dihedral_style none - turn off dihedral interactions
dihedral_style hybrid - define multiple styles of dihedral interactions
+dihedral_style zero - topology but no interactions
dihedral_style charmm - CHARMM dihedral
dihedral_style class2 - COMPASS (class 2) dihedral
dihedral_style harmonic - harmonic dihedral
diff --git a/doc/dihedral_style.txt b/doc/dihedral_style.txt
index b07cb056c9..6e76d887a9 100644
--- a/doc/dihedral_style.txt
+++ b/doc/dihedral_style.txt
@@ -86,7 +86,8 @@ links to the individual styles are given in the dihedral section of
"this page"_Section_commands.html#cmd_5.
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
-"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
+"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions
+"dihedral_style zero"_dihedral_zero.html - topology but no interactions :ul
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
diff --git a/doc/dihedral_zero.html b/doc/dihedral_zero.html
new file mode 100644
index 0000000000..ba12edcffc
--- /dev/null
+++ b/doc/dihedral_zero.html
@@ -0,0 +1,227 @@
+
+
+
+
+
+
+
+
+
+
+ dihedral_style zero command — LAMMPS documentation
+
+
+
+
+
+
+
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+ LAMMPS
+
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+
+
+
dihedral_style zero command
+
+
+
Examples
+
dihedral_style zero
+dihedral_coeff *
+
+
+
+
+
Description
+
Using a dihedral style of zero means dihedral forces and energies are
+not computed, but the geometry of dihedral quadruplets is still
+accessible to other commands.
+
As an example, the compute dihedral/local command can be used to
+compute the theta values for the list of quadruplets of dihderal atoms
+listed in the data file read by the read_data
+command. If no dihedral style is defined, this command cannot be used.
+
Note that the dihedral_coeff command must be
+used for all dihedral types, though no additional values are
+specified.
+
+
+
+
+
+
+
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\ No newline at end of file
diff --git a/doc/dihedral_zero.txt b/doc/dihedral_zero.txt
new file mode 100644
index 0000000000..85523847b7
--- /dev/null
+++ b/doc/dihedral_zero.txt
@@ -0,0 +1,42 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+dihedral_style zero command :h3
+
+[Syntax:]
+
+dihedral_style zero :pre
+
+[Examples:]
+
+dihedral_style zero
+dihedral_coeff * :pre
+
+[Description:]
+
+Using a dihedral style of zero means dihedral forces and energies are
+not computed, but the geometry of dihedral quadruplets is still
+accessible to other commands.
+
+As an example, the "compute
+dihedral/local"_compute_dihedral_local.html command can be used to
+compute the theta values for the list of quadruplets of dihderal atoms
+listed in the data file read by the "read_data"_read_data.html
+command. If no dihedral style is defined, this command cannot be used.
+
+Note that the "dihedral_coeff"_dihedral_coeff.html command must be
+used for all dihedral types, though no additional values are
+specified.
+
+[Restrictions:] none
+
+[Related commands:] none
+
+"dihedral_style none"_dihedral_none.html
+
+[Default:] none
diff --git a/doc/genindex.html b/doc/genindex.html
index c74d4bfaa6..1a6d68f591 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -234,6 +234,10 @@
+ angle_style zero
+
+
+
atom_modify
@@ -310,6 +314,10 @@
+ bond_style zero
+
+
+
boundary
@@ -835,12 +843,12 @@
dihedral_style multi/harmonic
-
-
dihedral_style nharmonic
+
+
dihedral_style none
@@ -858,6 +866,10 @@
+ dihedral_style zero
+
+
+
dimension
@@ -1548,6 +1560,10 @@
+ improper_style zero
+
+
+
include
@@ -2030,6 +2046,10 @@
+ pair_style zero
+
+
+
pair_write
diff --git a/doc/improper_none.html b/doc/improper_none.html
index 1b3ab5f4fb..a4ac43b6b1 100644
--- a/doc/improper_none.html
+++ b/doc/improper_none.html
@@ -140,15 +140,20 @@
Description
-
Using an improper style of none means improper forces are not
-computed, even if quadruplets of improper atoms were listed in the
+
Using an improper style of none means imroper forces and energies are
+not computed, even if quadruplets of improper atoms were listed in the
data file read by the read_data command.
+
See the improper_style zero command for a way to
+calculate improper statistics, but compute no improper interactions.
Restrictions
none
-
Related commands: none
+
+
diff --git a/doc/improper_none.txt b/doc/improper_none.txt
index 803cc23b02..af9964c743 100644
--- a/doc/improper_none.txt
+++ b/doc/improper_none.txt
@@ -18,12 +18,17 @@ improper_style none :pre
[Description:]
-Using an improper style of none means improper forces are not
-computed, even if quadruplets of improper atoms were listed in the
+Using an improper style of none means imroper forces and energies are
+not computed, even if quadruplets of improper atoms were listed in the
data file read by the "read_data"_read_data.html command.
+See the "improper_style zero"_improper_zero.html command for a way to
+calculate improper statistics, but compute no improper interactions.
+
[Restrictions:] none
-[Related commands:] none
+[Related commands:]
+
+"improper_style zero"_improper_zero.html
[Default:] none
diff --git a/doc/improper_style.html b/doc/improper_style.html
index 8577b1da6d..c7e48eca38 100644
--- a/doc/improper_style.html
+++ b/doc/improper_style.html
@@ -184,6 +184,7 @@ links to the individual styles are given in the improper section of
this page .
improper_style none - turn off improper interactions
+improper_style zero - topology but no interactions
improper_style hybrid - define multiple styles of improper interactions
improper_style class2 - COMPASS (class 2) improper
improper_style cvff - CVFF improper
diff --git a/doc/improper_style.txt b/doc/improper_style.txt
index e227a71de2..0bd1c10b58 100644
--- a/doc/improper_style.txt
+++ b/doc/improper_style.txt
@@ -65,6 +65,7 @@ links to the individual styles are given in the improper section of
"this page"_Section_commands.html#cmd_5.
"improper_style none"_improper_none.html - turn off improper interactions
+"improper_style zero"_improper_zero.html - topology but no interactions
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
"improper_style class2"_improper_class2.html - COMPASS (class 2) improper
diff --git a/doc/improper_zero.html b/doc/improper_zero.html
new file mode 100644
index 0000000000..6d7cc13a58
--- /dev/null
+++ b/doc/improper_zero.html
@@ -0,0 +1,228 @@
+
+
+
+
+
+
+
+
+
+
+ improper_style zero command — LAMMPS documentation
+
+
+
+
+
+
+
+
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+
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+
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+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
improper_style zero command
+
+
+
Examples
+
improper_style zero
+improper_coeff *
+
+
+
+
+
Description
+
Using an improper style of zero means improper forces and energies are
+not computed, but the geometry of improper quadruplets is still
+accessible to other commands.
+
As an example, the compute improper/local command can be used to
+compute the chi values for the list of quadruplets of improper atoms
+listed in the data file read by the read_data
+command. If no improper style is defined, this command cannot be
+used.
+
Note that the improper_coeff command must be
+used for all improper types, though no additional values are
+specified.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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\ No newline at end of file
diff --git a/doc/improper_zero.txt b/doc/improper_zero.txt
new file mode 100644
index 0000000000..7adbdbf05a
--- /dev/null
+++ b/doc/improper_zero.txt
@@ -0,0 +1,43 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+improper_style zero command :h3
+
+[Syntax:]
+
+improper_style zero :pre
+
+[Examples:]
+
+improper_style zero
+improper_coeff * :pre
+
+[Description:]
+
+Using an improper style of zero means improper forces and energies are
+not computed, but the geometry of improper quadruplets is still
+accessible to other commands.
+
+As an example, the "compute
+improper/local"_compute_improper_local.html command can be used to
+compute the chi values for the list of quadruplets of improper atoms
+listed in the data file read by the "read_data"_read_data.html
+command. If no improper style is defined, this command cannot be
+used.
+
+Note that the "improper_coeff"_improper_coeff.html command must be
+used for all improper types, though no additional values are
+specified.
+
+[Restrictions:] none
+
+[Related commands:] none
+
+"improper_style none"_improper_none.html
+
+[Default:] none
diff --git a/doc/pair_none.html b/doc/pair_none.html
index 6feb1cccc6..f3edd46ae5 100644
--- a/doc/pair_none.html
+++ b/doc/pair_none.html
@@ -152,12 +152,17 @@ data structures for binning are still allocated. If the neighbor skin
distance is small, then these data structures can consume a large
amount of memory. So you should either set the neighbor style to
nsq or set the skin distance to a larger value.
+See the pair_style zero for a way to trigger the
+building of a neighbor lists, but compute no pairwise interactions.
Restrictions
none
-
Related commands: none
+
+
diff --git a/doc/pair_none.txt b/doc/pair_none.txt
index 14aa9db2b0..c3ba80e9a6 100644
--- a/doc/pair_none.txt
+++ b/doc/pair_none.txt
@@ -33,8 +33,13 @@ distance is small, then these data structures can consume a large
amount of memory. So you should either set the neighbor style to
{nsq} or set the skin distance to a larger value.
+See the "pair_style zero"_pair_zero.html for a way to trigger the
+building of a neighbor lists, but compute no pairwise interactions.
+
[Restrictions:] none
-[Related commands:] none
+[Related commands:]
+
+"pair_style zero"_pair_zero.html
[Default:] none
diff --git a/doc/pair_style.html b/doc/pair_style.html
index db97b39651..1da7ba694e 100644
--- a/doc/pair_style.html
+++ b/doc/pair_style.html
@@ -208,6 +208,7 @@ in the pair section of pair_style none - turn off pairwise interactions
pair_style hybrid - multiple styles of pairwise interactions
pair_style hybrid/overlay - multiple styles of superposed pairwise interactions
+pair_style zero - neighbor list but no interactions
pair_style adp - angular dependent potential (ADP) of Mishin
pair_style airebo - AIREBO potential of Stuart
pair_style beck - Beck potential
diff --git a/doc/pair_style.txt b/doc/pair_style.txt
index c221cb058e..248753260b 100644
--- a/doc/pair_style.txt
+++ b/doc/pair_style.txt
@@ -97,7 +97,8 @@ in the pair section of "this page"_Section_commands.html#cmd_5.
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
-"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions :ul
+"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions
+"pair_style zero"_pair_zero.html - neighbor list but no interactions :ul
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
diff --git a/doc/pair_zero.html b/doc/pair_zero.html
new file mode 100644
index 0000000000..612eb8e395
--- /dev/null
+++ b/doc/pair_zero.html
@@ -0,0 +1,244 @@
+
+
+
+
+
+
+
+
+
+
+ pair_style zero command — LAMMPS documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
pair_style zero command
+
+
Syntax
+
+
+zero = style name of this pair style
+cutoff = global cutoff (distance units)
+
+
+
+
Examples
+
pair_style zero
+pair_coeff * *
+pair_coeff 1 2 3.0
+
+
+
+
+
Description
+
Define a global cutoff length for the purpose of building a neighbor
+list and acquiring ghost atoms, but do not compute any pairwise
+forces.
+
This can be useful for fixes or computes which require a neighbor list
+to enumerate pairs of atoms within some cutoff distance, but when
+pairwise forces are not otherwise needed. Examples are the fix bond/create , compute rdf ,
+compute voronoi/atom commands.
+
Note that the comm_modify cutoff command can be
+used to insure communication of ghost atoms even when a pair style is
+not defined, but it will not trigger neighbor list generation.
+
The following coefficients must be defined for each pair of atoms
+types via the pair_coeff command as in the examples
+above, or in the data file or restart files read by the
+read_data or read_restart
+commands, or by mixing as described below:
+
+cutoff (distance units)
+
+
This coefficient is optional. If not specified, the global cutoff
+specified in the pair_style command is used.
+
+
+
+
+
+
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+
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\ No newline at end of file
diff --git a/doc/pair_zero.txt b/doc/pair_zero.txt
new file mode 100644
index 0000000000..a891a392b1
--- /dev/null
+++ b/doc/pair_zero.txt
@@ -0,0 +1,57 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style zero command :h3
+
+[Syntax:]
+
+pair_style zero cutoff :pre
+
+zero = style name of this pair style
+cutoff = global cutoff (distance units) :l
+
+[Examples:]
+
+pair_style zero
+pair_coeff * *
+pair_coeff 1 2 3.0 :pre
+
+[Description:]
+
+Define a global cutoff length for the purpose of building a neighbor
+list and acquiring ghost atoms, but do not compute any pairwise
+forces.
+
+This can be useful for fixes or computes which require a neighbor list
+to enumerate pairs of atoms within some cutoff distance, but when
+pairwise forces are not otherwise needed. Examples are the "fix
+bond/create"_fix_bond_create.html, "compute rdf"_compute_rdf.html,
+"compute voronoi/atom"_compute_voronoi_atom.html commands.
+
+Note that the "comm_modify cutoff"_comm_modify.html command can be
+used to insure communication of ghost atoms even when a pair style is
+not defined, but it will not trigger neighbor list generation.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands, or by mixing as described below:
+
+cutoff (distance units) :ul
+
+This coefficient is optional. If not specified, the global cutoff
+specified in the pair_style command is used.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"pair_style none"_pair_none.html
+
+[Default:] none
diff --git a/doc/searchindex.js b/doc/searchindex.js
index b1ca3ec42a..0ffb7e3619 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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[3,6,320],advertis:8,advis:[371,438],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,196,197,202,209,210,212,213,214,215,218,219,220,221,223,224,234,240,242,244,250,257,261,262,263,264,266,267,268,274,279,280,281,283,304,305,318,332,342,355,361,367,368,369,371,372,373,376,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,223,376,391],afil:238,aforement:18,afresh:[292,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,198,200,201,202,206,207,209,210,217,218,219,220,221,223,227,236,247,248,249,250,251,256,257,258,260,266,267,268,274,279,280,281,283,286,290,294,302,304,307,316,321,323,324,325,327,328,329,330,331,335,337,339,343,346,347,353,360,366,367,369,370,372,374,375,376,377,378,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,197,223,240,290,346,360,371,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,224,371,439,440],aggreg:[6,12,65,68,69,79,95,112,119,240,256,302,304,318,471,503],aggress:[240,490],agilio:[9,13],agre:[3,8,190,369,378,411,440],agreement:[5,7],ahd:408,ahead:339,aidan:[0,5,7,9,13,364],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:196,akohlmei:[7,9,13,198,241],aktulga:[7,9,297,440],al2o3:447,al2o3_001:[122,305],al3:169,ala:[247,447],alain:9,alat:[285,426],alb:[437,460,462],albeit:303,albert:9,alchem:[89,164],alcohol:335,alcu:[377,382],alcu_eam:437,alderton:395,alejandr:[260,261],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,197,206,217,220,223,247,249,250,274,287,295,304,307,308,327,328,332,335,340,367,368,369,373,376,398,402,424,429,444,446,471,473,490],alia:[9,12,16],alias:[1,362],aliceblu:197,align:[6,12,29,41,71,172,190,213,217,242,364,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,198,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,253,255,256,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,305,306,307,308,309,310,311,312,316,317,319,320,321,322,323,324,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,351,356,359,360,361,362,363,364,366,369,370,371,372,373,375,376,377,378,379,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:344,alloc:[3,5,6,8,9,11,12,60,234,334,370,372,376,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,194,196,197,198,200,201,203,205,206,207,209,210,211,212,213,214,215,217,219,220,221,222,223,224,228,229,234,236,237,238,239,241,244,247,250,251,255,257,260,261,285,289,290,291,292,293,294,298,304,305,307,309,311,312,316,320,327,328,329,330,332,333,334,335,336,337,343,345,347,356,361,362,364,369,370,371,372,375,376,379,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,242,294,332,362,373,376,456],alo:392,alon:[6,7,220,300,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,196,209,220,242,247,248,252,257,259,294,304,307,309,313,317,318,327,331,332,338,341,343,364,367,368,369,371,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,201,247,286,294,295,299,369,377,380,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,200,347,356,370,389,457,476],alphanum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8,405,441],check:[3,6,8,11,12,15,17,39,41,71,93,190,207,213,217,218,219,224,233,236,242,243,290,303,307,320,328,330,335,343,345,360,369,370,371,372,373,376,399,410,413,431,440,471,473,474,476,484,490,493,494,502],checkf:190,checkqeq:440,checku:190,chem:[6,13,20,21,25,39,40,43,45,46,89,90,110,116,145,176,177,187,211,222,227,237,238,245,247,259,260,261,281,282,287,291,294,296,304,308,309,320,323,324,327,328,329,330,337,346,355,357,361,362,368,371,378,383,387,388,391,392,393,395,396,398,402,404,405,407,408,414,418,419,422,426,430,431,434,447,456,463,485,488,490,497],chemic:[9,122,164,169,193,194,206,207,236,295,300,301,327,362,439,440,452],chemistri:[9,294,295,297,382,402,439,440],chen:332,cheng:391,chenoweth:[439,440],chenoweth_2008:[439,440],chi:[95,159,192,285,295,297,403,405,503],chiefli:438,child:8,chip:[7,9,12,17,18,376,489],chipot:222,chiral:355,chmod:[11,12],cho:426,chocol:[7,197],choic:[3,6,9,12,15,16,18,40,41,54,89,145,148,149,163,174,190,209,213,214,217,220,223,224,238,244,247,258,260,287,295,304,327,356,362,367,368,371,373,376,409,422,431,435,476,485,486,489,490,496,497,501],choos:[1,3,6,7,8,12,16,17,18,29,39,54,89,121,160,161,196,218,219,220,221,224,233,244,247,258,260,262,263,264,265,266,267,268,290,291,308,320,324,338,361,362,368,466,471,473,485,491],chose:[460,462],chosen:[2,3,6,12,17,144,170,173,182,190,196,202,207,221,224,233,236,237,245,247,258,260,265,287,290,301,320,324,327,328,333,335,336,342,362,363,368,376,397,398,402,406,413,416,442,460,471,485,490,497],chri:168,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,92,96,107,109,118,150,165,167,209],chute:[4,9,10,239],ciccotti:307,cieplak:[6,176,488],cii:210,cij:210,ciko:2,circl:[42,71,316],circular:[3,6,148,191],circumst:18,circumv:[94,110,299],citat:[],cite:[3,7,8,12,244,447],civ:9,ckio:2,cko:2,cl1:169,clarendon:[29,395],clarifi:[7,460,462],clariti:345,clark:434,class2:[],classic:[0,3,5,6,7,8,9,234,287,294,299,332,357,402],classifi:[9,457,465],claus:474,clean:[6,12,14,15,17,484],cleanli:[475,505],clear:[],clearli:7,clebsch:144,clermont:[9,13],clever:480,click:[2,11,22,37,44,55,170,178,189,196,241,347,356,371,389,457],client:[241,243],climb:[259,371,490],clinic:[7,13],clo:[159,192,503],clock:[12,471,490],clockwis:338,close:[3,6,11,12,13,39,41,67,71,145,173,193,219,220,221,238,245,247,260,281,304,307,338,341,360,362,365,367,368,371,376,378,382,392,393,412,426,431,443,445,459,462,480,486,497,499],closer:[3,41,120,168,192,193,217,221,225,329,371],closest:[219,285,304,335,405,441,456,466],cloud:[447,497],clovertown:18,clsuter:72,clump1:[289,304],clump2:[289,304],clump3:[289,304],clump:304,cluster:[],clutter:[3,9],cmap:476,cmatrix:238,cmax:426,cmd:[11,12,287,487],cmdarg:11,cmin:426,cmm:[],cmoput:137,cn1:210,cn2:210,cna:[],cnn:210,cnr:[9,13],cnt:[409,480],co2:[40,169,307,370],coars:[7,9,29,36,40,54,182,289,304,320,407,442,485,488],coarser:[362,502],coarsest:144,code:[],coeff:[3,7,8,12,21,22,33,44,50,176,177,178,183,346,347,353,389,409,413,431,444,446,449,476],coeffcient:476,coeffici:[],coefficienct:396,coefficient0:400,coefficient1:400,coeffieci:[6,380,412],coeffincientn:400,coexist:[9,236,402],cohes:[6,403,426],coincid:[126,341,387,423,424,471],colberg:195,cold:[6,155,236,240,372,497],coldest:328,coleman8:9,coleman:[9,122,169,305],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,85,92,96,101,107,109,118,150,158,165,167,170,193,194,197,209,222,250,256,289,299,302,304,343,361,370,372,390,476,483,489,495,506],collid:[228,320,342],colliex:169,collinear:[3,289],collis:[3,247,320,338,342,399,406,469],colllis:320,colloid:[],colombo:39,colon:[198,343,477],color1:197,color2:197,color:[3,9,41,193,196,197,217,237,294,299],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,83,92,94,95,96,107,109,110,112,114,117,118,119,120,121,123,144,145,150,158,165,167,168,169,190,193,194,197,200,208,209,210,212,213,214,215,250,257,258,294,304,321,322,332,342,404,408,439,440,477,491,493,502],columnar:168,colvar:[],colvarmodul:12,com:[],comamnd:223,comand:220,comannd:376,comb3:[],comb:[],comb_1:296,comb_2:296,combiant:393,combin:[3,6,7,9,11,13,36,40,63,65,69,79,89,95,106,112,119,148,149,163,193,196,206,212,241,250,260,287,293,308,324,333,341,344,346,361,362,364,368,376,390,392,393,398,402,403,409,421,422,448,458,460,462,465,468,479,484,489,497,502],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,195,241,243,244,362,371,376,396,431,436,459,478],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,176,190,193,232,245,304,332,370,371,377,400,401,403,413,426,433,440,447,448,458,459,460,461,462,465,473,474,476,497,502],commerci:7,commit:9,commmand:[3,6,12,59,111,282,412,470,471,473,490,505],common:[],commonli:[3,6,12,17,25,57,59,108,110,172,193,196,198,357,407,416,448,460,462,476,479,488],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,173,174,196,197,217,218,219,221,222,223,241,243,247,249,250,251,260,286,293,295,296,297,304,308,320,332,343,359,361,372,373,374,376,398,399,435,473,474,485,486,502,504,506],communc:361,comp:[7,195,243,244,307,362,371,402,431,436,441,455,459,461],compact:[63,200,389,457],compani:[5,7],compar:[1,3,4,6,8,12,17,39,88,114,122,153,169,178,189,197,227,295,343,345,361,362,369,371,426,447,471,490,491,497,501],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,346,347,356,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,198,202,208,209,210,212,213,214,215,217,286,298,324,327,334,337,340,361,376,410,429,431,459,473,474,502],compens:[6,218,219,302,372,402],compet:331,competit:362,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,195,196,198,241,331,362,376,429,476,477,481,502],compl:17,complain:[11,12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,197,213,217,222,250,287,290,293,320,331,333,344,345,360,371,376,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,247,316,341,359,371,402,429,459,474,476,479,502],compli:[327,331],complic:[6,7,9,12,13,207,236,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,194,196,197,203,204,208,209,210,211,212,213,214,215,216,220,221,223,224,229,234,239,243,244,247,250,252,256,257,259,260,261,265,266,267,268,279,280,281,283,284,286,287,288,291,302,304,306,307,309,313,314,317,320,323,324,325,327,334,335,340,341,342,361,364,368,369,370,371,376,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,207,247,400],compound:[391,402,403,465],compres:[71,118,209],compress:[],compris:[40,341,441,464],compton:[122,169],comptu:3,compuat:362,comput:[],computation:[3,6,218,219,332,382],computational:497,compute_arrai:8,compute_fep:[202,422],compute_group_group:236,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,305],compute_scalar:8,compute_temp:8,compute_ti:202,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:341,concentr:[71,400],concept:[6,150,160,209,485],conceptu:[3,6,71,158,221,223,371,392,409,426,481],concern:[6,73,89,195,237],concetr:71,concis:[11,331],conclud:12,concret:8,concurr:[9,16,362,502],conden:[332,460,462],condens:[6,152,332,378,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:222,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,196,200,221,222,223,224,228,236,243,244,274,287,295,331,359,369,371,378,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,194,431,474],conform:[3,6,13,59,220,221,259,303,309,331,355,371,402,488],confus:[3,465],conjuct:396,conjug:[7,8,244,368,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,197,201,202,244,247,251,274,290,291,295,296,297,299,304,308,320,328,335,340,361,362,371,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,220,241,289,304,307,317,371,393,406,456,462,473,474,476,480,497],conput:3,consecut:[3,11,12,39,71,170,197,201,202,224,241,242,392,414,418,471,477,479],consequ:[1,6,207,332,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,194,197,201,202,208,210,213,217,219,220,224,248,261,286,304,327,328,331,332,335,362,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,244,245,323,324,325,376,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,198,203,204,209,223,224,227,229,234,237,244,245,246,257,260,262,263,264,265,266,267,268,269,270,272,273,274,275,277,278,279,280,281,282,283,291,294,299,301,303,304,323,324,325,326,336,361,362,364,370,371,376,378,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:206,consit:304,constant:[],constitu:[3,6,250,304,337,341,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,200,209,224,236,237,242,250,254,289,290,302,304,307,318,328,335,369,370,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,221,260,286,303,341,372,376,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,299,435,502],consumpt:359,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,194,196,197,198,200,201,202,206,208,209,210,212,213,214,215,217,222,224,229,232,238,242,243,244,247,258,274,285,286,289,290,292,294,297,301,304,305,310,320,327,331,332,341,342,345,360,362,370,371,374,375,377,378,379,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[9,12,18,440,492,494],context:[3,6,8,12,17,120,121,197,218,219,224,289,301,336,368,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,197,200,201,202,207,209,210,211,212,213,214,215,217,220,221,222,223,224,236,237,238,240,241,242,244,245,246,252,257,258,260,262,263,264,265,266,267,268,279,280,281,282,283,288,290,293,294,304,305,309,319,320,322,329,330,332,338,341,345,360,375,376,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,206,332,444,446],contour_integr:206,contract:[59,221,223,260,291,304],contradictori:3,contrain:307,contraint:274,contrari:[238,245],contrast:[1,6,42,55,64,152,155,194,223,343,444,446,468,505],contrib:332,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,202,207,208,209,210,212,213,214,215,221,236,244,247,250,251,255,261,281,282,289,290,298,301,304,305,307,334,361,369,371,379,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,194,196,200,206,207,217,221,222,223,240,241,244,245,260,262,263,264,265,266,267,268,291,296,304,311,312,323,324,325,332,336,359,361,373,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:206,controlfil:440,convect:93,conveni:[6,12,29,193,198,215,305,364,448,502],convent:[3,8,9,29,181,188,189,194,197,303,317,344,400,402,502],converg:[3,6,41,90,193,194,196,198,203,217,220,221,229,234,265,294,296,299,303,307,367,368,369,371,391,392,414,447,471,483,490],convers:[3,8,144,196,197,207,210,291,361,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,196,197,215,258,290,343,346,348,352,355,364,371,377,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,341],convinc:[7,12],cook:9,cooki:7,cool:[7,160,240,302],cooordin:[193,194],cooper:[5,7],coord123:118,coord1:[3,118,209,213,214],coord2:[3,118,209,213,214],coord3:[3,118,209,213,214],coord:[],coordb:447,coordbb:447,coordiat:369,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,198,200,203,208,209,212,213,214,217,218,219,220,221,222,223,224,227,229,230,234,236,239,240,241,242,243,244,245,257,259,260,262,263,264,266,267,268,281,284,285,286,289,290,291,301,302,304,306,307,309,314,317,318,319,320,322,330,331,332,339,340,342,343,364,369,370,371,376,377,378,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,209],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,196,332,371,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,376,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,289],coral:197,core:[],core_shel:152,coreshel:[6,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,196,341,342,364,464,476],cornflowerblu:197,cornsilk:197,corp:[],corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,194,196,223,236,238,244,260,261,281,289,291,294,331,337,341,361,371,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:206,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,197,203,224,229,234,245,254,260,261,297,304,307,317,319,338,341,371,372,376,394,424,429,473,474,476,486,501,503],correl:[],correpond:232,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,194,196,197,201,202,203,209,211,212,213,214,216,219,221,223,230,234,235,239,244,247,248,256,257,258,260,262,263,264,265,266,267,268,269,270,274,277,279,280,281,283,286,287,291,296,304,306,307,323,325,327,336,337,338,340,341,342,344,346,347,348,349,351,352,355,357,362,366,368,370,371,377,378,380,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],corrupt:3,cosin:[],cosineshift:27,cosmo:[238,243],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,196,197,209,213,214,217,218,219,233,260,296,332,361,362,374,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,238,372],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,194,196,197,201,202,209,210,213,217,223,234,243,293,294,295,299,302,304,306,320,321,327,331,332,333,337,341,343,345,353,358,360,367,369,372,376,379,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,295,297,333,361,362,369,376,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,203,204,207,209,212,213,214,216,217,224,229,233,236,242,260,274,290,307,323,324,341,362,369,370,371,373,376,404,408,431,494,502],counter:[3,338,471,482,484,490],counteract:236,counterbal:240,counterbalanc:29,counterpart:[193,304,471],counterproduct:18,coupl:[],courant:310,cours:[3,8,130,132,164,193,201,202,237,303,317,331,337,339,340,342,343,362,423,449,473,476,489,497,502,504],courtesi:364,cov:447,coval:[6,29,402,426,447,497],covari:238,cover:[6,71,190,197,206,247,402,464],coverag:[71,213],cpc:243,cpp:[1,3,6,8,9,11,12,13,89,193,201,202,234,307],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,197,211,227,245,333,359,362,376,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,372],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,372,497],craympi:376,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:206,create_faceset:206,create_group:195,create_nodeset:206,createatom:[],creation:[],crimson:197,critchlei:289,criteria:[3,120,171,196,197,218,219,220,255,369,436,464,478,481,502],criterion:[12,41,125,170,173,207,217,220,236,274,296,310,338,343,369,371,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,258,327,332,369],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,194,196,208,213,219,223,257,259,281,304,313,317,319,328,335,347,364,371,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:294,crystal:[3,4,6,13,73,110,285,286,330,364,372,476,480,494,497],crystallin:[6,106,286,364,461,497],crystallis:327,crystallogr:[122,169],crystallograph:[364,494],crystallographi:[122,169,364],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[377,400],ctemp_cor:227,cterm:309,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,217,227,341,364,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,215,218,219,220,222,233,238,244,246,320,323,324,325,326,328,335,408,494],cumul:[6,207,209,212,213,214,228,236,244,258,260,265,274,304,305,371],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,198,201,202,206,209,213,214,215,217,218,219,220,221,222,223,224,228,229,234,236,238,241,242,244,250,257,260,261,266,267,268,274,279,280,281,283,289,290,295,296,298,301,302,303,304,307,308,309,310,311,312,313,314,316,318,319,320,323,324,325,331,332,335,336,337,338,339,340,342,343,345,359,360,361,362,365,366,368,369,370,371,376,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,236,286],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[285,297],cutinn:[384,423,424],cutlo:[285,297],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,219,220,225,232,285,294,295,297,299,301,304,308,320,333,337,341,343,359,361,362,369,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:[],cutoff_inn:[],cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:327,cvel:309,cvff:[],cwiggl:[3,257,337,340,342,502],cyan:[2,196,197],cycl:[3,236,258,260,261,265],cyclic:[3,190],cygwin:12,cylind:[3,4,71,196,209,242,290,338,341,479],cylindr:[6,242,317,338],cypress:376,cyrot:382,cyrstal:286,d3q15:247,d3q19:247,d_double_doubl:15,d_e:332,d_flag2:293,d_flag:293,d_name:[117,193,293,322,486],d_single_doubl:15,d_single_singl:15,d_sx:293,d_sy:293,d_sz:293,daan:330,dai:12,daili:12,daivi:281,damag:[],dammak:299,damp:[3,6,200,205,244,245,246,251,260,261,265,291,294,295,299,304,323,324,336,338,339,368,369,371,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:245,damp_drud:245,dampen:[304,497],dampflag:[338,406],dan:17,danger:[3,12,236,343,396,494],dangl:173,daniel:9,darden:[362,395],darkblu:197,darkcyan:197,darken:196,darkgoldenrod:197,darkgrai:197,darkgreen:197,darkkhaki:197,darkmagenta:197,darkolivegreen:197,darkorang:197,darkorchid:197,darkr:197,darksalmon:197,darkseagreen:197,darkslateblu:197,darkslategrai:197,darkturquois:197,darkviolet:197,dasgupta:295,dash:[406,493],dat:[6,93,190,206,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,305],dataset:305,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,210],davenport:425,davi:337,david:[9,19,361,362,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,195,196,197,198,287,477,481],ddim:192,deactiv:422,dealt:243,debug:[6,7,11,12,13,14,17,122,126,169,170,287,292,359,361,376,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,257,293,304,333,491],decipher:364,declar:195,declin:320,decod:196,decompos:[89,448],decomposit:[3,5,7,18,62,206,287,308],decoupl:[6,497],decreas:[3,193,194,203,204,211,220,223,229,234,236,244,331,361],decrement:309,deepli:358,deeppink:197,deepskyblu:197,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,217,218,219,220,221,223,224,227,228,229,231,234,235,236,239,242,243,244,245,246,247,255,257,259,260,261,262,263,264,265,266,267,268,270,271,272,275,277,278,279,280,281,282,283,285,286,287,289,290,291,293,295,297,302,304,305,306,307,310,314,318,320,322,323,324,325,326,328,329,330,332,334,335,337,338,339,340,341,342,343,345,346,347,348,349,350,351,352,355,356,357,359,361,362,364,366,368,369,370,371,372,373,374,375,376,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,197,209,210,211,212,213,214,215,223,231,242,265,305,322,334,337,340,342,344,356,359,370,379,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,289],degrad:[8,18,286,362,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,196,209,220,227,236,238,239,244,245,250,260,261,265,266,267,268,279,280,281,283,287,289,303,304,307,323,324,325,330,346,348,352,355,357,369,395,400,408,486,494,497,503],degress:[150,209],del:490,delai:[3,6,12,372,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,200,209,210,212,213,214,215,218,220,233,236,260,305,323,324,343,345,360,370,372,375,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:206,deli:192,delimit:[474,502],deloc:[261,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:[],delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:[],delx:192,delz:192,dem:[],demand:299,demo:11,demon:284,demonstr:[294,426],den:290,dendrim:408,denniston:[9,247,249,250,251,286],denomin:[7,175],denot:[122,227,245,286,297,299,392,407,409,440,444,446],dens:[71,220,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,201,202,206,209,213,214,217,223,234,247,250,253,254,286,290,291,295,332,337,364,366,370,377,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[258,294],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,196,197,200,201,202,203,204,207,209,211,212,213,215,216,217,219,221,223,229,230,235,238,239,240,242,244,245,247,249,250,257,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,285,296,299,301,304,306,307,308,314,320,323,324,325,327,329,331,332,334,336,337,340,341,342,343,345,346,347,348,349,351,352,355,357,362,364,369,370,372,373,374,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:224,deposit:[],deprec:[3,295,439],depth:[51,148,196,332,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,210,221,223,236,244,257,260,262,263,264,265,266,267,268,285,291,295,299,329,330,332,337,338,341,368,370,378,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:285,descend:197,descent:[7,368],descib:[40,196,295],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,195,200,201,202,209,210,211,212,213,214,215,217,220,221,222,223,224,226,227,232,237,238,241,242,243,244,245,246,247,249,250,251,255,259,260,261,265,273,282,285,287,292,293,294,295,296,297,304,309,317,320,321,322,323,324,325,326,327,328,329,330,335,337,338,340,345,361,362,364,367,368,369,370,371,375,378,379,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:362,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,206,220,226,227,260,261,285,286,305,327,332,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,209,215,221,223,234,236,237,244,245,246,250,260,281,289,290,291,292,295,299,304,307,320,323,324,325,326,331,338,353,358,361,362,364,367,369,370,371,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,196],despit:497,destabil:382,destre:355,destroi:[11,39,218,219],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,194,196,197,200,201,202,206,209,210,211,212,213,215,217,219,220,221,222,223,224,234,236,237,238,239,241,242,244,246,247,251,257,258,259,260,261,262,263,264,265,266,267,268,272,274,279,280,281,282,283,286,289,290,291,293,294,296,297,298,304,307,308,320,323,324,325,326,327,328,330,331,332,333,334,335,336,343,345,347,356,361,362,365,369,370,372,373,376,377,378,379,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,235,290,331,371,391,408,413,471,473,476,487,490,502],determ:376,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,194,196,197,198,199,203,204,205,208,209,210,211,212,213,214,215,216,217,221,223,224,227,229,236,239,240,242,244,245,250,255,257,258,260,266,267,268,279,280,281,283,285,287,290,291,294,301,302,303,304,305,306,310,312,314,320,323,324,325,327,333,334,337,338,339,340,341,342,343,356,361,362,364,370,372,373,376,378,379,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:308,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,241,265,289,294,295,298,378,382,402,428,429,447,465,478],devemi:9,deviat:[258,265,285,404],deviator:9,devic:[1,3,12,15,17,241,376],device_typ:376,devin:[296,391],devis:428,dfactor:196,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,362],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,298,429],dhi:[59,192,223,290],dhug:[258,294],dhugoniot:[258,294],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,221,260,291,304,335,444,446],diagonalstyl:448,diagram:[41,122,169,189,217,287],diallo:408,diam:[196,197,290,370],diamet:[3,6,40,42,117,170,193,194,196,197,201,202,244,290,304,320,322,336,338,370,390,405,406,416,441,464,468,476,477,486],diamond:[364,402,426],diamter:[40,290],dick:6,dicsuss:257,dictat:[207,258],did:[3,12,369,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,334,361],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61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7,239,240,242,244,245,247,250,251,257,258,265,276,285,287,290,292,294,295,296,299,301,303,304,306,309,314,316,323,324,325,328,329,330,332,334,335,337,340,342,343,345,360,364,369,371,372,373,375,376,391,396,398,404,405,408,412,423,429,430,437,439,440,441,443,444,445,447,448,449,459,464,465,469,472,473,474,476,478,479,483,484,487,490,492,494,502,503],equat:[3,6,7,8,9,93,110,116,122,169,178,189,200,221,227,228,231,232,238,244,245,247,250,258,259,260,261,265,281,285,287,294,295,299,307,308,320,328,332,335,337,338,340,342,355,361,362,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:261,equidist:259,equil:[3,295,365,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,200,207,210,220,221,236,258,260,261,281,282,294,295,296,297,328,329,330,335,391,392,439,440,472,486],equilibria:335,equilibribum:[218,219],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,221,223,236,237,238,245,247,260,265,281,294,295,299,303,307,309,317,320,327,328,330,335,346,348,352,355,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:206,equival:[6,12,13,29,59,61,128,129,137,142,168,172,197,212,215,221,223,236,244,260,281,291,303,304,340,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[295,297],er3:169,eradiu:[40,117,194,402,476],eras:[306,329],erat:[223,424],erc:392,erfc:[392,414,431],erforc:[117,194],erg:501,erhart:[207,400,460,462],ermscal:379,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:337,erron:3,error:[],erta:406,ervel:[117,194,476],escap:[224,497],especi:[8,16,158,170,200,207,217,236,294,299,302,303,376,473],espresso:[9,298],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,210,265,286,336,362,378,392,414,462,481,494],essex:29,establish:[89,240],estim:[1,3,6,10,12,38,41,56,93,145,206,217,228,258,320,327,361,362,367,431,440,459,490,494],esu:501,esub:426,eta:[6,247,260,294,295,297,336,401,403,405,437,461,465,501],eta_dot:260,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:260,etap_dot:260,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,194,196,197,200,201,206,207,208,209,212,213,214,215,218,219,223,224,234,236,237,244,260,290,301,305,332,333,341,345,360,361,369,370,371,372,374,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[369,371,471,490],etot0:294,etot:[6,97,99,100,114,145,156,197,227,245,258,294,493,494],eu2:169,eu3:169,euler:[369,371],eulerian:206,euqat:450,europhi:247,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,194,196,197,201,202,203,204,206,208,209,210,211,212,213,214,215,216,223,229,237,239,240,242,243,244,245,286,292,295,306,310,314,323,324,325,334,337,340,342,343,345,361,362,367,369,376,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[345,474],evan:[158,281],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,369],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,194,197,200,201,202,207,208,209,212,213,214,215,217,218,219,221,223,224,227,242,245,258,260,261,286,290,299,301,304,305,316,320,328,332,335,337,341,343,354,361,367,369,371,376,381,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,217,247,412,466],event:[],eventu:[3,6,12,15,172,295,490],ever:[9,54,56,243,320],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,198,200,201,202,203,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,228,233,234,236,238,240,241,242,247,248,256,260,261,265,284,285,286,290,291,292,293,294,295,296,297,299,301,302,304,305,307,309,320,322,323,324,325,326,327,328,331,332,333,334,335,343,345,360,362,371,372,373,376,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[238,247,287,471],evolv:[247,287,333],ewald:[2,3,5,6,7,8,12,90,114,122,145,333,361,362,369,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,217,220,237,238,244,245,246,290,299,300,320,332,347,361,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,201,202,212,217,223,228,232,237,244,245,246,261,273,274,282,286,294,320,325,326,339,376,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,220,286],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,208,209,212,213,214,215,217,221,223,228,233,260,286,301,305,311,312,320,369,376,476,502],exceed:[3,41,59,217,223,260,320,484],excel:402,except:[1,2,5,6,8,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,197,200,203,209,210,212,216,217,221,223,230,235,236,239,242,244,246,260,261,262,263,264,265,266,267,268,269,270,273,274,277,279,280,281,282,283,287,296,297,304,306,307,317,320,323,325,326,332,336,340,343,344,345,346,347,348,349,351,352,355,356,357,361,362,364,366,370,371,372,374,375,376,377,378,380,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[211,402],exchang:[2,3,6,8,9,61,62,200,206,207,236,244,296,304,328,332,335,361,376,402,491],exchange:361,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,209,213,218,219,248,256,289,302,304,327,338,343,369,370,372,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,376,391,429,431,485,495],excurs:[260,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,196,241,298,345,360,363,375,472,474,484,487,490,502],exempl:447,exemplari:237,exemplifi:402,exert:[6,242,245,299,339,340,341,362],exhaust:[206,375,502],exhibit:[94,260,368,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,195,196,197,200,205,216,219,221,224,236,289,290,292,343,344,346,348,349,350,352,356,365,370,376,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,217,232,360,375,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,217,229,236,238,257,285,291,293,294,299,304,343,362,372,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,197,285,289,304,332,343,361,362,372,376,474],experi:[6,13,15,17,216,224,241,250,259,291,303,304,367,371,396,431,485,490],experienc:[6,12,249,250],experiment:[236,361,376,490],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,194,196,197,200,209,210,215,217,219,221,223,260,285,293,304,317,343,345,360,361,364,370,371,375,381,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,194,209,259,285,409,470,473,474,476,485],explanatori:[3,8,121,193,194,208,209,212,213,214,304,370,473,502],explantori:[3,300],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,201,202,223,311,312,347,366,378,379,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,213,216,223,230,235,237,239,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,293,294,296,304,306,307,323,325,326,332,336,340,346,348,349,351,352,355,357,370,376,377,378,380,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,287],explor:[122,169],expon:[3,295,297,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[206,396,399],express:[6,144,156,170,201,202,221,257,285,295,332,338,345,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,194,200,203,204,207,215,216,222,225,229,234,235,236,238,239,240,242,244,246,258,260,265,274,285,286,302,303,304,306,309,314,317,319,323,324,325,326,327,329,330,332,334,337,341,342,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,205,213,217,242,339,342,361,364,378,443,445,459,473,476,479],exterior:[3,6,168,341],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,197,212,217,219,260,292,293,294,304,320,369,370,373,374,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,201,202,297,371,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,196,211,221,223,260,330,402,461,497],extrema:422,extrins:206,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,334],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:294,f_harm:330,f_i:[29,437],f_id:[6,71,121,123,193,194,200,208,209,210,211,212,213,214,215,255,322,334,494,502],f_ij:437,f_indent:215,f_int:329,f_j:29,f_jj:93,f_k:437,f_langevin:332,f_max:[294,299],f_msst:258,f_r:[245,460,461,462],f_sigma:382,f_solid:330,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,205,213,214,337,339,340,341,342,364,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,238,290,320,330,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,196,197,201,202,210,217,221,223,224,236,241,244,246,247,258,260,261,265,287,291,295,303,307,310,312,320,324,328,335,336,337,341,352,362,364,370,376,378,379,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:361,fail:[3,11,12,59,174,221,224,361,369,371,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:241,fall:[3,6,197,212,290,474,502],fals:[88,343,345,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,194,197,198,217,218,219,221,224,260,285,303,304,320,337,348,352,367,371,372,464,474,476,481,494],farago:244,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,197,200,201,202,207,213,217,219,224,236,238,242,257,258,260,262,263,264,265,266,267,268,276,279,280,281,282,283,293,294,296,304,309,313,319,322,330,332,336,337,338,340,342,371,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,194,271,294,333,361,362,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,216,217,223,230,235,239,243,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,291,295,296,304,306,307,320,323,325,327,329,332,336,340,346,348,349,351,352,355,357,361,362,373,374,376,377,378,380,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,213,332,333,376,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:220,favorit:7,fbmc:327,fcc:[],fcm:[276,502],fdirect:227,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:206,featu:8,featur:[],fecr:400,feedback:[7,241],feel:[7,241,242,250,285,341,343,371,431],felling:428,felt:341,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,9,12,15,156,376,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,18,39,63,198,208,209,210,212,213,214,215,245,260,290,293,295,307,334,361,369,370,371,378,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,250,485],fewest:3,fextern:234,feynman:287,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,196],ffplai:196,fft:[1,3,7,11,12,14,15,90,113,114,145,286,361,362,485],fft_inc:[12,362],fft_lib:12,fft_path:12,fftbench:[361,495],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:456,fictiti:[6,203,204,229,234,238,287,303,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[317,433],figur:[1,3,8,12,294,473,474],fij:395,file0:285,file1:[11,13,285,331,345,370,481,483,487],file2:[11,13,331,345,370,481,483,487],file:[],file_from:195,filen:370,filenam:[3,12,13,38,41,56,190,193,194,196,197,198,206,209,210,211,212,213,214,215,217,222,232,285,289,292,295,296,297,300,301,304,305,331,332,358,359,360,370,371,377,378,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,194,197,478,483,506],filepo:301,fill:[7,9,170,196,290,332,364,372,382,429,440,479],filter:[197,206],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,198,207,220,221,232,233,236,259,285,290,291,299,303,367,369,371,372,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,203,229,330,372,376,502],finer:[144,170,502],finest:361,finger:[170,192,257,479],finish:[6,11,41,217,345,358,360,361,373,375,376,464,481,502,503],finit:[],finni:[7,400,457],finvers:227,fiorin:[9,222],fire:[],firebrick:197,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,198,200,201,209,210,212,213,214,215,217,220,223,232,236,237,242,247,257,258,259,260,285,287,292,293,294,296,301,304,307,309,317,318,320,321,322,329,330,331,332,334,338,343,345,346,353,364,369,370,371,372,375,376,377,378,381,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,232,303,320,378,382,411,426,431,452,459,461,484,502],five:[73,156,294,370,382,427,476,490],fix:[],fix_adapt:[164,202,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,207,290],fix_eo:9,fix_evapor:207,fix_flux:206,fix_gcmc:[207,370],fix_gl:238,fix_gld:238,fix_grav:290,fix_id:[3,221,258,260,262,263,264,265,266,267,268,291,294],fix_modifi:[],fix_mov:[192,338],fix_nh:8,fix_npt:238,fix_nvt:[207,236],fix_poem:[3,6],fix_pour:[3,224],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:307,fix_reax_bond:439,fix_rigid:[250,381],fix_saed_vtk:305,fix_setforc:8,fix_shak:307,fix_shardlow:9,fix_srd:3,fix_styl:265,fix_temp_rescal:326,fixedpoint:[221,260],fixextern:234,fixid:206,fji:395,flag1:[226,374],flag2:[226,374],flag:[3,8,9,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,194,196,197,198,215,220,222,226,241,244,248,250,256,257,286,293,304,317,319,320,327,331,340,343,359,362,370,374,375,376,378,408,413,426,429,456,471,473,474,476,477,478,480,481,482,486,502],flag_buck:386,flag_coul:[386,395,418],flag_lj:[395,418],flagfld:[384,423,424],flaghi:[3,384,423,424],flaglog:[384,423,424],flagn:226,flagvf:[384,423,424],flat:[6,332,337,338,342],flavor:[2,7,12],fld:[337,384,423,424],flen:379,flex_press:379,flexibl:[3,6,8,171,196,209,213,222,238,261,328,335,402,461,494],flip:[3,6,223,260,339,340],floor:502,flop:12,floralwhit:197,flow:[],fluctuat:[6,64,89,221,236,237,244,247,260,265,285,286,308,330,332,355,398],fluid:[],fluid_veloc:251,flush:[3,197,493],flux:[],flv:196,fly:[7,9,12,41,196,200,206,211,224,227,304,307,333,382,429,494,497],fmackai:9,fmag:225,fmass:287,fmax:[369,494],fmomentum:227,fmsec:[2,197,244,245,257,260,291,304,323,324,485,496,501,503],fname:360,fno:[9,12,16],fnorm:[369,494],fnpt:227,fnvt:227,foce:409,fock:379,focu:307,fogarti:[9,297,440],foil:[144,285,448],fold:[318,485],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,40,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,82,93,94,99,100,110,117,120,121,123,144,145,148,149,150,156,158,163,166,168,170,171,176,179,180,181,182,184,185,187,188,190,193,195,196,197,200,206,207,208,209,210,211,212,213,214,215,217,222,223,224,227,228,231,232,234,236,237,238,241,243,244,245,247,250,258,260,265,266,267,268,279,280,281,283,286,287,289,292,293,294,295,297,299,301,303,304,305,307,322,323,324,325,328,329,330,331,332,334,335,343,344,348,349,350,351,352,355,357,359,364,366,369,370,371,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,467,468,469,471,473,474,476,477,479,481,483,484,485,488,490,491,492,497,502,503,505],foo:[4,8,11,12,193,196,234,474,487,502],foot:6,footprint:[12,376],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:250,forcefield:[303,408],forcegroup:247,forcezero:367,ford:395,forestgreen:197,forev:71,forget:[245,497],forgiv:260,fork:[12,193],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,89,91,92,94,96,106,107,109,120,144,145,164,165,174,178,197,200,201,202,219,237,238,244,246,250,257,281,286,297,299,303,304,332,337,341,346,347,350,355,366,368,370,371,378,379,382,389,397,398,400,402,404,408,409,413,425,426,428,429,433,434,437,439,440,441,447,448,449,457,459,460,461,462,468,470,473,474,476,481,486,493,497,502],formal:[6,78,80,93,237,238,244,260,287,320,328,447],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,178,190,193,194,195,196,197,198,209,212,213,214,215,217,219,232,286,289,293,295,297,300,304,305,316,331,332,343,344,347,366,370,371,377,378,382,389,400,403,413,426,428,438,439,440,442,448,459,465,466,473,474,476,477,478,481,492,493,494,502,504],former:[6,12,16,39,41,197,217,332,336,382,384,482,488,502],formerli:[7,13],formul:[1,40,64,145,203,229,244,260,281,295,297,303,307,331,361,378,382,400,402,405,426,436],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,89,91,92,93,97,99,100,109,116,122,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,169,170,175,177,178,189,192,193,201,202,203,204,209,210,211,212,215,216,223,229,239,240,242,244,245,257,285,286,292,301,306,314,318,320,323,324,325,334,337,340,342,343,345,346,347,349,356,364,370,378,379,381,382,387,388,389,390,395,396,400,401,405,406,407,408,410,413,414,416,417,418,420,421,423,424,426,430,431,432,441,442,449,457,458,459,460,461,462,465,467,468,472,476,479,486,493,494,501,502,503],forth:[1,6,11,12,13,14,15,375,474,479,483],fortran:[3,6,9,11,12,13,234,400,409,426,439,440],fortun:8,forward:[3,8,89,360,371,376],foster:[382,436,437],foul:173,found:[3,6,9,12,73,164,193,220,222,236,241,247,286,327,333,345,360,372,389,392,395,471,477,478,493],four:[6,11,54,81,106,107,144,166,258,332,355,370,371,429,471],fourier:[],fourth:[6,108,303,317,327,387,433,447],fox:[6,122,176,455,488],fphi:[38,56,459],fpic:12,fplo:[38,56,459],fprime:459,fqdn:243,fqq:395,frac:[],fraction:[1,3,6,8,12,16,39,41,80,113,145,173,192,196,197,207,218,219,220,221,258,290,294,301,302,320,325,326,364,371,376,382,384,406,423,424,481,486],fragment:[42,241,301],fraig:42,frame:[8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:[211,447,459],resolv:[221,287,320,424],resort:3,resourc:[7,377,400],respa:[3,16,228,241,260,374,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,432,434,436,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,464,465,467,468,469,484,485,496,502],respecifi:429,respect:[1,6,9,10,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,59,70,71,89,91,99,100,113,116,122,126,147,152,155,157,164,168,169,176,177,179,180,181,182,184,185,187,188,190,194,196,197,213,214,219,220,221,223,239,242,244,245,247,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,295,296,304,305,309,317,319,332,337,340,346,348,349,351,352,355,357,359,361,362,366,369,370,375,376,377,378,380,382,383,384,385,386,387,388,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,441,442,446,447,448,449,458,459,460,461,462,463,465,467,468,469,473,477,486,489,497,502,504,506],respon:9,respond:[6,7,153,223,402,436],respons:[6,7,258,328,335],resquar:[],rest:[6,8,12,293,297,303,382,424,426,493,494,497],restart1:287,restart2:287,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,60,61,106,170,201,202,293,309,317,322,344,493,494],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,222,258,303,319,413],restratin:303,restrict:[],result:[1,2,3,6,7,9,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,45,46,47,48,49,51,53,54,56,63,64,66,67,71,75,89,92,93,96,106,107,109,113,114,116,118,119,120,121,122,123,145,147,150,153,157,164,165,167,169,170,173,176,177,179,180,181,182,184,185,187,188,190,192,193,194,196,197,200,203,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,227,230,232,235,236,237,239,244,245,247,251,258,260,262,263,264,265,266,267,268,269,270,277,279,280,281,282,283,286,287,295,296,301,302,304,306,307,320,323,325,328,329,330,332,333,334,336,337,338,340,342,345,346,348,349,351,352,355,357,361,362,371,374,376,377,378,380,383,384,385,386,387,388,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,426,427,429,431,432,433,434,436,440,441,442,449,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,480,481,485,486,487,488,490,501,502,503],resum:502,retain:[2,218,219,382,429,473],retart:[33,50,183,353],retir:[3,439],retreiv:8,retriev:[6,8,234,427,428,502],reus:[3,488],rev:[6,13,64,70,94,110,114,144,145,158,207,238,244,246,258,260,261,265,281,286,296,299,304,309,320,324,327,329,330,335,368,382,390,391,392,395,400,401,402,405,406,411,416,423,424,425,426,428,437,441,448,458,460,461,462,465,471],revers:[2,6,8,89,181,220,242,260,284,285,295,313,328,329,335,371,422,485,497],review:[144,295,309,327,429,438,448,471,490,497],rewind:360,rewrap:193,rewrit:[5,12],rewritten:19,rezwanur:436,rfac0:[144,448],rfactor:320,rfile:304,rg0:318,rgb:197,rh3:169,rh4:169,rhaphson:3,rheolog:6,rhi:459,rho0:[426,444,446,454,455],rho0_meam:426,rho:[],rho_0:[454,455],rho_alpha_beta:400,rho_bkgd:426,rho_colloid:337,rho_e:332,rho_fin:331,rho_i:[427,428],rho_initi:331,rho_ref_meam:426,rho_wal:337,rhodo:[9,10],rhodopsin:[1,10],rhohi:290,rholo:290,rhosum:[],ribier:368,richard:9,richardson:304,richi:[9,19],rick:[295,296,391,447],rick_and_stuart:296,ridg:[9,19],right:[3,6,11,12,41,146,170,188,189,192,194,217,220,242,247,257,284,345,364,392,476,479,486,502],rightmost:[41,217],rigid:[],rigidifi:304,rii:[91,92],rij:[94,110,218,219,285,396,397,398,456],rin:[408,419,420],ring:[],rino:[73,465],rinv:361,rirj:[338,406],rise:[],risi:[144,448],risk:[8,303,485],rix:[91,92],rjk:[218,219],rjone:[7,9,13],rlo:459,rmask:[3,502],rmass:3,rmax:[71,171,218],rmdir:487,rmin0:[144,448],rmin:[71,171,219,416],rmsd:331,rnemd:6,robert:9,robin:197,robust:[367,368,369],rock:426,rockett:437,rod:304,rodata:12,rodnei:299,roi:7,role:327,roll:12,ronchetti:110,room:[57,59],root:[11,89,91,92,195,327,331,376,400,483],rosati:39,rose:426,ross:426,rosski:287,rosybrown:197,rot:[6,93,287,303,327,503],rotat:[],rotation:110,rotaton:479,rough:[6,170,196,342],roughli:[7,10,12,41,153,196,211,236,244,245,259,260,274,291,304,320,323,324,327,362,371,376,443,445,478,485],round:[],rous:237,rout:[89,408,422],routin:[5,6,8,11,15,16,38,39,56,90,174,176,247,429,438,459,489],roux:[6,227,245,463,497],row:[6,65,66,68,69,75,79,92,95,96,107,109,112,118,119,120,123,150,158,165,167,168,169,209,210,212,213,214,215,250,304,332,334,342,402],royalblu:197,rozero:426,rperp:[257,313],rpi:289,rpm:12,rrespa:[1,3,5,7,8,16,201,202,257,260,372,377,378,379,380,381,383,384,385,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,430,432,434,436,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,464,465,467,468,469,485],rspace:3,rsq:[459,466],r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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.USER-CUDA package","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","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","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local 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/local command","compute dilatation/atom 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/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 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","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/spatial command","fix ave/spatial/sphere 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 enforce2d command","fix eos/cv command","fix eos/table 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 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/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway 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 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/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","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","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/conservative 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 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 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 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","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","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":218,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,194,196,197,198,199,201,202,203,205,206,207,209,213,214,215,218,219,221,222,223,224,228,233,236,237,242,244,245,246,247,248,250,255,258,260,261,265,281,282,286,287,290,291,292,293,294,296,299,301,302,304,305,320,322,327,328,329,330,333,335,337,339,343,356,359,361,362,364,365,367,368,370,372,373,374,376,379,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[211,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[201,202],addforc:203,addit:[12,13],addtorqu:204,adiabat:6,adjust_dt:310,adp:377,airebo:378,alloi:400,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:205,arrai:6,aspher:[6,9,84,148,262,266,270,271,279],atc:[9,206],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,205,207,208,293,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:216,awpmd:[9,379],balanc:[41,217],barostat:6,basal:67,beck:380,berendsen:[291,323],between:6,binary2txt:13,bodi:[6,8,9,42,68,149,263,267,272,280,381],bond:[8,13,69,218,219,220,300],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,221],brownian:384,buck:[385,386,394,425],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,209],citat:7,class2:[9,21,43,177,346,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[9,337,390,468],colvar:[9,13,222],com:[74,75,151],comb3:391,comb:[296,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,328],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,coreshel:9,correl:[210,211],cosin:[23,24,25,26,27,28,179],cossq:348,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:219,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:324,csvr:324,cubic:416,cuda:[9,14,113,116,147,157,203,216,230,235,239,260,269,306,307,323,325,336,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:[8,193,194],cut:[49,379,385,388,392,395,402,404,414,415,422,430,434],cvff:349,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,223],delete_atom:173,delete_bond:174,delta:24,deposit:224,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,9,29,395],direct:227,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:350,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:225,dreid:[6,408],drude:[6,9,155,226,227,245],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,196,198],dump_modifi:197,dynam:295,eam:[13,400],echo:199,edip:401,eff:[9,13,99,100,154,156,161,246,261,273,282,326,402],efield:229,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:230,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:233,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:234,fcc:285,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,202],field:[6,7],file:6,finit:6,fire:295,fix:[2,6,8,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,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:166,advanc:[3,244,386,476,487],advantag:[1,6,8,11,14,18,40,41,42,220,380,405,490,495],advect:[3,6,323],advertis:8,advis:[375,442],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,73,92,123,147,156,170,176,199,200,205,212,213,215,216,217,218,221,222,223,224,226,227,237,243,245,247,253,260,264,265,266,267,269,270,271,277,282,283,284,286,307,308,321,335,345,358,365,371,372,373,375,376,377,380,406,427,428,435,478,479,481,483,484,486,489,491],affin:[16,17,18,226,380,395],afil:241,aforement:18,afresh:[295,489,507],afshar:400,after:[2,3,5,6,8,9,11,12,15,21,22,33,40,41,42,45,51,59,60,61,63,65,73,150,151,152,153,154,155,156,159,160,161,162,164,165,172,173,175,176,179,180,185,195,196,197,198,199,200,201,203,204,205,209,210,212,213,220,221,222,223,224,226,230,239,250,251,252,253,254,259,260,261,263,269,270,271,277,282,283,284,286,289,293,297,305,307,310,319,324,326,327,328,330,331,332,333,334,338,340,342,346,349,350,356,364,370,371,373,374,376,378,379,380,381,382,386,393,395,404,405,406,407,413,414,415,426,427,428,430,431,432,433,437,441,443,444,451,452,461,462,464,465,466,469,476,478,480,481,482,483,484,486,487,489,491,493,495,498,499,502,506,507,508,509,510,511],afterrun:489,afterward:3,afterword:42,ag1:171,ag2:171,again:[6,11,12,16,17,64,146,152,158,166,196,200,226,243,293,349,364,375,427,428,476,478,479,481,483,488,495,497,507,509],against:[11,12,13,66,227,375,443,444],aggreg:[6,12,67,70,71,81,97,114,121,243,259,305,307,321,476,508],aggress:[243,495],agilio:[9,13],agre:[3,8,192,373,382,415,444],agreement:[5,7],ahd:412,ahead:342,aidan:[0,5,7,9,13,368],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:199,akohlmei:[7,9,13,201,244],aktulga:[7,9,300,444],al2o3:451,al2o3_001:[124,308],al3:171,ala:[250,451],alain:9,alat:[288,430],alb:[441,464,466],albeit:306,albert:9,alchem:[91,166],alcohol:338,alcu:[381,386],alcu_eam:441,alderton:399,alejandr:[263,264],alessandro:13,algebra:433,algorithm:[0,1,6,7,8,9,42,63,200,209,220,223,226,250,252,253,277,290,298,307,310,311,330,331,335,338,343,371,372,373,377,380,402,406,428,433,448,450,476,478,495],alia:[9,12,16],alias:[1,366],aliceblu:200,align:[6,12,29,42,73,174,192,216,220,245,368,481,484,502],alkali:406,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,165,166,167,168,169,170,171,172,173,174,175,176,178,180,185,191,192,193,196,197,198,199,200,201,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,256,258,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,319,320,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,348,349,350,354,359,361,363,364,365,366,367,368,370,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,392,393,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,502,506,507,508,509,510,511],allen:[29,91,399,409],allentildeslei:91,allign:3,allindex:347,alloc:[3,5,6,8,9,11,12,62,237,337,374,376,380,439,444,481,489],allocat:3,alloi:[],allosw:73,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,79,96,112,114,148,150,151,152,165,170,171,172,174,180,191,192,196,197,199,200,201,203,204,206,208,209,210,212,213,214,215,216,217,218,220,222,223,224,225,226,227,231,232,237,239,240,241,242,244,247,250,253,254,258,260,263,264,288,292,293,294,295,296,297,301,307,308,310,312,314,315,319,323,330,331,332,333,335,336,337,338,339,340,346,348,350,359,365,366,368,373,374,375,376,379,380,383,386,387,388,389,390,391,396,404,406,410,411,412,413,418,422,427,428,433,435,441,444,445,448,450,451,460,470,472,476,479,481,483,484,485,486,487,488,491,493,494,495,498,499,507,508],almost:[2,3,12,62,245,297,335,366,377,380,460],alo:396,alon:[6,7,223,303,443,444,479],alond:13,along:[6,8,9,12,29,41,73,91,124,170,171,172,195,196,199,212,223,245,250,251,255,260,262,297,307,310,312,316,320,321,330,334,335,341,344,346,368,371,372,373,375,396,399,410,413,416,418,422,430,443,444,463,481,484,491,492,507],alonso:[431,432],alpha:[6,12,52,204,250,289,297,298,302,373,381,384,387,396,400,402,404,405,407,412,417,418,430,436,440,465,467,499,502],alpha_:[],alpha_c:426,alpha_i:452,alpha_ialpha_j:[],alpha_lj:426,alphabet:[2,3,22,37,45,56,65,180,191,203,350,359,374,393,461,481],alphanumer:[3,65,203,296,304,348,374,507],alreadi:[3,7,8,9,12,16,17,18,43,172,173,175,198,208,212,216,217,220,222,226,254,295,297,323,346,347,374,375,400,411,413,420,428,460,470,473,477,481,482,486,491,507],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,73,74,75,77,79,83,91,93,94,96,98,108,109,110,111,112,113,118,120,122,123,125,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,164,165,166,167,168,169,172,173,174,175,176,178,180,191,192,194,195,196,197,198,199,200,201,203,204,205,206,208,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,232,237,238,239,240,241,243,244,247,248,249,250,260,261,263,264,265,266,267,268,269,270,271,276,279,280,282,283,284,285,286,288,289,290,292,293,294,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,316,317,320,321,323,326,327,328,329,330,334,335,336,337,339,341,344,346,347,348,350,356,359,363,365,366,368,369,370,373,374,375,376,377,379,380,386,390,391,393,397,398,399,400,404,405,406,409,410,412,413,414,422,426,427,430,433,435,437,439,440,441,442,445,446,448,455,456,458,459,461,462,463,464,465,466,467,469,476,478,479,480,481,482,483,484,485,486,488,489,490,491,493,494,495,496,499,500,501,502,503,505,506,507,508,509,511],alter:[3,6,8,9,11,12,42,61,149,150,151,152,153,155,158,159,160,161,164,165,172,176,196,197,199,201,204,205,212,221,222,223,224,226,262,263,302,305,307,309,317,323,331,338,345,372,375,413,481,486,488,491,507,508,511],altern:[1,6,8,11,12,17,18,95,172,196,203,213,226,234,244,248,263,296,307,330,331,338,351,355,365,372,373,381,382,396,401,402,404,405,407,415,418,426,430,431,432,437,441,442,452,462,464,466,469,479,481,482,494,496,499],although:[29,43,192,253,263,294,298,307,330,364,488,502,511],aluminum:473,alwai:[0,6,11,12,17,18,55,59,65,73,170,200,212,213,214,216,217,218,222,225,239,241,245,299,302,307,323,340,344,345,349,365,366,371,373,374,376,377,380,389,392,404,421,433,443,444,451,453,463,464,466,473,476,481,482,484,486,493,495,498,502,507,508],amap:200,amatrix:241,amaz:11,amazingli:13,amber2lmp:[],amber:[],ambient:199,ambigu:[3,65,203,507],amd:[17,380,433],amend:[],amino:9,amit:9,among:[16,147,210,250],amorph:[172,465],amount:[1,3,6,12,61,92,121,170,174,195,199,210,214,224,225,239,243,247,263,288,294,307,315,323,328,331,336,338,346,365,380,400,439,481,484],amplitud:[226,260,316,341,358,484,507],amu:239,amzallag:451,analag:[6,507],analalog:6,analog:[6,112,146,174,192,410],analys:[7,486],analysi:[7,9,13,65,66,75,201,303,304,313,347,433,452,481,491],analyt:[1,3,9,13,124,166,171,310,365,386,414,415,420,433,441,463],analyz:[6,8,13,375,433],andersen:310,anderson:[292,400],andr:[7,9,13],andrew:13,andzelm:460,ang:288,angl:[],angle1:306,angle2:306,angle_coeff:[],angle_cosineshift:27,angle_cosineshiftexp:[26,181],angle_cutof:412,angle_cutoff:412,angle_hybrid:29,angle_info:444,angle_styl:[],angle_typ:41,angleangl:[3,349,356,481],angleangletors:[3,179,481],anglecoeff:3,angletors:[3,179,185,481],angletyp:222,angmom:[],angmomi:[119,196,197,325],angmomx:[119,196,197,325],angmomz:[119,196,197,325],angstrom:[6,10,61,73,124,161,171,172,195,196,197,199,200,208,216,217,226,227,239,244,245,260,300,305,340,342,343,345,366,368,371,377,381,382,391,404,426,430,437,442,443,444,466,473,484,490,506,508],angular:[6,29,41,63,65,68,86,87,88,89,111,119,146,150,151,164,165,172,196,197,203,247,253,259,260,265,266,267,269,270,271,273,274,275,278,280,281,282,283,286,305,307,310,316,325,381,386,395,410,427,428,430,433,441,461,464,465,481,491,507,508],angularm:274,anharmon:[27,54,181,302,495],ani:[1,3,6,7,8,9,10,11,12,13,14,15,16,17,22,29,38,40,41,42,43,45,56,57,60,61,63,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,175,176,178,180,192,195,196,197,198,199,200,203,206,207,208,210,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,236,239,242,243,245,247,250,253,259,260,263,268,288,290,292,293,294,296,298,299,300,302,304,305,307,309,310,312,316,317,320,322,323,324,325,334,335,340,341,342,343,344,345,346,347,348,350,364,365,366,368,370,371,373,374,375,377,378,379,380,382,386,390,391,395,396,399,400,404,405,407,409,413,414,415,422,433,435,441,443,444,445,452,460,461,462,463,464,465,466,467,468,469,474,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,499,500,502,503,505,506,507,508,509,510,511],anihil:426,anim:[2,4,7,11,13,199,375],anion:[407,451],aniso:[3,224,226,263,264,265,266,267,268,269,270,271,294,307],anisotrop:[247,409,445],ann:434,annot:[7,462,464,465,466,469,481],annual:[476,495],anoth:[1,3,4,6,7,8,11,12,17,29,41,65,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7,413,418,422,426,438,443,444,451,461,466,467,469,470,472,473,481,482,486,491,493,502,506,507],charmm2lammp:13,charmm:[],chartreus:200,cheap:323,cheaper:[231,409,445],check:[3,6,8,11,12,15,17,40,42,73,95,192,210,216,220,221,222,227,236,239,245,246,293,306,310,323,331,333,338,346,348,364,373,374,375,376,377,380,403,414,417,435,444,476,478,479,481,489,495,498,499,507],checkf:192,checkqeq:444,checku:192,chem:[6,13,20,21,25,40,41,44,46,47,91,92,112,118,147,178,179,189,214,225,230,240,241,248,250,262,263,264,284,285,290,294,297,299,307,311,312,323,326,327,330,331,332,333,340,349,358,360,365,366,372,375,382,387,391,392,395,396,397,399,400,402,406,408,409,411,412,418,422,423,426,430,434,435,438,451,460,467,490,493,495,502],chemic:[9,124,166,171,196,197,209,210,239,298,303,304,330,366,443,444,456],chemistri:[9,297,298,300,386,406,443,444],chen:335,cheng:395,chenoweth:[443,444],chenoweth_2008:[443,444],chi:[97,161,195,288,298,300,361,407,409,508],chiefli:442,child:8,chip:[7,9,12,17,18,380,494],chipot:225,chiral:358,chmod:[11,12],cho:430,chocol:[7,200],choic:[3,6,9,12,15,16,18,41,42,55,91,147,150,151,165,176,192,212,216,217,220,223,226,227,241,247,250,261,263,290,298,307,330,359,366,371,372,375,377,380,413,426,435,439,481,490,491,494,495,501,502,506],choos:[1,3,6,7,8,12,16,17,18,29,40,55,91,123,162,163,199,221,222,223,224,227,236,247,250,261,263,265,266,267,268,269,270,271,293,294,311,323,327,341,365,366,372,470,476,478,490,496],chose:[464,466],chosen:[2,3,6,12,17,146,172,175,184,192,199,205,210,224,227,236,239,240,248,250,261,263,268,290,293,304,323,327,330,331,336,338,339,345,366,367,372,380,401,402,406,410,417,420,446,464,476,490,495,502],chri:170,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[68,77,94,98,109,111,120,152,167,169,212],chute:[4,9,10,242],ciccotti:310,cieplak:[6,178,493],cii:213,cij:213,ciko:2,circl:[43,73,319],circular:[3,6,150,194],circumst:18,circumv:[96,112,302],citat:[],cite:[3,7,8,12,247,451],civ:9,ckio:2,cko:2,cl1:171,clarendon:[29,399],clarifi:[7,464,466],clariti:348,clark:438,class2:[],classic:[0,3,5,6,7,8,9,237,290,297,302,335,360,406],classifi:[9,461,469],claus:479,clean:[6,12,14,15,17,489],cleanli:[480,510],clear:[],clearli:7,clebsch:146,clermont:[9,13],clever:485,click:[2,11,22,37,45,56,172,180,191,199,244,350,359,375,393,461],client:[244,246],climb:[262,375,495],clinic:[7,13],clo:[161,195,508],clock:[12,476,495],clockwis:341,close:[3,6,11,12,13,40,42,69,73,147,175,196,222,223,224,241,248,250,263,284,307,310,341,344,364,366,369,371,372,375,380,382,386,396,397,416,430,435,447,449,463,466,485,491,502,504],closer:[3,42,122,170,195,196,220,224,228,332,375],closest:[222,288,307,338,409,445,460,470],cloud:[451,502],clovertown:18,clsuter:74,clump1:[292,307],clump2:[292,307],clump3:[292,307],clump:307,cluster:[],clutter:[3,9],cmap:481,cmatrix:241,cmax:430,cmd:[11,12,290,492],cmdarg:11,cmin:430,cmm:[],cmoput:139,cn1:213,cn2:213,cna:[],cnn:213,cnr:[9,13],cnt:[413,485],co2:[41,171,310,374],coars:[7,9,29,36,41,55,184,292,307,323,411,446,490,493],coarser:[366,507],coarsest:146,code:[],coeff:[3,7,8,12,21,22,33,45,51,178,179,180,185,349,350,356,393,413,417,435,448,450,453,481],coeffcient:481,coeffici:[],coefficienct:400,coefficient0:404,coefficient1:404,coeffieci:[6,384,416],coeffincientn:404,coexist:[9,239,406],cohes:[6,407,430],coincid:[128,344,391,427,428,476],colberg:198,cold:[6,157,239,243,376,502],coldest:331,coleman8:9,coleman:[9,124,171,308],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,41,43,68,77,87,94,98,103,109,111,120,152,160,167,169,172,196,197,200,212,225,253,259,292,302,305,307,346,365,374,376,394,481,488,494,500,511],collid:[231,323,345],colliex:171,collinear:[3,292],collis:[3,250,323,341,345,403,410,473],colllis:323,colloid:[],colombo:40,colon:[201,346,482],color1:200,color2:200,color:[3,9,42,196,199,200,220,240,297,302],column:[3,6,9,12,13,43,65,67,68,69,70,71,73,77,79,81,83,85,94,96,97,98,109,111,112,114,116,119,120,121,122,123,125,146,147,152,160,167,169,170,171,192,196,197,200,203,211,212,213,215,216,217,218,253,260,261,297,307,324,325,335,345,408,412,443,444,482,496,498,507],columnar:170,colvar:[],colvarmodul:12,com:[],comamnd:226,comand:223,comannd:380,comb3:[],comb:[],comb_1:299,comb_2:299,combiant:397,combin:[3,6,7,9,11,13,36,41,65,67,71,81,91,97,108,114,121,150,151,165,196,199,209,215,244,253,263,290,296,311,327,336,344,347,349,365,366,368,372,380,394,396,397,402,406,407,413,425,426,452,462,464,466,469,472,484,489,494,502,507],come:[],comfort:[12,13],comm:[0,3,11,12,63,75,198,244,246,247,366,375,380,400,435,440,463,483],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,57,178,192,196,235,248,307,335,374,375,381,404,405,407,417,430,437,444,451,452,462,463,464,465,466,469,478,479,481,502,507],commerci:7,commit:9,commmand:[3,6,12,61,113,285,416,475,476,478,495,510],common:[],commonli:[3,6,12,17,25,59,61,110,112,174,196,199,201,360,411,420,452,464,466,481,484,493],commun:[1,3,6,7,8,10,11,12,14,15,16,18,41,42,60,63,64,73,170,175,176,199,200,220,221,222,224,225,226,244,246,250,252,253,254,263,289,296,298,299,300,307,311,323,335,346,363,365,376,377,378,380,402,403,439,474,478,479,490,491,507,509,511],communc:365,comp:[7,198,246,247,310,366,375,406,435,440,445,459,463,465],compact:[65,203,393,461],compani:[5,7],compar:[1,3,4,6,8,12,17,40,90,116,124,155,171,180,191,200,230,298,346,348,365,366,373,375,430,451,476,495,496,502,506],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,44,45,56,179,180,191,349,350,359,392,461],compat:[3,5,7,8,9,11,12,13,17,18,42,73,123,125,183,196,201,205,211,212,213,215,216,217,218,220,289,301,327,330,337,340,343,365,380,414,433,435,463,478,479,507],compens:[6,221,222,305,376,406],compet:334,competit:366,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,170,196,198,199,201,244,334,366,380,433,481,482,486,507],compl:17,complain:[11,12,17],complement:430,complementari:[7,396,418],complet:[3,6,9,11,12,15,42,61,73,200,216,220,225,253,290,293,296,323,334,336,347,348,364,375,380,407,448,450,468,476,481,486,489,493,495,498,502,507],complex:[6,8,11,12,13,25,41,43,64,96,112,146,148,160,172,173,250,319,344,363,375,406,433,463,479,481,484,507],compli:[330,334],complic:[6,7,9,12,13,210,239,479],complier:12,compon:[3,6,8,12,63,65,68,69,75,83,92,93,94,95,96,98,99,102,109,110,111,112,113,114,115,116,118,119,123,133,136,137,138,139,142,143,144,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,167,168,169,195,196,197,199,200,206,207,211,212,213,214,215,216,217,218,219,223,224,226,227,232,237,242,246,247,250,253,255,259,260,262,263,264,268,269,270,271,282,283,284,286,287,289,290,291,294,305,307,309,310,312,316,317,320,323,326,327,328,330,337,338,343,344,345,365,368,372,373,374,375,380,400,406,410,427,428,448,450,451,452,481,482,491,499,507,508],componenet:6,composit:[6,210,250,404],compound:[395,406,407,469],compres:[73,120,212],compress:[],compris:[41,344,445,468],compton:[124,171],comptu:3,compuat:366,comput:[],computation:[3,6,221,222,335,386],computational:502,compute_arrai:8,compute_fep:[205,426],compute_group_group:239,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[124,308],compute_scalar:8,compute_temp:8,compute_ti:205,compute_vector:8,compute_xrd:171,concaten:[2,3,510],concav:344,concentr:[73,404],concept:[6,152,162,212,490],conceptu:[3,6,73,160,224,226,375,396,413,430,486],concern:[6,75,91,198,240],concetr:73,concis:[11,334],conclud:12,concret:8,concurr:[9,16,366,507],conden:[335,464,466],condens:[6,154,335,382,398,404,418,469],condit:[],conducit:6,conduct:[],cone:484,confer:433,confid:[3,495],config:[12,196,478],configfil:225,configur:[1,2,6,12,15,17,38,61,128,174,192,195,196,199,203,224,225,226,227,231,239,246,247,277,290,298,334,363,373,375,382,386,405,430,433,462,464,466,469,476,481,483,484,495],confin:[481,495],conflict:[3,12,41,197,435,479],conform:[3,6,13,61,223,224,262,306,312,334,358,375,406,493],confus:[3,469],conjuct:400,conjug:[7,8,247,372,406,443,444],conjunct:[6,7,73,90,91,120,155,160,166,172,176,200,204,205,247,250,254,277,293,294,298,299,300,302,307,311,323,331,338,343,365,366,375,387,389,393,396,400,406,412,418,435,438,446,467,481,484,488,502,511],connect:[3,6,91,157,175,223,244,292,307,310,320,375,397,410,460,466,478,479,481,485,502],conput:3,consecut:[3,11,12,40,73,172,200,204,205,227,244,245,396,418,422,476,482,484],consequ:[1,6,210,335,417,495],conserv:[],consid:[6,9,72,73,80,91,121,154,157,158,175,196,197,200,204,205,211,213,216,220,222,223,227,251,264,289,307,330,331,334,335,338,366,393,406,413,444,445,451,460,476,477,479,482,483,484,486,489,491,499,502,507],consider:[6,8,247,248,326,327,328,380,490],consist:[3,6,8,9,11,12,41,43,67,71,81,97,109,114,117,118,121,152,155,157,172,184,195,201,206,207,212,226,227,230,232,237,240,247,248,249,260,263,265,266,267,268,269,270,271,272,273,275,276,277,278,280,281,282,283,284,285,286,294,297,302,304,306,307,326,327,328,329,339,365,366,368,374,375,380,382,386,388,394,396,406,409,413,416,427,428,430,433,435,445,448,450,451,463,470,479,481,482,483,484,485,486,493,502,507],consistent_fe_initi:209,consit:307,constant:[],constitu:[3,6,253,307,340,344,394,445],constitut:[448,450],constrain:[3,6,8,149,150,151,152,153,155,158,159,160,161,162,164,165,203,212,227,239,240,245,253,257,292,293,305,307,310,321,331,338,373,374,406,486,493,502],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,72,74,75,79,96,112,124,146,171,224,263,289,306,344,376,380,399,433,435,460,462,463,484,485,500,507],constructor:[8,11],consult:444,consum:[1,302,439,507],consumpt:363,contact:[],contact_stiff:[447,449],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,91,95,122,124,146,152,160,170,171,172,174,178,180,191,192,196,197,199,200,201,203,204,205,209,211,212,213,215,216,217,218,220,225,227,232,235,241,245,246,247,250,261,277,288,289,292,293,295,297,300,304,307,308,313,323,330,334,335,344,345,348,364,366,374,375,378,379,381,382,383,386,395,396,399,404,405,406,413,414,430,433,437,441,442,443,444,452,462,463,464,465,466,467,469,476,477,478,479,481,482,483,484,486,488,490,493,495,496,498,499,502,507,509,511],content:[9,12,18,444,497,499],context:[3,6,8,12,17,122,123,200,221,222,227,292,304,339,372,472,481,488,497,506,507,508],contibut:72,contigu:478,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,73,83,108,109,168,200,203,204,205,210,212,213,214,215,216,217,218,220,223,224,225,226,227,239,240,241,243,244,245,247,248,249,255,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,291,293,296,297,307,308,312,322,323,325,332,333,335,341,344,348,364,379,380,386,400,403,420,423,443,444,445,448,450,465,476,479,481,483,484,489,495,496,498,499,507,509],continuum:[6,7,9,209,335,448,450],contour_integr:209,contract:[61,224,226,263,294,307],contradictori:3,contrain:310,contraint:277,contrari:[241,248],contrast:[1,6,43,56,66,154,157,197,226,346,448,450,472,510],contrib:335,contribut:[3,5,6,7,8,9,12,13,17,65,68,70,72,73,76,77,79,82,88,91,92,93,94,95,98,107,109,111,113,114,115,116,118,120,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,205,210,211,212,213,215,216,217,218,224,239,247,250,253,254,258,264,284,285,292,293,301,304,307,308,310,337,365,373,375,383,400,403,404,406,413,427,428,433,435,443,444,451,493,499,502],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,91,95,128,146,181,196,197,199,203,209,210,220,224,225,226,243,244,247,248,263,265,266,267,268,269,270,271,294,299,307,314,315,326,327,328,335,339,363,365,377,406,409,433,443,444,447,449,462,466,476,478,490,496,497],control_typ:209,controlfil:444,convect:95,conveni:[6,12,29,196,201,218,308,368,452,507],convent:[3,8,9,29,183,190,191,197,200,306,320,347,404,406,507],converg:[3,6,42,92,196,197,199,201,206,220,223,224,232,237,268,297,299,302,306,310,371,372,373,375,395,396,418,451,476,488,495],convers:[3,8,146,199,200,210,213,294,365,396,397,398,406,418,422,426,438,479,495,506],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,73,95,172,179,196,199,200,218,261,293,346,349,351,355,358,368,375,381,404,433,464,466,473,479,481,482,483,488,498,502,506,507,509,511],convex:[43,344],convinc:[7,12],cook:9,cooki:7,cool:[7,162,243,305],cooordin:[196,197],cooper:[5,7],coord123:120,coord1:[3,120,212,216,217],coord2:[3,120,212,216,217],coord3:[3,120,212,216,217],coord:[],coordb:451,coordbb:451,coordiat:373,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,73,76,77,79,83,91,93,94,98,108,109,111,119,120,122,140,146,155,161,167,169,170,172,176,195,196,197,198,199,200,201,203,206,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,233,237,239,242,243,244,245,246,247,248,260,262,263,265,266,267,269,270,271,284,287,288,289,292,293,294,304,305,307,309,310,312,317,320,321,322,323,325,333,334,335,342,343,345,346,368,373,374,375,380,381,382,385,405,451,476,481,482,483,484,486,489,491,495,502,507,508],coordn:[120,212],coorind:[],copi:[0,3,4,8,11,12,15,17,41,125,199,335,375,393,443,479],copper:473,coproccesor:16,coprocessor:[1,4,7,9,16,17,380,494],coproprocessor:17,copy_arrai:8,copyright:[7,8,292],coral:200,core:[],core_shel:154,coreshel:[6,389,396,398],cornel:[6,178,493],corner123i:119,corner123x:119,corner123z:119,corner1i:119,corner1x:119,corner1z:119,corner2i:119,corner2x:119,corner2z:119,corner3i:119,corner3x:119,corner3z:119,corner:[3,6,41,119,199,344,345,368,468,481],cornflowerblu:200,cornsilk:200,corp:[],corpor:16,corr:395,correct:[3,6,9,11,12,16,17,61,91,92,107,108,116,122,154,159,166,197,199,226,239,241,247,263,264,284,292,294,297,334,340,344,365,375,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,481,496,499,502],correction_max_iter:209,correctli:[3,8,9,11,17,73,83,107,108,109,149,150,151,153,155,157,158,159,160,161,164,165,168,196,200,206,227,232,237,248,257,263,264,300,307,310,320,322,341,344,375,376,380,398,428,433,478,479,481,491,506,508],correl:[],correpond:235,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,72,73,91,101,102,115,118,119,120,121,124,125,133,136,137,138,139,140,142,143,144,146,149,150,159,166,170,171,178,179,180,181,182,183,184,186,187,189,190,192,195,196,197,199,200,204,205,206,212,214,215,216,217,219,222,224,226,233,237,238,242,247,250,251,259,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,289,290,294,299,307,309,310,326,328,330,339,340,341,343,344,345,347,349,350,351,352,354,355,358,360,366,370,372,374,375,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,441,443,444,445,446,451,452,453,462,463,464,465,466,469,471,472,473,476,478,479,481,482,484,494,495,496,498,499,502,507],correspondingli:[427,428,490],corrupt:3,cosin:[],cosineshift:27,cosmo:[241,246],cossq:[],cost:[1,6,10,11,12,17,40,42,73,115,124,147,171,199,200,212,216,217,220,221,222,236,263,299,335,365,366,378,396,418,422,433,435,462,478,490],costheta0:[462,464,466,469],costheta:441,costli:[11,92,241,376],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,73,77,91,94,98,109,111,115,118,120,152,162,167,169,185,196,197,199,200,204,205,212,213,216,220,226,237,246,296,297,298,302,305,307,309,323,324,330,334,335,336,340,344,346,348,356,362,364,371,373,376,380,383,408,412,413,416,443,444,477,478,479,481,483,485,488,489,496,497,502,507,508],coulomb:[3,5,6,7,8,9,10,12,14,15,18,74,92,113,114,122,147,173,177,298,300,336,365,366,373,380,387,389,390,391,392,395,396,397,398,399,406,410,411,413,418,422,426,429,435,438,443,444,446,451,461,466,467,469,472,486,493,499,502,506],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,42,65,70,79,95,120,122,123,160,170,176,206,207,210,212,215,216,217,219,220,227,232,236,239,245,263,277,293,310,326,327,344,366,373,374,375,377,380,408,412,435,499,507],counter:[3,341,476,487,489,495],counteract:239,counterbal:243,counterbalanc:29,counterpart:[196,307,476],counterproduct:18,coupl:[],courant:313,cours:[3,8,132,134,166,196,204,205,240,306,320,334,340,342,343,345,346,366,427,453,478,481,494,502,507,509],courtesi:368,cov:451,coval:[6,29,406,430,451,502],covari:241,cover:[6,73,192,200,209,250,406,468],coverag:[73,216],cpc:246,cpp:[1,3,6,8,9,11,12,13,91,196,204,205,237,310],cpu:[1,3,4,9,10,12,14,15,16,17,18,65,73,200,214,230,248,336,363,366,380,393,461,476,494,495,498,499,500,507],cpuremain:499,cr2:171,cr3:171,crack:[4,376],crada:[5,7],crai:[5,7,13,18,196],crash:[3,12,376,502],craympi:380,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:209,create_faceset:209,create_group:198,create_nodeset:209,createatom:[],creation:[],crimson:200,critchlei:292,criteria:[3,122,173,199,200,221,222,223,258,373,440,468,483,486,507],criterion:[12,42,127,172,175,210,220,223,239,277,299,313,341,346,373,375,395,406,410,451,486,495,496],criterioni:495,critic:[6,49,50,261,330,335,373],crmax:73,crmin:73,cross:[3,12,22,73,93,150,170,180,196,197,199,211,216,222,226,260,262,284,307,316,320,322,331,338,350,368,375,391,400,403,404,411,412,413,418,420,422,441,446,448,450,464,466,473,481,485,491,509],crossov:1,crossterm:481,crozier:[0,7,13],crucial:297,crystal:[3,4,6,13,75,112,288,289,333,368,376,481,485,499,502],crystallin:[6,108,289,368,465,502],crystallis:330,crystallogr:[124,171],crystallograph:[368,499],crystallographi:[124,171,368],cs1:171,cs_chunk:6,cs_im:[41,481],cs_re:[41,481],csanyi:[146,442,452],cscl:430,csequ:6,csh:[11,12,393],cshrc:[11,12],csic:[405,462,464,466,469],csinfo:6,csisi:[405,462,464,466,469],csld:[],cst:404,cstherm:6,cstyle:478,csvr:[],ctcm:[381,404],ctemp_cor:230,cterm:312,ctr:9,ctype:11,cu1:171,cu2:171,cu3au:430,cube:[6,42,170,175,220,230,344,368,502],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:386,cummul:[3,6,218,221,222,223,225,236,241,247,249,323,326,327,328,329,331,338,412,499],cumul:[6,210,212,215,216,217,231,239,247,261,263,268,277,307,308,375],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,41,42,43,61,63,65,73,75,83,91,107,108,114,122,123,136,147,152,160,162,168,170,173,176,195,196,197,198,199,200,201,204,205,209,212,216,217,218,220,221,222,223,224,225,226,227,231,232,237,239,241,244,245,247,253,260,263,264,269,270,271,277,282,283,284,286,292,293,298,299,301,304,305,306,307,310,311,312,313,314,315,316,317,319,321,322,323,326,327,328,334,335,338,339,340,341,342,343,345,346,348,363,364,365,366,369,370,372,373,374,375,380,386,393,395,399,404,406,407,410,413,414,417,427,428,430,431,432,435,441,443,444,447,448,449,450,453,464,466,467,470,476,477,478,479,481,482,483,484,485,487,488,489,491,493,495,496,498,499,507,508,509,510,511],curv:[6,172,239,289],curvatur:[409,445,473],custom:[],cut0:479,cut1:490,cut2:490,cut:[],cuthi:[288,300],cutinn:[388,427,428],cutlo:[288,300],cutmax:441,cutoff1:[392,399,418,422,426,429,438,446],cutoff2:[387,389,390,392,398,399,418,422,426,429,438,446],cutoff:[3,6,10,16,18,40,46,47,55,56,63,72,74,75,79,91,96,112,114,121,122,146,170,173,175,176,222,223,228,235,288,297,298,300,302,304,307,311,323,336,340,344,346,363,365,366,373,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,479,483,486,490,502,507],cutoff_glob:[],cutoff_inn:[],cutoffa:405,cutoffc:405,cuu3:404,cval:171,cvd:330,cvel:312,cvff:[],cwiggl:[3,260,340,343,345,507],cyan:[2,199,200],cycl:[3,239,261,263,264,268],cyclic:[3,192],cygwin:12,cylind:[3,4,73,199,212,245,293,341,344,484],cylindr:[6,245,320,341],cypress:380,cyrot:386,cyrstal:289,d3q15:250,d3q19:250,d_double_doubl:15,d_e:335,d_flag2:296,d_flag:296,d_name:[119,196,296,325,491],d_single_doubl:15,d_single_singl:15,d_sx:296,d_sy:296,d_sz:296,daan:333,dai:12,daili:12,daivi:284,damag:[],dammak:302,damp:[3,6,203,208,247,248,249,254,263,264,268,294,297,298,302,307,326,327,339,341,342,372,373,375,387,389,391,396,399,406,410,418,426,438,446,461,467,495,502],damp_com:248,damp_drud:248,dampen:[307,502],dampflag:[341,410],dan:17,danger:[3,12,239,346,400,499],dangl:175,daniel:9,darden:[366,399],darkblu:200,darkcyan:200,darken:199,darkgoldenrod:200,darkgrai:200,darkgreen:200,darkkhaki:200,darkmagenta:200,darkolivegreen:200,darkorang:200,darkorchid:200,darkr:200,darksalmon:200,darkseagreen:200,darkslateblu:200,darkslategrai:200,darkturquois:200,darkviolet:200,dasgupta:298,dash:[410,498],dat:[6,95,192,209,477],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,308],dataset:308,datatyp:3,date:[0,6,12,13,195,443,444,507],datom1:121,datom2:121,datom3:121,datom4:121,datum:[3,6,43,67,70,71,81,97,114,121,196,213],davenport:429,davi:340,david:[9,19,365,366,464,466],daw:[404,441],dbg:14,dcd:[3,6,7,196,198,199,200,201,290,482,486],ddim:195,deactiv:426,dealt:246,debug:[6,7,11,12,13,14,17,124,128,171,172,290,295,363,365,380,414,435,470,479,480,488,491,498,507],deby:[],decai:[96,396,473],decid:[3,6,12,16,73,260,296,307,336,496],decipher:368,declar:198,declin:323,decod:199,decompos:[91,452],decomposit:[3,5,7,18,64,209,290,311],decoupl:[6,502],decreas:[3,196,197,206,207,214,223,226,232,237,239,247,334,365],decrement:312,deepli:362,deeppink:200,deepskyblu:200,def:[12,13,479],defaul:63,defect:[6,72,170,433],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,186,187,189,190,191,192,193,194,195,196,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,237,238,239,242,245,246,247,248,249,250,258,260,262,263,264,265,266,267,268,269,270,271,273,274,275,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,298,300,305,307,308,309,310,313,317,321,323,325,326,327,328,329,331,332,333,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,358,359,360,361,363,365,366,368,370,372,373,374,375,376,377,378,379,380,382,383,384,385,387,388,389,390,391,392,393,394,396,397,399,400,401,402,403,405,406,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,433,434,435,436,437,438,440,441,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,484,485,486,487,490,491,492,493,495,496,498,499,502,503,504,505,506,507,508],definit:[2,3,6,8,12,13,80,82,122,146,200,212,213,214,215,216,217,218,226,234,245,268,308,325,337,340,343,345,347,359,363,374,383,386,394,401,402,406,416,441,448,450,452,468,479,481,483,490,492,506,507],defint:499,deform:[],deg2theta:171,deg:502,degener:[3,292],degrad:[8,18,289,366,490],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,81,96,97,99,101,102,104,106,107,112,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,171,172,178,179,182,183,190,192,195,199,212,223,230,239,241,242,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,306,307,310,326,327,328,333,349,351,355,358,360,373,399,404,412,491,499,502,508],degress:[152,212],del:495,delai:[3,6,12,376,403,499],deleg:413,delet:[2,3,7,8,12,55,59,62,65,170,175,176,203,212,213,215,216,217,218,221,223,236,239,263,308,326,327,346,348,364,374,376,379,435,460,481,482,483,484,492,493,498,503,505,507,508],delete_atom:[],delete_bond:[],delete_el:209,deli:195,delimit:[479,507],deloc:[264,406,451],delr:430,delt_lo:495,delta:[],delta_1:386,delta_3:386,delta_7:386,delta_conf:3,delta_ij:[430,441],delta_mu:[],delta_pi:386,delta_r:441,delta_sigma:386,delta_ua:[],delx:195,delz:195,dem:[],demand:302,demo:11,demon:287,demonstr:[297,430],den:293,dendrim:412,denniston:[9,250,252,253,254,289],denomin:[7,177],denot:[124,230,248,289,300,302,396,411,413,444,448,450],dens:[73,223,406],densiti:[3,6,7,9,18,41,42,61,105,122,132,146,158,170,172,204,205,209,212,216,217,220,226,237,250,253,256,257,289,293,294,298,335,340,368,370,374,381,386,404,430,431,432,441,445,451,455,457,458,459,481,490,491,499,506],density_continu:450,density_summ:450,depart:[0,7],departur:[261,297],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,71,72,73,81,96,97,108,114,115,118,119,120,121,125,146,149,155,159,160,166,172,173,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,203,204,205,206,207,210,212,214,215,216,218,219,220,222,224,226,232,233,238,241,242,243,245,247,248,250,252,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,288,299,302,304,307,309,310,311,317,323,326,327,328,330,332,334,335,337,339,340,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,373,374,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,434,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,487,491,493,495,498,499,501,507,508],dependend:6,depflag:12,dephas:[476,495],depos:227,deposit:[],deprec:[3,298,443],depth:[52,150,199,335,409,445],dequidt:9,der:[91,113,394,395,426,443,444,472,502],deriv:[6,7,8,9,38,57,65,91,146,166,192,213,224,226,239,247,260,263,265,266,267,268,269,270,271,288,294,298,302,332,333,335,340,341,344,372,374,382,386,394,399,406,407,411,420,424,425,430,433,443,444,461,463,472,502],derjagin:472,derlet:288,descend:200,descent:[7,372],descib:[41,199,298],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,72,73,75,92,116,119,122,124,136,146,147,150,151,152,156,157,160,163,165,166,170,171,172,174,175,184,189,192,196,197,198,203,204,205,212,213,214,215,216,217,218,220,223,224,225,226,227,229,230,235,240,241,244,245,246,247,248,249,250,252,253,254,258,262,263,264,268,276,285,288,290,295,296,297,298,299,300,307,312,320,323,324,325,326,327,328,329,330,331,332,333,338,340,341,343,348,365,366,368,371,372,373,374,375,379,382,383,385,387,388,389,391,392,393,394,395,396,399,404,406,407,409,410,411,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,440,441,442,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,469,471,472,473,474,476,478,479,481,482,483,484,485,491,494,495,498,507,508,509],descript:[],descriptor:[146,196,414],deserno:366,design:[0,3,6,7,8,9,11,13,14,15,17,124,154,157,171,209,223,229,230,263,264,288,289,308,330,335,383,384,385,388,391,396,398,406,426,427,428,431,432,441,444,463],desir:[2,3,6,7,11,12,14,15,16,33,41,51,61,73,92,95,118,123,147,154,172,185,195,212,218,224,226,237,239,240,247,248,249,253,263,284,292,293,294,295,298,302,307,310,323,326,327,328,329,334,341,356,362,365,366,368,371,373,374,375,400,404,412,427,428,462,464,466,477,478,479,481,485,490,495,496,498,499,507,508,509],desk:7,desktop:[4,6,7,10,12,199],despit:502,destabil:386,destre:358,destroi:[11,40,221,222],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,73,77,80,94,95,98,107,109,111,113,115,117,118,120,123,125,146,147,149,150,151,152,155,165,166,167,169,172,173,176,177,180,191,195,196,197,199,200,203,204,205,209,212,213,214,215,216,218,220,222,223,224,225,226,227,237,239,240,241,242,244,245,247,249,250,254,260,261,262,263,264,265,266,267,268,269,270,271,275,277,282,283,284,285,286,289,292,293,294,296,297,299,300,301,307,310,311,323,326,327,328,329,330,331,333,334,335,336,337,338,339,346,348,350,359,365,366,369,373,374,376,377,380,381,382,383,385,386,388,390,391,392,393,394,395,396,399,400,406,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,451,452,453,461,468,471,472,479,481,482,483,484,486,487,490,491,493,496,499,500,507,508,511],detect:[2,3,12,43,63,65,90,96,238,293,334,375,395,412,417,476,478,481,492,495,507],determ:380,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,73,91,107,113,115,118,124,125,133,147,160,161,170,171,172,195,196,197,199,200,201,202,206,207,208,211,212,213,214,215,216,217,218,219,220,224,226,227,230,232,239,242,243,245,247,248,253,258,260,261,263,269,270,271,282,283,284,286,288,290,293,294,297,304,305,306,307,308,309,313,315,317,323,326,327,328,330,336,337,340,341,342,343,344,345,346,359,365,366,368,374,376,377,380,382,383,390,395,399,403,404,408,410,413,414,422,430,433,435,444,445,451,460,463,467,472,478,481,482,484,486,488,491,495,497,498,500,506,507,508],determinist:311,detil:114,devan:[9,446],devanathan:466,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,244,268,292,297,298,301,382,386,406,432,433,451,469,483],devemi:9,deviat:[261,268,288,408],deviator:9,devic:[1,3,12,15,17,244,380],device_typ:380,devin:[299,395],devis:432,dfactor:199,dff:502,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,366],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,301,433],dhi:[61,195,226,293],dhug:[261,297],dhugoniot:[261,297],dia:430,diagnost:[],diagon:[3,6,87,146,147,148,224,263,294,307,338,448,450],diagonalstyl:452,diagram:[42,124,171,191,220,290],diallo:412,diam:[199,200,293,374],diamet:[3,6,41,43,119,172,196,197,199,200,204,205,247,293,307,323,325,339,341,374,394,409,410,420,445,468,472,481,482,491],diamond:[368,406,430],diamter:[41,293],dick:6,dicsuss:260,dictat: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:[443,444],eqp:399,eqq:399,equal:[2,3,6,8,11,12,17,40,42,55,65,67,70,71,73,78,81,90,91,95,97,114,116,121,123,125,147,150,166,168,170,172,195,199,200,203,204,205,206,207,210,213,214,215,218,219,220,224,226,227,232,239,240,242,243,245,247,248,250,253,254,260,261,268,279,288,290,293,295,297,298,299,302,304,306,307,309,312,317,319,326,327,328,331,332,333,335,337,338,340,343,345,346,348,364,368,373,375,376,377,379,380,395,400,402,408,409,412,416,427,433,434,441,443,444,445,447,448,449,451,452,453,463,468,469,473,477,478,479,481,483,484,488,489,492,495,497,499,507,508],equat:[3,6,7,8,9,95,112,118,124,171,180,191,203,224,230,231,234,235,241,247,248,250,253,261,262,263,264,268,284,288,290,297,298,302,310,311,323,331,335,338,340,341,343,345,358,365,366,394,399,400,402,406,407,410,415,427,428,430,435,445,448,450,455,456,458,459,473,502],equi:264,equidist:262,equil:[3,298,369,488,511],equilater:491,equilibr:[3,4,5,6,7,9,61,95,172,203,210,213,223,224,239,261,263,264,284,285,297,298,299,300,331,332,333,338,395,396,443,444,477,491],equilibria:338,equilibribum:[221,222],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,155,156,179,181,224,226,239,240,241,248,250,263,268,284,297,298,302,306,310,312,320,323,330,331,333,338,349,351,355,358,395,430,437,451,502],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:209,equival:[6,12,13,29,61,63,130,131,139,144,170,174,200,215,218,224,226,239,247,263,284,294,306,307,343,400,406,451,464,466,481,484,489,490,499,502],equlibrium:6,equliibr:[298,300],er3:171,eradiu:[41,119,197,406,481],eras:[309,332],erat:[226,428],erc:396,erfc:[396,418,435],erforc:[119,197],erg:506,erhart:[210,404,464,466],ermscal:383,ernst:9,eror:3,eros:430,erose_form:430,erot:[],errata:[464,466],erratum:340,erron:3,error:[],erta:410,ervel:[119,197,481],escap:[227,502],especi:[8,16,160,172,203,210,220,239,297,302,305,306,380,478],espresso:[9,301],essenti:[8,11,12,27,92,134,153,154,155,158,159,160,161,162,164,181,213,268,289,339,366,382,396,418,466,486,499],essex:29,establish:[91,243],estim:[1,3,6,10,12,38,42,57,95,147,209,220,231,261,323,330,365,366,371,435,444,463,495,499],esu:506,esub:430,eta:[6,250,263,297,298,300,339,405,407,409,441,465,469,506],eta_dot:263,eta_ij:441,eta_ji:407,etag:[41,481],etail:499,etap:263,etap_dot:263,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,93,94,95,99,115,116,119,121,147,149,152,153,154,155,156,158,159,160,161,162,164,166,172,174,175,176,185,196,197,199,200,203,204,209,210,211,212,215,216,217,218,221,222,226,227,237,239,240,247,263,293,304,308,335,336,344,348,364,365,373,374,375,376,378,404,405,413,426,428,433,439,443,444,462,464,466,469,476,479,481,482,483,488,490,491,495,496,497,498,499,500,502,506,507,509,511],ethernet:18,etol:[373,375,476,495],etot0:297,etot:[6,99,101,102,116,147,158,200,230,248,261,297,498,499],eu2:171,eu3:171,euler:[373,375],eulerian:209,euqat:454,europhi:250,ev_tal:8,evalu:[2,3,9,11,12,38,57,73,91,92,95,113,123,146,148,152,162,170,172,195,196,197,199,200,204,205,206,207,209,211,212,213,214,215,216,217,218,219,226,232,240,242,243,245,246,247,248,289,295,298,309,313,317,326,327,328,337,340,343,345,346,348,365,366,371,373,380,433,435,441,447,449,451,463,476,477,479,483,484,486,488,489,490,491,495,497,499,507,508],evalut:[348,479],evan:[160,284],evanseck:[6,20,178,391,493],evapor:[],evaul:[8,373],evdwl:[113,443,444,499],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,72,73,125,170,173,174,188,192,196,197,200,203,204,205,210,211,212,215,216,217,218,220,221,222,224,226,227,230,245,248,261,263,264,289,293,302,304,307,308,319,323,331,335,338,340,344,346,357,365,371,373,375,380,385,406,407,410,413,416,435,445,469,470,474,481,482,484,486,487,488,490,491,493,496,498,499,500,502,511],evenli:[3,42,147,192,220,250,416,470],event:[],eventu:[3,6,12,15,174,298,495],ever:[9,55,57,246,323],evera:[394,409,445,461],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,73,74,95,119,125,134,160,175,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,231,236,237,239,241,243,244,245,250,251,259,263,264,268,287,288,289,293,294,295,296,297,298,299,300,302,304,305,307,308,310,312,323,325,326,327,328,329,330,331,334,335,336,337,338,346,348,364,366,375,376,377,380,400,403,413,426,443,444,451,457,475,476,477,481,483,485,486,488,489,490,495,496,497,499,507,511],everyth:[8,113],everywher:[122,420],eviri:406,evolut:[241,250,290,476],evolv:[250,290,336],ewald:[2,3,5,6,7,8,12,92,116,124,147,336,365,366,373,387,389,390,396,399,406,418,422,438,446,461,463],ewald_disp:399,ewalddisp:3,exact:[22,42,45,73,128,166,175,180,220,223,240,241,247,248,249,293,302,303,323,335,350,365,393,483,488,495,507,509,511],exactli:[3,6,12,14,17,38,42,43,57,61,73,74,95,122,150,156,163,172,192,204,205,215,220,226,231,235,240,247,248,249,264,276,277,285,289,297,323,328,329,342,380,393,400,404,410,413,427,435,463,483,484,491,495,507],exager:502,examin:[6,8,9,17,223,289],examp:[479,507],exampl:[],exce:[3,6,16,17,18,42,60,73,174,211,212,215,216,217,218,220,224,226,231,236,263,289,304,308,314,315,323,373,380,481,507],exceed:[3,42,61,220,226,263,323,489],excel:406,except:[1,2,5,6,8,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,73,93,94,114,115,118,123,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,172,176,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,200,203,206,212,213,215,219,220,224,226,233,238,239,242,245,247,249,263,264,265,266,267,268,269,270,271,272,273,276,277,280,282,283,284,285,286,290,299,300,307,309,310,320,323,326,328,329,335,339,343,346,347,348,349,350,351,352,354,355,358,359,360,365,366,368,370,374,375,376,378,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,436,437,438,440,443,444,445,446,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,486,489,490,491,492,493,495,499,502,506,507,508,510],excess:[214,406],exchang:[2,3,6,8,9,63,64,203,209,210,239,247,299,307,331,335,338,365,380,406,496],exchange:365,excit:[9,406],exclud:[3,6,9,12,16,17,65,73,118,146,152,159,160,176,196,212,216,221,222,251,259,292,305,307,330,341,346,373,374,376,388,410,413,416,427,428,435,460,493],exclus:[1,3,9,12,16,91,380,395,433,435,490,500],excurs:[263,476],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,62,173,199,244,301,348,364,367,379,477,479,489,492,495,507],exempl:451,exemplari:240,exemplifi:406,exert:[6,245,248,302,342,343,344,366],exhaust:[209,379,507],exhibit:[96,263,372,406,490],exist:[3,6,7,8,11,12,13,16,37,56,61,70,72,128,172,173,191,198,199,200,203,208,219,222,224,227,239,292,293,295,346,347,349,351,352,353,355,359,369,374,380,401,402,413,443,460,470,477,479,481,482,483,492,493,494,507,508,509],exit:[2,3,11,12,42,59,196,220,235,364,379,479,480,489,498,507],exlanatori:3,exp:[],expand:[],expans:[12,146,196,492,507],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,73,107,153,164,170,192,220,232,239,241,260,288,294,296,297,302,307,346,366,376,393,430,433,435,476,479,481,483,486,490,495,507],expens:[6,10,73,200,288,292,307,335,346,365,366,376,380,479],experi:[6,13,15,17,219,227,244,253,262,294,306,307,371,375,400,435,490,495],experienc:[6,12,252,253],experiment:[239,365,380,495],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,42,61,65,67,70,71,73,74,75,78,79,81,90,97,152,160,192,196,197,199,200,203,212,213,218,220,222,224,226,263,288,296,307,320,346,348,364,365,368,374,375,379,385,404,416,451,453,468,479,482,483,486,488,491,502,507,511],explan:[3,6,61,119,146,196,197,212,262,288,413,475,478,479,481,490],explanatori:[3,8,123,196,197,211,212,215,216,217,307,374,478,507],explantori:[3,303],explic:434,explicit:[6,9,11,22,45,79,91,119,122,166,180,204,205,226,314,315,350,370,382,383,386,391,393,404,406,417,427,467,475,478,482,485],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,73,115,118,149,159,162,170,172,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,216,219,226,233,238,240,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,296,297,299,307,309,310,326,328,329,335,339,343,349,351,352,354,355,358,360,374,380,381,382,384,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,407,408,409,410,411,412,413,417,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,445,446,453,454,455,456,457,458,459,461,462,463,464,465,466,467,469,471,472,473,481,483,484,490,491,493,494,500,502],explictli:[16,494],exploit:[9,15,17,290],explor:[124,171],expon:[3,298,300,404,409,412,426,434,446],exponenti:[91,441,462,469,473,495,507],expos:11,exposit:[209,400,403],express:[6,146,158,172,204,205,224,260,288,298,335,341,348,386,404,406,420,430,451,452,461,507],expressiont:386,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,86,87,88,91,92,95,99,102,103,113,115,123,125,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,197,203,206,207,210,218,219,225,228,232,237,238,239,241,242,243,245,247,249,261,263,268,277,288,289,305,306,307,309,312,317,320,322,326,327,328,329,330,332,333,335,337,340,344,345,409,430,433,444,445,452,498,499],extent:[1,3,42,43,46,59,73,170,174,196,208,216,220,245,342,345,365,368,382,447,449,463,478,481,484],exterior:[3,6,170,344],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,73,107,115,116,118,124,147,149,150,151,153,155,158,159,160,161,162,164,165,171,172,173,174,178,200,215,220,222,263,295,296,297,307,323,373,374,377,378,399,410,413,416,430,435,478,479,481,484,493,502,507],extract:[3,6,11,13,36,65,91,113,121,123,125,204,205,300,375,396,407,430,452,479,486,498],extract_atom:11,extract_comput:[11,479],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,199,214,224,226,263,333,406,465,502],extrema:426,extrins:209,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[168,337],f_a:[464,465,466],f_ave:123,f_c:465,f_f:466,f_fix_id:297,f_harm:333,f_i:[29,441],f_id:[6,73,123,125,196,197,203,211,212,213,214,215,216,217,218,258,325,337,499,507],f_ij:441,f_indent:218,f_int:332,f_j:29,f_jj:95,f_k:441,f_langevin:335,f_max:[297,302],f_msst:261,f_r:[248,464,465,466],f_sigma:386,f_solid:333,f_ss:6,f_temp:[],face:[3,6,59,61,73,160,170,174,208,216,217,340,342,343,344,345,368,409,430,445,481,484],face_threshold:170,facet:170,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,241,293,323,333,410,451,493],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,74,91,95,107,114,121,122,124,146,166,171,174,178,189,195,196,199,200,204,205,213,220,224,226,227,239,244,247,249,250,261,263,264,268,290,294,298,306,310,313,315,323,327,331,338,339,340,344,355,366,368,374,380,382,383,386,387,389,391,396,397,398,400,401,402,406,410,413,417,418,430,433,435,437,438,444,446,453,462,467,478,481,484,485,490,493,495,496,499,502,506,507],factori:[3,479],factoriz:365,fail:[3,11,12,61,176,224,227,365,373,375,398,444,479],failur:[127,448,480,507],fairli:[11,435,490,495],faken:75,falcon:244,fall:[3,6,200,215,293,479,507],fals:[90,346,348,451,507],fame:8,famili:[469,478],familiar:[0,11],fan:441,far:[3,6,12,17,59,61,63,90,196,197,200,201,220,221,222,224,227,263,288,306,307,323,340,351,355,371,375,376,468,479,481,486,499],farago:247,farrel:[464,466],farther:196,fashion:[6,8,42,73,172,200,203,204,205,210,216,220,222,227,239,241,245,260,261,263,265,266,267,268,269,270,271,279,282,283,284,285,286,296,297,299,307,312,316,322,325,333,335,339,340,341,343,345,375,413,427,484,493,507,510],fasolino:415,fast:[6,7,9,12,13,17,40,196,197,274,297,336,365,366,388,427,428,433,461,463,483,488,490,499,508,511],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,110,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,219,220,226,233,238,242,246,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,294,298,299,307,309,310,323,326,328,330,332,335,339,343,349,351,352,354,355,358,360,365,366,377,378,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,461,462,463,464,465,466,469,471,472,473,476,484,490,494,502],fastest:[1,6,14,17,160,216,335,336,380,478],fatal:[3,498],fault:[72,444],faulti:12,fava:409,favor:223,favorit:7,fbmc:330,fcc:[],fcm:[279,507],fdirect:230,fdotr:414,fdt:[],fdti:91,fe2:171,fe3:171,fe_md_boundari:209,featu:8,featur:[],fecr:404,feedback:[7,244],feel:[7,244,245,253,288,344,346,375,435],felling:432,felt:344,femtosecond:506,fene:[],fennel:[396,418],fep:[],ferguson:[6,178,493],fermi:[1,9,12,15,158,380,466],fermion:[9,406],fernando:429,ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,18,40,65,201,211,212,213,215,216,217,218,248,263,293,296,298,310,337,365,373,374,375,382,451,478,481,486,490,492,500,507,509],fewer:[1,3,11,15,16,63,253,490],fewest:3,fextern:237,feynman:290,fff:479,ffield:[395,407,443,444,451],ffmpeg:[3,12,199],ffplai:199,fft:[1,3,7,11,12,14,15,92,115,116,147,289,365,366,490],fft_inc:[12,366],fft_lib:12,fft_path:12,fftbench:[365,500],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:460,fictiti:[6,206,207,232,237,241,290,306,396,418,422,460],field1:[482,486],field2:482,field:[],fifth:[320,437],figur:[1,3,8,12,297,478,479],fij:399,file0:288,file1:[11,13,288,334,348,374,486,488,492],file2:[11,13,334,348,374,486,488,492],file:[],file_from:198,filen:374,filenam:[3,12,13,38,42,57,192,196,197,199,200,201,209,212,213,214,215,216,217,218,220,225,235,288,292,295,298,299,300,303,304,307,308,334,335,362,363,364,374,375,381,382,386,396,404,405,407,415,430,431,432,437,441,442,443,444,451,452,462,463,464,465,466,469,477,478,479,482,483,488,492,499,507,509,510,511],filennam:488,filep:[3,196,197,200,483,488,511],filepo:304,fill:[7,9,172,199,293,335,368,376,386,433,444,484],filter:[200,209],final_integr:8,final_integrate_respa:8,finchham:[6,154,398],find:[0,3,4,6,7,8,11,12,13,14,16,38,40,57,63,73,75,91,123,175,192,201,210,223,224,235,236,239,262,288,293,294,302,306,371,373,375,376,396,413,418,422,430,451,461,463,502,507],find_custom:8,fine:[16,17,176,206,232,333,376,380,507],finer:[146,172,507],finest:365,finger:[172,195,260,484],finish:[6,11,42,220,348,362,364,365,377,379,380,468,486,507,508],finit:[],finni:[7,404,461],finvers:230,fiorin:[9,225],fire:[],firebrick:200,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,73,83,92,95,108,109,110,112,118,122,123,133,136,139,140,144,147,157,160,166,168,170,171,173,174,175,179,192,196,197,198,199,200,201,203,204,212,213,215,216,217,218,220,223,226,235,239,240,245,250,260,261,262,263,288,290,295,296,297,299,304,307,310,312,320,321,323,324,325,332,333,334,335,337,341,346,348,349,356,368,373,374,375,376,379,380,381,382,385,386,387,389,391,393,395,396,404,406,407,410,411,413,414,415,416,417,418,422,427,428,430,432,433,435,437,441,443,444,451,452,460,462,463,464,465,466,469,473,476,477,478,479,481,482,483,486,488,490,493,494,495,498,499,502,507,508,509,511],fischer:[6,9,19,20,178,391,493],fit:[3,6,9,12,38,57,192,235,306,323,382,386,415,430,435,456,463,465,489,507],five:[75,158,297,374,386,431,481,495],fix:[],fix_adapt:[166,205,426],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,210,293],fix_eo:9,fix_evapor:210,fix_flux:209,fix_gcmc:[210,374],fix_gl:241,fix_gld:241,fix_grav:293,fix_id:[3,224,261,263,265,266,267,268,269,270,271,294,297],fix_modifi:[],fix_mov:[195,341],fix_nh:8,fix_npt:241,fix_nvt:[210,239],fix_poem:[3,6],fix_pour:[3,227],fix_qbmsst:9,fix_qeq:[3,395],fix_rattl:310,fix_reax_bond:443,fix_rigid:[253,385],fix_saed_vtk:308,fix_setforc:8,fix_shak:310,fix_shardlow:9,fix_srd:3,fix_styl:268,fix_temp_rescal:329,fixedpoint:[224,263],fixextern:237,fixid:209,fji:399,flag1:[229,378],flag2:[229,378],flag:[3,8,9,11,12,14,15,16,17,41,68,76,77,83,90,93,94,98,108,109,111,124,167,171,175,196,197,199,200,201,218,223,225,229,244,247,251,253,259,260,289,296,307,320,322,323,330,334,343,346,363,366,374,378,379,380,382,412,417,430,433,460,476,478,479,481,482,483,485,486,487,491,507],flag_buck:390,flag_coul:[390,399,422],flag_lj:[399,422],flagfld:[388,427,428],flaghi:[3,388,427,428],flaglog:[388,427,428],flagn:229,flagvf:[388,427,428],flat:[6,335,340,341,345],flavor:[2,7,12],fld:[340,388,427,428],flen:383,flex_press:383,flexibl:[3,6,8,173,199,212,216,225,241,264,331,338,406,465,499],flip:[3,6,226,263,342,343],floor:507,flop:12,floralwhit:200,flow:[],fluctuat:[6,66,91,224,239,240,247,250,263,268,288,289,311,333,335,358,402],fluid:[],fluid_veloc:254,flush:[3,200,498],flux:[],flv:199,fly:[7,9,12,42,199,203,209,214,227,230,307,310,336,386,433,499,502],fmackai:9,fmag:228,fmass:290,fmax:[373,499],fmomentum:230,fmsec:[2,200,247,248,260,263,294,307,326,327,490,501,506,508],fname:364,fno:[9,12,16],fnorm:[373,499],fnpt:230,fnvt:230,foce:413,fock:383,focu:310,fogarti:[9,300,444],foil:[146,288,452],fold:[321,490],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,72,73,75,84,95,96,101,102,112,119,122,123,125,146,147,150,151,152,158,160,165,168,170,172,173,178,181,182,183,184,186,187,189,190,192,196,198,199,200,203,209,210,211,212,213,214,215,216,217,218,220,225,226,227,230,231,234,235,237,239,240,241,244,246,247,248,250,253,261,263,268,269,270,271,282,283,284,286,289,290,292,295,296,297,298,300,302,304,306,307,308,310,325,326,327,328,331,332,333,334,335,337,338,346,347,351,352,353,354,355,358,360,363,368,370,373,374,375,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,438,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,476,478,479,481,482,484,486,488,489,490,493,495,496,497,502,507,508,510],foo:[4,8,11,12,196,199,237,479,492,507],foot:6,footprint:[12,380],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:253,forcefield:[306,412],forcegroup:250,forcezero:371,ford:399,forestgreen:200,forev:73,forget:[248,502],forgiv:263,fork:[12,196],form:[2,3,6,8,12,19,22,45,55,65,68,76,77,79,83,91,93,94,96,98,108,109,111,122,146,147,166,167,176,180,200,203,204,205,222,240,241,247,249,253,260,284,289,300,302,306,307,335,340,344,349,350,353,358,370,372,374,375,382,383,386,393,401,402,404,406,408,412,413,417,429,430,432,433,437,438,441,443,444,445,451,452,453,461,463,464,465,466,472,475,478,479,481,486,491,498,502,507],formal:[6,80,82,95,240,241,247,263,290,323,331,451],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,79,180,192,196,197,198,199,200,201,212,215,216,217,218,220,222,235,289,292,296,298,300,303,307,308,319,334,335,346,347,350,370,374,375,381,382,386,393,404,407,417,430,432,442,443,444,446,452,463,469,470,478,479,481,482,483,486,497,498,499,507,509],former:[6,12,16,40,42,200,220,335,339,386,388,487,493,507],formerli:[7,13],formul:[1,41,66,147,206,232,247,263,284,298,300,306,310,334,365,382,386,404,406,409,430,440],formula:[2,3,6,7,13,21,22,37,45,55,56,72,75,91,93,94,95,99,101,102,111,118,124,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,171,172,177,179,180,191,195,196,204,205,206,207,212,213,214,215,218,219,226,232,242,243,245,247,248,260,288,289,295,304,309,317,321,323,326,327,328,337,340,343,345,346,348,349,350,352,359,368,374,382,383,385,386,391,392,393,394,399,400,404,405,409,410,411,412,414,417,418,420,421,422,424,425,427,428,430,434,435,436,445,446,453,461,462,463,464,465,466,469,471,472,477,481,484,491,498,499,506,507,508],forth:[1,6,11,12,13,14,15,379,479,484,488],fortran:[3,6,9,11,12,13,237,404,413,430,443,444],fortun:8,forward:[3,8,91,364,375,380],foster:[386,440,441],foul:175,found:[3,6,9,12,75,166,196,223,225,239,244,250,289,330,336,348,364,376,393,396,399,476,482,483,498],four:[6,11,55,83,108,109,146,168,261,335,358,374,375,433,476],fourier:[],fourth:[6,110,306,320,330,391,437,451],fox:[6,124,178,459,493],fphi:[38,57,463],fpic:12,fplo:[38,57,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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.USER-CUDA package","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_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/local command","compute angmom/chunk command","compute basal/atom command","compute body/local 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/local command","compute dilatation/atom 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/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 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/spatial command","fix ave/spatial/sphere 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 enforce2d command","fix eos/cv command","fix eos/table 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 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/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway 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 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/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","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/conservative 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 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 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 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","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":221,"default":[37,40,41,56,59,60,61,63,64,73,91,92,96,107,108,110,112,113,124,128,129,146,152,160,161,165,171,172,175,177,191,194,195,196,197,199,200,201,202,204,205,206,208,209,210,212,216,217,218,221,222,224,225,226,227,231,236,239,240,245,247,248,249,250,251,253,258,261,263,264,268,284,285,289,290,293,294,295,296,297,299,302,304,305,307,308,323,325,330,331,332,333,336,338,340,342,346,359,363,365,366,368,369,371,372,374,376,377,378,380,383,386,388,406,427,428,433,435,443,444,460,461,476,477,478,481,482,484,486,488,489,490,493,495,497,498,499,500,501,506,508,509,510],"function":507,"long":[214,387,389,390,391,392,396,398,399,418,422,426,438,446],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[204,205],addforc:206,addit:[12,13],addtorqu:207,adiabat:6,adjust_dt:313,adp:381,airebo:382,alloi:404,amber2lmp:13,amber:6,angl:[8,67],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:68,append:208,arrai:6,aspher:[6,9,86,150,265,269,273,274,282],atc:[9,209],atom:[6,7,8,66,69,72,73,74,75,78,79,80,82,83,85,89,96,100,101,104,105,106,112,116,117,119,146,147,170,208,210,211,296,507],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:219,awpmd:[9,383],balanc:[42,220],barostat:6,basal:69,beck:384,berendsen:[294,326],between:6,binary2txt:13,bodi:[6,8,9,43,70,151,266,270,275,283,385],bond:[8,13,71,221,222,223,303],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:386,born:[387,398],boundari:[7,59],box:[6,60,224],brownian:388,buck:[389,390,398,429],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:72,ch2lmp:13,chain:13,change_box:61,charmm:[6,20,178,391,426],chunk:[6,68,73,77,94,98,109,111,120,152,167,169,212],citat:7,class2:[9,21,44,179,349,392],clear:62,cluster:74,cmm:9,cna:75,code:6,coeffici:6,colloid:[9,340,394,472],colvar:[9,13,225],com:[76,77,153],comb3:395,comb:[299,395],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,507],compute_modifi:107,condit:7,conduct:[6,331],conserv:401,constant:6,constraint:7,contact:[78,126],contact_radiu:[],coord:79,core:6,coreshel:9,correl:[213,214],cosin:[23,24,25,26,27,28,181],cossq:351,coul:[387,389,390,391,392,396,397,398,411,418,422,426,438,446],coupl:6,creat:222,create_atom:172,create_bond:173,create_box:174,createatom:13,creation:7,csld:327,csvr:327,cubic:420,cuda:[9,14,115,118,149,159,206,219,233,238,242,263,272,309,310,326,328,339,387,389,391,392,404,410,411,418,419,421,424,436,462,464],custom:[8,196,197],cut:[50,383,389,392,396,399,406,408,418,419,426,434,438],cvff:352,damag:[80,127],data2xmovi:13,data:6,databas:13,deby:[396,418],dec:[],defgrad:133,deform:[155,156,226],delete_atom:175,delete_bond:176,delta:24,deposit:227,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],diagnost:7,diel:397,dielectr:177,diffract:9,diffus:6,dihedr:[8,81],dihedral_coeff:180,dihedral_styl:[2,178,179,181,182,183,184,185,186,187,188,189,190,191,192,193],dilat:82,dimens:194,dipol:[6,9,29,399],direct:230,discuss:6,disp:6,displac:[83,90],displace_atom:195,distanc:353,distribut:[7,12],document:0,dpd:[9,84,85,400,401,402],drag:228,dreid:[6,412],drude:[6,9,157,229,230,248],dsf:[396,418],dsmc:403,dump:[6,8,196,197,198,199,201],dump_modifi:200,dynam:298,eam:[13,404],echo:202,edip:405,eff:[9,13,101,102,156,158,163,249,264,276,285,329,406],efield:232,eim:407,elast:6,emac:13,energi:[129,402],enforce2d:233,ensembl:7,erot:[86,87,88,89],error:[3,128],evapor:236,event:90,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],exp:[27,181],expand:[47,421],extend:[8,11],extern:237,fcc:288,fdt:402,featur:[7,8,507],feb:0,fene:[46,47],fep:[9,13,91,205],field:[6,7],file:6,finit:6,fire:298,fix:[2,6,8,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,2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