| |
|
|
|
@@ -1026,6 +1041,8 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).
(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
+(4) The USER-DPD package was created by James Larentzos, Timothy
+Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).
If the Library is not listed as lib/package, then it is a third-party
library not included in the LAMMPS distribution. See the
src/package/Makefile.lammps file for info on where to download the
@@ -1200,8 +1217,32 @@ theory.
Arkansas. Contact him directly if you have questions.
+
+
4.20. USER-DPD package
+
This package implements the dissipative particle dynamics (DPD) method
+under isothermal, isoenergetic, isobaric and isenthalpic conditions.
+The DPD equations of motion are integrated efficiently through the
+Shardlow splitting algorithm.
+
See these doc pages and their related commands to get started:
+
+
There are example scripts for using this package in examples/USER/dpd.
+
The people who created this package are James Larentzos
+(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
+engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
+Contact them directly if you have questions.
+
-
4.20. USER-DRUDE package
+
4.21. USER-DRUDE package
This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.
See these doc pages and their related commands to get started:
@@ -1221,7 +1262,7 @@ Agilio Padua.
-
4.21. USER-EFF package
+
4.22. USER-EFF package
This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
@@ -1255,7 +1296,7 @@ have questions.
-
4.22. USER-FEP package
+
4.23. USER-FEP package
This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.
See these doc pages and their related commands to get started:
@@ -1270,7 +1311,7 @@ Contact him directly if you have questions.
-
4.23. USER-H5MD package
+
4.24. USER-H5MD package
This package contains a dump h5md command for
performing a dump of atom properties in HDF5 format. HDF5 files are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
@@ -1284,7 +1325,7 @@ directly if you have questions.
-
4.24. USER-INTEL package
+
4.25. USER-INTEL package
This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
@@ -1296,7 +1337,7 @@ Intel(R) Xeon Phi(TM) coprocessor.
-
4.25. USER-LB package
+
4.26. USER-LB package
This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.
@@ -1308,7 +1349,7 @@ Western Ontario. Contact them directly if you have questions.
-
4.26. USER-MGPT package
+
4.27. USER-MGPT package
This package contains a fast implementation for LAMMPS of
quantum-based MGPT multi-ion potentials. The MGPT or model GPT method
derives from first-principles DFT-based generalized pseudopotential
@@ -1331,7 +1372,7 @@ Contact them directly if you have any questions.
-
4.27. USER-MISC package
+
4.28. USER-MISC package
The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (*.cpp and *.h).
@@ -1348,7 +1389,7 @@ about the feature or its coding.
-
4.28. USER-MOLFILE package
+
4.29. USER-MOLFILE package
This package contains a dump molfile command which uses molfile
plugins that are bundled with the
VMD molecular visualization and
@@ -1367,7 +1408,7 @@ application itself.
-
4.29. USER-OMP package
+
4.30. USER-OMP package
This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
@@ -1378,7 +1419,7 @@ styles, and fix styles.
-
4.30. USER-PHONON package
+
4.31. USER-PHONON package
This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.
@@ -1390,7 +1431,7 @@ if you have questions.
-
4.31. USER-QMMM package
+
4.32. USER-QMMM package
This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the Quantum ESPRESSO package.
@@ -1407,7 +1448,7 @@ without changes to LAMMPS itself.
-
4.32. USER-QTB package
+
4.33. USER-QTB package
This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
@@ -1429,7 +1470,7 @@ have questions.
-
4.33. USER-REAXC package
+
4.34. USER-REAXC package
This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
@@ -1457,7 +1498,7 @@ questions.
-
4.34. USER-SMD package
+
4.35. USER-SMD package
This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:
@@ -1481,7 +1522,7 @@ you have questions.
-
4.35. USER-SMTBQ package
+
4.36. USER-SMTBQ package
This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
potential for the description of ionocovalent bonds in oxides.
There are example scripts for using this package in
@@ -1495,7 +1536,7 @@ them directly if you have any questions.
-
4.36. USER-SPH package
+
4.37. USER-SPH package
This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt
index 251bfa33b3..864c0afd92 100644
--- a/doc/Section_packages.txt
+++ b/doc/Section_packages.txt
@@ -201,6 +201,7 @@ USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sd
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
+USER-DPD, dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
@@ -245,6 +246,9 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
+(4) The USER-DPD package was created by James Larentzos, Timothy
+Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).
+
If the Library is not listed as lib/package, then it is a third-party
library not included in the LAMMPS distribution. See the
src/package/Makefile.lammps file for info on where to download the
@@ -455,6 +459,33 @@ Arkansas. Contact him directly if you have questions.
:line
+USER-DPD package :h4
+
+This package implements the dissipative particle dynamics (DPD) method
+under isothermal, isoenergetic, isobaric and isenthalpic conditions.
+The DPD equations of motion are integrated efficiently through the
+Shardlow splitting algorithm.
+
+See these doc pages and their related commands to get started:
+
+"compute dpd"_compute_dpd.html
+"compute dpd/atom"_compute_dpd_atom.html
+"fix_eos/cv"_fix_eos_table.html
+"fix_eos/table"_fix_eos_table.html
+"fix_shardlow"_fix_shardlow.html
+"pair_dpd/conservative"_pair_dpd_conservative.html
+"pair_dpd/fdt"_pair_dpd_fdt.html
+"pair_dpd/fdt/energy"_pair_dpd_fdt.html :ul
+
+There are example scripts for using this package in examples/USER/dpd.
+
+The people who created this package are James Larentzos
+(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
+engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
+Contact them directly if you have questions.
+
+:line
+
USER-DRUDE package :h4
This package implements methods for simulating polarizable systems
diff --git a/doc/_sources/Section_packages.txt b/doc/_sources/Section_packages.txt
index 90c21bfa38..dee6c8632d 100644
--- a/doc/_sources/Section_packages.txt
+++ b/doc/_sources/Section_packages.txt
@@ -246,6 +246,8 @@ The current list of user-contributed packages is as follows:
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-DIFFRACTION | virutal x-ray and electron diffraction | Shawn Coleman (ARL) | :doc:`compute xrd ` | USER/diffraction | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| USER-DPD | dissipative particle dynamics (DPD) | Larentzos & Mattox & Brennan (5) | src/USER-DPD/README | USER/dpd | - | - |
++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-DRUDE | Drude oscillators | Dequidt & Devemy & Padua (3) | :doc:`tutorial ` | USER/drude | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-EFF | electron force field | Andres Jaramillo-Botero (Caltech) | :doc:`pair_style eff/cut ` | USER/eff | `eff `_ | - |
@@ -324,6 +326,9 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
+(4) The USER-DPD package was created by James Larentzos, Timothy
+Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).
+
If the Library is not listed as lib/package, then it is a third-party
library not included in the LAMMPS distribution. See the
src/package/Makefile.lammps file for info on where to download the
@@ -557,6 +562,36 @@ Arkansas. Contact him directly if you have questions.
----------
+USER-DPD package
+----------------
+
+This package implements the dissipative particle dynamics (DPD) method
+under isothermal, isoenergetic, isobaric and isenthalpic conditions.
+The DPD equations of motion are integrated efficiently through the
+Shardlow splitting algorithm.
+
+See these doc pages and their related commands to get started:
+
+* :doc:`compute dpd `
+* :doc:`compute dpd/atom `
+* :doc:`fix_eos/cv `
+* :doc:`fix_eos/table `
+* :doc:`fix_shardlow `
+* :doc:`pair_dpd/conservative `
+* :doc:`pair_dpd/fdt `
+* :doc:`pair_dpd/fdt/energy `
+
+There are example scripts for using this package in examples/USER/dpd.
+
+The people who created this package are James Larentzos
+(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
+engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
+Contact them directly if you have questions.
+
+
+----------
+
+
USER-DRUDE package
------------------
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 1508bee6d2..a79054cb4f 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,195,196,201,208,209,211,212,213,214,217,218,219,220,222,223,233,239,241,243,249,256,260,261,262,263,265,266,267,273,278,279,280,282,303,304,317,331,341,354,360,366,367,368,370,371,372,375,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,222,375,391],afil:237,aforement:18,afresh:[291,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,199,200,201,205,206,208,209,216,217,218,219,220,222,226,235,246,247,248,249,250,255,256,257,259,265,266,267,273,278,279,280,282,285,289,293,301,303,306,315,320,322,323,324,326,327,328,329,330,334,336,338,342,345,346,352,359,365,366,368,369,371,373,374,375,376,377,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,196,222,239,289,345,359,370,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,223,370,439,440],aggreg:[6,12,65,68,69,79,95,112,119,239,255,301,303,317,471,503],aggress:[239,490],agilio:[9,13],agre:[3,8,190,368,377,411,440],agreement:[5,7],ahd:408,ahead:338,aidan:[0,5,7,9,13,363],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:195,akohlmei:[7,9,13,197,240],aktulga:[7,9,296,440],al2o3:447,al2o3_001:[122,304],al3:169,ala:[246,447],alain:9,alat:[284,426],alb:[437,460,462],albeit:302,albert:9,alchem:[89,164],alcohol:334,alcu:[376,382],alcu_eam:437,alderton:395,alejandr:[259,260],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,196,205,216,219,222,246,248,249,273,286,294,303,306,307,326,327,331,334,339,366,367,368,372,375,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,361],aliceblu:196,align:[6,12,29,41,71,172,190,212,216,241,363,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,252,254,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,311,315,316,318,319,320,321,322,323,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,350,355,358,359,360,361,362,363,365,368,369,370,371,372,374,375,376,377,378,380,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:343,alloc:[3,5,6,8,9,11,12,60,233,333,369,371,375,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,195,196,197,199,200,202,204,205,206,208,209,210,211,212,213,214,216,218,219,220,221,222,223,227,228,233,235,236,237,238,240,243,246,249,250,254,256,259,260,284,288,289,290,291,292,293,297,303,304,306,308,310,311,315,319,326,327,328,329,331,332,333,334,335,336,342,344,346,355,360,361,363,368,369,370,371,374,375,378,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,241,293,331,361,372,375,456],alo:392,alon:[6,7,219,299,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,195,208,219,241,246,247,251,256,258,293,303,306,308,312,316,317,326,330,331,337,340,342,363,366,367,368,370,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,200,246,285,293,294,298,368,376,379,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,199,346,355,369,389,457,476],alphanumer:[3,63,199,292,300,344,369,502],alreadi:[3,7,8,9,12,16,17,18,4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7,21,22,37,43,44,55,177,178,189,345,346,355,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,410,429,431,459,473,474,502],compens:[6,217,218,301,371,402],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,429,476,477,481,502],compl:17,complain:[12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,402,429,459,474,476,479,502],compli:[326,330],complic:[6,7,9,12,13,206,235,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,381,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,206,246,400],compound:[391,402,403,465],compres:[71,118,208],compress:[],compris:[40,340,441,464],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,382],computational:497,compute_arrai:8,compute_fep:[201,422],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:340,concentr:[71,400],concept:[6,150,160,208,485],conceptu:[3,6,71,158,220,222,370,392,409,426,481],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,502],conden:[331,460,462],condens:[6,152,331,377,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,431,474],conform:[3,6,13,59,219,220,258,302,308,330,354,370,402,488],confus:[3,465],conjuct:396,conjug:[7,8,243,367,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,219,240,288,303,306,316,370,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,392,414,418,471,477,479],consequ:[1,6,206,331,413,490],conserv:[3,29,199,206,219,226,227,236,239,243,245,246,250,255,257,259,273,303,306,307,322,323,327,334,335,339,370,395,396,406,420,447,485,490],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,243,244,322,323,324,375,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,298,435,502],consumpt:358,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,493,494,502,504],continuum:[6,7,9,205,331,444,446],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,444,446,468,505],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:205,controlfil:440,convect:93,conveni:[6,12,29,193,197,214,304,363,448,502],convent:[3,8,9,29,181,188,189,196,302,316,343,400,402,502],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,391,392,414,447,471,483,490],convers:[3,8,144,195,196,206,209,290,360,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,340,381],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:447,coordbb:447,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,385,392,394],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:[3,6,40,117,195,340,341,363,464,476],cornflowerblu:196,cornsilk:196,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,394,424,429,473,474,476,486,501,503],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,404,408,409,412,439,440,472,473,474,476,478,480,483,484,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,404,408,431,494,502],counter:[337,471,482,484,490],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,471],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,423,449,473,476,489,497,502,504],courtesi:363,cov:447,coval:[6,29,402,426,447,497],covari:237,cover:[6,71,190,196,205,246,402,464],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,497],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,436,464,478,481,502],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,480,494,497],crystallin:[6,106,285,363,461,497],crystallis:326,crystallogr:[122,169],crystallograph:[363,494],crystallographi:[122,169,363],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:[376,400],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,216,226,340,363,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,408,494],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,235,285],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[284,296],cutinn:[384,423,424],cutlo:[284,296],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:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:381,cutoff_inn:381,cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,502],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,479],cylindr:[6,241,316,337],cypress:375,cyrot:382,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,486],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:244,damp_drud:244,dampen:[303,497],dampflag:[337,406],dan:17,danger:[3,12,235,342,396,494],dangl:173,daniel:9,darden:[361,395],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[406,493],dat:[6,93,190,205,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:425,davi:336,david:[9,19,360,361,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,477,481],ddim:192,deactiv:422,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,256,292,303,332,491],decipher:363,declar:194,declin:319,decod:195,decompos:[89,448],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,497],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,288],degrad:[8,18,285,361,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,395,400,408,486,494,497,503],degress:[150,208],del:490,delai:[3,6,12,371,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[474,502],deloc:[260,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:3,delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:381,delx:192,delz:192,dem:381,demand:298,demo:11,demon:283,demonstr:[293,426],den:289,dendrim:408,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,392,407,409,440,444,446],dens:[71,219,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:223,deposit:[],deprec:[294,439],depth:[51,148,195,331,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459,485],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,195],despit:497,destabil:382,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,234,289,330,370,391,408,413,471,473,476,487,490,502],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:307,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,382,402,428,429,447,465,478],devemi:9,deviat:[257,264,284,404],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,391],devis:428,dfactor:195,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,429],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,444,446],diagonalstyl:448,diagram:[41,122,169,189,216,286],diallo:408,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,381,390,405,406,416,441,464,468,476,477,486],diamond:[363,402,426],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,262,263,265,266,26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44,360,409,475,487,502,505],elsewher:[8,256,319,426,438,439,440,488,494,502],elt:426,emac:[],email:[0,3,5,7,8,9,11,403],emb:[3,9,340],emb_lin_neg:426,embed:[3,5,7,11,12,13,29,90,146,168,331,376,400,403,422,426,427,428,437,457,466,474],embt:177,emi:[7,9],emil:9,emol:[439,440,494],emphas:406,empir:[205,323,377,402],emploi:[9,285,294,298,461],empti:[3,57,71,168,172,303,360,371,413,476,487,488,502],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,85,89,99,100,101,102,103,104,108,113,115,116,122,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,147,148,149,152,154,156,157,161,162,164,168,169,176,177,179,180,181,182,183,184,185,187,188,189,190,193,194,196,197,199,200,201,202,203,204,206,210,213,215,217,218,219,221,222,223,228,229,232,233,234,235,236,237,238,240,241,242,243,244,245,246,247,248,249,250,252,253,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,276,277,278,279,280,281,282,284,285,286,288,289,293,294,295,296,297,298,299,300,302,303,305,306,308,309,310,311,312,313,315,316,318,319,322,324,325,326,327,328,329,331,332,334,335,336,337,338,339,340,343,345,347,348,350,351,352,354,355,356,361,368,370,374,375,376,377,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,467,468,469,474,477,478,479,483,485,495,502,506],enclos:[2,6,12,172,193,291,344,426,447,472,474,484,502],encod:[13,39,42,193,195,196,292,409],encompass:[3,6,40,42,57,59,120,171,315,333,457,479],encount:[3,8,12,59,110,211,374,481,502],encourag:[7,8,297,317],end12i:117,end12x:117,end12z:117,end1i:117,end1x:117,end1z:117,end2i:117,end2x:117,end2z:117,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,42,57,59,71,117,173,174,177,192,193,195,196,197,200,201,209,211,213,214,219,222,236,241,243,245,258,259,260,273,290,302,303,308,319,322,323,324,325,327,330,331,334,338,341,342,359,360,369,370,374,375,396,400,405,412,425,429,441,444,446,448,449,466,471,474,476,477,478,479,481,483,484,488,492,494,497,502,506],end_of_step:8,endbondtors:[3,177,183,476],endif:8,energet:[219,377,440],energi:[],energy_compon:447,energy_update_freq:440,enforc:[6,57,58,107,192,193,194,195,197,199,206,219,222,259,283,285,295,303,306,344,360,414,473,502,503],enforce2d:[],eng:[11,65,69,112,193,233,342,344,391,428],eng_previ:344,engin:[205,222,288,308,328,400,427],engr:[439,440],enhanc:[201,205,471],enlarg:[59,195],enough:[3,40,61,88,170,171,173,174,216,244,289,293,298,303,332,336,337,340,371,375,392,435,476,480,481],enpub:400,enrti:[],ensembl:[],ensight:6,ensur:[3,6,144,193,206,210,220,235,236,259,309,330,361,382,399,422,458,465],enter:[57,160,403,429,465,490],enthalpi:[127,261,262,263,400,493,494,502],entir:[0,2,3,6,11,14,15,41,42,63,82,83,90,113,114,116,120,122,145,150,169,170,196,199,200,201,208,212,213,216,219,221,232,235,236,239,243,244,255,259,261,262,263,264,265,266,267,284,286,288,301,303,317,331,333,344,375,395,418,431,459,476,484,485],entireti:464,entiti:[6,8,40,42,193,303],entri:[3,8,12,38,42,56,65,69,79,95,112,119,122,131,134,135,136,137,138,140,141,142,168,190,196,211,212,213,221,231,293,342,369,382,401,426,433,440,448,458,459,460,461,462,465,502],entropi:490,entry1:[38,56,196,389,459],entry2:196,entryn:196,enumer:[171,193],enumuer:6,env:375,environ:[1,3,6,11,12,16,17,18,195,237,242,284,375,376,382,389,391,401,402,437,460,473,487,502],epair:[111,196,404,408,439,440,494],epen:[439,440],epfl:[237,242],epp:395,epq:395,eps0:468,eps14:422,epsilon0:462,epsilon:[3,6,36,45,46,50,53,54,89,176,200,201,235,303,319,336,340,366,368,380,381,387,388,390,392,393,394,395,405,407,408,409,412,413,414,415,416,417,418,419,420,421,422,425,430,434,441,442,452,458,464,467,468,485,497,501],epsilon_0:469,epsilon_14:387,epsilon_:441,epsilon_d:393,epsilon_i:[405,431,441],epsilon_i_:441,epsilon_i_a:[405,441],epsilon_i_b:[405,441],epsilon_i_c:[405,441],epsilon_ij:431,epsilon_j:[405,431,441],epsilon_j_:441,epsilon_j_a:[405,441],epsilon_j_b:[405,441],epsilon_j_c:[405,441],epsilon_lj:441,epton:436,eqch:165,eqeq:[439,440],eqp:395,eqq:395,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,71,76,79,88,89,93,95,112,114,119,121,123,145,148,164,166,168,170,192,195,196,199,200,201,202,203,206,209,210,211,214,215,216,220,222,223,228,235,236,238,239,241,243,244,246,249,250,256,257,264,275,284,286,289,291,293,294,295,298,300,302,303,305,308,313,315,322,323,324,327,328,329,331,333,334,336,339,341,342,344,359,363,368,370,371,372,374,375,391,396,398,404,405,408,412,423,429,430,437,439,440,441,443,444,445,447,448,449,459,464,465,469,472,473,474,476,478,479,483,484,487,490,492,494,502,503],equat:[3,6,7,8,9,93,110,116,122,169,178,189,199,220,226,227,230,231,237,243,244,246,249,257,258,259,260,264,280,284,286,293,294,298,306,307,319,327,331,334,336,337,339,341,354,360,361,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:260,equidist:258,equil:[3,294,364,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,391,392,439,440,472,486],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,402,476],eras:[305,328],erat:[222,424],erc:392,erfc:[392,414,431],erforc:117,erg:501,erhart:[206,400,460,462],ermscal:378,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:336,erron:3,error:[],erta:406,ervel:[117,476],escap:[223,497],especi:[8,11,16,158,170,199,206,216,235,293,298,301,302,375,473],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,392,414,462,481,494],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,431,440,459,490,494],esu:501,esub:426,eta:[6,246,259,293,294,296,335,401,403,405,437,461,465,501],eta_dot:259,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[368,370,471,490],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,493,494],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:450,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[344,474],evan:[158,280],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,368],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,216,246,412,466],event:[],eventu:[3,6,12,15,172,294,490],ever:[54,56,242,319],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[237,246,286,471],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,219,285],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,476,502],exceed:[3,41,59,216,222,259,319,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[210,402],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,402,491],exchange:360,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,375,391,429,431,485,495],excurs:[259,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,472,474,484,487,490,502],exempl:447,exemplari:236,exemplifi:402,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,502],exhibit:[94,259,367,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,216,231,359,374,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,474],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,396,431,485,490],experienc:[6,12,248,249],experiment:[235,360,375,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,208,258,284,409,470,473,474,476,485],explanatori:[3,8,121,193,207,208,211,212,213,303,369,473,502],explantori:[3,299],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[205,396,399],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,443,445,459,473,476,479],exterior:[3,6,168,340],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,402,461,497],extrema:422,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:293,f_harm:329,f_i:[29,437],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,494,502],f_ij:437,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:437,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,460,461,462],f_sigma:382,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:240,fall:[3,6,196,211,289,474,502],fals:[88,342,344,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,464,474,476,481,494],farago:243,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,212,331,332,375,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,502],fdirect:226,fdotr:410,fdt:[231,307],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:400,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,431],felling:428,felt:340,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,375,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,249,485],fewest:3,fextern:233,feynman:286,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,12,14,15,90,113,114,145,285,360,361,485],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,495],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:456,fictiti:[6,202,203,228,233,237,286,302,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[316,433],figur:[1,3,8,11,12,293,473,474],fij:395,file0:284,file1:[11,13,284,330,344,369,481,483,487],file2:[11,13,330,344,369,481,483,487],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,196,478,483,506],filepo:300,fill:[7,9,170,195,289,331,363,371,382,429,440,479],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,202,228,329,371,375,502],finer:[144,170,502],finest:360,finger:[170,192,256,479],finish:[6,11,41,216,344,357,359,360,372,374,375,464,481,502,503],finit:[],finni:[7,400,457],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,231,302,319,377,382,411,426,431,452,459,461,484,502],five:[73,156,293,369,382,427,476,490],fix:[],fix_adapt:[164,201,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:306,fix_reax_bond:439,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:395,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,10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68,69,79,95,112,117,118,119,121,123,321],input:[],input_doubl:3,inquir:309,insensit:12,insert:[3,5,7,8,12,59,170,199,223,235,241,289,360,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,196,207,212,213,223,224,232,235,241,246,249,289,303,319,336,338,339,340,341,342,358,363,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[246,395,446],instal:[],instanc:[6,11,200,221,237,338,404,409,431,437,474,497],instantan:[6,63,219,220,236,237,259,264,285,290,293,298,300,303,326,482,494],instanti:[6,11,12,205,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,201,208,211,212,213,214,216,220,221,235,243,246,249,250,285,291,301,303,321,339,358,360,361,364,371,375,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,240,288],instruct:[],insuffici:[3,6,12],insult:259,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,195,196,202,217,218,223,228,229,232,233,235,238,243,255,291,292,301,303,319,331,336,340,341,342,344,359,369,371,375,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,195,196,206,208,212,213,217,218,219,223,225,233,235,236,237,240,243,244,245,246,285,288,289,292,293,298,303,319,321,323,326,330,331,350,360,363,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,210,236,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,199,208,209,211,212,213,214,216,217,218,219,227,232,239,249,257,259,264,300,303,304,319,327,331,333,334,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,219,243,245,258,295,303,360,370,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,199,200,201,217,218,219,234,235,240,241,243,245,249,273,284,286,288,289,294,296,302,303,310,311,319,320,326,331,335,336,337,340,341,346,347,348,349,351,355,360,361,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,258,328,329,376,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:340,interest:[1,5,7,8,9,11,13,71,169,286,326,329,361,401,424,439,440,474,502],interf:375,interfac:[],interfer:[12,259,377],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,340,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,195,258,284,354,370,474,475,484,488],intermix:471,intermolecular:377,intern:[],internal_element_set:205,internal_quadratur:205,internet:242,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,195,196,205,231,246,284,360,361,370,382,431,440,453,459,460],interpret:[2,6,11,195,211,406,449,471,474,490,502],interrupt:293,intersect:[3,6,122,196,340,342,479],intersert:340,interspers:368,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,194,209,243,259,293,298,299,311,447,453,471,490,502],intestieti:122,intial:[6,375,377],intiial:[41,481],intiti:[3,318],intra:303,intra_energi:235,intramolecular:[29,235],introduc:[6,9,94,110,195,259,293,298,303,354,360,376,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:363,inv:[122,169,304],invalid:[3,12,71,91,173,273,370,423,424,478],invari:[110,137,142,144],invent:306,invers:[],invert:[1,6,174,285],invis:340,invoc:[168,219,375,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,227,228,229,232,233,234,235,236,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,255,256,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,294,295,296,297,298,299,300,301,303,304,305,306,308,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,345,347,348,350,351,354,356,359,360,361,362,363,368,370,375,376,377,379,383,384,385,386,387,388,390,391,392,395,396,4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462,463,465,467,468,469,473,477,485,486,489,497,502,504,506],respon:9,respond:[6,7,153,222,402,436],respons:[6,7,257,327,334],resquar:[],rest:[6,8,12,292,296,302,382,424,426,493,494,497],restart1:286,restart2:286,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,60,61,106,170,200,201,292,308,316,321,493,494],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,221,257,302,318,413],restratin:302,restrict:[],result:[1,2,3,6,7,9,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,45,46,47,48,49,51,53,54,56,63,64,66,67,71,75,89,92,93,96,106,107,109,113,114,116,118,119,120,121,122,123,145,147,150,153,157,164,165,167,169,170,173,176,177,179,180,181,182,184,185,187,188,190,192,193,195,196,199,202,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,226,229,231,234,235,236,238,243,244,246,250,257,259,261,262,263,264,265,266,267,268,269,276,278,279,280,281,282,285,286,294,295,300,301,303,305,306,319,322,324,327,328,329,331,332,333,335,336,337,339,341,344,345,347,348,350,351,354,356,360,361,370,373,375,376,377,379,383,384,385,386,387,388,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,426,427,429,431,432,433,434,436,440,441,442,449,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,480,481,485,486,487,488,490,501,502,503],resum:502,retain:[2,217,218,382,429,473],retart:[33,50,183,352],retir:439,retreiv:8,retriev:[6,8,233,427,428,502],reus:[3,488],rev:[6,13,64,70,94,110,114,144,145,158,206,237,243,245,257,259,260,264,280,285,295,298,303,308,319,323,326,328,329,334,367,382,390,391,392,395,400,401,402,405,406,411,416,423,424,425,426,428,437,441,448,458,460,461,462,465,471],revers:[2,6,8,89,181,219,241,259,283,284,294,312,327,328,334,370,422,485,497],review:[144,294,308,326,429,438,448,471,490,497],rewind:359,rewrap:193,rewrit:[5,12],rewritten:19,rezwanur:436,rfac0:[144,448],rfactor:319,rfile:303,rg0:317,rgb:196,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:336,rho_e:331,rho_fin:330,rho_i:[427,428],rho_initi:330,rho_ref_meam:426,rho_wal:336,rhodo:10,rhodopsin:[1,10],rhohi:289,rholo:289,rhosum:[],ribier:367,richardson:303,richi:[9,19],rick:[294,295,391,447],rick_and_stuart:295,ridg:[9,19],right:[3,6,11,12,41,146,170,188,189,192,216,219,241,246,256,283,344,363,392,476,479,486,502],rightmost:[41,216],rigid:[],rigidifi:303,rii:[91,92],rij:[94,110,217,218,284,396,397,398,456],rin:[408,419,420],ring:[],rino:[73,465],rinv:360,rirj:[337,406],rise:[],risi:[144,448],risk:[8,302,485],rix:[91,92],rjk:[217,218],rjone:[7,9,13],rlo:459,rmask:[3,502],rmass:3,rmax:[71,171,217],rmdir:487,rmin0:[144,448],rmin:[71,171,218,416],rmsd:330,rnemd:6,robert:9,robin:196,robust:[366,367,368],rock:426,rockett:437,rod:303,rodata:12,rodnei:298,roi:7,role:326,roll:12,ronchetti:110,room:[57,59],root:[11,89,91,92,194,326,330,375,400,483],rosati:39,rose:426,ross:426,rosski:286,rosybrown:196,rot:[6,93,286,302,326,503],rotat:[],rotation:110,rotaton:479,rough:[6,170,195,341],roughli:[7,10,12,41,153,195,210,235,243,244,258,259,273,290,303,319,322,323,326,361,370,375,443,445,478,485],round:[],rous:236,rout:[89,408,422],routin:[5,6,8,11,15,16,38,39,56,90,174,176,246,429,438,459,489],roux:[6,226,244,463,497],row:[6,65,66,68,69,75,79,92,95,96,107,109,112,118,119,120,123,150,158,165,167,168,169,208,209,211,212,213,214,249,303,331,333,341,402],royalblu:196,rozero:426,rperp:[256,312],rpi:288,rpm:12,rrespa:[1,3,5,7,8,16,200,201,256,259,371,376,377,378,379,380,381,383,384,385,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,430,432,434,436,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,464,465,467,468,469,485],rspace:3,rsq:[459,466],rsurfac:331,ru3:169,ru4:169,rub:20,rubia:[427,428],rudd:[431,459],rudra:[7,9],rudranarayan:[7,288],ruiz:206,rule:[],run1:[6,374,502],run2:[6,357,359,374,502],run3:[6,374,502],run4:[6,374,502],run5:[6,374,502],run6:[6,374,502],run7:[6,374,476,477,481,502],run8:[6,374,502],run:[],run_styl:[],runloop:359,runtim:[12,17,195,375],russia:9,rutherford:331,rutuparna:[460,462],ryan:9,ryckaert:[306,354],rycroft:168,rydberg:429,s00:436,s0st:6,s2050:1,s2629:400,s319:205,s_fact:309,s_i:[6,402],s_ij:6,sack:7,saddl:[258,370],saddlebrown:196,sadigh:[206,400,427,428],saed_vtk:122,safe:[12,195,226,244,375],safe_zon:3,safest:[3,319],safeti:309,safezon:440,safran:468,sagui:[361,395],sai:[1,3,12,13,196,439,440,474],said:368,sakai:461,sall:[9,447],salmon:196,salt:[393,404,426,476],salter:447,same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,57,59,62,63,65,69,71,72,77,79,81,84,86,87,89,90,91,92,93,94,95,97,100,106,107,108,110,112,113,114,116,117,119,120,121,144,145,146,147,148,149,150,151,152,153,156,157,158,159,160,1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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 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 body/rounded/polygon 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":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[210,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,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:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380,381],bond:[8,13,69,217,218,219,299],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:[6,58,220],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,390,468],colvar:[9,13,221],com:[74,75,151],comb3:391,comb:[295,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],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:[6,327],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:416,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:8,cut:[49,378,385,388,392,395,402,404,414,415,422,430,434],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],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:[6,29,395],direct:226,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:349,distribut:[7,12],document:0,dpd:[82,83,396,397,398],drag:224,dreid:[6,408],drude:[6,9,155,225,226,244],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,197],dump_modifi:196,dynam:294,eam:[13,400],echo:198,edip:401,eff:[9,13,99,100,154,156,161,245,260,272,281,325,402],efield:228,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:229,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:232,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:233,fcc:284,fdt:398,featur:[7,8,502],fene:[45,46],fep:[9,13,89,201],field:[6,7],file:6,finit:6,fire:294,fix:[2,6,8,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,3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:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,195,196,201,208,209,211,212,213,214,217,218,219,220,222,223,233,239,241,243,249,256,260,261,262,263,265,266,267,273,278,279,280,282,303,304,317,331,341,354,360,366,367,368,370,371,372,375,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,222,375,391],afil:237,aforement:18,afresh:[291,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,199,200,201,205,206,208,209,216,217,218,219,220,222,226,235,246,247,248,249,250,255,256,257,259,265,266,267,273,278,279,280,282,285,289,293,301,303,306,315,320,322,323,324,326,327,328,329,330,334,336,338,342,345,346,352,359,365,366,368,369,371,373,374,375,376,377,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,196,222,239,289,345,359,370,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,223,370,439,440],aggreg:[6,12,65,68,69,79,95,112,119,239,255,301,303,317,471,503],aggress:[239,490],agilio:[9,13],agre:[3,8,190,368,377,411,440],agreement:[5,7],ahd:408,ahead:338,aidan:[0,5,7,9,13,363],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:195,akohlmei:[7,9,13,197,240],aktulga:[7,9,296,440],al2o3:447,al2o3_001:[122,304],al3:169,ala:[246,447],alain:9,alat:[284,426],alb:[437,460,462],albeit:302,albert:9,alchem:[89,164],alcohol:334,alcu:[376,382],alcu_eam:437,alderton:395,alejandr:[259,260],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,196,205,216,219,222,246,248,249,273,286,294,303,306,307,326,327,331,334,339,366,367,368,372,375,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,361],aliceblu:196,align:[6,12,29,41,71,172,190,212,216,241,363,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,252,254,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,311,315,316,318,319,320,321,322,323,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,350,355,358,359,360,361,362,363,365,368,369,370,371,372,374,375,376,377,378,380,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:343,alloc:[3,5,6,8,9,11,12,60,233,333,369,371,375,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,195,196,197,199,200,202,204,205,206,208,209,210,211,212,213,214,216,218,219,220,221,222,223,227,228,233,235,236,237,238,240,243,246,249,250,254,256,259,260,284,288,289,290,291,292,293,297,303,304,306,308,310,311,315,319,326,327,328,329,331,332,333,334,335,336,342,344,346,355,360,361,363,368,369,370,371,374,375,378,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,241,293,331,361,372,375,456],alo:392,alon:[6,7,219,299,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,195,208,219,241,246,247,251,256,258,293,303,306,308,312,316,317,326,330,331,337,340,342,363,366,367,368,370,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,200,246,285,293,294,298,368,376,379,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,199,346,355,369,389,457,476],alphanumer:[3,63,199,292,300,344,369,502],alreadi:[3,7,8,9,12,16,17,18,4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rashev:400,bare:[226,242,244],barost:[226,497],barostat:[],barostt:6,barr:391,barrat:298,barrett:67,barrier:[3,4,6,258,356,370,391,404,490],bartel:285,bartok2010:448,bartok2013:448,bartok:[9,144,438,448],bartok_2010:438,bartok_phd:438,bary:501,barycent:315,basal:[],base:[3,4,6,8,9,11,12,13,14,15,20,63,64,71,78,89,93,106,115,122,150,152,169,170,172,193,194,195,196,199,205,212,213,216,217,218,222,223,227,235,240,243,247,249,273,285,286,289,292,294,296,303,304,308,309,319,326,361,375,377,379,382,396,402,405,408,409,410,412,414,423,427,428,434,436,437,447,458,461,462,465,471,473,476,477,478,480,483,486,487,490,491,494,501,502,503,506],bash:389,bashford:[6,20,176,387,488],basi:[3,6,12,40,144,150,170,204,243,245,285,319,336,363,412,486,502],basic:[6,7,8,12,17,41,117,145,195,196,205,216,259,260,284,340,376,378,429,470,478,497],basin:[88,370,471,490],bask:[400,426,437],bath:[9,293,298],batom1:[69,119,121,193,196],batom2:[69,119,121,193,196],bayli:[6,176,488],bb13:177,bcc:[3,4,7,64,70,73,363,426,428],bcolor:[3,195,196],bdiam:[3,195,196],be2:169,bead:[5,7,10,13,40,45,46,162,203,219,286,456],beam:223,bear:[6,236],becau:13,becaus:[0,1,3,6,8,12,16,17,18,40,41,42,59,64,71,72,77,94,110,120,132,144,150,155,160,170,171,172,176,193,194,195,196,197,202,208,216,217,218,219,220,222,228,234,235,236,237,242,243,244,245,256,259,260,273,280,289,293,294,298,303,316,321,326,327,330,331,334,338,339,340,341,342,348,360,366,368,370,371,374,375,381,387,389,392,394,396,402,403,405,406,407,408,409,413,422,423,424,426,431,441,456,457,463,464,473,474,476,478,479,480,483,485,486,488,490,497,502,503,504,506],beck:[],becker:[376,400],beckman:240,becom:[1,2,3,6,7,8,18,39,41,54,57,59,71,172,193,195,196,216,217,218,219,222,235,237,246,258,259,300,301,322,323,336,337,339,340,341,360,361,366,370,377,390,392,400,402,405,414,431,437,441,458,465,468,476,477,479,486,502],been:[1,2,3,6,7,8,9,11,12,13,16,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,45,46,47,48,49,51,53,54,56,57,59,60,63,65,69,71,89,113,116,117,118,119,121,123,147,148,149,150,151,152,153,157,158,159,160,162,163,171,172,173,174,176,177,179,180,181,182,184,185,187,188,190,192,193,195,196,197,202,204,206,207,208,209,211,212,213,214,215,216,219,220,221,222,223,229,234,235,238,240,241,243,244,246,247,248,249,250,254,256,257,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,288,289,290,293,295,297,300,301,303,305,306,315,320,322,323,324,331,332,333,335,336,337,338,339,341,342,345,347,348,350,351,354,356,359,360,361,368,371,375,376,377,379,383,384,385,386,387,388,390,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,428,429,432,433,434,436,439,440,441,442,449,456,458,459,460,461,462,464,465,467,468,469,471,473,474,476,477,478,479,480,482,486,490,493,494,502,503,504,505],befor:[1,2,3,6,8,9,12,14,17,22,29,39,40,41,44,59,66,71,74,75,81,91,92,96,106,107,108,109,118,150,153,158,159,165,170,171,173,174,178,191,192,196,200,201,202,203,204,206,208,211,212,213,214,215,216,220,225,226,234,235,240,242,243,244,246,249,256,259,265,266,267,278,279,282,285,292,293,294,297,298,303,304,305,320,322,323,324,330,336,337,338,342,346,365,366,368,370,375,403,406,422,426,429,457,466,471,473,474,477,478,479,480,481,483,484,486,490,493,494,497,502,503,504,505,506],began:[5,12],begin:[3,8,12,38,39,56,71,121,123,171,190,192,193,196,200,201,205,207,208,209,211,212,213,214,216,222,231,273,288,301,304,319,321,324,333,338,341,342,357,359,360,361,362,364,367,369,370,371,374,375,400,429,431,437,444,446,447,449,456,459,469,471,476,483,490,492,494,501,502,504],behalf:3,behav:[3,27,179,367,368],behavior:[3,174,190,193,195,197,219,220,223,235,236,237,240,243,244,245,259,289,293,298,319,322,323,331,367,382,402,426,469,470,478,482,502,504],behaviour:[6,243],behind:[8,242,257,293,319,360],beig:196,belak:7,believ:11,bellott:[6,20,176,387,488],bellow:350,belong:[2,3,40,71,124,173,206,208,212,235,249,303,342,369,443,476],below:[1,2,3,5,6,8,9,11,12,15,16,17,22,38,39,40,41,42,44,54,56,59,60,63,65,68,69,71,77,79,93,95,116,117,120,121,122,144,145,150,156,158,164,168,169,170,173,174,176,178,189,190,192,193,195,196,199,200,202,203,205,208,209,210,211,212,213,215,216,218,219,220,222,223,228,231,233,235,238,239,241,243,244,249,256,257,259,264,265,266,267,278,279,282,284,289,292,293,294,301,302,303,305,306,313,316,319,320,321,322,323,324,327,328,329,331,334,336,337,342,344,346,358,360,363,365,366,368,369,370,372,375,376,377,378,382,383,384,387,388,389,390,392,395,400,402,403,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,442,448,449,456,457,459,464,465,467,468,469,470,471,474,476,477,478,479,481,483,484,486,488,489,490,492,493,494,496,497,502,503,506],bench:[1,6,11,12],benchmark:[1,7,10,11,12,13,14,15,16,17,18,41,216,360,489],beneath:223,benedict:429,benefici:[61,372],benefit:[1,236,485],bennet:89,beowulf:7,berardi:[405,441],beraun:331,berendsen:[],berensen:303,berkelei:168,berkowitz:360,berlin:[7,9,308],bern:[3,286,2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,compass:[7,21,22,37,43,44,55,177,178,189,345,346,355,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,410,429,431,459,473,474,502],compens:[6,217,218,301,371,402],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,429,476,477,481,502],compl:17,complain:[12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,402,429,459,474,476,479,502],compli:[326,330],complic:[6,7,9,12,13,206,235,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,381,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,206,246,400],compound:[391,402,403,465],compres:[71,118,208],compress:[],compris:[40,340,441,464],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,382],computational:497,compute_arrai:8,compute_fep:[201,422],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:340,concentr:[71,400],concept:[6,150,160,208,485],conceptu:[3,6,71,158,220,222,370,392,409,426,481],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,502],conden:[331,460,462],condens:[6,152,331,377,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,431,474],conform:[3,6,13,59,219,220,258,302,308,330,354,370,402,488],confus:[3,465],conjuct:396,conjug:[7,8,243,367,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,219,240,288,303,306,316,370,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,392,414,418,471,477,479],consequ:[1,6,206,331,413,490],conserv:[3,29,199,206,219,226,227,236,239,243,245,246,250,255,257,259,273,303,306,307,322,323,327,334,335,339,370,395,396,406,420,447,485,490],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,243,244,322,323,324,375,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,298,435,502],consumpt:358,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,493,494,502,504],continuum:[6,7,9,205,331,444,446],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,444,446,468,505],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:205,controlfil:440,convect:93,conveni:[6,12,29,193,197,214,304,363,448,502],convent:[3,8,9,29,181,188,189,196,302,316,343,400,402,502],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,391,392,414,447,471,483,490],convers:[3,8,144,195,196,206,209,290,360,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,340,381],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:447,coordbb:447,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,385,392,394],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:[3,6,40,117,195,340,341,363,464,476],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,394,424,429,473,474,476,486,501,503],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,404,408,409,412,439,440,472,473,474,476,478,480,483,484,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,404,408,431,494,502],counter:[337,471,482,484,490],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,471],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,423,449,473,476,489,497,502,504],courtesi:363,cov:447,coval:[6,29,402,426,447,497],covari:237,cover:[6,71,190,196,205,246,402,464],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,497],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,436,464,478,481,502],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,480,494,497],crystallin:[6,106,285,363,461,497],crystallis:326,crystallogr:[122,169],crystallograph:[363,494],crystallographi:[122,169,363],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:[376,400],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,216,226,340,363,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,408,494],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,235,285],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[284,296],cutinn:[384,423,424],cutlo:[284,296],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:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:381,cutoff_inn:381,cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,502],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,479],cylindr:[6,241,316,337],cypress:375,cyrot:382,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,486],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:244,damp_drud:244,dampen:[303,497],dampflag:[337,406],dan:17,danger:[3,12,235,342,396,494],dangl:173,daniel:9,darden:[361,395],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[406,493],dat:[6,93,190,205,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:425,davi:336,david:[9,19,360,361,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,477,481],ddim:192,deactiv:422,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,256,292,303,332,491],decipher:363,declar:194,declin:319,decod:195,decompos:[89,448],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,497],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,288],degrad:[8,18,285,361,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,395,400,408,486,494,497,503],degress:[150,208],del:490,delai:[3,6,12,371,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[474,502],deloc:[260,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:3,delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:381,delx:192,delz:192,dem:381,demand:298,demo:11,demon:283,demonstr:[293,426],den:289,dendrim:408,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,392,407,409,440,444,446],dens:[71,219,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:223,deposit:[],deprec:[294,439],depth:[51,148,195,331,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459,485],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,195],despit:497,destabil:382,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,234,289,330,370,391,408,413,471,473,476,487,490,502],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:307,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,382,402,428,429,447,465,478],devemi:9,deviat:[257,264,284,404],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,391],devis:428,dfactor:195,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,429],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,444,446],diagonalstyl:448,diagram:[41,122,169,189,216,286],diallo:408,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,381,390,405,406,416,441,464,468,476,477,486],diamond:[363,402,426],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,2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43,244,246,249,257,258,259,260,264,280,284,286,293,294,298,306,307,319,327,331,334,336,337,339,341,354,360,361,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:260,equidist:258,equil:[3,294,364,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,391,392,439,440,472,486],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,402,476],eras:[305,328],erat:[222,424],erc:392,erfc:[392,414,431],erforc:117,erg:501,erhart:[206,400,460,462],ermscal:378,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:336,erron:3,error:[],erta:406,ervel:[117,476],escap:[223,497],especi:[8,11,16,158,170,199,206,216,235,293,298,301,302,375,473],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,392,414,462,481,494],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,431,440,459,490,494],esu:501,esub:426,eta:[6,246,259,293,294,296,335,401,403,405,437,461,465,501],eta_dot:259,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[368,370,471,490],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,493,494],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:450,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[344,474],evan:[158,280],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,368],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,216,246,412,466],event:[],eventu:[3,6,12,15,172,294,490],ever:[54,56,242,319],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[237,246,286,471],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,219,285],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,476,502],exceed:[3,41,59,216,222,259,319,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[210,402],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,402,491],exchange:360,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,375,391,429,431,485,495],excurs:[259,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,472,474,484,487,490,502],exempl:447,exemplari:236,exemplifi:402,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,502],exhibit:[94,259,367,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,216,231,359,374,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,474],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,396,431,485,490],experienc:[6,12,248,249],experiment:[235,360,375,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,208,258,284,409,470,473,474,476,485],explanatori:[3,8,121,193,207,208,211,212,213,303,369,473,502],explantori:[3,299],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[205,396,399],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,443,445,459,473,476,479],exterior:[3,6,168,340],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,402,461,497],extrema:422,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:293,f_harm:329,f_i:[29,437],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,494,502],f_ij:437,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:437,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,460,461,462],f_sigma:382,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:240,fall:[3,6,196,211,289,474,502],fals:[88,342,344,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,464,474,476,481,494],farago:243,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,212,331,332,375,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,502],fdirect:226,fdotr:410,fdt:[231,307],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:400,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,431],felling:428,felt:340,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,375,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,249,485],fewest:3,fextern:233,feynman:286,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,12,14,15,90,113,114,145,285,360,361,485],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,495],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:456,fictiti:[6,202,203,228,233,237,286,302,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[316,433],figur:[1,3,8,11,12,293,473,474],fij:395,file0:284,file1:[11,13,284,330,344,369,481,483,487],file2:[11,13,330,344,369,481,483,487],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,196,478,483,506],filepo:300,fill:[7,9,170,195,289,331,363,371,382,429,440,479],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,202,228,329,371,375,502],finer:[144,170,502],finest:360,finger:[170,192,256,479],finish:[6,11,41,216,344,357,359,360,372,374,375,464,481,502,503],finit:[],finni:[7,400,457],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,231,302,319,377,382,411,426,431,452,459,461,484,502],five:[73,156,293,369,382,427,476,490],fix:[],fix_adapt:[164,201,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:306,fix_reax_bond:439,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:395,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,195,196,197,214,219,221,225,240,243,247,249,255,256,285,292,303,316,318,319,326,330,339,342,358,361,369,373,374,375,377,408,413,426,429,456,471,473,474,476,477,478,480,481,482,486,502],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:225,flagvf:[384,423,424],flat:[6,331,336,337,341],flavor:[2,7,12],fld:[9,336,384,423,424],flen:378,flex_press:378,flexibl:[3,6,8,171,195,208,212,221,237,260,327,334,402,461,494],flip:[3,6,222,259,338,339],floor:502,flop:12,floralwhit:196,flow:[],fluctuat:[6,64,89,220,235,236,243,246,259,264,284,285,307,329,331,354,398],fluid:[],fluid_veloc:250,flush:[3,196,493],flux:[],flv:195,fly:[7,9,12,41,195,199,205,210,223,226,303,306,332,382,429,494,497],fmackai:9,fmag:224,fmass:286,fmax:[368,494],fmomentum:226,fmsec:[2,196,243,244,256,259,290,303,322,323,485,496,501,503],fname:359,fno:[12,16],fnorm:[368,494],fnpt:226,fnvt:226,foce:409,fock:378,focu:306,fogarti:[9,296,440],foil:[144,284,448],fold:[317,485],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,40,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,82,93,94,99,100,110,117,120,121,123,144,145,148,149,150,156,158,163,166,168,170,171,176,179,180,181,182,184,185,187,188,190,193,194,195,196,199,205,206,207,208,209,210,211,212,213,214,216,221,222,223,226,227,230,231,233,235,236,237,240,242,243,244,246,249,257,259,264,265,266,267,278,279,280,282,285,286,288,291,292,293,294,296,298,300,302,303,304,306,321,322,323,324,327,328,329,330,331,333,334,342,343,347,348,349,350,351,354,356,358,363,365,368,369,370,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,467,468,469,471,473,474,476,477,479,481,483,484,485,488,490,491,492,497,502,503,505],foo:[4,8,11,12,193,195,233,474,487,502],foot:6,footprint:[12,375],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:249,forcefield:[302,408],forcegroup:246,forcezero:366,ford:395,forestgreen:196,forev:71,forget:[244,497],forgiv:259,fork:[12,193],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,89,91,92,94,96,106,107,109,120,144,145,164,165,174,178,196,199,200,201,218,236,237,243,245,249,256,280,285,296,298,302,303,331,336,340,345,346,349,354,365,367,369,370,377,378,382,389,397,398,400,402,404,408,409,413,425,426,428,429,433,434,437,439,440,441,447,448,449,457,459,460,461,462,468,470,473,474,476,481,486,493,497,502],formal:[6,78,80,93,236,237,243,259,286,319,327,447],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,178,190,193,194,195,196,197,208,211,212,213,214,216,218,231,285,288,292,294,296,299,303,304,315,330,331,342,343,346,365,369,370,376,377,382,389,400,403,413,426,428,438,439,440,442,448,459,465,466,473,474,476,477,478,481,492,493,494,502,504],former:[6,12,16,39,41,196,216,331,335,382,384,482,488,502],formerli:[7,13],formul:[1,40,64,145,202,228,243,259,280,294,296,302,306,330,360,377,382,400,402,405,426,436],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,89,91,92,93,97,99,100,109,116,122,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,169,170,175,177,178,189,192,193,200,201,202,203,208,209,210,211,214,215,222,228,238,239,241,243,244,256,284,285,291,300,305,313,317,319,322,323,324,333,336,339,341,342,344,345,346,348,355,363,369,377,378,380,382,387,388,389,390,395,396,400,401,405,406,407,408,410,413,414,416,417,418,420,421,423,424,426,430,431,432,441,442,449,457,458,460,461,462,465,467,468,472,476,479,486,493,494,501,502,503],forth:[1,6,11,12,13,14,15,374,474,479,483],fortran:[3,6,9,11,12,13,233,400,409,426,439,440],fortun:8,forward:[3,8,89,359,370,375],foster:[382,436,437],foul:173,found:[3,6,9,12,73,164,193,219,221,235,240,246,285,326,332,344,359,371,389,392,395,471,477,478,493],four:[6,11,54,81,106,107,144,166,257,331,354,369,370,429,471],fourier:[],fourth:[6,108,302,316,326,387,433,447],fox:[6,122,176,455,488],fphi:[38,56,459],fpic:12,fplo:[38,56,459],fprime:459,fqdn:242,fqq:395,frac:[],fraction:[1,3,6,8,12,16,39,41,80,113,145,173,192,195,196,206,217,218,219,220,257,289,293,300,301,319,324,325,363,370,375,382,384,406,423,424,481,486],fragment:[42,240,300],fraig:[42,381],frame:[85,144,196,205,257,293,338,405],framer:[195,196],framework:[5,237,376,448],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,89,164,201,284,319,328,329,330,331,367,370,378,402,422,429,437,468,473],freedom:[3,6,8,97,99,100,102,104,105,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,208,219,226,235,237,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,303,306,322,323,324,329,368,395,494,497,503],freeli:[0,6,7,12,148,149,163,168,195],freez:[],frenkel:[235,329],freq:204,frequenc:[3,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465],input1:[65,68,69,79,95,112,117,118,119,121,123,321],input2:[65,68,69,79,95,112,117,118,119,121,123,321],input:[],input_doubl:3,inquir:309,insensit:12,insert:[3,5,7,8,12,59,170,199,223,235,241,289,360,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,196,207,212,213,223,224,232,235,241,246,249,289,303,319,336,338,339,340,341,342,358,363,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[246,395,446],instal:[],instanc:[6,11,200,221,237,338,404,409,431,437,474,497],instantan:[6,63,219,220,236,237,259,264,285,290,293,298,300,303,326,482,494],instanti:[6,11,12,205,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,201,208,211,212,213,214,216,220,221,235,243,246,249,250,285,291,301,303,321,339,358,360,361,364,371,375,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,240,288],instruct:[],insuffici:[3,6,12],insult:259,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,195,196,202,217,218,223,228,229,232,233,235,238,243,255,291,292,301,303,319,331,336,340,341,342,344,359,369,371,375,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,195,196,206,208,212,213,217,218,219,223,225,233,235,236,237,240,243,244,245,246,285,288,289,292,293,298,303,319,321,323,326,330,331,350,360,363,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,210,236,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,199,208,209,211,212,213,214,216,217,218,219,227,232,239,249,257,259,264,300,303,304,319,327,331,333,334,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,219,243,245,258,295,303,360,370,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,199,200,201,217,218,219,234,235,240,241,243,245,249,273,284,286,288,289,294,296,302,303,310,311,319,320,326,331,335,336,337,340,341,346,347,348,349,351,355,360,361,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,258,328,329,376,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:340,interest:[1,5,7,8,9,11,13,71,169,286,326,329,361,401,424,439,440,474,502],interf:375,interfac:[],interfer:[12,259,377],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,340,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,195,258,284,354,370,474,475,484,488],intermix:471,intermolecular:377,intern:[],internal_element_set:205,internal_quadratur:205,internet:242,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,195,196,205,231,246,284,360,361,370,382,431,440,453,459,460],interpret:[2,6,11,195,211,406,449,471,474,490,502],interrupt:293,intersect:[3,6,122,196,340,342,479],intersert:340,interspers:368,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,194,209,243,259,293,298,299,311,447,453,471,490,502],intestieti:122,intial:[6,375,377],intiial:[41,481],intiti:[3,318],intra:303,intra_energi:235,intramolecular:[29,235],introduc:[6,9,94,110,195,259,293,298,303,354,360,376,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:363,inv:[122,169,304],invalid:[3,12,71,91,173,273,370,423,424,478],invari:[110,137,142,144],invent:306,invers:[],invert:[1,6,174,285],invis:340,invoc:[168,219,375,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,227,228,229,232,233,234,235,236,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,255,256,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,294,295,296,297,298,299,300,301,303,304,305,306,308,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,345,347,348,350,351,354,356,359,360,361,362,363,3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01,302,303,305,306,308,316,318,319,320,322,323,324,325,327,328,329,330,331,333,334,335,336,337,339,340,341,342,344,345,347,348,350,351,352,354,356,359,360,361,363,365,367,368,369,370,371,374,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,426,427,428,429,431,432,433,434,435,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,465,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,506],young:[406,443,445],your:[0,1,2,3,4,5,6,7,8,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,59,61,111,113,116,120,147,148,149,153,157,163,168,170,171,172,173,174,176,177,179,180,181,182,184,185,187,188,190,192,193,194,195,202,205,209,211,214,215,217,218,219,220,222,223,229,234,235,238,240,243,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,289,292,295,301,303,305,306,308,321,322,324,327,331,333,334,335,336,337,339,340,341,342,345,347,348,350,351,354,356,361,363,369,370,371,374,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,399,400,401,403,404,405,406,407,408,409,410,411,414,415,416,417,418,419,420,421,422,423,426,427,428,429,431,432,433,434,436,437,439,440,441,442,449,456,458,459,460,461,462,465,467,468,469,470,473,474,476,478,479,480,483,484,485,486,487,488,489,493,494,501,502,504,506],yourself:[6,8,12,13,220,369],yplane:337,ypo:170,ysu:[3,193,321,477],yuan:9,yukawa:[],yukawa_1_1:466,yxz:473,yzx:473,z_i:[402,462,469],z_j:[462,469],z_meam:426,zachari:13,zannoni:405,zbl:[],zblcut:462,zblcutinn:448,zblcutout:448,zblexpscal:462,zblz:448,zcm:303,zcylind:337,zepeda:206,zero:[3,4,6,9,11,12,26,27,39,41,48,49,59,61,63,66,71,72,75,89,90,92,94,96,105,106,107,108,109,110,112,113,114,116,117,118,119,120,121,122,125,144,145,148,149,150,151,158,159,162,163,165,167,168,169,170,172,173,174,176,179,188,190,192,193,195,196,199,200,201,202,204,206,207,208,209,210,211,212,213,214,215,216,217,218,220,222,227,228,229,232,234,235,236,237,239,243,244,245,246,247,249,255,256,257,259,264,273,276,286,291,292,293,294,295,298,300,301,303,304,305,306,310,311,313,319,321,326,327,329,331,334,335,336,337,338,339,341,342,343,344,350,363,366,368,369,370,371,375,378,382,383,385,386,387,390,392,395,396,397,398,402,405,407,408,409,410,414,416,418,419,422,424,425,426,429,431,436,440,441,442,447,456,459,463,465,469,471,472,473,476,477,479,481,483,484,485,486,490,491,494,497,502,503,504,506],zeta:[3,246,294,403],zfactor:195,zflag:[157,158,247,249,255,303,326],zhang:[303,327,406],zhi:[3,6,172,193,204,330,336,339,341,476,479,494],zhi_bound:[6,193],zhou:[13,382,403,437,460,462],zhu:455,ziegenhain:13,ziegler:[288,426,457,462,469],zimmerman2004:205,zimmerman2010:205,zimmerman:[9,70,205,382],zlat:[222,241,494],zlib:193,zlim:447,zlo:[3,6,172,193,204,330,336,338,339,341,476,479,494],zlo_bound:[6,193],zmax:[204,246,502],zmin:[246,502],zn2:169,zone:[122,304],zoom:[3,193,195,196],zorig:71,zplane:337,zr4:169,zrest:318,zsu:[3,193,321,477],zwall:336,zwall_veloc:246,zxy:473,zybin:440,zyx:473},titles:["LAMMPS 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 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 body/rounded/polygon 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":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[210,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,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:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380,381],bond:[8,13,69,217,218,219,299],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:[6,58,220],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,390,468],colvar:[9,13,221],com:[74,75,151],comb3:391,comb:[295,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],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:[6,327],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:416,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:8,cut:[49,378,385,388,392,395,402,404,414,415,422,430,434],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],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:[6,29,395],direct:226,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:349,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:224,dreid:[6,408],drude:[6,9,155,225,226,244],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,197],dump_modifi:196,dynam:294,eam:[13,400],echo:198,edip:401,eff:[9,13,99,100,154,156,161,245,260,272,281,325,402],efield:228,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:229,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:232,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:233,fcc:284,fdt:398,featur:[7,8,502],fene:[45,46],fep:[9,13,89,201],field:[6,7],file:6,finit:6,fire:294,fix:[2,6,8,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313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