202,203,205,209,215,216,224,228,229,230,249,250,253,254,270,272,273,274,275,276,277,278,304,309,317,318,325,326,338,339,340,347,351,375,377,390,418,422,446,458,459,462,464,477,482,492,494,506,512,513],control_typ:215,controlfil:459,convect:99,conveni:[6,12,28,202,207,222,319,380,467,483,519,524],convent:[3,8,28,189,196,197,203,206,316,331,359,416,418,524],converg:[3,6,41,96,202,203,205,207,212,224,227,228,236,243,275,286,292,307,309,312,316,321,384,385,386,388,408,409,431,466,492,504,511],convers:[3,8,152,205,206,216,219,304,377,409,410,411,418,431,435,439,453,495,511,523],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,202,205,206,219,222,268,303,306,358,361,363,367,370,380,388,394,416,446,480,482,489,495,497,498,499,504,514,518,523,524,527,529],convex:[42,356],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,249,315],cooordin:[202,203],cooper:[5,7],coord123:125,coord1:[3,125,218],coord2:[3,125,218],coord3:[3,125,218],coord:[],coordb:466,coordbb:466,coordiat:386,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,243,245,248,249,250,251,252,253,254,267,269,270,272,273,274,276,277,278,293,296,297,298,299,302,303,304,314,315,317,320,321,323,328,331,332,333,334,335,337,345,346,347,354,355,357,358,380,386,387,388,393,394,395,398,417,466,492,497,498,499,500,502,505,507,511,518,524,525],coordn:[125,218],coords:466,copi:[0,3,4,8,9,11,12,14,16,40,131,205,347,388,406,458,495,519],copper:489,coproccesor:15,coprocessor:[1,7,9,15,16,393,510],coproprocessor:16,copy_arrai:8,copyright:[7,8,302],coral:206,core:[],core_shel:160,cores:518,coreshel:[4,6,9],coreshell:[],cornel:[6,184,509],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,205,356,357,380,484,497,519],cornflowerblu:206,cornsilk:206,corp:9,corpor:15,corr:408,correct:[3,6,9,11,12,15,16,61,86,95,96,112,113,118,121,127,160,165,172,184,203,205,230,237,245,247,253,270,271,293,302,304,307,346,352,356,377,388,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,497,512,515,518,519],correction_max_iter:215,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,243,254,264,270,271,310,317,321,331,334,353,356,388,389,393,411,441,446,494,495,497,507,519,523,525],correl:[],correpond:[240,241],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,241,243,244,248,253,256,257,266,267,268,270,272,273,274,275,276,277,278,279,280,284,288,290,291,293,295,297,299,300,304,309,317,318,320,321,342,352,353,355,356,357,359,361,362,363,364,366,367,370,372,378,383,385,387,388,394,395,397,400,401,402,403,404,405,406,407,408,409,412,413,416,417,418,419,420,421,422,423,424,425,426,429,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,451,452,453,455,456,458,459,460,461,466,467,468,477,478,479,480,481,482,483,485,487,488,489,492,494,495,497,498,500,510,511,512,514,515,518,524],correspondingli:[440,441,506],corrupt:3,cosin:[],cosineshift:26,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,205,206,218,224,225,226,242,270,309,347,377,378,391,409,431,435,446,448,477,494,506],costheta0:[477,480,482,485],costheta:456,costli:[11,96,247,389],couett:4,coul:[],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,243,252,306,307,308,312,315,317,320,335,336,342,346,347,348,352,356,358,360,368,374,376,384,386,389,393,395,396,421,425,426,429,458,459,493,494,495,497,499,501,504,505,512,513,518,524,525],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,308,310,348,377,378,386,393,400,402,403,404,405,408,409,410,411,412,418,423,424,426,431,435,439,442,448,453,458,459,461,466,476,482,483,485,488,502,509,515,518,523],coulommb:6,cound:3,count:[1,3,6,8,11,12,15,41,65,71,81,99,125,127,128,166,176,182,184,212,213,216,218,221,223,224,231,236,242,245,251,270,284,303,320,321,338,339,356,378,386,387,388,390,393,421,425,448,515,516,524],counter:[3,353,492,503,505,511],counteract:245,counterbal:[237,249],counterbalanc:28,counterclockwis:184,counterpart:[202,492],counterproduct:17,coupl:[],couple:[4,6,11,12],courant:324,cours:[3,8,138,140,172,202,210,211,246,316,331,346,352,354,355,357,358,378,440,468,494,497,510,518,524,527],courtesi:380,cov:466,coval:[6,9,28,418,443,466,518],covari:247,cover:[6,12,75,198,206,215,256,418,484],coverag:75,cpc:252,cpp:[1,3,6,8,9,11,12,13,95,202,210,211,243,321],cpu:[1,3,9,10,12,14,15,16,17,65,75,206,220,234,254,348,375,378,393,406,476,492,510,511,514,515,516,524],cpuremain:515,cpus:12,cr2:177,cr3:177,crack:[4,389],crada:[5,7],crai:[5,7,13,17,202],crash:[3,12,389,518],craympi:393,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:302,criteria:[3,127,179,205,206,225,226,227,265,386,455,484,499,502,524],criterion:[12,41,133,178,181,216,224,227,245,284,309,324,353,358,386,388,408,418,423,466,502,511,512],criterioni:511,critic:[6,48,49,268,342,347,386],crmax:75,crmin:75,cross:[3,12,21,75,97,129,156,176,186,202,203,205,217,226,230,267,269,293,317,327,331,334,343,350,362,380,388,404,413,415,416,424,425,426,431,433,435,456,461,463,465,480,482,489,497,501,507,527],crossov:1,crossterm:497,crozier:[0,7,13],crucial:307,crystal:[3,4,6,13,77,117,297,298,299,345,380,389,497,501,515,518],crystallin:[6,113,299,380,481,518],crystallis:342,crystallogr:[130,177],crystallograph:[380,515],crystallographi:[130,177,380],cs1:177,cs_chunk:6,cs_im:[40,497],cs_re:[40,497],csanyi:[152,457,467],cscl:443,csequ:6,csh:[11,12,406],cshrc:[11,12],csic:[417,477,480,482,485],csinfo:6,csisi:[417,477,480,482,485],csld:[],cst:416,cstherm:6,cstyle:494,csvr:[],ctcm:[394,416],ctemp_core:234,cterm:323,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:443,cube:[6,176,181,234,356,380,518],cubes:[41,224],cubic:[],cuda:[],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cufft:[],cuh:399,cummul:[3,6,222,225,226,227,229,242,247,253,255,335,338,339,340,341,343,350,425,515],cumul:[6,216,218,221,235,245,253,268,270,275,284,317,319,388],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,112,113,119,127,128,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,243,245,247,250,251,253,259,265,267,270,271,276,277,278,284,286,290,291,292,293,295,302,303,308,309,311,314,315,316,317,318,321,322,323,324,325,326,327,328,330,332,333,334,335,338,339,340,346,347,350,351,352,353,354,355,357,358,360,375,376,377,378,381,382,383,385,386,387,388,393,399,406,408,412,414,416,418,419,423,426,427,430,440,441,443,444,445,448,456,458,459,462,463,464,465,468,480,482,483,486,492,493,494,495,497,498,499,500,501,503,504,505,507,509,511,512,514,515,519,524,525,526,527,528,529],curv:[6,178,245,286,292,299],curvatur:[422,460,489],custom:[],cut0:495,cut1:506,cut2:506,cut:[],cuthi:[297,298,310],cutinn:[401,440,441],cutlo:[297,298,310],cutmax:456,cutoff1:[405,412,431,435,439,442,453,461],cutoff2:[400,402,403,405,411,412,431,435,439,442,453,461,483],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,226,227,232,240,241,297,298,307,308,310,312,314,317,322,335,348,352,356,358,375,377,378,386,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,466,467,468,469,470,471,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,495,499,502,506,518,524],cutoffa:417,cutoffc:417,cuu3:416,cval:177,cvd:342,cvel:323,cvff:[],cwiggl:[3,267,352,355,357,524],cyan:[2,205,206],cycl:[3,245,268,270,271,275],cyclic:[3,184,198],cygwin:12,cylind:[3,4,75,205,218,251,292,303,353,356,382,500],cylinder_d:382,cylindr:[6,251,331,353],cypress:393,cyrot:399,cyrstal:299,d3q15:256,d3q19:256,d_double_double:14,d_e:347,d_flag2:306,d_flag:306,d_name:[124,202,306,337,507],d_single_double:14,d_single_single:14,d_sx:306,d_sy:306,d_sz:306,daan:345,dai:12,daili:12,daivi:293,damag:[],dammak:312,damp:[3,6,209,214,253,254,255,260,270,271,275,292,304,307,308,312,317,338,339,351,353,354,385,386,388,400,402,404,409,412,418,423,431,439,453,461,476,483,511,518],damp_com:254,damp_drud:254,dampen:[317,518],dampflag:[353,423],dan:16,danger:[3,12,245,358,413,515],dangl:181,daniel:9,darden:[378,412],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:308,dash:[423,514],dat:[6,99,198,215,493],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,319],dataset:319,datatyp:3,date:[0,4,6,12,13,201,458,459,524],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,42,68,71,73,84,102,119,126,202,219],davenport:442,davi:352,david:[9,18,377,378,480,482],daw:[416,456],dbg:[],dcd:[3,6,7,202,204,205,206,207,300,498,502],dcs:9,ddim:201,deactiv:439,dealt:252,debug:[6,7,11,12,13,16,57,130,134,177,178,300,305,375,377,427,448,486,495,496,504,507,514,524],deby:[],decai:[100,409,489],decid:[3,6,12,15,75,267,306,317,348,512,519],decipher:380,deck:306,declar:204,declin:335,decod:205,decompos:[95,467],decomposit:[3,5,7,17,64,215,300,322],decoupl:[6,518],decreas:[3,202,203,212,213,220,227,230,236,237,243,245,253,346,377],decrement:323,deepli:374,deeppink:206,deepskyblu:206,def:[12,13,495],defaul:63,defect:[6,74,176,446],defgrad:[],defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,241,243,244,245,248,251,252,253,254,255,256,265,267,269,270,271,272,273,274,275,276,277,278,280,281,282,285,288,289,290,291,293,294,295,297,298,299,300,302,303,304,306,308,310,315,317,318,319,320,321,324,328,332,333,335,337,338,339,340,341,343,344,345,347,349,350,352,353,354,355,356,357,358,360,361,362,363,364,365,366,367,370,371,372,373,375,377,378,380,383,385,386,387,388,389,390,391,392,393,395,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,417,418,420,421,422,423,424,425,426,427,429,431,432,433,434,435,436,437,438,439,440,441,442,446,447,448,449,450,451,452,453,455,456,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,497,498,500,501,502,503,506,507,508,509,511,512,514,515,518,520,521,522,523,524,525,526],definit:[2,3,6,8,12,13,82,85,127,152,206,218,219,220,221,222,230,239,251,275,319,337,349,352,355,357,359,371,375,387,396,399,407,414,418,429,456,463,465,467,484,495,497,499,506,508,523,524],defint:515,deform:[],deg2theta:177,deg:518,degener:[3,302],degrad:[8,17,299,378,506],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,245,247,248,253,254,259,270,271,275,276,277,278,290,291,293,295,300,302,316,317,321,338,339,340,345,361,363,367,370,372,386,412,416,425,507,515,518,525],degrees:198,degress:[158,218],del:511,delai:[3,6,12,389,415,515],deleg:426,delet:[2,3,7,8,12,54,59,62,65,176,181,182,209,218,219,221,222,225,227,242,245,270,319,338,339,358,360,376,387,389,392,448,475,497,498,499,500,508,509,514,519,520,522,524,525],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[318,495,524],dellago:[6,237],deloc:[271,418,466],delr:443,delt_lo:511,delta:[],delta_1:399,delta_3:399,delta_7:399,delta_conf:3,delta_ij:[443,456],delta_pi:399,delta_r:456,delta_sigma:399,deltah_f:241,delx:201,delz:201,demand:312,demo:11,demon:296,demonstr:[307,443],den:303,dendrim:425,dendtrit:382,denniston:[9,256,258,259,260,299],denomin:[7,183],denot:[130,234,237,254,299,310,312,409,424,426,459,463,465],dens:[75,227,418],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,210,211,215,218,224,230,243,256,259,263,264,299,303,304,306,308,347,352,380,383,387,394,395,399,416,443,444,445,450,451,456,460,466,470,472,473,474,497,506,507,515,523],density_continuity:465,density_summation:465,dent:382,depart:[0,7],departur:[268,307],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,241,244,247,248,249,251,253,254,256,258,259,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,297,298,309,312,314,317,318,320,321,322,328,335,338,339,340,342,344,346,347,349,352,355,356,357,358,360,361,362,363,364,366,367,370,372,378,380,386,387,389,390,391,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,416,417,418,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,447,449,450,451,452,453,455,456,458,459,460,461,466,467,468,476,477,478,480,481,482,483,485,487,488,489,492,494,497,499,500,503,507,509,511,514,515,517,524,525],dependend:6,depflags:12,dephas:[492,511],depos:231,deposit:[],deprec:[3,308,458],deprect:218,depth:[51,156,205,347,420,422,460],dequidt:9,der:[95,118,407,408,439,458,459,488],deriv:[6,7,8,9,37,56,65,95,152,172,198,219,228,230,237,245,253,267,270,272,273,274,275,276,277,278,297,298,304,308,312,344,345,347,352,353,356,385,387,395,399,407,412,418,419,424,433,437,438,443,446,458,459,476,478,479,488,518],derjagin:488,derlet:[297,298],descend:206,descent:[7,385],descib:[40,205,308],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,241,246,247,250,251,252,253,254,255,256,258,259,260,265,269,270,271,275,283,294,297,298,300,305,306,307,308,309,310,317,318,323,331,335,336,337,338,339,340,341,342,343,344,345,350,352,353,355,360,377,378,380,384,385,386,387,388,392,395,396,398,400,401,402,404,405,406,407,408,409,412,416,418,419,420,422,423,424,426,429,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,450,451,455,456,457,458,459,460,461,466,467,468,475,476,477,478,479,480,481,482,483,485,487,488,489,490,492,494,495,497,498,499,500,501,507,510,511,514,519,524,525,527],descript:[],descriptor:[152,202,427],deserno:378,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,215,227,233,234,270,271,297,298,299,319,342,347,396,397,398,401,404,409,411,418,439,440,441,444,445,456,459,478],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,201,218,222,228,230,243,245,246,253,254,255,259,270,293,302,303,304,305,308,312,317,320,321,335,338,339,340,341,346,353,368,374,377,378,380,384,386,387,388,413,416,425,440,441,477,480,482,493,494,495,497,501,506,511,512,514,515,516,524,525,527],desk:7,desktop:[4,6,7,10,12,205],despit:518,destabil:399,destre:370,destroi:[9,11,39,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,112,114,116,118,120,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,243,245,246,247,248,250,251,253,255,256,260,267,268,269,270,271,272,273,274,275,276,277,278,282,284,290,291,293,294,295,299,302,303,304,306,307,309,310,311,317,321,322,335,338,339,340,341,342,343,345,346,347,348,349,350,351,358,360,362,371,377,378,381,386,387,389,390,393,394,395,396,398,399,401,403,404,405,406,407,408,409,412,413,418,419,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,447,448,450,451,455,458,459,460,466,467,468,476,484,487,488,490,495,497,498,499,500,502,503,506,507,509,512,515,516,519,524,525,529],detect:[2,3,12,42,63,65,94,100,244,303,346,388,408,425,430,492,494,497,508,511,524],determ:[],determin:[1,3,6,8,9,12,14,39,40,42,51,59,60,61,63,64,71,75,95,112,118,120,123,129,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,241,245,248,249,251,253,254,259,265,267,268,270,276,277,278,290,291,293,295,297,298,300,303,304,307,314,315,316,317,318,319,320,324,326,328,335,338,339,340,342,348,349,352,353,354,355,356,357,358,371,377,378,380,387,389,390,393,395,396,403,408,412,415,416,420,421,423,426,427,435,443,446,448,451,459,460,466,475,478,479,483,488,494,497,498,500,502,504,507,511,513,514,516,523,524,525],determinist:322,detil:119,devan:[9,461],devanathan:482,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,250,275,302,307,308,311,395,399,418,445,446,466,485,499],devemi:9,deviat:[268,275,297,298,421],deviator:9,devic:[1,3,12,14,16,250,393],device_typ:393,devin:[309,408],devis:445,dfactor:205,dff:518,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,378],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,311,446],dhi:[61,201,230,303],dhug:[268,307],dhugoniot:[268,307],dia:443,diagnost:[],diagon:[3,6,91,129,152,153,154,228,270,304,317,350,463,465],diagonalstyl:467,diagram:[41,130,177,197,224,300],diallo:425,diam:[205,206,303,387],diamet:[3,6,40,42,124,178,202,203,205,206,210,211,253,303,306,317,335,337,351,353,387,407,422,423,433,460,484,488,497,498,507],diamond:[380,418,443],diamter:[40,303],dick:6,dicsuss:267,dictat:[216,268],did:[3,12,386,413,415,416,423,448,480,482,505],didn:3,die:17,diel:[],dielectr:[],diff:[3,6,12,174,349,377],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,244,245,246,247,248,249,250,253,254,256,267,270,271,272,273,274,276,277,278,280,282,285,288,289,290,291,295,297,298,300,302,304,307,308,309,312,315,317,321,323,331,333,335,338,339,340,343,344,345,347,350,351,352,353,356,360,361,371,374,376,377,378,380,381,384,385,387,388,390,391,392,393,394,395,399,403,404,406,407,408,413,414,416,418,420,422,423,424,426,429,431,432,434,435,442,443,444,445,447,448,449,450,451,452,456,458,459,460,461,462,463,465,466,467,468,476,477,478,479,480,482,484,485,488,491,492,494,495,497,499,500,501,502,505,506,507,509,511,512,514,515,516,518,523,524,525,527],differenti:[1,3,6,28,198,318,377,409,456,481],difficult:[228,300,393,425,506],difficulti:[100,117,321,458],diffract:[7,9,130,177,319],diffus:[],diffuse:[4,6],digit:[2,3,206,360,446,524],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:26,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:418,dij:321,dilat:[],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,201,230,251,353,380,443,500,523,524,525],dimdim:524,dimems:299,dimens:[],dimensinon:75,dimension:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,269,299,347,380,384,388,456,497,507],dimensionless:[115,133,134,136,139,141,143,148,152,347,378,467,488],dimensions:319,diment:3,dimentionless:147,dimer:[6,317,443],dimgrai:206,dimstr:[41,224],dinola:[304,338],dintel_offload_noaffinity:15,dipol:[],dipolar:[4,28,40,202,203,337,518],dir1:508,dir2:508,dir:[1,3,4,8,10,11,12,268,297,298,307,334,456,458,459,495,508,524],dirac:152,direc:456,direct:[],directli:[3,6,8,9,11,12,95,124,129,152,154,202,203,204,205,212,236,247,251,256,299,318,319,339,351,353,354,355,356,380,385,393,394,395,400,402,403,409,412,416,418,431,435,448,453,461,475,495,507,508,509,515,524],directoi:[],directori:[],disabl:[3,12,15,347,430,495,510,524],disadvantag:[6,224],disallow:[202,230,270],disappear:499,discard:[2,3,41,75,220,224,348,356,494,499,500],discontinu:[198,386,437],discourag:443,discov:[13,348],discret:[6,8,40,42,205,206,253,256,292],discuss:[],disk:[6,92,93,100,171,200,231,245,303,495],disloc:[74,446],disord:[39,74,446],disp:[],dispar:460,disperion:[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,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,489,495,498,499,500,504,506,516,524,529],enclos:[2,6,12,180,202,305,360,443,466,493,495,505,524],encod:[13,39,42,202,205,206,306,426],encompass:[3,6,40,42,59,61,127,179,330,349,476,500],encount:[3,8,12,61,117,221,392,502,524],encourag:[7,8,311,333],end12i:124,end12x:124,end12z:124,end1i:124,end1x:124,end1z:124,end2i:124,end2x:124,end2z:124,end:[1,2,3,5,6,8,11,12,14,15,16,17,18,37,40,41,42,57,59,61,75,124,181,182,185,201,202,203,205,206,207,210,211,219,221,222,227,230,237,246,251,253,255,269,270,271,284,292,304,316,317,323,335,338,339,340,341,343,346,347,350,354,357,358,376,377,387,388,392,393,413,416,422,429,442,446,460,463,465,467,468,486,492,495,497,498,499,500,502,504,505,509,513,515,518,524,529],end_of_step:8,endbondtors:[3,185,191,497],endif:8,energet:[227,395,459],energi:[],energy_compon:466,energy_update_freq:459,enforc:[6,9,59,60,114,201,202,203,204,205,207,209,216,227,230,270,296,299,309,317,321,360,377,431,494,524,525],enforce2d:[],eng:[11,68,73,119,202,243,358,360,408,445],eng_previ:360,engiliti:9,engilitycorp:9,engin:230,engineer:[215,302,323,344,416],enginer:444,enhanc:[211,215,237,492],enlarg:[61,205],enough:[3,40,63,94,178,179,181,182,224,254,303,307,312,317,348,352,353,356,389,393,409,454,497,501,502],enpub:416,ensembl:[],ensight:6,ensur:[3,6,152,202,203,216,220,228,245,246,270,324,346,378,399,415,439,477,485],enter:[59,168,419,446,485,511],enthalpi:[135,272,273,274,318,416,514,515,524],entir:[0,2,3,6,11,14,41,42,65,88,89,96,120,121,123,127,129,130,153,158,177,178,206,209,210,211,218,224,227,229,237,242,245,246,249,253,254,266,270,272,273,274,275,276,277,278,297,298,300,302,315,317,318,333,347,349,360,393,412,435,448,478,479,497,505,506],entireti:484,entiti:[6,8,40,42,202,317],entri:[3,8,12,37,42,56,68,73,84,102,119,126,129,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,241,307,358,387,399,417,443,450,451,452,459,467,477,478,479,480,481,482,485,524],entries:206,entropi:511,entry1:[37,56,206,406,450,451,478,479],entry2:206,entryn:206,enumer:[179,202,490],enumuer:6,env:393,environ:[1,3,6,11,12,15,16,17,205,247,252,297,298,393,394,399,406,408,417,418,456,480,494,508,524],eos:[9,240,241],epair:[118,206,395,421,425,458,459,515],epen:[458,459],epfl:[247,252],epp:412,epq:412,eps0:488,eps14:439,eps:[455,476],epsilon0:482,epsilon:[3,6,35,45,46,50,53,54,95,184,210,211,245,317,335,352,356,384,386,398,404,405,407,409,410,411,412,420,422,424,425,426,429,430,431,432,433,434,435,436,437,438,439,442,447,453,460,461,471,477,483,484,487,488,506,518,523],epsilon_0:489,epsilon_14:404,epsilon_:460,epsilon_d:410,epsilon_i:[422,448,460],epsilon_i_:460,epsilon_i_a:[422,460],epsilon_i_b:[422,460],epsilon_i_c:[422,460],epsilon_ij:448,epsilon_j:[422,448,460],epsilon_j_:460,epsilon_j_a:[422,460],epsilon_j_b:[422,460],epsilon_j_c:[422,460],epsilon_lj:460,epton:455,eqch:173,eqeq:[458,459],eqp:412,eqq:412,equal:[2,3,6,8,11,12,16,39,41,54,65,68,71,73,75,80,84,94,95,99,102,119,121,126,128,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,245,246,248,249,251,253,254,256,259,260,267,268,275,286,287,297,298,300,303,305,307,308,309,312,314,316,317,318,320,323,328,330,338,339,340,343,344,345,347,349,350,352,355,357,358,360,376,380,386,388,389,390,392,393,395,408,413,414,421,422,425,429,440,446,447,456,458,459,460,462,463,464,466,467,468,478,479,484,485,489,493,494,495,497,499,500,504,505,508,511,513,515,524,525],equat:[3,6,7,8,9,99,117,123,130,177,186,197,209,228,234,235,237,239,240,241,247,253,254,256,259,268,269,270,271,275,293,297,298,300,307,308,312,318,321,322,335,343,347,350,352,353,355,357,377,378,382,407,412,413,414,418,419,420,423,428,440,441,443,448,451,460,463,465,470,471,473,474,479,489,518],equation:[247,297,298,370],equi:271,equidist:269,equil:[3,308,381,504,529],equilater:507,equilibr:[3,4,5,6,7,9,61,99,178,209,216,219,227,228,245,268,270,271,293,294,304,307,308,309,310,343,344,345,350,408,409,458,459,493,507],equilibria:350,equilibribum:[225,226],equilibrium:[1,3,4,6,7,20,23,25,26,27,28,31,34,35,37,38,43,47,48,49,51,53,56,58,61,161,162,185,187,228,230,245,246,247,254,256,270,275,293,307,308,312,316,321,323,331,335,342,343,345,350,361,363,367,370,408,443,452,466,518],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,28,61,63,136,137,145,150,176,180,206,221,222,228,230,245,253,270,293,304,316,317,355,395,413,418,466,480,482,483,497,500,505,506,515,518],equlibrium:6,equliibr:[308,310],er3:177,eradiu:[40,124,203,418,497],eras:[320,344],erat:[230,441],erc:409,erfc:[409,431,448],erforc:[124,203],erg:523,erhart:[216,416,480,482],ermscal:396,ernst:9,eror:3,eros:443,erose_form:443,erot:[],errata:[480,482],erratum:352,erron:3,error:[],erta:423,ervel:[124,203,497],escap:[231,518],especi:[8,15,166,178,209,216,224,245,307,312,315,316,393,494],espresso:[9,311],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,219,299,351,378,395,409,431,482,502,515],essential:[8,275],essex:28,establish:[95,249],estim:[1,3,6,10,12,37,41,56,99,153,215,224,235,268,335,342,377,378,384,448,459,478,479,511,515],estimat:3,esu:523,esub:443,eta:[6,256,270,307,308,310,351,417,419,422,456,481,485,523],eta_dot:270,eta_ij:456,eta_ji:419,etag:[40,497],etail:515,etap:270,etap_dot:270,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,243,245,246,253,270,303,314,319,347,348,356,360,376,377,386,387,388,389,391,416,417,426,439,441,446,454,458,459,477,480,482,485,492,495,497,498,499,504,506,507,511,512,513,514,515,516,518,523,524,527,529],ethernet:17,etol:[386,388,492,511],etot0:307,etot:[6,104,106,107,121,153,164,206,234,254,268,307,514,515],eu2:177,eu3:177,euler:[386,388],eulerian:215,euqat:469,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,246,248,249,251,252,253,254,299,305,308,320,324,328,338,339,340,349,352,355,357,358,360,384,386,446,448,450,451,456,462,464,466,478,479,492,493,495,499,500,502,504,505,506,507,511,513,515,524,525],evaluat:[377,378,524],evalut:[360,495],evan:[166,293],evanseck:[6,19,184,404,509],evapor:[],evaul:[8,386],evdwl:[118,154,458,459,515],even:[3,6,8,12,14,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,251,254,268,270,271,299,303,312,314,317,319,330,335,343,347,350,352,356,358,369,377,384,386,388,393,398,418,419,423,426,429,448,460,485,486,490,497,498,500,502,503,504,506,507,509,512,514,515,516,518,529],evenli:[3,41,57,153,198,224,256,429,486],event:[],eventu:[3,6,12,14,180,511],eventual:308,ever:[9,54,56,252,335],everaer:[407,422,460,476],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,242,243,245,247,249,250,251,256,257,266,270,271,275,286,292,296,297,298,299,303,304,305,306,307,308,309,310,312,314,315,317,318,319,321,323,332,335,337,338,339,340,341,342,343,346,347,348,349,350,358,360,376,378,388,389,390,393,413,415,426,439,458,459,466,472,491,492,493,497,499,501,502,504,505,506,511,512,513,515,516,519,524,529],everyth:[8,118,519],everywher:[127,433],eviri:418,evolut:[237,247,256,300,492],evolv:[256,300,348],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,348,377,378,386,400,402,403,409,412,418,431,435,453,461,476,478,483],ewald_disp:412,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,224,227,246,247,253,254,255,303,312,313,335,347,362,377,406,499,504,511,524,527,529],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,198,210,211,221,224,230,235,240,246,253,254,255,271,283,284,294,299,306,307,335,340,341,354,393,406,413,416,423,426,440,448,450,451,478,479,499,500,507,511,524],exager:518,examin:[6,8,16,227,299],examp:[495,524],exampl:[],exce:[3,6,15,16,17,41,60,75,180,217,218,221,222,224,228,230,235,242,270,299,314,319,325,326,335,386,393,497,524],exceed:[3,41,61,224,230,270,335,505],excel:418,except:[1,2,5,6,8,10,11,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,244,245,248,251,253,255,270,271,272,273,274,275,276,277,278,279,280,283,284,288,290,291,293,294,295,300,309,310,317,320,321,331,335,341,347,355,358,359,360,361,362,363,364,366,367,370,371,372,377,378,380,383,387,388,389,391,392,393,394,395,397,400,401,402,403,404,405,406,407,408,409,411,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,444,449,452,453,455,458,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,494,495,497,499,500,502,505,506,507,508,509,511,515,518,523,524,525,528],exception:495,excess:[220,418],exchang:[2,3,6,8,63,64,209,215,216,237,245,249,253,309,317,343,347,350,377,393,418,512],exchange:377,excit:418,excite:418,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,202,218,225,226,257,266,302,315,317,342,353,358,386,387,389,401,423,426,429,440,441,448,475,509],exclude:389,exclus:[1,3,12,15,95,184,408,446,448,506,516],excurs:[270,492],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,205,250,311,360,376,379,392,493,495,505,508,511,524],exempl:466,exemplari:246,exemplifi:418,exert:[6,251,254,286,312,354,355,356,378],exhaust:[215,392,524],exhibit:[100,237,249,270,385,418,506],exist:[3,6,7,8,11,12,13,15,36,55,57,61,71,74,134,178,179,197,204,205,206,209,214,223,226,228,231,245,302,303,305,306,358,359,361,363,364,365,367,371,381,387,414,426,458,475,486,493,495,497,498,499,508,509,510,519,524,525,527],exit:[2,3,11,12,41,59,202,224,376,392,495,496,505,514,516,524],exlanatori:3,exp6:[],exp:[],expand:[],expans:[12,152,202,508,524],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,198,224,236,245,247,267,297,298,304,306,307,312,317,358,378,389,406,443,446,448,492,495,497,499,502,506,511,524],expens:[6,75,206,297,298,302,317,347,358,377,378,389,393,495],experi:[6,13,14,223,231,250,259,269,304,316,317,384,388,413,448,506,511],experienc:[6,12,258,259],experiment:[16,245,377,393,511],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,15,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,270,286,297,298,306,317,331,358,360,376,377,380,387,388,392,398,416,429,466,468,484,495,498,499,502,504,507,518,519,524,529],explan:[3,6,61,124,129,152,202,203,218,269,297,298,426,491,494,495,497,506],explanatori:[3,8,128,202,203,217,218,221,317,387,494,524],explantori:[3,313],explic:447,explicit:[6,9,11,21,44,81,95,124,127,172,186,210,211,230,318,325,326,362,377,383,395,396,399,404,406,416,418,430,440,483,491,494,498,501,519],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,244,246,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,306,307,309,317,320,321,340,341,347,355,361,363,364,366,367,370,372,387,393,394,395,397,400,401,402,403,404,405,406,407,408,409,410,412,413,415,416,417,419,420,421,422,423,424,425,426,430,431,432,433,434,435,436,437,438,439,440,444,446,448,449,450,451,452,453,455,460,461,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,485,487,488,489,497,499,500,506,507,509,510,516,518,519],explictli:[15,510],exploit:[14,16,300],explor:[130,177],expon:[3,308,310,318,416,420,422,425,439,447,461],exponenti:[95,420,456,477,485,489,511,524],expos:11,exposit:[215,413,415],express:[6,152,164,178,210,211,228,267,297,298,308,318,347,353,360,399,416,418,433,443,466,467,476,524],expression:360,expressiont:399,extend:[],extens:[3,6,9,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,243,244,245,247,248,249,251,253,255,268,270,275,284,297,298,299,315,316,317,320,323,328,331,332,334,338,339,340,341,342,344,345,347,349,352,356,357,422,443,446,459,460,467,514,515,523],extensiv:[65,209,515],extent:[1,3,41,42,45,59,75,176,180,202,214,224,251,354,357,377,380,395,462,464,478,479,494,497,500],exterior:[3,6,176,356],extern:[],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,270,305,306,307,317,335,386,387,390,391,412,423,426,429,443,448,494,495,497,500,509,518,524],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,210,211,310,388,409,419,443,467,495,502,514],extract_atom:11,extract_comput:[11,495],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,205,220,228,230,270,345,418,481,518],extrema:439,extreme:418,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,349],f_a:[480,481,482],f_ave:128,f_c:481,f_f:482,f_fix_id:307,f_foo:524,f_harm:345,f_i:[28,456],f_id:[6,75,128,131,202,203,209,217,218,219,220,221,222,265,337,349,515,524],f_ij:456,f_indent:222,f_int:344,f_j:28,f_jj:99,f_k:456,f_langevin:347,f_max:[307,312],f_msst:268,f_r:[254,480,481,482],f_sigma:399,f_solid:345,f_ss:6,face:[3,6,59,61,75,166,176,180,214,352,354,355,356,357,380,422,443,460,497,500],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,247,303,335,345,423,458,466,509],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,245,250,253,255,256,268,270,271,275,300,304,308,316,318,321,324,326,335,339,343,350,351,352,356,367,378,380,387,393,395,396,399,400,402,404,409,410,411,413,414,418,423,426,430,431,443,446,448,450,451,452,453,459,461,468,477,483,494,497,500,501,506,509,511,512,515,518,523,524],factori:[3,495],factoriz:377,fail:[3,9,11,12,61,182,228,231,377,386,388,411,459,495],failur:[133,463,496,524],fairli:[11,448,506,511,519],faken:77,falcon:250,fall:[3,6,206,221,303,495,524],fals:[94,358,466,524],fame:8,famili:[485,494],familiar:[0,11,519],fan:456,far:[3,6,12,16,59,61,63,94,202,203,206,207,224,225,226,228,231,270,297,298,316,317,335,352,363,367,384,388,389,484,495,497,502,515],farago:253,farrel:[480,482],farther:202,fashion:[6,8,41,75,178,206,209,210,211,216,224,226,231,245,247,251,267,268,270,272,273,274,275,276,277,278,287,290,291,293,294,295,306,307,309,317,323,327,334,337,345,347,351,352,353,355,357,388,426,440,500,509,524,528],fasolino:428,fast:[6,7,9,12,13,16,39,202,203,281,307,348,377,378,401,440,441,446,476,478,479,499,504,506,515,525,529],faster:[1,6,9,11,12,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,244,248,252,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,304,308,309,317,320,321,335,342,344,347,351,355,361,363,364,366,367,370,372,377,378,390,391,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,500,506,510,518],fastest:[1,6,16,166,347,348,393,494],fatal:[3,514],fault:[74,459],faulti:12,fava:422,favor:227,favorit:7,fbmc:342,fcc:[],fcm:[287,524],fcold:237,fdirect:234,fdotr:427,fdt:[],fdti:95,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:416,feedback:[7,250],feel:[7,250,251,259,297,298,356,358,388,448],felling:445,felt:356,femtosecond:523,fene:[],fennel:[409,431],fep:[],ferguson:[6,184,509],fermi:[1,9,10,12,14,164,393,482],fermion:418,fernando:442,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,207,217,218,219,221,222,237,254,270,303,306,308,321,349,377,386,387,388,395,466,494,497,502,506,508,516,527],fewer:[1,3,11,14,15,63,259,506],fewest:3,fextern:243,feynman:300,fff:495,ffield:[408,419,458,459,466],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,96,120,121,153,299,377,378,506],fft_inc:[12,378],fft_lib:12,fft_path:12,fftbench:[377,516],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:475,fictiti:[6,212,213,236,243,247,300,316,409,431,435,475],field1:[498,502],field2:498,field:[],fifth:[6,331,420,452],figshar:297,figur:[1,3,8,12,307,494,495,519],fij:412,file0:[297,298],file1:[11,13,241,297,298,346,360,387,502,504,508],file2:[11,13,241,346,360,387,502,504,508],file:[],file_from:204,filen:387,filenam:[3,12,13,37,41,56,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,241,297,298,302,305,308,309,310,313,314,317,318,319,346,347,374,375,376,387,388,394,395,399,409,416,417,419,420,428,443,444,445,450,451,452,456,457,458,459,466,467,477,478,479,480,481,482,485,493,494,495,498,499,504,508,515,524,527,528,529],filennam:504,filep:[3,202,203,206,499,504,529],filepo:314,fill:[7,9,178,205,303,347,380,389,399,446,459,500,519],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,411],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,198,207,216,227,228,240,241,242,245,269,297,298,303,304,312,316,384,386,388,389,409,426,431,435,443,450,451,466,476,478,479,518,519,524],find_custom:8,fine:[15,16,182,212,236,345,389,393,519,524],finer:[152,178,524],finest:377,finger:[178,201,267,500],finish:[6,11,41,224,360,374,376,377,390,392,393,484,502,524,525],finit:[],finni:[7,416,476],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,241,245,246,251,256,267,268,269,270,297,298,300,305,306,307,309,314,317,321,323,331,332,333,335,336,337,344,345,346,347,349,353,358,360,361,368,380,386,387,388,389,392,393,394,395,398,399,400,402,404,406,408,409,416,418,419,420,423,424,426,427,428,429,430,431,435,440,441,443,445,446,448,450,451,452,456,458,459,466,467,475,477,478,479,480,481,482,485,489,492,493,494,495,497,498,499,502,504,506,509,510,511,514,515,518,519,524,525,526,527,529],fischer:[6,9,18,19,184,404,509],fit:[3,6,9,12,37,56,198,240,316,335,395,399,428,443,448,450,451,471,478,479,481,505,519,524],five:[77,164,307,387,399,444,497,511],fix:[],fix_deposit:3,fix_ehex07:[],fix_flux:215,fix_heat:237,fix_id:[3,228,268,270,272,273,274,275,276,277,278,304,307],fix_manifoldforc:519,fix_modifi:[],fix_nh:8,fix_nv:519,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:321,fix_reax_bond:458,fix_saed_vtk:319,fix_setforc:8,fix_shak:321,fix_srd:3,fixedpoint:[228,270],fixextern:243,fixid:215,fji:412,flag1:[233,391],flag2:[233,391],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,199,202,203,205,206,207,222,227,229,233,250,253,257,259,266,267,299,306,317,331,334,335,342,346,355,358,373,375,378,387,391,392,393,395,425,430,443,446,475,490,492,494,495,497,498,499,501,502,503,507,519,524],flag_buck:403,flag_coul:[403,412,435],flag_lj:[412,435],flagfld:[401,440,441],flaghi:[3,401,440,441],flaglog:[401,440,441],flagn:233,flagvf:[401,440,441],flat:[6,347,352,353,357],flavor:[2,7,12],fld:[352,440,441],flen:396,flex_press:396,flexibl:[3,6,8,179,205,218,229,247,271,343,350,418,481,515],flip:[3,6,230,270,354,355],floor:524,flop:12,floralwhit:206,flow:[],fluctuat:[6,66,95,228,245,246,253,256,270,275,297,298,299,304,322,345,347,370,414],fluid:[],fluid_veloc:260,flush:[3,206,514],flux:[],flv:205,fly:[7,9,12,41,205,209,215,220,231,234,317,321,348,399,446,515,518],fmackai:9,fmag:232,fmass:300,fmax:[386,515],fmomentum:234,fmsec:[2,206,253,254,267,270,304,317,338,339,506,517,523,525],fname:376,fno:[9,15],fnorm:[386,515],fnpt:234,fnve:237,fnvt:234,foce:426,fock:396,focu:321,fogarti:[9,310,459],foil:[152,297,298,467],fold:[333,506],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,241,243,245,246,247,250,252,253,254,256,259,268,270,275,276,277,278,290,291,293,295,299,300,302,305,306,307,308,310,312,314,316,317,318,319,321,337,338,339,340,343,344,345,346,347,349,350,358,359,363,364,365,366,367,370,372,375,380,383,386,387,388,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,451,452,453,455,456,457,458,459,460,461,463,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,494,495,497,498,500,502,504,505,506,509,511,512,513,518,519,524,525,528],foo:[4,8,11,12,202,205,243,318,495,508,524],foo_species:318,foot:6,footprint:[12,393],fopenmp:[9,15,17],forc:[],force_uvm:16,forceatom:259,forcefield:[316,425],forcegroup:256,forcezero:384,ford:412,forestgreen:206,forev:75,forget:[254,518],forgiv:270,fork:[],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,152,153,172,173,182,186,206,209,210,211,226,246,247,253,255,259,267,293,299,310,312,316,317,318,347,352,356,361,362,365,370,383,385,387,388,395,396,399,406,414,416,418,421,425,426,430,442,443,445,446,450,451,452,453,456,458,459,460,466,467,468,476,478,480,481,482,488,491,494,495,497,502,507,514,518,524],formal:[6,82,85,99,246,247,253,270,300,335,343,466],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,198,202,203,204,205,206,207,218,221,222,224,226,240,241,299,302,306,308,310,313,317,318,319,330,346,347,358,359,362,383,387,388,394,395,399,406,416,419,420,430,443,445,450,451,457,458,459,461,467,478,479,485,486,494,495,497,498,499,502,513,514,515,524,526,527],formation:241,former:[6,12,15,39,41,206,224,347,351,399,401,503,509,524],formerli:[7,13],formul:[1,6,9,40,66,153,212,236,253,270,293,308,310,316,321,346,377,395,399,416,418,422,443,455],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,222,223,230,236,248,249,251,253,254,267,297,298,299,305,314,320,328,333,335,338,339,340,349,352,355,357,358,360,361,362,364,371,380,387,395,396,398,399,404,405,406,407,412,413,416,417,422,423,424,425,427,430,431,433,434,435,437,438,440,441,443,447,448,449,460,461,468,476,477,478,480,481,482,485,487,488,493,497,500,507,514,515,523,524,525],forth:[1,6,11,12,13,14,392,495,500,504],fortran:[3,6,9,11,12,13,243,416,426,443,458,459],fortun:8,forward:[3,8,95,376,388,393],foster:[399,455,456],foul:181,found:[3,6,9,12,77,172,202,227,229,237,245,250,256,262,299,342,348,360,376,389,406,409,412,492,498,499,514],four:[6,11,54,87,113,114,152,174,268,347,370,387,388,446,492],fourier:[],fourth:[6,115,316,331,342,404,420,452,466],fox:[6,130,184,474,509],fphi:[37,56,478,479],fpic:12,fplo:[37,56,478,479],fprime:[478,479],fqdn:252,fqq:412,fraction:[1,3,6,8,12,15,39,41,85,120,153,181,201,205,206,216,225,226,227,228,268,303,307,314,315,335,340,341,380,388,393,399,401,420,423,440,441,502,507],fragment:[42,250,314],fraig:42,frame:[91,152,206,215,268,307,354,422],framer:[205,206],framework:[5,247,394,467],franc:9,frattl:237,fraunhof:9,free:[5,6,7,9,13,28,62,65,74,95,172,210,211,297,298,335,344,345,346,347,385,388,396,418,439,446,449,456,488,494],freedom:[3,6,8,104,106,107,109,111,112,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,227,234,245,247,253,254,259,270,271,275,276,277,278,290,291,293,295,300,302,317,321,338,339,340,345,386,412,515,518,525],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[6,237,245,345],freq:214,frequenc:[3,6,15,39,113,206,220,284,299,300,307,312,375,413,418,459,466,492,506,511,524,528],frequent:[3,66,70,74,76,77,81,96,100,117,152,206,225,226,237,242,343,350,448,483,504,516],fri:[268,307],friction:[4,5,6,9,10,42,209,247,253,307,312,317,347,351,353,423,507],friedrich:324,from:[],front:[268,307,354],frontend:[205,311],frozen:[6,123,182,244,246,254,389,421],fs2:[6,99],fscale:250,fstr:524,fstring:495,ftol:[386,388,492,511],fuchsia:206,fuction:409,fudg:321,fugac:245,fugacity_coeff:245,fulfil:6,full:[1,2,3,6,9,12,16,37,39,40,99,205,219,220,229,237,256,297,298,318,377,378,393,399,416,418,419,422,483,497,499,504,505,509,511,516,518,528],full_energi:[3,245],fuller:386,fulli:[3,6,82,247,252,297,298,386,388,409,456,457,497,519,526,527],fulton:416,fumi:400,func:[495,524],funcfl:416,functionaliri:229,fund:[0,7],fundament:[335,523],funn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354,494,495,497,499,511,524,528],immediat:[330,524],immens:3,immers:[256,317],impact:[1,4,6,8,9,235,342,395,516],impart:[3,6,248,335,357],impei:[6,431],implement:[1,3,6,8,9,12,16,17,26,82,88,89,95,117,130,160,166,177,178,186,187,197,218,229,233,237,239,247,249,250,253,256,258,259,260,268,270,293,296,299,300,306,307,310,311,312,318,321,322,323,335,342,347,351,370,376,377,378,386,388,393,394,396,399,408,409,411,413,414,416,417,418,426,431,435,439,443,455,458,459,460,480,482,494,495,506,511,518,524,526,527],impli:[3,6,40,61,95,153,201,205,210,211,212,230,236,253,316,338,340,341,377,380,406,495],implicit:[],implicitli:8,implict:410,imporop:387,important:345,impos:[2,6,75,123,167,201,209,212,213,223,236,237,238,243,248,251,260,261,269,284,297,298,301,320,328,331,332,334,335,342,343,344,345,350,351,352,355,356,357,386,388,390,491,505,516],impose:248,imposs:[1,3,306,497],improp:[],improper:[3,8,362,368,370,371,387,497],improper_coeff:[],improper_styl:[],impropercoeff:[3,373],impropertyp:226,imprortant:107,improtant:[210,211],improv:[0,1,9,15,39,41,206,224,237,249,270,299,393,425,431,446,448,459,477,481],imrop:369,in3:177,inaccur:[1,3,6,181,268,377],inaccuraci:356,inact:425,inappropri:178,incid:[130,177,231],includ:[],include:[12,374],includelink:9,includig:[360,376],inclus:[],inclusion:12,incom:250,incompat:[3,11,262,286,292,427],incomplet:[3,11,497],incompress:[271,418],inconsist:[3,182,227,498],inconveni:380,incorpor:[307,399,410,519],incorrect:[3,161,253,443],incorrectli:[3,380,423,524],increas:[1,3,6,17,37,56,59,61,120,130,153,198,202,203,205,206,220,225,226,227,230,237,240,241,245,253,304,315,316,317,343,346,350,377,378,388,393,395,418,422,450,451,459,478,479,481,495,506,511,524],increasingli:418,increment:[3,11,140,212,213,223,224,231,236,242,270,303,323,324,358,376,392,429,466,492,495,509,511,524],incur:[16,218,242,347,494],inde:161,indefatig:7,indefinit:344,indent:[],independ:[4,6,9,11,12,15,16,41,61,65,86,99,128,131,164,178,201,209,217,218,219,221,222,224,227,228,229,230,231,246,248,253,254,256,259,270,299,304,308,312,317,319,323,334,345,347,380,423,446,492,495,514,525],indetermin:[202,203,206],index:[0,3,6,8,11,12,37,39,40,56,57,71,73,128,129,131,176,198,202,206,217,219,240,241,250,252,300,319,347,358,359,360,383,392,448,450,451,458,459,478,479,486,497,512,524],indianr:206,indic:[2,3,6,8,11,12,15,20,40,42,54,67,70,72,78,83,87,88,89,96,97,99,101,113,115,123,126,128,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,198,202,205,210,211,228,270,299,317,347,358,361,370,377,387,389,408,415,419,426,443,446,448,452,458,459,466,480,482,494,496,497,499,515,519,524],indigo:206,indirectli:[6,306,524],indistinguish:253,indium:467,individu:[],induc:[],industri:7,ineffici:[3,6,40,66,70,74,76,77,81,100,117,152,166,205,230,270,299,377,390],inelig:216,inerti:441,inertia:[],inertiai:129,inertiax:129,inertiaz:129,inexpens:[247,506],inf:[2,3,12,350,500],infer:[3,104,106,107,172,212,213,224,225,226,236,250,302,335,343,350,380,406,419,497,509,515],infil:[3,13,317,494],infin:[3,386,502,515],infininti:205,infinit:[3,231,244,251,253,256,299,335,347,353,354,378,380,418,497,501,523],infinitesim:6,inflect:[410,433,476],influenc:[3,9,41,85,160,267,303,377,378,448,480,481,482],inform:[0,1,2,3,6,7,8,9,11,12,13,14,16,39,41,42,61,63,64,65,71,96,126,128,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,242,243,244,245,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,266,269,279,280,281,282,283,284,285,286,287,288,289,292,296,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,319,320,321,324,331,332,333,335,336,338,339,340,341,342,343,344,346,349,350,351,352,354,355,356,357,359,375,377,378,381,385,386,387,388,389,391,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,415,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,453,455,456,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,494,495,497,498,499,501,502,504,509,511,512,514,516,524,526,527,528,529],informat:[8,12,498],infrequ:[6,270,413,492,511,516],infti:[410,440,441],ingtegr:399,inher:[377,386,448],inherit:[6,483],inhomogen:[17,347,448],inidividu:386,init:[3,8,315,466],init_fil:347,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,37,39,40,41,56,59,61,64,75,85,87,94,95,113,114,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,241,245,246,250,251,252,253,254,256,261,266,267,268,269,270,275,284,286,299,300,301,306,307,312,315,316,317,320,322,332,334,335,337,342,344,345,346,347,348,349,352,353,354,355,357,358,360,377,381,385,386,388,395,396,412,413,415,446,450,451,457,458,459,466,478,479,492,494,495,497,499,500,502,504,505,507,511,512,515,518,524,525,527,529],initial:[2,3,6,87,113,180,524],initial_integr:8,initial_integrate_respa:8,initialis:457,initialt:347,inlclud:11,inlin:495,inner2:[404,424],inner:[3,8,15,57,202,251,360,376,384,385,386,388,392,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,486,487,488,489,490,506,511,524],inner_distance_cutoff:425,innergroup:259,innermost:[37,56,75,391,478,479,506],innernod:259,innner:437,inordin:348,inorgan:[6,485],inp:[229,360,467,485],input1:[68,71,73,84,102,119,124,125,126,128,129,131,337],input2:[68,71,73,84,102,119,124,125,126,128,129,131,337],input:[],input_doubl:3,inquir:324,insensit:12,insert:[3,5,7,8,9,12,61,178,209,231,245,251,303,377,467,475,495,501,518],insertion:[3,231,245,303],insid:[2,3,6,8,11,75,129,141,147,178,202,203,206,217,231,232,237,242,245,251,256,259,303,317,335,352,354,355,356,357,358,375,380,495,496,497,499,500,507,524],inside:[256,433,495,511],insight:[6,13],instabl:[256,412,465],instal:[1,3,6,8,9,11,12,14,15,16,176,202,204,205,207,378,388,403,404,427,431,435,439,446,492,498,499,504,512,519,529],install:[],instanc:[6,9,11,210,229,247,354,421,426,448,456,495,518],instantan:[6,65,227,228,246,247,270,275,299,304,307,312,314,317,342,503,515],instanti:[6,11,12,215,426,494],instead:[1,3,6,8,11,12,13,16,17,40,41,61,63,65,74,75,98,113,128,156,160,182,184,198,202,203,211,218,221,222,224,228,229,245,253,256,259,260,299,305,306,315,317,337,355,375,377,378,381,389,393,402,403,416,430,432,439,443,446,449,476,483,492,500,504,511,513,518,524],institut:[9,250,302],instruct:[3,4,6,8,9,10,11,12,13,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,244,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,309,317,320,321,355,361,363,364,366,367,370,372,378,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,460,461,468,477,478,480,481,482,483,485,487,488,489,500,506,518],instruction:11,insuffici:[3,6,12],insult:270,insur:[3,6,11,12,16,39,40,63,77,112,114,178,179,198,202,203,205,206,212,225,226,231,236,238,242,243,245,248,253,266,305,306,315,317,335,347,352,356,357,358,360,376,387,389,393,407,422,426,454,460,478,490,494,495,497,498,502,505,506,514,515,524,525],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,243,245,246,247,250,253,254,255,256,299,302,303,306,307,312,317,335,337,339,342,346,347,366,377,380,401,413,414,415,429,443,458,459,463,465,467,492,494,495,496,497,505,506,507,511,514,524,525],integer:[3,497],integr:[],integral:[300,450,451],integrate_ulsph:[],intel:[],intel_cpu:[12,15],intel_phi:[12,15],intend:[3,6,8,12,13,35,220,246,457,497],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,242,249,259,268,270,275,314,317,319,335,343,347,349,350,514,515,523],intensiv:[65,209,515],intepol:524,inter:[17,42,63,64,158,181,182,202,227,253,255,269,309,317,377,388,399,507,518,524,527,529],interact:[1,3,6,7,8,9,10,11,12,14,15,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,244,245,250,251,253,255,259,284,297,298,300,302,303,308,310,316,317,318,325,326,335,336,342,347,351,352,353,356,357,362,363,364,365,367,369,371,377,378,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,459,460,461,463,465,466,467,468,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,492,495,497,499,501,502,506,507,509,514,515,518,527],interatom:[3,4,7,9,10,178,202,269,344,345,394,399,416,418,427,443,446,466,481,524],intercept:130,interchang:6,interconnect:17,interconvert:418,intereract:39,interesect:356,interest:[1,5,7,8,9,11,13,75,177,300,342,345,378,417,441,458,459,495,524],interf:[393,519],interfac:[],interfer:[12,270,395],interg:[6,518],intergr:506,interi:441,interior:[3,6,41,356,500],interlac:443,interleav:[6,178,505],intermedi:[6,12,61,205,269,297,298,370,388,495,496,505,509],intermix:492,intermolecular:[154,395],intern:[],internal:[3,205,211,303,524],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:252,interpenetr:443,interpentr:[470,471,473],interpol:[6,14,37,56,110,198,205,206,215,240,241,256,297,298,377,378,388,399,448,450,451,459,472,478,479,480],interpret:[2,6,11,205,221,423,468,492,495,511,524],interrupt:307,intersect:[3,6,130,206,356,358,500],intersert:356,interspers:386,interstiti:[176,446],intertia:[3,103],interv:[3,6,99,204,219,253,270,307,312,313,326,466,472,492,511,524],intestieti:130,intial:[6,393,395],intiial:[41,502],intiti:[3,334],intra:317,intra_energi:245,intramolecular:[28,154,245],introduc:[6,9,100,117,205,237,270,307,312,317,370,377,394,409,418,431,435,439,477,511,524],introduct:[],intuit:380,inv:[130,177,319],invalid:[3,12,75,97,181,284,388,440,441,499],invari:[117,145,150,152],invent:321,invers:[],inverse:518,invert:[1,6,182,299],invis:356,invoc:[176,227,393,463,465,495],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,96,97,98,103,113,114,116,121,122,123,128,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,198,202,203,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,236,237,238,242,243,244,245,246,248,249,250,251,253,254,255,256,257,258,259,260,261,262,263,264,266,267,269,270,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,317,319,320,321,323,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,361,363,364,366,367,370,372,376,377,378,379,380,386,388,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,427,431,432,433,434,435,436,437,438,439,440,441,444,448,449,452,453,455,460,461,463,465,467,468,477,478,480,481,482,483,485,486,487,488,489,491,494,495,496,498,500,502,505,506,508,509,511,514,515,518,524,525],invokd:3,invoke:[3,12,16],involv:[3,6,7,8,12,65,119,126,127,128,158,182,209,216,225,245,256,302,305,310,335,377,385,386,388,398,415,422,429,477,480,482,493,494,500,502,506,511,512],ioff:[387,497],ion:[6,7,9,160,296,331,347,378,399,410,419,421,443,446,466,476,482,489,497,518],ionic:[6,9,400,402,410,418,419,453,466,518],ioniz:[408,418],ionocoval:9,iparam:[3,226],ipi:[],ipp:[],ir3:177,ir4:177,irregular:[6,41,60,224,228,230,270,317],irrelev:452,irrespect:[440,441],irrevers:[234,318],is_act:[3,524],is_avail:[3,524],is_defin:[3,524],isbn:488,isele:[377,378],isenthalp:[9,270,271,272,273,274],ismail:[377,378,403,435],isn:[3,8,11,12,237,249],iso:[3,228,234,254,270,271,272,273,274,275,276,277,278,304,312,317,518],isobar:[9,270,271,276,277,278,322,414],isodem:418,isoenerget:[9,322,414],isoenthalp:[322,414],isol:[3,181,358],isomorph:300,isotherm:[9,245,270,271,276,277,278,304,322,414],isotop:306,isotrop:[6,100,253,304,377,378,401,422,440,441],isovolum:319,isralewitz:323,issu:[1,3,6,9,11,12,13,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,61,75,77,87,113,123,155,165,184,185,187,188,189,190,192,193,195,196,198,205,212,223,227,228,230,231,236,237,238,244,245,248,253,268,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,300,304,306,309,317,320,321,334,338,339,340,345,355,357,360,361,363,364,366,367,370,372,378,387,388,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,460,461,468,475,477,478,480,481,482,483,485,487,488,489,497,499,500,506,509,514,515,524,525],issue:215,ital:[458,459],itali:13,item:[6,7,8,41,202,206,224],iter:[3,6,12,39,41,65,204,212,213,223,224,228,234,236,243,251,286,292,299,308,309,317,321,332,342,358,360,376,384,385,386,388,392,466,492,502,506,511,515,516,524],iterat:[12,386],ith:[75,128,131,217,218,219,220,221,222,337,349,515,524],itself:[2,3,6,7,8,9,11,12,13,17,42,61,99,118,169,202,204,205,206,207,219,220,229,234,254,265,269,311,317,347,358,360,387,388,409,419,422,426,427,450,451,478,479,495,501,504,505,509,524,529],itset:507,ityp:[3,57,126,127,178,214,226,310,486],itype1:127,itype2:127,itypen:127,ivector:8,ivori:206,ixcm:317,ixi:[42,317,387],ixx:[42,103,317,387,524],ixy:[103,387,524],ixz:[42,103,317,387,524],iycm:317,iyi:[42,103,317,387,524],iyz:[42,103,317,387,524],izcm:317,izrailev:323,izumi:481,izz:[42,103,317,387,524],j0jt:99,j20:219,j_m:152,jackson:447,jacobi:3,jacobsen:385,jacs:[6,184,509],jagreat:13,jame:[9,18],janssen:[297,298],januari:443,jaramillo:[7,9,13,418],jarzynski:323,jatempl:9,jcc:9,jcp:352,jec:13,jeff:13,jello:270,jensen:[253,377],jeremi:[9,445],jerom:9,jewett:13,jiang:[254,518],jiao:[9,13],jiht:[7,9],jik:399,jim:7,jku:[7,9],jmake:12,jmm:152,joannopoulo:268,job:[12,62,321,505],jochim:[270,271],john:[7,9,13,204],johnson:[9,13],join:[6,423,500],joint:[3,302,425],jon:[9,74],jonathan:9,jone:[1,3,6,7,9,10,12,13,45,46,66,95,118,121,184,209,215,237,304,335,352,356,378,380,386,395,398,402,403,404,405,407,412,422,424,425,426,429,430,431,432,433,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff 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 hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff 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 hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute rigid/local command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian 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_coeff 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 dsmc 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 hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/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_modify 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 none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[36,39,40,55,59,60,61,63,64,75,95,96,100,112,113,115,117,118,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,242,245,246,251,253,254,255,256,257,259,265,268,270,271,275,293,294,299,300,303,304,305,306,307,309,312,314,315,317,319,335,337,342,343,344,345,348,350,352,354,358,371,375,377,378,380,381,384,385,387,389,390,391,393,396,399,401,418,440,441,446,448,458,459,475,476,492,493,494,497,498,500,502,504,505,506,509,511,513,514,515,516,517,523,525,527,528],"function":524,"long":[220,400,402,403,404,405,409,411,412,431,435,439,453,461,483],"new":8,"static":12,acceler:1,account:519,ackland:66,acknowledg:7,adapt:[210,211],addforc:212,adding:519,addition:[12,13,519],addtorqu:213,adiabat:6,adjust_dt:324,adp:394,after:519,airebo:395,alloi:416,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:214,arrai:6,aspher:[6,90,156,272,276,280,281,290],asphere:9,atc:[9,215],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,214,216,217,306,524],atom_modifi:39,atom_styl:40,attract:5,aveforc:223,awpmd:[9,396],axel:519,balanc:[41,224],barostat:6,basal:70,bcc:297,beck:397,berendsen:[304,338],between:6,binary2txt:13,bodi:[6,8,42,71,157,273,277,282,291,398],body:9,bond:[8,13,72,73,225,226,227,313],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:399,born:[400,411],boundari:[7,59],box:[6,60,228],branch:519,brownian:401,buck:[402,403,411,442],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:519,change_box:61,charmm:[6,19,184,404,439],chunk:[6,69,75,79,86,98,103,114,116,125,158,173,175,218,332],citat:7,class2:[9,20,43,185,361,405],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,352,407,488],colvar:[13,229],colvars:9,com:[78,79,159],comb3:408,comb:[309,408],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,524],compute_modifi:112,condit:7,conduct:[6,343],constant:[6,524],constraint:7,contact:[80,132],coord:81,core:6,coreshell:9,correl:[219,220],cosin:[22,23,24,25,26,27,187],cossq:363,coul:[400,402,403,404,405,409,410,411,424,431,435,439,453,461],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:339,csvr:339,cubic:433,cuda:[],custom:[8,202,203],cut:[49,396,402,405,409,412,418,421,431,432,439,447,453,483],cvff:364,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[409,431],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:23,deposit:231,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],diagnost:7,diel:410,dielectr:183,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:85,dimens:200,dipol:[6,28,86,412],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:201,distanc:365,distribut:[7,12],document:0,dpd:[9,88,89,413,414],drag:232,dreid:425,dreiding:6,drude:[6,9,163,233,234,254,518],dsf:[409,431],dsmc:415,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:308,eam:[13,416],echo:208,edip:417,eff:[9,13,106,107,162,164,169,255,271,283,294,341,418],efield:236,ehex:237,eim:419,elastic:6,emac:13,energi:[135,414],enforce2d:238,ensembl:7,erot:[90,91,92,93],error:[3,134],evapor:242,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],exp6:420,exp:[26,187],expand:[46,434],extend:[8,11],extern:243,fcc:[297,298],fdt:414,featur:[7,8,519,524],fene:[45,46],fep:[9,13,95,211],field:[6,7],file:6,finit:6,fire:308,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,2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\ No newline at end of file diff --git a/doc/html/timer.html b/doc/html/timer.html index a9fecb6090..0c61197504 100644 --- a/doc/html/timer.html +++ b/doc/html/timer.html @@ -132,7 +132,7 @@
off = do not collect or print any timing information @@ -141,24 +141,26 @@ full = like normal but also include CPU and thread utilzation sync = explicitly synchronize MPI tasks between sections nosync = do not synchronize MPI tasks between sections (default) +timeout elapse = set walltime limit to elapse +every Ncheck = perform timeout check every Ncheck steps
timer full sync
+timer timeout 2:00:00 every 100
timer loop
Select the level of detail LAMMPS performs its CPU timings.
+Select the level of detail at which LAMMPS performs its CPU timings.
During a simulation run LAMMPS collects information about how much time is spent in different sections of the code and thus can provide -valuable information for determining performance and load imbalance -problems. This can be done at different levels of detail and -accuracy. For more information about the timing output, see this -discussion of screen output.
+information for determining performance and load imbalance problems. +This can be done at different levels of detail and accuracy. For more +information about the timing output, see this discussion of screen output.The off setting will turn all time measurements off. The loop setting will only measure the total time for a run and not collect any detailed per section information. With the normal setting, timing @@ -171,8 +173,27 @@ utilization and thread utilization, when multi-threading is enabled.
call which meaures load imbalance more accuractly, though it can also slow down the simulation. Using the nosync setting (which is the default) turns off this synchronization. -Multiple keywords can be specified. For keywords that are mutually -exclusive, the last one specified takes effect.
+With the timeout keyword a walltime limit can be imposed that +affects the run and minimize commands. If +the time limit is reached, the run or energy minimization will exit on +the next step or iteration that is a multiple of the Ncheck value +specified with the every keyword. All subsequent run or minimize +commands in the input script will be skipped until the timeout is +reset or turned off by a new timer command. The timeout elapse +value can be specified as off or unlimited to impose no timeout +condition (which is the default). The elapse setting can be +specified as a single number for seconds, two numbers separated by a +colon (MM:SS) for minutes and seconds, or as three numbers separated +by colons for hours, minutes, and seconds.
+The every keyword sets how frequently during a run or energy +minimization the wall clock will be checked. This check count applies +to the outer iterations or time steps during minimizations or r-RESPA runs, respectively. Checking for timeout too often, +can slow a calculation down. Checking too infrequently can make the +timeout measurement less accurate, with the run being stopped later +than desired.
+Multiple keywords can be specified with the timer command. For +keywords that are mutually exclusive, the last one specified takes +effect.
Note
Using the full and sync options provides the most detailed @@ -196,7 +217,11 @@ can just use the loop or off setting.
timer normal nosync
+timer normal nosync
+timer timeout off
+timer every 10
+