From 59149e72ff3d527d32a5c5f4a1a34ecd0ed60fb3 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 28 Aug 2015 20:40:16 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13944 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_start.html | 130 +++++++++++++++++++++++++++------------ doc/Section_start.txt | 135 +++++++++++++++++++++++++++++------------ doc/searchindex.js | 2 +- 3 files changed, 190 insertions(+), 77 deletions(-) diff --git a/doc/Section_start.html b/doc/Section_start.html index 5090972279..90bb1e4987 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -1739,40 +1739,91 @@ timesteps. When the run concludes, LAMMPS prints the final thermodynamic state and a total run time for the simulation. It then appends statistics about the CPU time and storage requirements for the simulation. An example set of statistics is shown here:

-
Loop time of 49.002 on 2 procs for 2004 atoms
+
Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+97.0% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
 

 

-
Pair   time (%) = 35.0495 (71.5267)
-Bond   time (%) = 0.092046 (0.187841)
-Kspce  time (%) = 6.42073 (13.103)
-Neigh  time (%) = 2.73485 (5.5811)
-Comm   time (%) = 1.50291 (3.06703)
-Outpt  time (%) = 0.013799 (0.0281601)
-Other  time (%) = 2.13669 (4.36041)
+
MPI task timings breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.9808     | 2.0134     | 2.0318     |   1.4 | 71.60
+Bond    | 0.0021894  | 0.0060319  | 0.010058   |   4.7 |  0.21
+Kspace  | 0.3207     | 0.3366     | 0.36616    |   3.1 | 11.97
+Neigh   | 0.28411    | 0.28464    | 0.28516    |   0.1 | 10.12
+Comm    | 0.075732   | 0.077018   | 0.07883    |   0.4 |  2.74
+Output  | 0.00030518 | 0.00042665 | 0.00078821 |   1.0 |  0.02
+Modify  | 0.086606   | 0.086631   | 0.086668   |   0.0 |  3.08
+Other   |            | 0.007178   |            |       |  0.26
 

 

-
Nlocal:    1002 ave, 1015 max, 989 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    8720 ave, 8724 max, 8716 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    354141 ave, 361422 max, 346860 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
+
Nlocal:    501 ave 508 max 490 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Nghost:    6586.25 ave 6628 max 6548 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:    177007 ave 180562 max 170212 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
 

 

-
Total # of neighbors = 708282
-Ave neighs/atom = 353.434
+
Total # of neighbors = 708028
+Ave neighs/atom = 353.307
 Ave special neighs/atom = 2.34032
-Number of reneighborings = 42
-Dangerous reneighborings = 2
+Neighbor list builds = 26
+Dangerous builds = 0
 

 

-
The first section gives the breakdown of the CPU run time (in seconds)
-into major categories.  The second section lists the number of owned
-atoms (Nlocal), ghost atoms (Nghost), and pair-wise neighbors stored
-per processor.  The max and min values give the spread of these values
-across processors with a 10-bin histogram showing the distribution.
-The total number of histogram counts is equal to the number of
-processors.

+
The first section provides a global loop timing summary. The loop time
+is the total wall time for the section. The second line provides the
+CPU utilzation per MPI task; it should be close to 100% times the number
+of OpenMP threads (or 1). Lower numbers correspond to delays due to
+file i/o or unsufficient thread utilization. The Performance line is
+provided for convenience to help predicting the number of loop
+continuations required and for comparing performance with other similar
+MD codes.

+
The second section gives the breakdown of the CPU run time (in seconds)
+into major categories:

+
    
+
  • Pair stands for all non-bonded force computation
    • 
+
  • Bond stands for bonded interactions: bonds, angles, dihedrals, impropers
    • 
+
  • Kspace stands for reciprocal space interactions: Ewald, PPPM, MSM
    • 
+
  • Neigh stands for neighbor list construction
    • 
+
  • Comm stands for communicating atoms and their properties
    • 
+
  • Output stands for writing dumps and thermo output
    • 
+
  • Modify stands for fixes and computes called by them
    • 
+
  • Other is the remaining time
    • 
+

+
For each category, there is a breakdown of the least, average and most
+amount of wall time a processor spent on this section. Also you have the
+variation from the average time. Together these numbers allow to gauge
+the amount of load imbalance in this segment of the calculation. Ideally
+the difference between minimum, maximum and average is small and thus
+the variation from the average close to zero. The final column shows
+the percentage of the total loop time is spent in this section.

+
When using the timers full setting, and additional column
+is present that also prints the CPU utilization in percent. In addition,
+when using timers full and the package omp command are
+active, a similar timing summary of time spent in threaded regions to
+monitor thread utilization and load balance is provided. A new enrty is
+the Reduce section, which lists the time spend in reducing the per-thread
+data elements to the storage for non-threaded computation. These thread
+timings are taking from the first MPI rank only and and thus, as the
+breakdown for MPI tasks can change from MPI rank to MPI rank, this
+breakdown can be very different for individual ranks. Here is an example
+output for this optional output section:

+
Thread timings breakdown (MPI rank 0):
+Total threaded time 0.6846 / 90.6%
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+—————————————————————
+Pair    | 0.5127     | 0.5147     | 0.5167     |   0.3 | 75.18
+Bond    | 0.0043139  | 0.0046779  | 0.0050418  |   0.5 |  0.68
+Kspace  | 0.070572   | 0.074541   | 0.07851    |   1.5 | 10.89
+Neigh   | 0.084778   | 0.086969   | 0.089161   |   0.7 | 12.70
+Reduce  | 0.0036485  | 0.003737   | 0.0038254  |   0.1 |  0.55

+
The third section lists the number of owned atoms (Nlocal), ghost atoms
+(Nghost), and pair-wise neighbors stored per processor.  The max and min
+values give the spread of these values across processors with a 10-bin
+histogram showing the distribution. The total number of histogram counts
+is equal to the number of processors.

 
The last section gives aggregate statistics for pair-wise neighbors
 and special neighbors that LAMMPS keeps track of (see the
 special_bonds command).  The number of times
@@ -1789,21 +1840,24 @@ takes place.

 minimize command, additional information is printed,
 e.g.

 
Minimization stats:
-  E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
-  Gradient 2-norm init/final= 1920.78 20.9992
-  Gradient inf-norm init/final= 304.283 9.61216
-  Iterations = 36
-  Force evaluations = 177
+  Stopping criterion = linesearch alpha is zero
+  Energy initial, next-to-last, final =
+         -6372.3765206     -8328.46998942     -8328.46998942
+  Force two-norm initial, final = 1059.36 5.36874
+  Force max component initial, final = 58.6026 1.46872
+  Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
+  Iterations, force evaluations = 701 1516
 

 

-
The first line lists the initial and final energy, as well as the
-energy on the next-to-last iteration.  The next 2 lines give a measure
-of the gradient of the energy (force on all atoms).  The 2-norm is the
-“length” of this force vector; the inf-norm is the largest component.
-The last 2 lines are statistics on how many iterations and
-force-evaluations the minimizer required.  Multiple force evaluations
-are typically done at each iteration to perform a 1d line minimization
-in the search direction.

+
The first line prints the criterion that determined the minimization
+to be completed. The third line lists the initial and final energy,
+as well as the energy on the next-to-last iteration.  The next 2 lines
+give a measure of the gradient of the energy (force on all atoms).
+The 2-norm is the “length” of this force vector; the inf-norm is the
+largest component. Then some information about the line search and
+statistics on how many iterations and force-evaluations the minimizer
+required.  Multiple force evaluations are typically done at each
+iteration to perform a 1d line minimization in the search direction.

 
If a kspace_style long-range Coulombics solve was
 performed during the run (PPPM, Ewald), then additional information is
 printed, e.g.

diff --git a/doc/Section_start.txt b/doc/Section_start.txt
index f259d22385..fca3963560 100644
--- a/doc/Section_start.txt
+++ b/doc/Section_start.txt
@@ -1745,36 +1745,92 @@ thermodynamic state and a total run time for the simulation.  It then
 appends statistics about the CPU time and storage requirements for the
 simulation.  An example set of statistics is shown here:
 
-Loop time of 49.002 on 2 procs for 2004 atoms :pre
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+97.0% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s :pre
 
-Pair   time (%) = 35.0495 (71.5267)
-Bond   time (%) = 0.092046 (0.187841)
-Kspce  time (%) = 6.42073 (13.103)
-Neigh  time (%) = 2.73485 (5.5811)
-Comm   time (%) = 1.50291 (3.06703)
-Outpt  time (%) = 0.013799 (0.0281601)
-Other  time (%) = 2.13669 (4.36041) :pre
+MPI task timings breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.9808     | 2.0134     | 2.0318     |   1.4 | 71.60
+Bond    | 0.0021894  | 0.0060319  | 0.010058   |   4.7 |  0.21
+Kspace  | 0.3207     | 0.3366     | 0.36616    |   3.1 | 11.97
+Neigh   | 0.28411    | 0.28464    | 0.28516    |   0.1 | 10.12
+Comm    | 0.075732   | 0.077018   | 0.07883    |   0.4 |  2.74
+Output  | 0.00030518 | 0.00042665 | 0.00078821 |   1.0 |  0.02
+Modify  | 0.086606   | 0.086631   | 0.086668   |   0.0 |  3.08
+Other   |            | 0.007178   |            |       |  0.26 :pre
 
-Nlocal:    1002 ave, 1015 max, 989 min
-Histogram: 1 0 0 0 0 0 0 0 0 1 
-Nghost:    8720 ave, 8724 max, 8716 min 
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    354141 ave, 361422 max, 346860 min 
-Histogram: 1 0 0 0 0 0 0 0 0 1 :pre
+Nlocal:    501 ave 508 max 490 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Nghost:    6586.25 ave 6628 max 6548 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:    177007 ave 180562 max 170212 min
+Histogram: 1 0 0 0 0 0 0 1 1 1 :pre
 
-Total # of neighbors = 708282
-Ave neighs/atom = 353.434
+Total # of neighbors = 708028
+Ave neighs/atom = 353.307
 Ave special neighs/atom = 2.34032
-Number of reneighborings = 42
-Dangerous reneighborings = 2 :pre
+Neighbor list builds = 26
+Dangerous builds = 0 :pre
 
-The first section gives the breakdown of the CPU run time (in seconds)
-into major categories.  The second section lists the number of owned
-atoms (Nlocal), ghost atoms (Nghost), and pair-wise neighbors stored
-per processor.  The max and min values give the spread of these values
-across processors with a 10-bin histogram showing the distribution.
-The total number of histogram counts is equal to the number of
-processors.
+The first section provides a global loop timing summary. The loop time
+is the total wall time for the section. The second line provides the
+CPU utilzation per MPI task; it should be close to 100% times the number
+of OpenMP threads (or 1). Lower numbers correspond to delays due to
+file i/o or unsufficient thread utilization. The {Performance} line is
+provided for convenience to help predicting the number of loop
+continuations required and for comparing performance with other similar
+MD codes.
+
+The second section gives the breakdown of the CPU run time (in seconds)
+into major categories:
+
+{Pair} stands for all non-bonded force computation
+{Bond} stands for bonded interactions: bonds, angles, dihedrals, impropers
+{Kspace} stands for reciprocal space interactions: Ewald, PPPM, MSM
+{Neigh} stands for neighbor list construction
+{Comm} stands for communicating atoms and their properties
+{Output} stands for writing dumps and thermo output
+{Modify} stands for fixes and computes called by them
+{Other} is the remaining time :ul
+
+For each category, there is a breakdown of the least, average and most
+amount of wall time a processor spent on this section. Also you have the
+variation from the average time. Together these numbers allow to gauge
+the amount of load imbalance in this segment of the calculation. Ideally
+the difference between minimum, maximum and average is small and thus
+the variation from the average close to zero. The final column shows
+the percentage of the total loop time is spent in this section.
+
+When using the "timers full"_timers.html setting, and additional column
+is present that also prints the CPU utilization in percent. In addition,
+when using {timers full} and the "package omp"_package.html command are
+active, a similar timing summary of time spent in threaded regions to 
+monitor thread utilization and load balance is provided. A new enrty is
+the {Reduce} section, which lists the time spend in reducing the per-thread
+data elements to the storage for non-threaded computation. These thread
+timings are taking from the first MPI rank only and and thus, as the
+breakdown for MPI tasks can change from MPI rank to MPI rank, this
+breakdown can be very different for individual ranks. Here is an example
+output for this optional output section:
+
+Thread timings breakdown (MPI rank 0):
+Total threaded time 0.6846 / 90.6%
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.5127     | 0.5147     | 0.5167     |   0.3 | 75.18
+Bond    | 0.0043139  | 0.0046779  | 0.0050418  |   0.5 |  0.68
+Kspace  | 0.070572   | 0.074541   | 0.07851    |   1.5 | 10.89
+Neigh   | 0.084778   | 0.086969   | 0.089161   |   0.7 | 12.70
+Reduce  | 0.0036485  | 0.003737   | 0.0038254  |   0.1 |  0.55
+
+
+The third section lists the number of owned atoms (Nlocal), ghost atoms
+(Nghost), and pair-wise neighbors stored per processor.  The max and min
+values give the spread of these values across processors with a 10-bin
+histogram showing the distribution. The total number of histogram counts
+is equal to the number of processors.
 
 The last section gives aggregate statistics for pair-wise neighbors
 and special neighbors that LAMMPS keeps track of (see the
@@ -1794,20 +1850,23 @@ If an energy minimization was performed via the
 e.g.
 
 Minimization stats:
-  E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
-  Gradient 2-norm init/final= 1920.78 20.9992
-  Gradient inf-norm init/final= 304.283 9.61216
-  Iterations = 36
-  Force evaluations = 177 :pre
+  Stopping criterion = linesearch alpha is zero
+  Energy initial, next-to-last, final = 
+         -6372.3765206     -8328.46998942     -8328.46998942
+  Force two-norm initial, final = 1059.36 5.36874
+  Force max component initial, final = 58.6026 1.46872
+  Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
+  Iterations, force evaluations = 701 1516 :pre
 
-The first line lists the initial and final energy, as well as the
-energy on the next-to-last iteration.  The next 2 lines give a measure
-of the gradient of the energy (force on all atoms).  The 2-norm is the
-"length" of this force vector; the inf-norm is the largest component.
-The last 2 lines are statistics on how many iterations and
-force-evaluations the minimizer required.  Multiple force evaluations
-are typically done at each iteration to perform a 1d line minimization
-in the search direction.
+The first line prints the criterion that determined the minimization
+to be completed. The third line lists the initial and final energy,
+as well as the energy on the next-to-last iteration.  The next 2 lines
+give a measure of the gradient of the energy (force on all atoms).
+The 2-norm is the "length" of this force vector; the inf-norm is the
+largest component. Then some information about the line search and
+statistics on how many iterations and force-evaluations the minimizer
+required.  Multiple force evaluations are typically done at each
+iteration to perform a 1d line minimization in the search direction.
 
 If a "kspace_style"_kspace_style.html long-range Coulombics solve was
 performed during the run (PPPM, Ewald), then additional information is
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 10bb7511c2..883c7a7f7e 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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41,ag1:163,ag2:163,again:[6,11,12,17,62,140,144,146,150,158,187,190,215,230,277,332,345,356,406,407,450,452,453,455,457,462,469,471,481,483],against:[11,12,13,64,216,356,420,421],aggreg:[6,12,65,68,69,79,92,108,115,230,246,289,291,304,450,482],aggress:[230,469],agilio:[9,13],agre:[3,8,184,354,363,394,421],agreement:[5,7],ahd:391,ahead:325,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:189,akohlmei:[7,9,13,191,231],aktulga:[7,9,284,421],al2o3_001:[118,292],al3:163,ala:237,alain:9,alat:[272,408],alb:[418,440,442],albeit:290,albert:9,alchem:[87,158],alcohol:321,alcu:[362,367],alcu_eam:418,alderton:380,alejandr:[250,251],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,190,199,209,212,215,237,239,240,262,274,291,294,313,314,318,321,326,352,353,354,358,361,385,407,425,427,450,452,469],alia:12,alias:[1,347],aliceblu:190,align:[6,12,29,41,71,166,184,205,209,232,349,455,458,476],alkali:385,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,152,157,158,159,160,161,162,163,164,165,166,167,168,170,172,177,183,184,187,188,189,190,191,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,243,245,246,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,302,303,305,306,307,308,309,310,313,314,315,316,317,318,319,320,321,323,324,325,326,327,328,329,330,331,332,333,336,341,344,345,346,347,348,349,351,354,355,356,357,358,360,361,362,363,364,366,367,368,370,371,372,373,374,376,377,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,401,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,470,472,473,474,476,480,481,482,483,484,485],allen:[29,87,380,388],allentildeslei:87,allign:3,allindex:330,alloc:[3,5,6,8,9,11,12,60,224,320,355,357,361,416,421,455,463],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,143,144,157,162,163,164,166,172,183,184,187,189,190,191,193,194,196,198,199,200,202,203,204,205,206,207,209,211,212,213,214,215,216,220,221,224,226,227,228,229,231,234,237,240,241,245,247,250,251,272,276,278,279,280,281,285,291,292,294,295,297,298,302,306,313,314,315,316,318,319,320,321,322,323,329,331,333,341,346,347,349,354,355,356,357,360,361,364,367,368,369,370,371,372,377,383,385,389,390,391,392,401,406,407,412,418,421,422,425,427,436,445,447,450,453,455,457,458,459,460,461,462,465,467,468,469,472,473,474,481,482],almost:[2,3,12,60,232,281,318,347,358,361,436],alo:377,alon:[6,7,212,287,420,421,453],alond:13,along:[6,8,9,12,29,40,87,118,163,164,186,187,189,212,232,237,238,242,247,249,281,291,294,295,299,303,304,313,317,318,324,327,329,349,352,353,354,356,377,380,389,392,395,397,401,408,420,421,439,455,458,465,466,481],alonso:[409,410],alpha:[6,51,194,237,273,281,286,354,362,365,368,377,381,383,384,386,391,396,397,408,413,417,441,443,473,476],alpha_:443,alpha_c:405,alpha_i:[428,443],alpha_ialpha_j:443,alpha_lj:405,alphabet:[2,3,22,37,44,55,63,172,183,193,333,341,355,374,437,455],alphanumer:[3,63,193,280,288,331,355,481],alreadi:[3,7,8,12,42,164,165,167,188,198,202,205,206,209,211,215,241,279,281,306,329,355,356,381,390,392,399,407,436,445,448,451,455,456,460,465,481],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,150,151,152,153,154,156,157,158,159,160,161,162,164,165,166,167,168,170,172,183,184,185,187,188,189,190,191,193,194,195,196,198,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,221,224,225,226,227,228,230,231,234,235,236,237,247,248,250,251,252,253,254,255,256,261,264,265,267,268,269,270,272,273,274,276,277,278,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,299,300,303,304,306,309,310,311,312,313,317,318,319,320,322,324,327,329,331,333,338,341,344,346,347,349,350,351,354,355,356,357,358,360,361,367,371,372,374,378,379,380,381,383,384,385,388,389,391,392,393,401,405,406,408,412,414,416,417,418,419,422,423,425,431,432,434,435,436,437,438,439,440,441,442,443,450,452,453,454,455,456,457,458,459,460,462,463,464,465,467,468,469,470,473,474,475,476,477,479,480,481,482,483,485],alter:[3,6,8,9,11,12,41,59,142,143,144,145,147,150,151,152,153,156,157,164,168,187,189,191,194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olecular:464,biophys:231,biosym:13,bird:382,bisect:[41,209,444],bisector:[6,377,397,401],bispectrum:[63,140,428],bisqu:190,bit:[3,12,17,39,224,235,412,439,463,476],bitmap:[3,439,445],bitrat:[189,190],bitzek:353,bkgd_dyn:408,bla:12,black:190,blais:[9,13],blanchedalmond:190,blank:[2,3,12,38,56,107,184,189,276,291,355,356,367,384,408,414,428,438,439,440,441,442,452,453,455,481],blast:318,blend:408,block:[2,3,6,91,140,164,166,167,277,327,349,361,367,385,418,428,458,469,476],blocksiz:361,blow:[3,262,323,327,429],blown:3,blue:[2,189,190,212],bluegen:[187,346],blueviolet:190,board:[347,380],bodi:[],body_nparticl:8,bodyflag:455,bodyforc:237,bodyforcei:237,bodyforcex:237,bodyforcez:237,bodystyl:[240,291],boff:[355,455],bogaert:313,bogu:[3,147,213],bogusz:88,bohr:[383,385,442,480],boltzmann:[6,7,9,87,91,112,142,144,145,146,147,150,151,152,153,154,156,202,212,234,237,238,239,240,241,254,322,381,470,480],bond:[],bond_coeff:[],bond_graph_cutoff:421,bond_harmon:[8,48,49],bond_harmonicshift:49,bond_info:421,bond_interact:199,bond_styl:[],bond_typ:[168,436],bondangl:[3,21,33,455],bondbond13:[3,171,455],bondbond:[3,21,33,455],bondchk:421,bondcoeff:3,bondtyp:[210,211,355,436],bonu:[3,483],book:447,bookkeep:412,bookmark:0,boost:[1,3,12,64,357],bop:[],border:[3,7,16,61,318,482],boresch:87,boreschkarplu:87,born:[],boron:385,borrow:295,bose:286,botero:[7,9,13,385],both:[1,3,6,7,8,9,11,12,14,15,16,17,18,27,37,39,40,54,55,57,59,61,62,63,68,69,71,83,87,88,108,113,115,116,128,143,144,149,152,154,157,164,166,167,168,173,183,184,187,189,192,193,194,195,200,202,203,205,206,207,210,211,212,213,214,215,220,226,228,230,232,234,235,237,238,246,247,250,251,255,256,262,267,270,276,280,281,282,288,291,294,295,303,306,310,314,315,316,318,321,323,324,326,327,328,331,332,341,347,351,354,355,356,357,359,361,363,367,368,369,370,371,372,373,375,380,381,383,384,385,388,389,391,392,393,397,399,401,402,403,405,406,407,411,412,415,422,423,438,440,441,442,448,450,452,453,455,456,457,458,462,467,472,473,476,481,483,484,485],bottleneck:[1,3,453],bottom:[8,9,147,190,215,225,237,268,314,321,349,467],bottomwal:208,bounc:[3,306],bound:[3,6,17,26,27,41,42,57,59,71,153,166,173,186,187,190,204,205,209,215,216,220,226,235,250,277,306,323,324,325,326,327,328,346,354,385,455,458,469,476,481,482],boundar:3,boundari:[],boundary_dynam:199,boundary_faceset:199,boundary_integr:199,bount:11,box:[],boxcolor:[189,190],boxxlo:11,bpa:361,bpclermont:[9,13],bptype:436,br1:163,bracket:[2,3,6,41,63,71,117,119,193,201,202,203,204,205,206,207,209,320,473,481],bragg:[118,163],branc:11,branch:11,branicio:73,breakabl:[7,44,55],breakag:[78,210],breakdown:[1,12,15,88,107,420,421,450,469],brennan:436,brenner:[363,437],brick:[3,41,62,152,166,209,455,457,459],brief:[1,5,6,7,8,12,233,363,367,421,469],briefli:[6,10,274,376],brilliantov:389,bristol:[5,7],brittl:417,broader:453,broadli:8,broken:[2,54,65,69,70,78,107,115,168,210,250,367,457,467,474,483],brook:6,brought:186,brown:[7,9,13,15,16,118,141,190],brownain:369,brownian:[],brownw:7,brows:0,browser:[4,189],bryantsev:391,bsd:12,bstyle:[40,42],btype:[69,115,165,187,377,397,401,405,436],buc:370,buck:[],buckingham:[7,194,195,282,347,368,370,371,379,437],buffer:[3,8,189,190,472],bufi:189,bug:[],bui:189,build:[],builder:[7,13],built:[1,2,3,4,6,8,9,11,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,43,45,46,47,48,49,50,51,53,54,55,56,64,67,78,80,83,86,87,96,97,98,99,100,101,105,109,111,112,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,148,150,151,155,156,158,162,170,171,173,174,175,176,177,178,179,181,182,183,184,187,188,191,193,196,197,198,200,208,210,211,212,214,216,221,222,223,225,226,227,228,229,231,233,234,236,237,238,239,240,241,243,244,248,249,250,251,252,253,254,255,256,257,258,259,260,261,263,265,266,267,268,269,270,272,273,274,276,277,280,281,282,283,284,285,286,287,288,291,293,294,295,296,297,298,299,300,302,306,309,311,312,313,314,315,316,318,319,321,322,324,325,330,331,332,334,335,336,337,338,340,341,342,347,356,357,358,361,362,363,365,366,367,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,450,453,456,458,464,468,469,470],bulatov:[409,410],bulk:[4,6,10,70,237,272,278,378,408,412,417,424,426,459],bullet:7,bump:234,bunch:8,bundl:[9,189,191],burlywood:190,bussi1:310,bussi2:310,bussi:[228,310],buyl:[9,188],bybe:9,c1060:14,c11:[203,408],c12:203,c13:203,c1n:203,c2050:14,c21:203,c22:203,c23:203,c2n:203,c31:203,c32:203,c33:203,c34:203,c3n:203,c41:203,c42:203,c43:203,c44:203,c_0:[318,434,435],c_1:[68,69,117,118,163,187,190,227,280,292,329],c_2:[69,117,118,160,162,163,187,292,320,329],c_3:[117,292],c_cluster:6,c_cstherm:6,c_dist:117,c_doubl:11,c_e:318,c_flux:91,c_forc:117,c_gauss:387,c_hb:391,c_id:[6,63,71,87,117,119,187,201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50,255,256,267,268,270,273,277,282,288,289,291,292,295,303,304,306,308,309,310,311,313,314,316,323,327,332,349,355,366,384,385,388,389,395,406,407,408,409,410,438,440,441,442,444,458,465,476,481],centimet:480,central:[3,61,70,76,77,116,122,140,240,272,294,304,355,414,420,421,455],centro:[],centroid:[3,274,444,465],cerda:346,ceriotti2:228,ceriotti:[13,228,233],certain:[1,2,3,6,8,12,17,39,71,113,117,119,168,187,189,201,202,203,204,205,206,207,212,224,225,291,293,307,320,331,338,345,357,392,412,421,443,457,461,476,481],certainli:232,cerutti:347,cfg:[3,6,7,13,187,188,189,190,191],cfile:421,cfl:[128,296],cfor:295,cg_type:423,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:294,ch2lmp:[],ch3:294,ch5md:188,chain3:357,chain:[],challeng:[6,295],chalopin:286,champaign:[231,346,347,406],chandler:[362,383],chandrasekhar:[6,397],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,128,146,147,148,164,165,166,168,184,186,187,188,189,190,191,193,194,195,196,197,199,200,205,206,208,209,210,211,212,213,214,215,216,220,221,223,225,228,230,231,232,234,236,237,238,240,246,247,248,250,251,252,253,254,255,256,262,267,268,269,270,272,273,277,278,280,281,285,288,289,290,291,293,294,295,306,309,310,311,312,314,315,316,317,318,319,321,324,327,329,347,352,354,356,359,361,381,385,389,392,406,407,408,412,420,421,437,450,451,452,453,455,456,457,458,459,460,461,463,464,465,466,467,470,473,477,479,480,481,482,483],change_box:[],changeabl:187,channel:[4,196],chapter:[274,347],charact:[2,3,6,12,38,41,56,63,184,187,189,190,191,193,209,280,288,331,355,360,385,396,418,420,421,439,452,453,457,462,463,481,483,484,485],character:[6,67,70,116,140,428,450,469],characterist:[235,306,315],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,163,164,187,191,193,194,195,200,216,221,226,280,282,283,284,288,308,321,346,347,355,368,370,376,377,379,380,383,385,386,392,397,401,405,415,420,421,437,442,443,445,447,448,455,456,460,465,467,476,480,481],charmm2lammp:13,charmm:[],chartreus:190,cheap:306,cheaper:[220,388,422],check:[3,6,8,11,12,15,17,39,41,71,91,184,200,205,209,210,211,216,223,226,232,233,290,294,306,314,316,321,329,331,345,354,355,356,357,358,361,382,393,396,412,421,436,450,452,453,455,463,469,472,473],checkf:184,checkqeq:421,checku:184,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,141,170,171,181,214,219,227,228,235,237,249,250,251,268,269,274,278,281,283,291,295,306,309,310,313,314,315,316,323,332,340,342,346,347,353,356,363,368,372,373,376,377,378,380,381,385,387,388,390,391,397,401,402,405,408,411,412,415,436,443,464,467,469,476],chemic:[9,118,158,163,187,199,200,226,282,287,288,313,347,420,421,432],chemistri:[9,281,282,284,367,385,420,421],chen:318,cheng:376,chenoweth:[420,421],chenoweth_2008:[420,421],chi:[92,153,186,272,282,284,386,388,482],chiefli:419,child:8,chip:[7,12,17,361,468],chipot:214,chiral:340,chmod:[11,12],cho:408,chocol:[7,190],choic:[3,6,12,15,16,18,40,41,54,87,141,143,157,168,184,202,205,206,209,212,215,216,228,234,237,248,250,274,282,291,313,341,347,352,353,356,358,361,392,405,412,416,455,464,465,468,469,475,476,480],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,154,155,189,210,211,212,213,216,223,234,237,248,250,252,253,254,255,256,278,306,310,324,346,347,353,445,450,452,464,470],chose:[440,442],chosen:[2,3,6,12,17,140,164,167,176,184,189,195,200,213,216,223,226,227,235,237,248,250,254,274,277,288,306,310,313,314,319,321,322,328,347,348,353,361,385,389,395,396,399,423,440,450,464,469,476],chri:162,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,144,159,161,202],chute:[4,10,229],ciccotti:294,cieplak:[6,170,467],cii:203,cij:203,circl:302,circular:[3,6,143,185],circumst:18,circumv:286,citat:[],cite:[3,7,8,12,234],cko:2,cl1:163,clarendon:[29,380],clarifi:[7,440,442],clariti:331,clark:415,class2:[],classic:[0,3,5,6,7,8,9,224,274,281,286,318,342,385],classifi:[9,437],claus:453,clean:[6,12,14,15,17,463],cleanli:[454,484],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:459,click:[2,11,22,37,44,55,164,172,183,189,231,333,341,356,374,437],client:[231,233],climb:[249,356,469],clinic:[7,13],clo:[153,186,482],clock:[12,450,469],clockwis:324,close:[3,6,11,12,13,39,41,67,141,167,187,211,212,213,228,235,237,250,268,291,294,324,327,345,347,350,352,353,356,361,363,367,377,378,408,412,424,426,442,459,465,476,478],closer:[3,41,116,162,186,187,209,213,217,315,356],closest:[211,272,291,321,388,422,436,445],cloud:476,clovertown:18,clsuter:72,clump1:[276,291],clump2:[276,291],clump3:[276,291],clump:291,cluster:[],clutter:[3,9],cmap:455,cmatrix:228,cmax:408,cmd:[11,12,274,466],cmin:408,cmm:[],cn1:203,cn2:203,cna:[],cnn:203,cnr:[9,13],cnt:[392,459],co2:[40,163,294,355],coars:[7,9,29,36,40,54,176,276,291,306,390,423,467],coarser:[347,481],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,170,171,172,177,332,333,338,374,392,396,412,425,427,429,455,457],coeffcient:455,coeffici:[],coefficienct:381,coefficient0:383,coefficient1:383,coeffieci:[6,365],coeffincientn:383,coexist:[9,226,385],cohes:[6,386,408],coincid:[122,327,372,406,407,450],colberg:188,cold:[6,149,230,357,476],coldest:314,coleman8:9,coleman:[9,118,163,292],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,144,152,159,161,164,187,190,202,214,240,246,276,286,289,291,329,346,355,357,375,395,455,462,468,474,485],collid:[220,306,328],colliex:163,collinear:[3,276],collis:[3,237,306,324,328,382,389,448],colllis:306,colloid:[],colombo:39,colon:[191,329,456],color1:190,color2:190,color:[3,9,41,187,189,190,209,227,281,286],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,144,152,159,161,162,163,184,187,190,193,201,202,203,204,205,206,207,240,247,248,281,291,307,308,318,328,387,391,420,421,456,470,472,481],colvar:[],colvarmodul:12,com:[],comamnd:215,comand:[212,457],comannd:361,comb3:[],comb:[],comb_1:283,comb_2:283,combiant:378,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,143,157,187,189,199,204,231,240,250,274,280,310,319,327,330,332,346,347,349,353,361,375,377,378,385,386,392,404,405,428,438,440,442,447,458,463,476,481],come:[],comfort:[12,13],comm:[0,3,12,61,73,188,231,233,234,347,356,361,381,412,417,439],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,170,184,187,235,291,318,355,356,362,383,384,386,396,408,414,421,428,438,439,440,441,442,452,453,455,476,481],commerci:7,commmand:[3,6,12,59,107,269,449,450,452,469,484],common:[],commonli:[3,6,12,17,25,57,59,105,166,187,189,191,342,390,399,428,440,442,455,458,467],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,167,168,189,190,209,210,211,213,214,215,231,233,237,239,240,241,250,273,280,282,283,284,291,306,318,329,346,357,358,359,361,382,416,452,453,457,464,465,483,485],communc:346,comp:[7,188,233,234,294,347,356,385,412,417,422,435,439,441],compact:[63,193,374,437],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,147,162,163,172,183,190,219,282,329,331,346,347,354,356,408,450,469,470,476,480],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,171,172,183,332,333,341,373,437],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,175,187,191,195,201,202,203,204,205,206,207,209,273,285,310,313,320,323,326,346,361,393,412,439,452,453,481],compens:[6,210,211,289,357,385],compet:317,competit:347,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,162,187,188,189,191,231,317,347,361,455,456,460],compl:17,complain:[12,17],complement:408,complementari:[7,377,397],complet:[3,6,9,12,15,41,59,71,190,205,209,214,240,274,277,280,306,317,319,331,345,356,361,386,425,427,444,450,455,460,463,467,469,472,476,481],complex:[6,8,11,12,13,25,40,42,62,140,152,164,165,237,302,327,344,356,385,439,453,455,458,481],compli:[313,317],complic:[6,7,9,12,13,200,226,453],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,159,160,161,187,189,190,196,197,201,202,203,204,205,206,207,208,212,213,215,216,221,224,229,233,234,237,240,242,246,247,249,250,251,254,255,256,267,268,270,271,273,274,275,278,289,291,293,294,295,299,300,303,306,309,310,311,313,320,321,326,327,328,346,349,353,354,355,356,361,381,385,389,406,407,425,427,428,455,456,465,473,481,482],componenet:6,composit:[6,200,237,383],compound:[376,385,386],compres:[71,114,202],compress:[3,6,9,12,59,71,114,167,187,189,190,202,215,248,254,278,281],compris:[40,327,395,422,444],compton:[118,163],comptu:[3,6],compuat:347,comput:[],computation:[3,6,210,211,318,367],computational:476,compute_arrai:8,compute_fep:[195,405],compute_group_group:226,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,292],compute_scalar:8,compute_temp:8,compute_ti:195,compute_vector:8,compute_xrd:163,concaten:[2,3,484],concav:327,concentr:383,concept:[6,144,154,202,464],conceptu:[3,6,71,152,213,215,356,377,392,408,460],concern:[6,73,87,188,227],concis:[11,317],conclud:12,concret:8,concurr:[9,16,347],conden:[318,440,442],condens:[6,146,318,363,379,383,397],condit:[],conducit:6,conduct:[],cone:458,confid:[3,469],config:[12,187,452],configfil:214,configur:[1,2,6,12,15,17,38,59,122,166,184,186,187,189,193,213,214,215,216,220,226,233,234,262,274,282,317,344,354,356,363,367,384,408,438,440,442,450,455,457,458,469],confin:[455,469],conflict:[3,12,40,412,453],conform:[3,6,13,59,212,213,249,290,295,317,340,356,385,467],confus:3,conjuct:381,conjug:[7,8,234,353,385,420,421],conjunct:[6,7,71,86,87,114,147,152,158,164,168,190,194,195,234,237,241,262,277,278,282,283,284,286,291,306,314,321,326,346,347,356,368,370,374,377,381,385,391,397,412,415,423,443,455,458,462,476,485],connect:[3,6,87,149,167,212,231,276,291,294,303,356,378,389,436,442,452,453,459,476],conput:3,consecut:[3,11,12,39,71,164,190,194,195,216,231,232,377,397,401,450,456,458],consequ:[1,6,318,396,469],conserv:[3,193,200,212,219,220,227,230,234,236,237,241,246,248,250,262,291,294,309,310,314,321,322,326,356,380,381,389,403,464,469],consid:[6,9,70,71,78,87,115,149,150,167,187,190,194,195,201,203,205,209,211,212,216,238,251,273,291,313,314,317,318,321,347,374,385,392,421,422,436,450,451,453,456,457,458,460,463,465,473,476,481],consider:[6,8,234,235,309,310,311,361,464],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,144,147,149,164,176,186,191,196,197,202,215,216,219,221,224,227,234,235,236,247,250,252,253,254,255,256,257,258,260,261,262,263,265,266,267,268,269,270,278,281,286,288,290,291,309,310,311,312,322,346,347,349,355,356,361,363,367,369,375,377,385,388,392,406,407,408,412,422,425,427,439,445,453,455,456,458,459,460,467,476,481],consistent_fe_initi:199,consit:291,constant:[],constitu:[3,6,240,291,323,327,375,422],constitut:[425,427],constrain:[3,6,8,142,143,144,145,147,150,151,152,153,154,156,157,193,202,216,226,227,232,240,244,276,277,289,291,294,304,314,321,354,355,385,460,467,476],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,140,163,213,250,273,290,327,357,361,380,412,436,438,439,458,459,481],constructor:8,consult:421,consum:[1,286,416,481],consumpt:344,contact:[],contact_stiff:[424,426],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,144,152,162,163,164,166,170,172,183,184,187,189,190,191,193,194,195,199,201,202,203,204,205,206,207,209,214,216,221,228,232,233,234,235,237,248,262,272,273,276,277,279,281,284,288,291,292,296,306,313,317,318,327,328,331,345,347,355,356,359,360,362,363,364,367,376,377,380,383,384,385,392,393,408,414,418,419,420,421,428,438,439,440,441,442,443,450,451,452,453,455,456,457,458,460,462,464,467,469,472,473,476,481,483,485],content:[12,18,421,471,473],context:[3,6,8,12,17,117,190,210,211,216,276,288,322,353,447,455,462,471,480,481,482],contibut:70,contigu:452,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,160,190,193,194,195,200,202,203,204,205,206,207,209,212,213,214,215,216,226,227,228,230,231,232,234,235,236,242,247,248,250,252,253,254,255,256,267,268,269,270,275,277,280,281,291,292,295,305,306,308,315,316,318,324,327,331,345,360,361,367,381,382,399,402,420,421,422,425,427,441,450,453,455,457,458,463,469,472,473,481,483],continuum:[6,7,9,199,318,425,427],contour_integr:199,contract:[59,213,215,250,278,291],contradictori:3,contrain:294,contraint:262,contrari:[228,235],contrast:[1,6,42,55,64,149,215,329,425,427,447,484],contrib:318,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,195,200,201,202,203,204,205,206,207,213,226,234,237,240,241,245,251,268,269,276,277,285,288,291,292,294,320,346,354,356,364,381,382,383,385,392,406,407,412,420,421,467,473,476],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,173,187,189,193,199,200,209,213,214,215,230,231,234,235,250,252,253,254,255,256,278,283,291,297,298,309,310,311,318,322,344,346,358,385,388,420,421,424,426,438,442,450,452,464,470,471],control_typ:199,controlfil:421,convect:91,conveni:[6,12,29,187,191,207,292,349,428,481],convent:[3,8,9,29,175,182,183,190,290,303,330,383,385,481],converg:[3,6,41,88,187,189,191,196,209,212,213,221,224,254,281,283,286,290,294,352,353,354,356,376,377,397,450,462,469],convers:[3,8,140,189,190,200,203,278,346,377,378,379,385,397,401,405,415,453,469,480],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,164,171,187,189,190,207,248,329,332,334,337,340,349,356,362,383,440,442,448,453,455,456,457,462,472,476,480,481,483,485],convex:327,convinc:[7,12],cook:9,cooki:7,cool:[7,154,230,289],cooordin:187,cooper:[5,7],coord123:114,coord1:[3,114,202,205,206],coord2:[3,114,202,205,206],coord3:[3,114,202,205,206],coord:[],coordiat:354,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,147,153,159,161,162,164,168,186,187,188,189,190,191,193,196,201,202,204,205,206,209,210,211,212,213,214,215,216,219,221,222,224,226,229,230,231,232,233,234,235,247,249,250,252,253,255,256,268,271,272,273,276,277,278,288,289,291,293,294,295,300,303,304,305,306,308,316,317,318,325,326,328,329,349,354,355,356,361,362,363,366,384,450,455,456,458,460,463,465,469,476,481,482],coordn:[114,202],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,189,318,356,374,420,453],copper:448,coproccesor:16,coprocessor:[1,4,7,9,16,17,361,468],coproprocessor:17,copy_arrai:8,copyright:[7,8,276],coral:190,core:[],core_shel:146,coreshel:[6,9,370,377,379],cornel:[6,170,467],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,189,327,328,349,444,455],cornflowerblu:190,cornsilk:190,corpor:16,corr:376,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,146,151,158,189,215,228,234,250,251,268,276,278,281,317,323,327,346,356,362,363,364,365,366,367,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,446,447,448,455,470,473,476],correction_max_iter:199,correctli:[3,8,9,11,17,71,81,102,103,142,143,145,147,149,150,151,152,153,156,157,160,187,190,196,216,221,224,235,244,250,251,284,291,294,303,305,324,327,356,357,361,379,407,452,453,455,465,480,482],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,142,143,151,158,163,170,171,172,173,174,175,176,178,179,181,182,184,187,189,190,194,195,196,202,204,205,206,208,211,213,215,222,224,225,229,234,237,238,246,247,248,250,252,253,254,255,256,257,262,265,267,268,270,273,274,278,283,291,293,294,309,311,313,322,323,324,326,327,328,330,332,333,334,335,336,337,340,342,347,351,353,355,356,362,363,365,368,369,370,371,372,373,374,375,376,377,380,381,383,384,385,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,417,418,420,421,422,423,428,429,438,439,440,441,442,444,446,447,448,450,452,453,455,456,458,468,469,470,472,473,476,481],correspondingli:[406,407,464],cosin:[],cosineshift:27,cosmo:[228,233],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,163,189,190,202,205,206,209,210,211,223,250,283,318,346,347,359,377,397,401,412,438,452,464],costheta0:[438,440,442],costheta:418,costli:[11,88,228,357],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,144,154,159,161,177,187,189,190,194,195,200,202,203,205,209,215,224,233,280,281,282,286,289,291,293,306,307,313,317,318,319,323,327,329,331,338,343,345,352,354,357,361,364,387,391,392,420,421,451,452,453,455,457,459,462,463,471,476,481,482],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,141,165,169,282,284,319,346,347,354,361,368,370,371,372,373,376,377,378,379,380,385,389,390,392,397,401,405,412,415,420,421,423,437,442,443,447,460,467,473,476,480],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,152,162,168,196,197,200,202,204,205,206,208,209,216,221,223,226,232,250,262,277,294,309,310,327,347,354,355,356,358,361,387,391,412,473,481],counter:[324,450,461,463,469],counterbal:230,counterpart:[187,291,450],counterproduct:18,coupl:[],courant:296,cours:[3,8,126,128,158,187,194,195,227,290,303,317,323,325,326,328,329,347,406,429,452,455,468,476,481,483],coval:[6,29,385,408,476],covari:228,cover:[6,71,184,190,199,237,385,395,444],coverag:[71,205],cpc:233,cpp:[1,3,6,8,9,11,12,13,87,187,194,195,224,294],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,190,193,219,235,319,344,347,361,374,437,450,468,469,472,473,474],cpuremain:473,cr2:163,cr3:163,crack:[4,357],crada:[5,7],crai:[5,7,13,18,187],crash:[3,12,357,476],craympi:361,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:199,create_faceset:199,create_group:188,create_nodeset:199,createatom:[],creation:[],crimson:190,critchlei:276,criteria:[3,116,165,189,190,210,211,212,245,354,417,444,457,460,481],criterion:[41,121,162,164,167,200,209,212,226,262,283,296,324,329,354,356,376,385,389,460,469,470],criterioni:469,critic:[48,49,248,313,318,354],cross:[3,12,22,71,89,143,172,187,189,201,205,211,215,247,249,268,291,299,303,305,314,321,333,349,356,372,381,382,383,390,391,392,397,399,401,418,423,425,427,440,442,455,459,465,483],crossov:1,crossterm:455,crozier:[0,7,13],crucial:281,crystal:[4,6,13,73,272,273,316,357,459,473,476],crystallin:[6,273,349,441,476],crystallis:313,crystallogr:[118,163],crystallograph:[349,473],crystallographi:[118,163,349],cs1:163,cs_chunk:6,cs_im:[40,455],cs_re:[40,455],csanyi:[140,419,428],cscl:408,csequ:6,csh:[11,12,374],cshrc:[11,12],csic:[384,438,440,442],csinfo:6,csisi:[384,438,440,442],csld:[],cst:383,cstherm:6,cstyle:452,csvr:[],ctcm:[362,383],ctemp_cor:219,cterm:295,ctr:9,ctype:11,cu1:163,cu2:163,cu3au:408,cube:[6,41,162,167,209,219,327,349,476],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:367,cummul:[3,6,207,210,211,212,214,223,228,234,236,306,309,310,311,312,314,321,391,473],cumul:[6,200,202,204,205,206,220,226,234,248,250,254,262,291,292,356],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,144,152,160,162,165,168,187,188,189,190,191,194,195,199,200,202,205,206,207,209,210,211,212,213,214,215,216,220,221,224,226,228,231,232,234,240,247,250,251,255,256,262,267,268,270,276,282,283,285,288,289,290,291,294,295,296,297,298,299,300,302,304,305,306,309,310,311,317,318,321,322,323,324,325,326,328,329,331,344,345,346,347,350,351,353,354,355,356,361,367,374,376,380,383,385,386,389,393,396,406,407,408,409,410,412,418,420,421,424,425,426,427,429,440,442,443,445,450,451,452,453,455,456,457,458,459,461,462,463,465,467,469,470,472,473,481,482,483,484,485],curv:[6,164,226,273],curvatur:[388,422,448],custom:[],cut0:453,cut1:464,cut2:464,cut:[],cuthi:[272,284],cutinn:[369,406,407],cutlo:[272,284],cutmax:418,cutoff1:[373,380,397,401,405,415,423],cutoff2:[368,370,371,373,379,380,397,401,405,415,423],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,162,165,167,211,212,217,272,281,282,284,286,288,291,306,319,323,327,329,346,347,354,357,358,359,361,362,363,364,365,366,367,368,369,370,371,372,373,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,428,429,430,431,432,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,453,457,460,464,476],cutoffa:384,cutoffc:384,cuu3:383,cval:163,cvd:313,cvel:295,cvff:[],cwiggl:[3,247,323,326,328,481],cyan:[2,189,190],cycl:[3,226,248,250,251,254],cyclic:[3,184],cygwin:12,cylind:[3,4,189,232,277,324,327,458],cylindr:[6,232,303,324],cypress:361,cyrot:367,cyrstal:273,d3q15:237,d3q19:237,d_double_doubl:15,d_e:318,d_flag2:280,d_flag:280,d_name:[113,187,280,308,465],d_single_doubl:15,d_single_singl:15,d_sx:280,d_sy:280,d_sz:280,daan:316,dai:12,daili:12,daivi:268,damag:[],dammak:286,damp:[3,6,193,198,234,235,236,241,250,251,254,278,281,286,291,309,310,322,324,325,353,354,356,368,370,372,377,380,385,389,397,405,415,423,437,443,469,476],damp_com:235,damp_drud:235,dampen:[291,476],dampflag:[324,389],dan:17,danger:[3,12,226,329,381,473],dangl:167,daniel:9,darden:[347,380],darkblu:190,darkcyan:190,darken:189,darkgoldenrod:190,darkgrai:190,darkgreen:190,darkkhaki:190,darkmagenta:190,darkolivegreen:190,darkorang:190,darkorchid:190,darkr:190,darksalmon:190,darkseagreen:190,darkslateblu:190,darkslategrai:190,darkturquois:190,darkviolet:190,dasgupta:282,dash:[389,472],dat:[6,91,184,199,451],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,292],dataset:292,datatyp:3,date:[0,6,12,13,420,421,481],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,187,203],davi:323,david:[9,19,346,347,440,442],daw:[383,418],dbg:14,dcd:[3,6,7,187,188,189,190,191,274,456,460],ddim:186,deactiv:405,dealt:233,debug:[6,7,11,12,13,14,17,118,122,163,164,274,279,344,346,361,393,412,445,453,454,457,462,465,472,481],deby:[],decai:[377,448],decid:[3,6,12,16,71,247,280,291,319,470],decipher:349,declar:188,declin:306,decod:189,decompos:[87,428],decomposit:[3,5,7,18,62,199,274],decoupl:[6,476],decreas:[3,187,196,197,212,215,221,224,234,317,346],decrement:295,deepli:343,deeppink:190,deepskyblu:190,def:[12,13,453],defaul:61,defect:[6,70,162],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,170,171,172,173,174,175,176,178,179,181,182,183,184,185,186,187,188,189,190,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,219,220,221,224,225,226,229,232,233,234,235,236,237,245,247,249,250,251,252,253,254,255,256,258,259,260,263,265,266,267,268,269,270,272,273,274,276,277,278,280,282,284,289,291,292,293,294,296,300,304,306,308,309,310,311,312,314,315,316,318,320,321,323,324,325,326,327,328,329,331,332,333,334,335,336,337,340,341,342,344,346,347,349,351,353,354,355,356,357,358,359,360,361,363,364,365,366,368,369,370,371,372,373,374,375,377,378,380,381,382,384,385,387,388,389,390,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,411,412,413,414,415,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,455,456,458,459,460,461,464,465,466,467,469,470,472,473,476,477,478,479,480,481,482],definit:[2,3,6,8,12,13,78,80,116,140,190,202,203,204,205,206,207,215,232,254,292,308,320,323,326,328,330,341,344,355,364,367,375,385,395,418,425,427,428,444,453,455,457,464,466,480,481],defint:473,deform:[],deg2theta:163,deg:476,degener:[3,276],degrad:[8,18,273,347,464],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,163,164,170,171,174,175,182,184,186,189,202,212,219,226,228,229,234,235,240,250,251,254,255,256,267,268,270,274,276,290,291,294,309,310,311,316,332,334,337,340,342,354,380,383,391,465,473,476,482],degress:[144,202],del:469,delai:[3,6,12,357,382,473],deleg:392,delet:[2,3,7,8,12,54,57,60,63,162,167,168,193,202,203,204,205,206,207,210,212,223,226,250,292,309,310,329,331,345,355,357,360,412,455,456,458,466,467,472,477,479,481,482],delete_atom:[],delete_bond:[],delete_el:199,deli:186,delimit:[453,481],deloc:[251,385],delr:408,delt_lo:469,delta:[],delta_1:367,delta_3:367,delta_7:367,delta_conf:3,delta_ij:[408,418],delta_mu:[3,200],delta_pi:367,delta_r:418,delta_sigma:367,delx:186,delz:186,demand:286,demo:11,demon:271,demonstr:[281,408],den:277,dendrim:391,denniston:[9,237,239,240,241,273],denomin:[7,169],denot:[118,219,235,273,284,286,377,390,392,421,425,427],dens:[71,212,385],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,150,162,164,194,195,199,202,205,206,209,215,224,237,240,243,244,273,277,278,282,318,323,349,351,355,362,367,383,408,409,410,418,422,431,433,434,435,455,464,465,473,480],density_continu:427,density_summ:427,depart:[0,7],departur:[248,281],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,142,147,151,152,158,164,165,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,189,190,193,194,195,196,197,200,202,204,205,207,208,209,211,213,221,222,225,228,229,230,232,234,235,237,239,240,247,250,252,253,254,255,256,257,265,267,268,270,272,283,286,288,291,293,294,300,306,309,310,311,313,315,317,318,320,322,323,326,327,328,329,331,332,333,334,335,336,337,340,342,347,349,354,355,357,358,359,361,362,363,365,366,367,368,369,370,371,372,373,374,375,376,377,378,380,381,383,384,385,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,408,409,411,413,414,415,417,418,420,421,422,423,428,429,437,438,439,440,441,442,443,444,446,447,448,450,452,455,457,458,461,465,467,469,472,473,475,481,482],dependend:6,depflag:12,dephas:[450,469],depos:216,deposit:[],deprec:282,depth:[51,143,189,318,388,422],dequidt:9,der:[87,107,375,376,405,420,421,447,476],deriv:[6,7,8,38,56,63,87,140,158,184,203,213,215,226,234,247,250,252,253,254,255,256,272,278,282,286,315,316,318,323,324,327,353,355,363,367,375,380,385,386,390,399,403,404,408,420,421,437,439,447,476],derjagin:447,derlet:272,descend:190,descent:[7,353],descib:[40,282],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,143,144,148,149,152,155,157,158,162,163,164,166,167,176,181,184,187,188,193,194,195,202,203,204,205,206,207,209,212,213,214,215,216,218,219,227,228,231,232,233,234,235,236,237,239,240,241,245,249,250,251,254,261,269,272,274,279,280,281,282,283,284,291,295,303,306,307,308,309,310,311,312,313,314,315,316,321,323,324,326,331,346,347,349,352,353,354,355,356,360,363,364,366,368,369,370,372,373,374,375,376,377,380,383,385,386,388,389,390,392,397,398,399,400,401,402,403,404,405,406,407,408,411,417,418,419,420,421,422,423,428,429,436,437,438,439,440,441,442,443,446,447,448,450,452,453,455,456,458,459,465,468,469,472,481,482,483],descript:[],descriptor:[140,187,393],deserno:347,design:[0,3,6,7,8,9,11,13,14,15,17,118,146,149,163,199,212,218,219,250,251,272,273,292,313,318,364,365,366,369,372,377,379,385,405,406,407,409,410,418,421,439,464],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,146,164,177,186,200,202,207,213,215,224,226,227,234,235,236,240,250,268,276,277,278,279,282,286,291,294,306,309,310,311,312,317,324,338,343,346,347,349,352,354,355,356,381,383,391,406,407,438,440,442,451,452,453,455,459,464,469,470,472,473,481,482,483],desk:7,desktop:[4,6,7,10,12,17,189],despit:476,destabil:367,destre:340,destroi:[11,39,210,211],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,142,143,144,147,157,158,159,161,164,165,168,169,172,183,187,189,190,193,194,195,199,202,203,204,205,207,209,211,212,213,214,215,216,224,226,227,228,229,231,232,234,236,237,241,247,248,249,250,251,252,253,254,255,256,260,262,267,268,269,270,273,276,277,278,280,281,283,284,285,291,294,306,309,310,311,312,313,314,316,317,318,319,320,321,322,329,331,333,341,346,347,350,354,355,357,358,361,362,363,364,366,367,369,371,372,373,374,375,376,377,380,381,385,386,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,407,408,411,412,417,420,421,422,428,429,437,444,446,447,453,455,456,457,458,460,461,464,465,467,470,473,474,481,482,485],detect:[2,3,12,61,63,86,225,277,317,356,376,391,396,450,452,455,466,469,481],determ:361,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,152,153,162,163,164,186,187,189,190,191,192,196,197,198,201,202,203,204,205,206,207,208,209,213,215,216,219,221,226,229,230,232,234,235,240,245,247,248,250,255,256,267,268,270,272,274,278,281,288,289,290,291,292,293,296,298,300,306,309,310,311,313,319,320,323,324,325,326,327,328,329,341,346,347,349,355,357,358,361,363,364,371,376,380,382,383,387,389,392,393,401,408,412,421,422,436,439,443,447,452,455,456,458,460,462,465,469,471,472,474,480,481,482],detil:108,devan:[9,423],devanathan:442,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,231,254,276,281,282,285,363,367,385,410,457],devemi:9,deviat:[248,254,272,387],deviator:9,devic:[1,3,12,15,17,231,361],device_typ:361,devin:[283,376],devis:410,dfactor:189,dff:476,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,347],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,285],dhi:[59,186,215,277],dhug:[248,281],dhugoniot:[248,281],dia:408,diagnost:[],diagon:[3,6,83,140,141,213,250,278,291,321,425,427],diagonalstyl:428,diagram:[41,118,163,183,209,274],diallo:391,diam:[189,190,277,355],diamet:[3,6,40,113,164,187,189,190,194,195,234,277,291,306,322,324,355,375,388,389,395,399,422,444,447,455,456,465],diamond:[349,385,408],diamter:[40,277],dick:6,dicsuss:247,dictat:[200,248],did:[3,12,354,381,382,383,389,412,440,442,463],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,160,320,346],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,142,143,144,145,147,150,151,152,153,154,156,157,158,164,165,167,172,183,184,186,187,189,190,193,195,198,200,202,204,209,210,211,212,213,214,215,219,225,226,227,228,229,230,231,234,235,237,247,250,251,252,253,255,256,258,260,263,265,266,267,270,272,274,276,278,281,282,283,286,289,291,294,295,303,304,306,309,310,311,314,315,316,318,321,322,323,324,327,331,332,341,343,345,346,347,349,350,352,353,355,356,358,359,360,361,362,363,367,371,372,374,375,376,381,383,385,388,389,390,392,395,397,398,400,401,408,409,410,411,412,414,418,420,421,422,423,424,425,427,428,429,437,438,439,440,442,444,447,448,449,450,452,453,455,457,458,459,460,463,464,465,467,469,470,472,473,474,476,480,481,482,483],differenti:[1,3,6,29,184,346,377,418,441],difficult:[213,274,361,391,464],difficulti:[294,420],diffract:[],diffus:[],digit:[2,3,190,331],dih_table1:184,dih_table2:184,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:211,dihydrid:385,dij:294,dilat:[],dim1:3,dim2:3,dim:[3,59,71,142,145,146,147,150,151,152,153,154,156,164,186,205,215,232,324,349,408,458,480,481,482],dimdim:481,dimems:273,dimens:[],dimension:[3,39,112,118,140,142,144,145,146,147,150,151,152,153,154,156,163,185,202,205,249,273,318,349,352,356,418,455,465],dimensionless:[105,121,122,124,127,129,131,136,140,318,347,428,447],dimentionless:135,dimer:[6,291,408],dimgrai:190,dimstr:[41,209],dinola:[278,309],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,187,308,476],dir1:466,dir2:466,dir:[1,3,4,8,11,12,248,272,281,305,418,420,421,453,466,481],dirac:140,direc:418,direct:[],directli:[3,6,8,9,11,12,87,113,140,187,188,189,196,221,228,232,237,273,292,310,322,324,325,326,327,349,353,361,362,363,368,370,371,377,380,383,385,397,401,412,415,423,436,453,465,466,467,473,481],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,191,214,233,276,282,285,302,306,315,316,356,360,362,363,367,374,376,377,383,384,386,393,394,405,408,409,410,414,418,419,420,421,428,438,440,441,442,453,455,456,457,466,481],disabl:[3,12,16,318,396,453,468],disadvantag:[6,209],disallow:[187,215,250],disappear:457,discard:[2,3,41,71,205,209,319,327,452,457,458],discontinu:[9,184,354,403],discourag:408,discov:[13,319],discret:[6,8,40,42,189,190,234,237],discuss:[],disk:[6,84,85,157,185,216,226,277,453],disloc:70,disord:[39,70],disp:[],dispar:422,disperion:[380,401],dispers:[3,6,7,9,162,273,346,347,371,380,401,406,412,421,439],displac:[],displace_atom:[],displace_box:59,displacemet:458,displai:[11,13,22,37,44,55,172,183,187,189,333,341,374,437],dispters:3,dissip:[6,227,234,273,315,316,369,381,389,406,407,437],dissolut:210,dist:[6,69,91,108,117,187,274,290,382,436,450,482],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,153,159,162,164,165,166,167,171,186,187,189,190,198,202,205,206,210,211,212,213,215,216,217,220,226,232,237,247,248,249,250,254,262,272,273,277,281,282,289,290,291,294,295,299,303,304,305,306,313,314,316,317,318,321,323,324,325,326,327,328,332,346,347,349,352,354,356,357,358,361,364,365,366,367,368,369,370,371,372,373,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,395,396,397,398,399,400,401,402,403,404,405,406,407,408,411,412,413,414,415,416,417,418,420,421,422,423,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,453,455,458,464,465,469,473,476,480,482],distinct:[6,219,288,346,422],distinguish:[6,86,140,240,385],distort:362,distrbut:362,distribut:[],distro:[111,374,417,418],ditto:[8,11,12,14,15,16,17,18,115,211,453],div:8,divd:117,diverg:[3,12,39,291,316,457,476,483],divid:[3,6,16,41,91,112,117,126,128,141,161,162,172,183,190,202,203,204,209,215,272,314,321,326,346,354,356,386,421,464,472,481],divis:[6,237,367,395,405,452,455,473,481],dl_poli:7,dlambda:158,dlammps_async_imd:231,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,189],dlammps_gzip:[3,12,187,189,317,455,456,460],dlammps_jpeg:[3,12,189],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,189],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,187],dlen:465,dlmp_intel_offload:[12,16],dlo:[59,186,215,277],dlvo:[7,375,447],dm_lb:237,dmax:[306,352],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,143,144,157,159,161,164,165,166,172,183,187,188,189,190,191,193,194,195,200,201,202,203,204,205,206,207,216,226,234,235,245,250,251,255,256,260,267,268,269,270,277,280,291,303,306,309,310,311,320,324,327,329,331,333,341,345,354,355,356,361,362,363,366,374,376,377,383,384,386,391,392,394,395,408,409,410,412,414,417,418,419,428,437,438,440,442,444,453,455,456,457,458,460,463,464,465,472,473,481,482,483,484],docuement:422,dodgerblu:190,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,143,144,147,152,154,158,163,164,165,166,168,170,172,177,183,184,186,187,188,189,190,193,199,200,202,205,208,209,211,212,213,215,219,221,223,226,227,230,232,234,235,237,240,246,250,251,252,253,255,256,267,268,269,270,278,279,280,284,286,289,291,306,309,311,313,314,318,321,322,323,326,327,328,329,334,335,337,338,340,345,346,347,348,349,355,356,357,362,363,364,365,366,367,369,371,372,373,375,376,377,378,380,381,382,383,384,385,387,388,389,390,392,393,394,395,396,399,400,402,403,404,406,407,408,409,410,412,418,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,442,443,444,446,447,448,450,451,452,453,455,456,457,458,459,462,463,465,466,467,468,469,472,473,476,481,485],doegenomestolif:7,doesn:[3,7,8,12,164,187,200,205,206,303,355,357,361,363,376,384,394,420,421,438,440,441,442,455,457],dof:[3,8,112,143,144,157,202,291,482],dof_per_atom:[144,202],dof_per_chunk:[144,202],doff:[355,455],doi:[6,214],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,153,163,166,186,188,189,190,193,200,209,213,215,216,230,233,237,250,251,274,286,291,318,323,324,346,347,356,361,382,412,450,452,455,459,472],domin:[1,385,469],don:[0,8,11,12,13,116,167,196,221,235,280,327,408,453,455],donadio:310,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,158,161,164,167,184,187,189,190,199,200,202,204,205,206,207,209,210,211,212,213,215,216,224,226,231,232,234,235,242,250,255,256,267,268,270,271,273,274,275,280,288,291,292,294,306,309,310,311,313,315,316,329,331,345,346,347,354,356,357,360,361,363,371,383,392,393,394,401,407,408,412,420,436,439,444,450,451,452,453,456,459,460,463,473,474,476,481,482],donor:391,dot:[141,160,196,221,229,249],doti:[367,418],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,215,224,279,327,331,345,347,360,361,367,386,390,420,421,451,455,459,463,468,481,482],dover:199,down:[3,6,7,8,11,39,71,213,234,306,322,361,385,412,454,474],downhil:[352,353],download:[5,7,8,9,11,12,13,17,231,393,419],downsid:6,downward:288,dozen:[8,12,107,193,420,421],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:243,dproduct:364,dr_ewald:[118,292],drag:[],dragforc:237,drai:[248,281],drain:[230,322,354],dramat:[59,186,210,211,212,213,215,250,306,309,310,347,361,412,452],drautz:367,draw:189,drawback:280,drawn:[187,189,190,227,450],drayleigh:[248,281],dreid:[],drfourth:105,drho:[113,362,383],drift:[6,103,105,227,228,234,235,246,289,306,464,472,476],drive:[11,12,197,213,215,229,250,272,278,291,325,356],driven:[6,176],driver:[6,12,14,15,193,224,231],drop:[3,190,381],droplet:392,drsquar:105,drude:[],dry:223,dsecriptor:393,dsf:[],dsmc:[],dstyle:277,dt_collis:237,dt_lb:237,dt_md:237,dt_srd:306,dtilt:[59,215],dtneb:469,dtqm:281,dtype:[115,211],dual:[17,306,361],dudarev:163,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,126,140,141,142,143,145,147,150,151,152,153,154,156,157,159,163,164,167,168,187,189,193,196,197,204,208,210,211,212,213,214,215,216,221,222,223,224,227,228,231,232,234,235,236,237,240,241,242,246,247,248,249,250,254,262,272,275,277,289,290,291,293,303,305,306,307,309,310,311,312,313,315,316,318,322,323,325,326,327,329,347,352,354,356,357,358,378,381,383,387,388,392,406,407,412,418,420,422,423,436,439,440,442,445,447,448,450,452,455,456,457,464,469,472,473,474,476,481,482],duffi:318,duin:[9,282,287,420,421],duke:347,dummi:[12,29,441],dump1:460,dump2:460,dump2vtk_tri:134,dump:[],dump_atom:8,dump_custom:8,dump_h5md:188,dump_modifi:[],dumpcustom:8,dumptimestep:460,dunbrack:[6,20,170,372,467],dunweg:[234,236],duplic:[2,3,14,15,16,17,18,19,41,42,165,209,228,272,455,480],dupont:[5,7,13],durat:[37,55,142,143,145,146,147,149,150,151,152,153,156,157,183,190,202,226,286,318,341,389,437],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,128,146,165,168,184,187,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,246,247,249,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,299,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,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59,460],enpub:383,ensembl:[],ensight:6,ensur:[3,6,140,187,200,213,226,227,250,296,317,347,367,382,405,436,438],enter:[57,154,386,469],enthalpi:[123,252,253,383,472,473,481],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,144,163,164,190,193,194,195,202,205,206,209,212,214,223,226,227,230,234,235,246,250,252,253,254,255,256,272,274,276,289,291,304,318,320,331,361,380,401,412,439,455,463,464],entireti:[395,444],entiti:[6,8,40,42,187,291],entri:[3,8,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,162,184,190,204,205,206,214,281,329,355,367,384,408,414,421,428,438,439,440,441,442],entropi:469,entry1:[38,56,190,374,439],entry2:190,entryn:190,enumer:[165,187],enumuer:6,env:361,environ:[1,3,6,11,12,16,17,18,189,228,233,272,361,362,367,374,376,384,385,418,440,452,466,481],epair:[107,190,387,391,420,421,473],epen:[420,421],epfl:[228,233],epp:380,epq:380,eps0:447,eps14:405,epsilon0:442,epsilon:[3,6,36,45,46,50,53,54,87,170,194,195,226,291,306,323,327,352,354,366,372,373,375,377,378,379,380,388,390,391,392,395,396,397,398,399,400,401,402,403,404,405,411,415,422,423,432,438,444,446,447,464,476,480],epsilon_0:448,epsilon_14:372,epsilon_:422,epsilon_d:378,epsilon_i:[388,412,422],epsilon_i_:422,epsilon_i_a:[388,422],epsilon_i_b:[388,422],epsilon_i_c:[388,422],epsilon_ij:412,epsilon_j:[388,412,422],epsilon_j_:422,epsilon_j_a:[388,422],epsilon_j_b:[388,422],epsilon_j_c:[388,422],epsilon_lj:422,epton:417,eqch:159,eqeq:[420,421],eqp:380,eqq:380,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,143,158,160,164,189,190,193,194,195,196,197,200,203,204,207,208,209,213,215,216,221,226,227,229,230,232,234,235,237,240,241,247,248,254,264,272,274,277,279,281,282,283,286,288,290,291,293,295,300,302,309,310,311,314,315,316,318,320,321,323,326,328,329,331,345,354,356,357,358,360,361,376,381,387,388,391,406,411,418,420,421,422,424,425,426,428,429,439,444,448,451,452,453,455,457,458,462,463,466,469,471,473,481,482],equat:[3,6,7,8,9,91,112,118,163,172,183,193,213,219,220,228,234,235,237,240,248,249,250,251,254,268,272,274,281,282,286,294,306,314,318,321,323,324,326,328,340,346,347,375,380,381,385,386,389,394,406,407,408,412,422,425,427,431,432,434,435,443,448,476],equi:251,equidist:249,equil:[3,282,350,462,485],equilater:465,equilibr:[3,4,5,6,7,9,59,91,164,193,200,203,212,213,226,248,250,251,268,269,281,282,283,284,314,315,316,321,376,377,420,421,451,465],equilibria:321,equilibribum:[210,211],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,147,148,171,173,213,215,226,227,228,235,237,250,254,268,281,286,290,294,295,303,306,313,314,316,321,332,334,337,340,376,408,414,476],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:199,equival:[6,12,13,59,124,125,133,138,162,166,190,204,207,213,215,226,234,250,268,278,290,291,326,381,385,440,442,455,458,463,464,473,476],equlibrium:6,equliibr:[282,284],er3:163,eradiu:[40,113,385,455],eras:[293,315],erat:[215,407],erc:377,erfc:[377,397,412],erforc:113,erg:480,erhart:[200,383,440,442],ermscal:364,ernst:9,eror:3,eros:408,erose_form:408,erot:[],errata:[440,442],erratum:323,erron:3,error:[],erta:389,ervel:[113,455],escap:[216,476],especi:[8,11,16,152,164,193,200,209,226,281,286,289,290,361,452],espresso:[9,285],essenti:[8,11,12,27,88,128,145,146,147,150,151,152,153,154,156,173,203,254,273,322,347,363,377,397,442,460,473],essex:29,establish:[87,230],estim:[1,3,6,10,12,38,41,56,91,141,199,209,220,248,306,313,346,347,352,412,421,439,469,473],esu:480,esub:408,eta:[6,237,250,281,282,284,322,384,386,388,418,441,480],eta_dot:250,eta_ij:418,eta_ji:386,etag:[40,455],etail:473,etap:250,etap_dot:250,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,142,144,145,146,147,148,150,151,152,153,154,156,158,164,166,167,168,177,187,189,190,193,199,200,201,202,204,205,206,207,210,211,215,216,224,226,227,234,250,277,288,292,318,319,327,331,345,346,354,355,356,357,359,383,384,392,405,407,416,420,421,438,440,442,450,453,455,456,457,462,464,465,469,471,472,473,476,480,481,483,485],ethernet:18,etol:[354,356,450,469],etot0:281,etot:[6,94,96,97,110,141,150,190,219,235,248,281,472,473],eu2:163,eu3:163,euler:[354,356],eulerian:199,euqat:430,europhi:237,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,144,154,162,164,187,189,190,194,195,196,197,199,201,202,203,204,205,206,207,208,215,221,227,229,230,232,233,234,235,273,279,282,293,296,300,309,310,311,320,323,326,328,329,331,346,347,352,354,361,412,418,424,426,439,450,451,453,457,458,460,462,463,464,465,469,471,473,481,482],evalut:[331,453],evan:[152,268],evanseck:[6,20,170,372,467],evapor:[],evaul:[8,354],evdwl:[107,420,421,473],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,165,166,180,184,187,190,193,194,195,200,201,202,204,205,206,207,209,210,211,213,215,216,219,232,235,248,250,251,273,286,288,291,292,302,306,314,318,321,323,327,329,339,346,352,354,356,361,366,385,386,389,392,412,422,445,455,456,458,460,461,462,464,465,467,470,472,473,474,476,485],evenli:[3,41,141,184,209,237,395,445,455],event:[],eventu:[3,6,12,15,166,282,469],ever:[54,56,233,306],evera:[375,388,422,437],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,128,152,167,187,188,189,190,191,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,220,223,224,226,228,230,231,232,237,238,246,250,251,254,271,272,273,277,278,279,280,281,282,283,284,286,288,289,291,292,294,295,306,308,309,310,311,312,313,314,317,318,319,320,321,329,331,345,347,356,357,358,361,381,382,392,405,420,421,433,449,450,451,455,457,459,460,462,463,464,469,470,471,473,481,485],everyth:[8,107],everywher:[116,399],eviri:385,evolut:[228,237,274,450],evolv:[237,274,319],ewald:[2,3,5,6,7,8,12,88,110,118,141,319,346,347,354,368,370,371,377,380,385,397,401,415,423,437,439,457],ewald_disp:380,ewalddisp:3,exact:[22,41,44,71,122,158,167,172,209,212,227,228,234,235,236,277,286,287,306,318,333,346,374,457,462,469,483,485],exactli:[3,6,12,14,17,38,41,56,59,71,91,143,148,155,164,184,194,195,204,209,215,220,227,234,235,236,251,261,262,269,273,281,306,311,312,325,361,374,381,383,389,392,395,406,412,439,457,458,465,469,481],exager:476,examin:[6,8,9,212,273],examp:[453,481],exampl:[],exce:[3,6,16,17,18,41,58,71,166,202,205,206,209,213,215,220,223,250,273,297,298,306,354,361,455,481],exceed:[3,41,59,209,215,250,306,463],excel:385,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,164,168,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,190,193,196,202,203,204,208,209,213,215,222,225,226,229,232,234,236,250,251,252,253,254,255,256,257,261,262,265,267,268,269,270,274,283,284,291,293,294,303,306,309,311,312,318,322,329,331,332,333,334,335,336,337,340,341,342,346,347,349,351,355,356,357,359,360,361,362,363,365,368,369,370,371,372,373,374,375,376,377,379,380,381,383,384,385,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,407,409,413,414,415,417,420,421,422,423,429,437,438,439,440,441,442,444,446,447,448,450,452,453,455,457,458,460,463,464,465,466,467,469,473,476,480,481,482,484],excess:385,exchang:[2,3,6,8,9,61,62,193,199,200,226,234,283,291,314,318,321,346,361,385,470],exchange:346,excit:[9,385],exclud:[3,6,9,12,16,17,63,71,112,140,144,151,152,168,187,202,205,210,211,238,246,276,289,291,313,324,329,354,355,357,369,389,392,406,407,412,436,467],exclus:[1,3,9,12,16,87,361,376,412,464,474],excurs:450,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,165,189,231,285,331,345,348,360,451,453,463,466,469,481],exemplari:227,exemplifi:385,exert:[6,232,235,286,325,326,327,347],exhaust:[199,360,481],exhibit:[250,353,385,464],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,164,165,183,188,189,190,193,198,208,211,213,216,226,276,277,279,329,332,334,335,337,341,350,355,361,392,420,445,451,453,455,456,457,466,467,468,481,482,483],exit:[2,3,11,12,41,57,187,209,345,360,453,454,463,472,481],exlanatori:3,exp:[],expand:[],expans:[12,140,187,466],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,145,156,162,184,209,221,226,228,247,272,278,280,281,286,291,329,347,357,374,408,412,450,453,455,457,460,464,469,481],expens:[6,10,71,190,272,276,291,318,329,346,347,357,361,453],experi:[6,13,15,17,208,216,231,240,249,278,290,291,352,356,381,412,464,469],experienc:[6,12,239,240],experiment:[346,361,469],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,144,152,184,187,189,190,193,202,203,207,209,211,213,215,250,272,280,291,303,329,331,345,346,349,355,356,360,366,383,395,429,444,448,453,456,457,460,462,465,476,481,485],explan:[3,6,59,113,140,187,202,249,272,392,449,452,453,455,464],explanatori:[3,8,117,187,201,202,204,205,206,291,355,452,481],explantori:[3,287],explic:411,explicit:[6,9,11,22,44,77,87,113,116,158,172,194,195,215,297,298,333,351,363,364,367,372,374,383,385,396,406,443,449,452,456,459],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,142,151,154,162,164,170,171,173,174,175,176,178,179,181,182,184,187,190,196,205,208,215,222,225,227,229,234,250,252,253,254,255,256,257,265,267,268,270,280,281,283,291,293,294,309,311,312,318,322,332,334,335,336,337,340,342,355,361,362,363,365,368,369,370,371,372,373,374,375,376,377,378,380,381,382,383,384,386,387,388,389,390,391,392,395,396,397,398,399,400,401,402,403,404,405,406,409,412,413,414,415,417,422,423,429,430,431,432,433,434,435,437,438,439,440,441,442,443,444,446,447,448,455,457,464,465,467,468,474,476],explictli:[16,468],exploit:[9,15,17,274],explor:[118,163],expon:[3,282,284,383,388,391,405,411,423],exponenti:[87,418,438,448,469,481],expos:11,exposit:[199,381,382],express:[6,140,150,164,194,195,213,247,272,282,318,324,331,367,383,385,399,408,428,437,481],expressiont:367,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,193,196,197,200,207,208,214,217,221,224,225,226,228,229,230,232,234,236,248,250,254,262,272,273,289,290,291,293,295,300,303,305,309,310,311,312,313,315,316,318,320,323,327,328,388,408,421,422,428,472,473],extent:[1,3,41,45,57,71,162,166,187,198,205,209,232,325,328,346,349,363,424,426,439,452,455,458],exterior:[3,6,327],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,142,143,145,147,150,151,152,153,154,156,157,163,164,165,166,170,190,204,209,211,250,279,280,281,291,306,354,355,358,359,380,389,392,395,408,412,452,453,455,458,467,476,481],extract:[3,6,11,13,36,63,87,107,115,117,119,194,195,284,356,377,386,408,428,453,460,472],extract_atom:11,extract_comput:[11,453],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,189,213,215,250,316,385,441,476],extrema:405,extrins:199,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[160,320],f_a:[440,441,442],f_ave:117,f_c:441,f_f:442,f_fix_id:281,f_harm:316,f_i:418,f_id:[6,71,117,119,187,193,201,202,203,204,205,206,207,245,308,320,473,481],f_ij:418,f_indent:207,f_int:315,f_jj:91,f_k:418,f_langevin:318,f_max:[281,286],f_msst:248,f_r:[235,440,441,442],f_sigma:367,f_solid:316,f_ss:6,f_temp:235,face:[3,6,57,59,71,152,162,166,198,205,206,323,325,326,327,328,349,388,408,422,455,458],face_threshold:162,facet:162,facil:[0,12],facilit:[6,13],fact:[6,8,16,228,306,316,389,467],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,140,158,163,166,170,181,187,189,190,194,195,203,209,213,215,216,226,231,234,236,237,248,250,251,254,274,278,290,294,296,298,306,310,314,321,322,323,327,337,347,349,361,363,364,367,368,370,372,377,378,379,381,385,389,392,396,397,408,412,414,415,421,423,429,438,443,452,455,458,459,464,467,469,470,473,476,480,481],factori:[3,453],factoriz:346,fail:[3,11,12,59,168,213,216,346,354,356,379,421,453],failur:[121,425],fairli:[11,412,464,469],faken:73,falcon:231,fall:[3,6,190,204,277,453],fals:[86,329,331,481],fame:8,famili:452,familiar:[0,11],fan:418,far:[3,6,12,17,57,59,61,86,187,190,191,209,210,211,213,216,250,272,290,291,306,323,334,337,352,356,357,444,453,455,460,473],farago:234,farrel:[440,442],farther:187,fashion:[6,8,41,71,164,190,193,194,195,200,205,209,211,216,226,228,232,247,248,250,252,253,254,255,256,264,267,268,269,270,280,281,283,291,295,299,305,308,316,318,322,323,324,326,328,356,392,406,458,467,481,484],fasolino:394,fast:[6,7,9,12,13,17,39,187,259,281,319,346,347,369,406,407,437,439,457,462,464,473,482,485],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,142,151,170,171,173,174,175,176,178,179,181,182,184,187,190,193,196,208,209,222,225,229,233,234,250,252,253,254,255,256,257,265,267,268,270,278,282,283,291,293,294,306,309,311,313,315,318,322,332,334,335,336,337,340,342,346,347,358,359,361,362,363,365,367,368,369,370,371,372,373,374,375,376,377,380,381,383,384,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,409,413,414,415,417,422,423,429,437,438,439,440,441,442,444,446,447,448,450,464,468,476],fastest:[6,14,17,152,205,318,319,361,452],fatal:[3,472],fault:[70,421],faulti:12,fava:388,favor:212,favorit:7,fbmc:313,fcc:[],fcm:[264,481],fdirect:219,fdotr:393,fdti:87,fe2:163,fe3:163,fe_md_boundari:199,featu:8,featur:[],fecr:383,feedback:[7,231],feel:[7,231,232,240,272,327,329,356,412],felling:410,felt:327,femtosecond:480,fene:[],fennel:[377,397],fep:[],ferguson:[6,170,467],fermi:[1,12,15,150,361,442],fermion:[9,385],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,191,201,202,203,204,205,206,207,235,250,277,280,282,294,320,346,354,355,356,363,452,455,460,464,466,474,481,483],fewer:[1,3,11,15,16,61,240,464],fewest:3,fextern:224,feynman:274,fff:453,ffield:[376,386,420,421],ffmpeg:[3,12,189],ffplai:189,fft:[1,3,7,12,14,15,88,109,110,141,273,346,347,464],fft_inc:[12,347],fft_lib:12,fft_path:12,fftbench:[346,474],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,196,197,221,224,228,274,290,377,397,401,436],field1:[456,460],field2:456,field:[],fifth:[303,414],figur:[1,3,8,11,12,281,452,453],fij:380,file0:272,file1:[11,13,272,317,331,355,460,462,466],file2:[11,13,317,331,355,460,462,466],file:[],file_from:188,filenam:[3,12,13,38,41,56,184,187,189,190,191,199,202,203,204,205,206,207,209,214,272,276,279,282,283,284,287,288,291,292,317,318,343,344,345,356,362,363,367,377,383,384,386,394,408,409,410,414,418,419,420,421,428,438,439,440,441,442,451,452,453,456,457,462,466,473,481,483,484,485],filennam:462,filep:[3,187,190,457,462,485],filepo:288,fill:[7,164,189,277,318,349,357,367,421,458],filter:[190,199],final_integr:8,final_integrate_respa:8,finchham:[6,146,379],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,167,184,191,200,212,213,223,226,249,272,278,286,290,352,354,356,357,377,392,397,401,408,437,439,476,481],find_custom:8,fine:[16,17,168,196,221,316,357,361,481],finer:[140,164,481],finest:346,finger:[164,186,247,458],finish:[6,11,41,209,331,343,345,346,358,360,361,444,460,481,482],finit:[],finni:[7,383,437],finvers:219,fiorin:[9,214],fire:[352,353,354,356,469],firebrick:190,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,149,152,158,160,162,163,165,166,167,171,184,187,188,189,190,191,193,200,202,203,204,205,206,207,209,212,215,226,227,232,237,247,248,249,250,272,274,279,280,281,283,288,291,294,295,303,304,306,307,308,315,316,317,318,320,324,329,331,332,338,349,354,355,356,357,360,361,362,363,366,367,368,370,372,374,376,377,383,385,386,389,390,393,394,396,397,401,406,407,408,410,412,414,418,420,421,428,436,438,439,440,441,442,450,451,452,453,455,456,457,460,462,464,467,468,469,472,473,476,481,482,483,485],fischer:[6,9,19,20,170,372,467],fit:[3,6,9,12,38,56,184,290,306,363,367,394,408,412,432,439,441,463,481],five:[73,150,281,355,367,409,455,469],fix:[],fix_adapt:[158,195,405],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,200,277],fix_evapor:200,fix_flux:199,fix_gcmc:[200,355],fix_gl:228,fix_gld:228,fix_grav:277,fix_id:[3,213,248,250,252,253,254,255,256,278,281],fix_modifi:[],fix_mov:[186,324],fix_nh:8,fix_npt:228,fix_nvt:[200,226],fix_poem:[3,6],fix_pour:[3,216],fix_qbmsst:9,fix_qeq:[3,376],fix_rattl:294,fix_reax_bond:420,fix_rigid:[240,366],fix_saed_vtk:292,fix_setforc:8,fix_shak:294,fix_srd:3,fix_styl:254,fix_temp_rescal:312,fixedpoint:[213,250],fixextern:224,fixid:199,fji:380,flag1:[218,359],flag2:[218,359],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,159,163,167,187,189,190,191,207,212,214,218,231,234,238,240,246,247,273,280,291,303,305,306,313,317,326,329,344,347,355,359,360,361,363,391,396,408,436,450,452,453,455,456,457,459,460,461,465,481],flag_buck:371,flag_coul:[371,380,401],flag_lj:[380,401],flagfld:[369,406,407],flaghi:[3,369,406,407],flaglog:[369,406,407],flagn:218,flagvf:[369,406,407],flat:[6,318,323,324,328],flavor:[2,7,12],fld:[9,323,369,406,407],flen:364,flex_press:364,flexibl:[3,6,8,165,189,202,205,214,228,251,314,321,385,441,473],flip:[3,6,215,250,325,326],floor:481,flop:12,floralwhit:190,flow:[],fluctuat:[6,64,87,213,226,227,234,237,250,254,272,273,316,318,340],fluid:[],fluid_veloc:241,flush:[3,190,472],flux:[],flv:189,fly:[7,9,12,41,189,193,199,216,219,291,294,319,367,473,476],fmackai:9,fmag:217,fmass:274,fmax:[354,473],fmomentum:219,fmsec:[2,190,234,235,247,250,278,291,309,310,464,475,480,482],fname:345,fno:12,fnorm:[354,473],fnpt:219,fnvt:219,foce:392,fock:364,focu:294,fogarti:[9,284,421],foil:[140,272,428],fold:[304,464],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,143,144,150,152,157,160,162,164,165,170,173,174,175,176,178,179,181,182,184,187,188,189,190,193,199,200,201,202,203,204,205,206,207,209,214,215,216,219,220,224,226,227,228,231,233,234,235,237,240,248,250,254,255,256,267,268,270,273,274,276,279,280,281,282,284,286,288,290,291,292,294,308,309,310,311,314,315,316,317,318,320,321,329,330,334,335,336,337,340,342,344,349,351,354,355,356,361,362,363,364,365,366,367,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,425,427,428,429,430,431,432,433,434,435,436,438,439,440,441,442,443,444,446,447,448,450,452,453,455,456,457,458,460,462,463,464,467,469,470,471,476,481,482,484],foo:[4,8,11,12,187,189,224,453,466,481],foot:6,footprint:[12,361],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:240,forcefield:[290,391],forcegroup:237,forcezero:352,ford:380,forestgreen:190,forev:71,forget:[235,476],forgiv:250,fork:[12,187],form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,158,159,168,172,190,193,194,195,211,227,228,234,236,240,247,268,273,284,286,290,291,318,323,327,332,333,340,351,353,355,356,363,364,367,374,383,385,387,391,392,396,408,410,414,415,418,420,421,422,428,429,437,439,440,441,442,447,449,452,453,455,460,465,472,476,481],formal:[6,78,80,91,227,228,234,250,274,306,314],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,172,184,187,188,189,190,191,202,204,205,206,207,209,211,273,276,280,282,284,287,291,292,302,317,318,329,330,333,351,355,356,362,363,367,374,383,386,396,408,410,419,420,421,423,428,439,445,452,453,455,456,457,460,471,472,473,481,483],former:[6,12,16,39,41,190,209,318,322,367,369,461,467,481],formerli:[7,13],formul:[1,40,64,141,196,221,234,250,268,282,284,290,294,317,346,363,367,383,385,388,408,417],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,163,164,169,171,172,183,187,194,195,196,197,202,203,204,207,208,215,221,229,230,232,234,235,247,272,273,279,288,293,300,304,306,309,310,311,320,323,326,328,329,331,332,333,335,341,349,355,363,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_integrate_respa:8,initialis:419,initialt:318,inlclud:11,inlcud:481,inlin:453,inner2:[372,390],inner:[3,8,16,187,232,331,345,352,353,354,356,360,362,363,364,365,366,367,368,369,370,371,372,373,375,376,377,378,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,417,419,420,421,422,423,428,429,430,431,432,433,434,435,436,438,439,440,441,442,444,445,446,447,448,464,469],inner_distance_cutoff:391,innergroup:240,innermost:[38,56,359,439,464],innernod:240,innner:403,inordin:319,inorgan:6,inp:[214,331,428],input1:[65,68,69,79,92,108,113,114,115,117,119,308],input2:[65,68,69,79,92,108,113,114,115,117,119,308],input:[],input_doubl:3,inquir:296,insensit:12,insert:[3,5,7,8,12,59,164,193,216,226,232,277,346,428,436,453,459,476],insid:[2,3,6,8,11,71,129,135,164,187,190,201,205,206,216,217,223,226,232,237,240,277,291,306,323,325,326,327,328,329,344,349,399,453,454,455,457,458,465,469,474,481],insight:[6,13],instabl:[237,380,427],instal:[],instanc:[6,11,214,228,325,387,392,412,418,453,476],instantan:[6,63,212,213,227,228,250,254,273,278,281,286,288,291,313,461,473],instanti:[6,11,12,199,392,452],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,63,70,71,90,117,143,146,168,184,187,195,202,204,205,206,207,209,213,214,234,237,240,241,273,279,289,291,308,326,344,346,347,350,357,361,370,371,383,396,398,405,408,450,458,462,469,471,476,481],institut:[9,231,276],instruct:[3,6,8,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,142,151,162,170,171,173,174,175,176,178,179,181,182,184,185,189,196,208,222,225,229,234,250,252,253,254,255,256,257,265,267,268,270,283,291,293,294,309,311,322,332,334,335,336,337,340,342,347,361,362,363,365,368,369,370,371,372,373,375,376,377,380,381,383,384,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,409,413,414,415,417,422,423,429,438,439,440,441,442,444,446,447,448,464,476],insuffici:[3,6,12],insult:250,insur:[3,6,11,12,17,39,40,61,73,102,104,164,165,184,187,189,190,196,210,211,216,221,222,223,224,226,229,234,246,279,280,289,291,306,318,323,327,328,329,331,345,355,357,361,375,388,392,416,422,439,452,453,455,456,460,463,464,472,473,481,482],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,113,115,117,119,140,162,164,167,168,170,174,175,179,184,186,187,189,190,200,202,205,206,210,211,212,216,218,224,226,227,228,231,234,235,236,237,273,276,277,280,281,286,291,306,308,310,313,317,318,336,346,349,369,381,382,395,408,420,421,425,427,428,450,452,453,455,463,464,465,469,472,481,482],integr:[],integrate_ulsph:297,intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,8,12,13,36,227,419,455],intens:[1,3,6,9,63,66,74,75,86,89,90,91,93,103,104,105,106,112,114,116,117,118,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,159,160,161,163,193,202,203,204,205,206,207,209,210,211,212,220,223,230,240,248,250,254,288,291,292,306,314,318,320,321,472,473],intepol:481,inter:[14,18,42,61,62,144,167,168,187,212,234,236,249,283,291,346,356,367,465,476,481,483,485],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,77,79,87,88,92,107,108,110,112,115,116,122,123,124,125,127,128,129,130,131,132,133,135,136,137,138,140,141,143,157,158,162,165,166,167,168,169,170,172,176,177,183,187,193,194,195,210,211,212,225,226,231,232,234,236,240,262,272,274,276,282,284,290,291,297,298,306,307,313,318,322,323,324,327,328,333,334,335,337,341,346,347,354,355,356,357,358,359,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,417,418,421,422,423,425,427,428,429,436,437,438,440,441,442,443,444,445,446,447,448,450,453,455,457,459,460,464,465,467,472,473,476,483],interatom:[3,4,7,164,187,249,315,316,362,367,383,385,393,408,441,481],intercept:118,interchang:6,interconnect:18,interconvert:385,intereract:39,interesect:327,interest:[1,5,7,8,9,11,13,71,163,274,313,316,347,384,407,420,421,453,481],interf:361,interfac:[],interfer:[12,250,363],interg:[6,476],intergr:[464,468],interi:407,interior:[3,6,41,327,458],interlac:408,interleav:[6,164,463],intermedi:[6,12,59,189,249,272,340,356,453,454,463,467],intermix:450,intermolecular:363,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,99,101,118,141,144,146,163,171,184,189,190,193,194,195,199,211,215,219,231,243,244,248,250,254,273,291,295,332,334,337,340,344,354,355,430,431,439,453,455,457,460,469,472,473,474,480,481,482,483],internal_element_set:199,internal_quadratur:199,internet:233,interpenetr:408,interpentr:[431,432,434],interpol:[6,15,38,56,100,184,189,190,199,237,272,346,347,356,367,412,421,433,439,440],interpret:[2,6,11,189,204,389,429,450,453,469,481],interrupt:281,intersect:[3,6,118,190,327,329,458],intersert:327,interspers:354,interstiti:162,intertia:[3,93],interv:[3,6,91,188,203,234,281,286,287,298,433,450,469,481],intestieti:118,i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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 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 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 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 temp command","compute temp/asphere 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/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 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/sphere command","fix nphug command","fix npt/asphere 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/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 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 fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style 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 meam command","pair_style meam/spline","pair_style meam/sw/spline","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 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_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":210,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,144,152,153,157,163,164,167,169,183,185,186,187,189,190,191,192,194,195,196,198,199,200,202,205,206,207,210,211,213,214,215,216,220,223,226,227,232,234,235,236,237,238,240,245,248,250,251,254,268,269,273,274,277,278,279,280,281,283,286,288,289,291,292,306,308,313,314,315,316,319,321,323,325,329,341,344,346,347,349,350,352,353,355,357,358,359,361,364,367,369,385,406,407,412,420,421,436,437,450,451,452,455,456,458,460,462,463,464,467,469,471,472,473,474,475,480,482,483,484],"function":481,"long":[368,370,371,372,373,377,379,380,397,401,405,415,423],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[194,195],addforc:196,addit:[12,13],addtorqu:197,adiabat:6,adjust_dt:296,adp:362,airebo:363,alloi:383,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:198,arrai:6,aspher:[6,82,143,252,255,258,259,267],atc:[9,199],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,162,198,200,201,280,481],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:208,awpmd:[9,364],balanc:[41,209],barostat:6,basal:67,beck:365,berendsen:[278,309],between:6,binary2txt:13,bodi:[6,8,42,68,260,366],bond:[8,13,69,210,211,212,287],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:367,born:[368,379],boundari:[7,57],box:[6,58,213],brownian:369,buck:[370,371,379],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,170,372,405],chunk:[6,66,71,75,90,93,104,106,114,144,159,161,202],citat:7,class2:[21,43,171,332,373],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[323,375,447],colvar:[9,13,214],com:[74,75,145],comb3:376,comb:[283,376],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,481],compute_modifi:102,condit:7,conduct:[6,314],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:203,cosin:[23,24,25,26,27,28,173],cossq:334,coul:[368,370,371,372,373,377,378,379,390,397,401,405,415,423],coupl:6,creat:211,create_atom:164,create_bond:165,create_box:166,createatom:13,creation:7,csld:310,csvr:310,cubic:399,cuda:[9,14,109,112,142,151,196,208,222,225,229,250,257,293,294,309,311,322,368,370,372,373,383,389,390,397,398,400,403,413,438,440],custom:8,cut:[49,364,370,373,377,380,385,387,397,398,405,411,415],cvff:335,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[377,397],deform:[147,148,215],delete_atom:167,delete_bond:168,delta:24,deposit:216,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,9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,peri:417,period:25,phonon:[9,13,273],pimd:274,piston:325,planeforc:275,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:417,poem:276,point:282,polariz:6,poli:[369,406,407],polym:13,polymorph:418,post:7,potenti:[2,6,8],pour:277,pppm:6,prd:450,pre:7,press:278,pressur:112,previou:12,print:[279,451],problem:[3,4],process:[6,7],processor:452,profil:152,properti:[6,113,114,115,280],pymol_aspher:13,python:[11,13,453],qbmsst:281,qeq:[282,283,284],qmmm:[9,285],qtb:[9,286],quadrat:182,quantiti:6,quartic:[35,54],quip:419,quit:454,ramp:153,rattl:294,rdf:116,read_data:455,read_dump:456,read_restart:457,reax:[13,284,287,288,420,421],reaxc:9,rebo:363,recent:289,reduc:117,refer:481,reflect:326,region:[8,117,154,155,327,458,481],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,181,182,183,184,185,186,187,188,189,190,191,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,225,226,227,228,229,230,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,286,287,288,289,291,292,293,295,296,297,298,299,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,349,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,477,478,479,481,482,483,484,485],relax:213,replic:459,replica:[6,7],report:3,requir:12,rerun:460,rescal:[311,312],reset:220,reset_timestep:461,resquar:422,restart2data:13,restart:[6,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,462],restrain:290,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485],rho:126,rhosum:433,rigid:[6,83,98,240,291],ring:340,rotat:156,rule:2,run:[6,11,12,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,463],run_styl:464,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,423],self:305,serial:11,set:[6,465],setforc:293,setvel:300,shake:294,share:[11,12],shell:[6,466],shield:282,shift:[26,27,48,49,173],simpl:31,simul:6,size:6,slater:282,slice:119,sllod:[268,269],small:291,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,295,296,297,298,299,300,302,424,425,426,427],smooth:[403,404],sna:140,snad:140,snap:428,snapshot:6,snav:140,soft:[405,429],solver:2,sourc:7,spatial:[205,206],spc:6,speci:288,special:[7,412,481],special_bond:467,sph:[9,430,431,432,433,434,435],sphere:[84,85,157,206,240,253,256,265,270],spheric:6,spline:[409,410],spring:[303,304,305,316],squar:28,srd:[306,328],srp:436,standard:9,start:[12,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328],state:308,stationari:244,stop:[194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328],store:[307,308],strategi:1,streitz:377,stress:141,structur:2,style:[1,2,6,8],submit:8,suffix:468,summari:6,swap:[200,212],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485],system:6,tabl:[0,6,38,56,184,439,440],tad:469,taitwat:[434,435],temp:[142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,309,310,311,312],temper:470,temperatur:6,tersoff:[440,441,442],test:11,tfmc:313,thermal:[6,314],thermo:[6,471],thermo_modifi:472,thermo_styl:473,thermodynam:[6,8],thermostat:6,thole:443,time:[6,207],timer:474,timestep:475,tip3p:6,tip4p:[6,377,397,401,405],tip:12,tlsph:425,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:317,tool:13,torqu:159,transform:219,tri:[266,444],tri_surfac:426,triangle_mesh_vertic:134,triclin:6,tstat:381,ttm:318,tune:319,type:7,ulsph:427,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:342,uncomput:477,undump:478,unfix:479,unit:480,user:[9,12,14,16,18],vacf:160,val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\ No newline at end of file
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afterward:3,afterword:41,ag1:163,ag2:163,again:[6,11,12,17,62,140,144,146,150,158,187,190,215,230,277,332,345,356,406,407,450,452,453,455,457,462,469,471,481,483],against:[11,12,13,64,216,356,420,421],aggreg:[6,12,65,68,69,79,92,108,115,230,246,289,291,304,450,482],aggress:[230,469],agilio:[9,13],agre:[3,8,184,354,363,394,421],agreement:[5,7],ahd:391,ahead:325,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:189,akohlmei:[7,9,13,191,231],aktulga:[7,9,284,421],al2o3_001:[118,292],al3:163,ala:237,alain:9,alat:[272,408],alb:[418,440,442],albeit:290,albert:9,alchem:[87,158],alcohol:321,alcu:[362,367],alcu_eam:418,alderton:380,alejandr:[250,251],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,190,199,209,212,215,237,239,240,262,274,291,294,313,314,318,321,326,352,353,354,358,361,385,407,425,427,450,452,469],alia:12,alias:[1,347],aliceblu:190,align:[6,12,29,41,71,166,184,205,209,232,349,455,458,476],alkali:385,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,152,157,158,159,160,161,162,163,164,165,166,167,168,170,172,177,183,184,187,188,189,190,191,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,243,245,246,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,302,303,305,306,307,308,309,310,313,314,315,316,317,318,319,320,321,323,324,325,326,327,328,329,330,331,332,333,336,341,344,345,346,347,348,349,351,354,355,356,357,358,360,361,362,363,364,366,367,368,370,371,372,373,374,376,377,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,401,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,470,472,473,474,476,480,481,482,483,484,485],allen:[29,87,380,388],allentildeslei:87,allign:3,allindex:330,alloc:[3,5,6,8,9,11,12,60,224,320,355,357,361,416,421,455,463],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,143,144,157,162,163,164,166,172,183,184,187,189,190,191,193,194,196,198,199,200,202,203,204,205,206,207,209,211,212,213,214,215,216,220,221,224,226,227,228,229,231,234,237,240,241,245,247,250,251,272,276,278,279,280,281,285,291,292,294,295,297,298,302,306,313,314,315,316,318,319,320,321,322,323,329,331,333,341,346,347,349,354,355,356,357,360,361,364,367,368,369,370,371,372,377,383,385,389,390,391,392,401,406,407,412,418,421,422,425,427,436,445,447,450,453,455,457,458,459,460,461,462,465,467,468,469,472,473,474,481,482],almost:[2,3,12,60,232,281,318,347,358,361,436],alo:377,alon:[6,7,212,287,420,421,453],alond:13,along:[6,8,9,12,29,40,87,118,163,164,186,187,189,212,232,237,238,242,247,249,281,291,294,295,299,303,304,313,317,318,324,327,329,349,352,353,354,356,377,380,389,392,395,397,401,408,420,421,439,455,458,465,466,481],alonso:[409,410],alpha:[6,12,51,194,237,273,281,286,354,362,365,368,377,381,383,384,386,391,396,397,408,413,417,441,443,473,476],alpha_:443,alpha_c:405,alpha_i:[428,443],alpha_ialpha_j:443,alpha_lj:405,alphabet:[2,3,22,37,44,55,63,172,183,193,333,341,355,374,437,455],alphanumer:[3,63,193,280,288,331,355,481],alreadi:[3,7,8,12,42,164,165,167,188,198,202,205,206,209,211,215,241,279,281,306,329,355,356,381,390,392,399,407,436,445,448,451,455,456,460,465,481],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,150,151,152,153,154,156,157,158,159,160,161,162,164,165,166,167,168,170,172,183,184,185,187,188,189,190,191,193,194,195,196,198,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,221,224,225,226,227,228,230,231,234,235,236,237,247,248,250,251,252,253,254,255,256,261,264,265,267,268,269,270,272,273,274,276,277,278,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,299,300,303,304,306,309,310,311,312,313,317,318,319,320,322,324,327,329,331,333,338,341,344,346,347,349,350,351,354,355,356,357,358,360,361,367,371,372,374,378,379,380,381,383,384,385,388,389,391,392,393,401,405,406,408,412,414,416,417,418,419,422,423,425,431,432,434,435,436,437,438,439,440,441,442,443,450,452,453,454,455,456,457,458,459,460,462,463,464,465,467,468,469,470,473,474,475,476,477,479,480,481,482,483,485],alter:[3,6,8,9,11,12,41,59,142,143,144,145,147,150,151,152,153,156,15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7,219,226,227,232,234,235,240,246,250,255,256,267,268,270,273,277,282,288,289,291,292,295,303,304,306,308,309,310,311,313,314,316,323,327,332,349,355,366,384,385,388,389,395,406,407,408,409,410,438,440,441,442,444,458,465,476,481],centimet:480,central:[3,61,70,76,77,116,122,140,240,272,294,304,355,414,420,421,455],centro:[],centroid:[3,274,444,465],cerda:346,ceriotti2:228,ceriotti:[13,228,233],certain:[1,2,3,6,8,12,17,39,71,113,117,119,168,187,189,201,202,203,204,205,206,207,212,224,225,291,293,307,320,331,338,345,357,392,412,421,443,457,461,476,481],certainli:232,cerutti:347,cfg:[3,6,7,13,187,188,189,190,191],cfile:421,cfl:[128,296],cfor:295,cg_type:423,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:294,ch2lmp:[],ch3:294,ch5md:188,chain3:357,chain:[],challeng:[6,295],chalopin:286,champaign:[231,346,347,406],chandler:[362,383],chandrasekhar:[6,397],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,128,146,147,148,164,165,166,168,184,186,187,188,189,190,191,193,194,195,196,197,199,200,205,206,208,209,210,211,212,213,214,215,216,220,221,223,225,228,230,231,232,234,236,237,238,240,246,247,248,250,251,252,253,254,255,256,262,267,268,269,270,272,273,277,278,280,281,285,288,289,290,291,293,294,295,306,309,310,311,312,314,315,316,317,318,319,321,324,327,329,347,352,354,356,359,361,381,385,389,392,406,407,408,412,420,421,437,450,451,452,453,455,456,457,458,459,460,461,463,464,465,466,467,470,473,477,479,480,481,482,483],change_box:[],changeabl:187,channel:[4,196],chapter:[274,347],charact:[2,3,6,12,38,41,56,63,184,187,189,190,191,193,209,280,288,331,355,360,385,396,418,420,421,439,452,453,457,462,463,481,483,484,485],character:[6,67,70,116,140,428,450,469],characterist:[235,306,315],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,163,164,187,191,193,194,195,200,216,221,226,280,282,283,284,288,308,321,346,347,355,368,370,376,377,379,380,383,385,386,392,397,401,405,415,420,421,437,442,443,445,447,448,455,456,460,465,467,476,480,481],charmm2lammp:13,charmm:[],chartreus:190,cheap:306,cheaper:[220,388,422],check:[3,6,8,11,12,15,17,39,41,71,91,184,200,205,209,210,211,216,223,226,232,233,290,294,306,314,316,321,329,331,345,354,355,356,357,358,361,382,393,396,412,421,436,450,452,453,455,463,469,472,473],checkf:184,checkqeq:421,checku:184,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,141,170,171,181,214,219,227,228,235,237,249,250,251,268,269,274,278,281,283,291,295,306,309,310,313,314,315,316,323,332,340,342,346,347,353,356,363,368,372,373,376,377,378,380,381,385,387,388,390,391,397,401,402,405,408,411,412,415,436,443,464,467,469,476],chemic:[9,118,158,163,187,199,200,226,282,287,288,313,347,420,421,432],chemistri:[9,281,282,284,367,385,420,421],chen:318,cheng:376,chenoweth:[420,421],chenoweth_2008:[420,421],chi:[92,153,186,272,282,284,386,388,482],chiefli:419,child:8,chip:[7,12,17,361,468],chipot:214,chiral:340,chmod:[11,12],cho:408,chocol:[7,190],choic:[3,6,12,15,16,18,40,41,54,87,141,143,157,168,184,202,205,206,209,212,215,216,228,234,237,248,250,274,282,291,313,341,347,352,353,356,358,361,392,405,412,416,455,464,465,468,469,475,476,480],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,154,155,189,210,211,212,213,216,223,234,237,248,250,252,253,254,255,256,278,306,310,324,346,347,353,445,450,452,464,470],chose:[440,442],chosen:[2,3,6,12,17,140,164,167,176,184,189,195,200,213,216,223,226,227,235,237,248,250,254,274,277,288,306,310,313,314,319,321,322,328,347,348,353,361,385,389,395,396,399,423,440,450,464,469,476],chri:162,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,144,159,161,202],chute:[4,10,229],ciccotti:294,cieplak:[6,170,467],cii:203,cij:203,circl:302,circular:[3,6,143,185],circumst:18,circumv:286,citat:[],cite:[3,7,8,12,234],cko:2,cl1:163,clarendon:[29,380],clarifi:[7,440,442],clariti:331,clark:415,class2:[],classic:[0,3,5,6,7,8,9,224,274,281,286,318,342,385],classifi:[9,437],claus:453,clean:[6,12,14,15,17,463],cleanli:[454,484],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:459,click:[2,11,22,37,44,55,164,172,183,189,231,333,341,356,374,437],client:[231,233],climb:[249,356,469],clinic:[7,13],clo:[153,186,482],clock:[12,450,469],clockwis:324,close:[3,6,11,12,13,39,41,67,141,167,187,211,212,213,228,235,237,250,268,291,294,324,327,345,347,350,352,353,356,361,363,367,377,378,408,412,424,426,442,459,465,476,478],closer:[3,41,116,162,186,187,209,213,217,315,356],closest:[211,272,291,321,388,422,436,445],cloud:476,clovertown:18,clsuter:72,clump1:[276,291],clump2:[276,291],clump3:[276,291],clump:291,cluster:[],clutter:[3,9],cmap:455,cmatrix:228,cmax:408,cmd:[11,12,274,466],cmin:408,cmm:[],cn1:203,cn2:203,cna:[],cnn:203,cnr:[9,13],cnt:[392,459],co2:[40,163,294,355],coars:[7,9,29,36,40,54,176,276,291,306,390,423,467],coarser:[347,481],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,170,171,172,177,332,333,338,374,392,396,412,425,427,429,455,457],coeffcient:455,coeffici:[],coefficienct:381,coefficient0:383,coefficient1:383,coeffieci:[6,365],coeffincientn:383,coexist:[9,226,385],cohes:[6,386,408],coincid:[122,327,372,406,407,450],colberg:188,cold:[6,149,230,357,476],coldest:314,coleman8:9,coleman:[9,118,163,292],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,144,152,159,161,164,187,190,202,214,240,246,276,286,289,291,329,346,355,357,375,395,455,462,468,474,485],collid:[220,306,328],colliex:163,collinear:[3,276],collis:[3,237,306,324,328,382,389,448],colllis:306,colloid:[],colombo:39,colon:[191,329,456],color1:190,color2:190,color:[3,9,41,187,189,190,209,227,281,286],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,144,152,159,161,162,163,184,187,190,193,201,202,203,204,205,206,207,240,247,248,281,291,307,308,318,328,387,391,420,421,456,470,472,481],colvar:[],colvarmodul:12,com:[],comamnd:215,comand:[212,457],comannd:361,comb3:[],comb:[],comb_1:283,comb_2:283,combiant:378,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,143,157,187,189,199,204,231,240,250,274,280,310,319,327,330,332,346,347,349,353,361,375,377,378,385,386,392,404,405,428,438,440,442,447,458,463,476,481],come:[],comfort:[12,13],comm:[0,3,12,61,73,188,231,233,234,347,356,361,381,412,417,439],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,170,184,187,235,291,318,355,356,362,383,384,386,396,408,414,421,428,438,439,440,441,442,452,453,455,476,481],commerci:7,commmand:[3,6,12,59,107,269,449,450,452,469,484],common:[],commonli:[3,6,12,17,25,57,59,105,166,187,189,191,342,390,399,428,440,442,455,458,467],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,167,168,189,190,209,210,211,213,214,215,231,233,237,239,240,241,250,273,280,282,283,284,291,306,318,329,346,357,358,359,361,382,416,452,453,457,464,465,483,485],communc:346,comp:[7,188,233,234,294,347,356,385,412,417,422,435,439,441],compact:[63,193,374,437],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,147,162,163,172,183,190,219,282,329,331,346,347,354,356,408,450,469,470,476,480],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,171,172,183,332,333,341,373,437],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,175,187,191,195,201,202,203,204,205,206,207,209,273,285,310,313,320,323,326,346,361,393,412,439,452,453,481],compens:[6,210,211,289,357,385],compet:317,competit:347,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,162,187,188,189,191,231,317,347,361,455,456,460],compl:17,complain:[12,17],complement:408,complementari:[7,377,397],complet:[3,6,9,12,15,41,59,71,190,205,209,214,240,274,277,280,306,317,319,331,345,356,361,386,425,427,444,450,455,460,463,467,469,472,476,481],complex:[6,8,11,12,13,25,40,42,62,140,152,164,165,237,302,327,344,356,385,439,453,455,458,481],compli:[313,317],complic:[6,7,9,12,13,200,226,453],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,159,160,161,187,189,190,196,197,201,202,203,204,205,206,207,208,212,213,215,216,221,224,229,233,234,237,240,242,246,247,249,250,251,254,255,256,267,268,270,271,273,274,275,278,289,291,293,294,295,299,300,303,306,309,310,311,313,320,321,326,327,328,346,349,353,354,355,356,361,381,385,389,406,407,425,427,428,455,456,465,473,481,482],componenet:6,composit:[6,200,237,383],compound:[376,385,386],compres:[71,114,202],compress:[3,6,9,12,59,71,114,167,187,189,190,202,215,248,254,278,281],compris:[40,327,395,422,444],compton:[118,163],comptu:[3,6],compuat:347,comput:[],computation:[3,6,210,211,318,367],computational:476,compute_arrai:8,compute_fep:[195,405],compute_group_group:226,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,292],compute_scalar:8,compute_temp:8,compute_ti:195,compute_vector:8,compute_xrd:163,concaten:[2,3,484],concav:327,concentr:383,concept:[6,144,154,202,464],conceptu:[3,6,71,152,213,215,356,377,392,408,460],concern:[6,73,87,188,227],concis:[11,317],conclud:12,concret:8,concurr:[9,16,347],conden:[318,440,442],condens:[6,146,318,363,379,383,397],condit:[],conducit:6,conduct:[],cone:458,confid:[3,469],config:[12,187,452],configfil:214,configur:[1,2,6,12,15,17,38,59,122,166,184,186,187,189,193,213,214,215,216,220,226,233,234,262,274,282,317,344,354,356,363,367,384,408,438,440,442,450,455,457,458,469],confin:[455,469],conflict:[3,12,40,412,453],conform:[3,6,13,59,212,213,249,290,295,317,340,356,385,467],confus:3,conjuct:381,conjug:[7,8,234,353,385,420,421],conjunct:[6,7,71,86,87,114,147,152,158,164,168,190,194,195,234,237,241,262,277,278,282,283,284,286,291,306,314,321,326,346,347,356,368,370,374,377,381,385,391,397,412,415,423,443,455,458,462,476,485],connect:[3,6,87,149,167,212,231,276,291,294,303,356,378,389,436,442,452,453,459,476],conput:3,consecut:[3,11,12,39,71,164,190,194,195,216,231,232,377,397,401,450,456,458],consequ:[1,6,318,396,469],conserv:[3,193,200,212,219,220,227,230,234,236,237,241,246,248,250,262,291,294,309,310,314,321,322,326,356,380,381,389,403,464,469],consid:[6,9,70,71,78,87,115,149,150,167,187,190,194,195,201,203,205,209,211,212,216,238,251,273,291,313,314,317,318,321,347,374,385,392,421,422,436,450,451,453,456,457,458,460,463,465,473,476,481],consider:[6,8,234,235,309,310,311,361,464],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,144,147,149,164,176,186,191,196,197,202,215,216,219,221,224,227,234,235,236,247,250,252,253,254,255,256,257,258,260,261,262,263,265,266,267,268,269,270,278,281,286,288,290,291,309,310,311,312,322,346,347,349,355,356,361,363,367,369,375,377,385,388,392,406,407,408,412,422,425,427,439,445,453,455,456,458,459,460,467,476,481],consistent_fe_initi:199,consit:291,constant:[],constitu:[3,6,240,291,323,327,375,422],constitut:[425,427],constrain:[3,6,8,142,143,144,145,147,150,151,152,153,154,156,157,193,202,216,226,227,232,240,244,276,277,289,291,294,304,314,321,354,355,385,460,467,476],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,163,213,250,273,290,327,357,361,380,412,436,438,439,458,459,481],constructor:8,consult:421,consum:[1,286,416,481],consumpt:344,contact:[],contact_stiff:[424,426],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,144,152,162,163,164,166,170,172,183,184,187,189,190,191,193,194,195,199,201,202,203,204,205,206,207,209,214,216,221,228,232,233,234,235,237,248,262,272,273,276,277,279,281,284,288,291,292,296,306,313,317,318,327,328,331,345,347,355,356,359,360,362,363,364,367,376,377,380,383,384,385,392,393,408,414,418,419,420,421,428,438,439,440,441,442,443,450,451,452,453,455,456,457,458,460,462,464,467,469,472,473,476,481,483,485],content:[12,18,421,471,473],context:[3,6,8,12,17,117,190,210,211,216,276,288,322,353,447,455,462,471,480,481,482],contibut:70,contigu:452,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,160,190,193,194,195,200,202,203,204,205,206,207,209,212,213,214,215,216,226,227,228,230,231,232,234,235,236,242,247,248,250,252,253,254,255,256,267,268,269,270,275,277,280,281,291,292,295,305,306,308,315,316,318,324,327,331,345,360,361,367,381,382,399,402,420,421,422,425,427,441,450,453,455,457,458,463,469,472,473,481,483],continuum:[6,7,9,199,318,425,427],contour_integr:199,contract:[59,213,215,250,278,291],contradictori:3,contrain:294,contraint:262,contrari:[228,235],contrast:[1,6,42,55,64,149,215,329,425,427,447,484],contrib:318,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,195,200,201,202,203,204,205,206,207,213,226,234,237,240,241,245,251,268,269,276,277,285,288,291,292,294,320,346,354,356,364,381,382,383,385,392,406,407,412,420,421,467,473,476],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,173,187,189,193,199,200,209,213,214,215,230,231,234,235,250,252,253,254,255,256,278,283,291,297,298,309,310,311,318,322,344,346,358,385,388,420,421,424,426,438,442,450,452,464,470,471],control_typ:199,controlfil:421,convect:91,conveni:[6,12,29,187,191,207,292,349,428,481],convent:[3,8,9,29,175,182,183,190,290,303,330,383,385,481],converg:[3,6,41,88,187,189,191,196,209,212,213,221,224,254,281,283,286,290,294,352,353,354,356,376,377,397,450,462,469],convers:[3,8,140,189,190,200,203,278,346,377,378,379,385,397,401,405,415,453,469,480],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,164,171,187,189,190,207,248,329,332,334,337,340,349,356,362,383,440,442,448,453,455,456,457,462,472,476,480,481,483,485],convex:327,convinc:[7,12],cook:9,cooki:7,cool:[7,154,230,289],cooordin:187,cooper:[5,7],coord123:114,coord1:[3,114,202,205,206],coord2:[3,114,202,205,206],coord3:[3,114,202,205,206],coord:[],coordiat:354,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,147,153,159,161,162,164,168,186,187,188,189,190,191,193,196,201,202,204,205,206,209,210,211,212,213,214,215,216,219,221,222,224,226,229,230,231,232,233,234,235,247,249,250,252,253,255,256,268,271,272,273,276,277,278,288,289,291,293,294,295,300,303,304,305,306,308,316,317,318,325,326,328,329,349,354,355,356,361,362,363,366,384,450,455,456,458,460,463,465,469,476,481,482],coordn:[114,202],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,189,318,356,374,420,453],copper:448,coproccesor:16,coprocessor:[1,4,7,9,16,17,361,468],coproprocessor:17,copy_arrai:8,copyright:[7,8,276],coral:190,core:[],core_shel:146,coreshel:[6,9,370,377,379],cornel:[6,170,467],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,189,327,328,349,444,455],cornflowerblu:190,cornsilk:190,corpor:16,corr:376,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,146,151,158,189,215,228,234,250,251,268,276,278,281,317,323,327,346,356,362,363,364,365,366,367,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,446,447,448,455,470,473,476],correction_max_iter:199,correctli:[3,8,9,11,17,71,81,102,103,142,143,145,147,149,150,151,152,153,156,157,160,187,190,196,216,221,224,235,244,250,251,284,291,294,303,305,324,327,356,357,361,379,407,452,453,455,465,480,482],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,142,143,151,158,163,170,171,172,173,174,175,176,178,179,181,182,184,187,189,190,194,195,196,202,204,205,206,208,211,213,215,222,224,225,229,234,237,238,246,247,248,250,252,253,254,255,256,257,262,265,267,268,270,273,274,278,283,291,293,294,309,311,313,322,323,324,326,327,328,330,332,333,334,335,336,337,340,342,347,351,353,355,356,362,363,365,368,369,370,371,372,373,374,375,376,377,380,381,383,384,385,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,417,418,420,421,422,423,428,429,438,439,440,441,442,444,446,447,448,450,452,453,455,456,458,468,469,470,472,473,476,481],correspondingli:[406,407,464],cosin:[],cosineshift:27,cosmo:[228,233],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,163,189,190,202,205,206,209,210,211,223,250,283,318,346,347,359,377,397,401,412,438,452,464],costheta0:[438,440,442],costheta:418,costli:[11,88,228,357],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,144,154,159,161,177,187,189,190,194,195,200,202,203,205,209,215,224,233,280,281,282,286,289,291,293,306,307,313,317,318,319,323,327,329,331,338,343,345,352,354,357,361,364,387,391,392,420,421,451,452,453,455,457,459,462,463,471,476,481,482],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,141,165,169,282,284,319,346,347,354,361,368,370,371,372,373,376,377,378,379,380,385,389,390,392,397,401,405,412,415,420,421,423,437,442,443,447,460,467,473,476,480],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,152,162,168,196,197,200,202,204,205,206,208,209,216,221,223,226,232,250,262,277,294,309,310,327,347,354,355,356,358,361,387,391,412,473,481],counter:[324,450,461,463,469],counterbal:230,counterpart:[187,291,450],counterproduct:18,coupl:[],courant:296,cours:[3,8,126,128,158,187,194,195,227,290,303,317,323,325,326,328,329,347,406,429,452,455,468,476,481,483],coval:[6,29,385,408,476],covari:228,cover:[6,71,184,190,199,237,385,395,444],coverag:[71,205],cpc:233,cpp:[1,3,6,8,9,11,12,13,87,187,194,195,224,294],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,190,193,219,235,319,344,347,361,374,437,450,468,469,472,473,474],cpuremain:473,cr2:163,cr3:163,crack:[4,357],crada:[5,7],crai:[5,7,13,18,187],crash:[3,12,357,476],craympi:361,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:199,create_faceset:199,create_group:188,create_nodeset:199,createatom:[],creation:[],crimson:190,critchlei:276,criteria:[3,116,165,189,190,210,211,212,245,354,417,444,457,460,481],criterion:[12,41,121,162,164,167,200,209,212,226,262,283,296,324,329,354,356,376,385,389,460,469,470],criterioni:469,critic:[48,49,248,313,318,354],cross:[3,12,22,71,89,143,172,187,189,201,205,211,215,247,249,268,291,299,303,305,314,321,333,349,356,372,381,382,383,390,391,392,397,399,401,418,423,425,427,440,442,455,459,465,483],crossov:1,crossterm:455,crozier:[0,7,13],crucial:281,crystal:[4,6,13,73,272,273,316,357,459,473,476],crystallin:[6,273,349,441,476],crystallis:313,crystallogr:[118,163],crystallograph:[349,473],crystallographi:[118,163,349],cs1:163,cs_chunk:6,cs_im:[40,455],cs_re:[40,455],csanyi:[140,419,428],cscl:408,csequ:6,csh:[11,12,374],cshrc:[11,12],csic:[384,438,440,442],csinfo:6,csisi:[384,438,440,442],csld:[],cst:383,cstherm:6,cstyle:452,csvr:[],ctcm:[362,383],ctemp_cor:219,cterm:295,ctr:9,ctype:11,cu1:163,cu2:163,cu3au:408,cube:[6,41,162,167,209,219,327,349,476],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:367,cummul:[3,6,207,210,211,212,214,223,228,234,236,306,309,310,311,312,314,321,391,473],cumul:[6,200,202,204,205,206,220,226,234,248,250,254,262,291,292,356],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,144,152,160,162,165,168,187,188,189,190,191,194,195,199,200,202,205,206,207,209,210,211,212,213,214,215,216,220,221,224,226,228,231,232,234,240,247,250,251,255,256,262,267,268,270,276,282,283,285,288,289,290,291,294,295,296,297,298,299,300,302,304,305,306,309,310,311,317,318,321,322,323,324,325,326,328,329,331,344,345,346,347,350,351,353,354,355,356,361,367,374,376,380,383,385,386,389,393,396,406,407,408,409,410,412,418,420,421,424,425,426,427,429,440,442,443,445,450,451,452,453,455,456,457,458,459,461,462,463,465,467,469,470,472,473,481,482,483,484,485],curv:[6,164,226,273],curvatur:[388,422,448],custom:[],cut0:453,cut1:464,cut2:464,cut:[],cuthi:[272,284],cutinn:[369,406,407],cutlo:[272,284],cutmax:418,cutoff1:[373,380,397,401,405,415,423],cutoff2:[368,370,371,373,379,380,397,401,405,415,423],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,162,165,167,211,212,217,272,281,282,284,286,288,291,306,319,323,327,329,346,347,354,357,358,359,361,362,363,364,365,366,367,368,369,370,371,372,373,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,428,429,430,431,432,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,453,457,460,464,476],cutoffa:384,cutoffc:384,cuu3:383,cval:163,cvd:313,cvel:295,cvff:[],cwiggl:[3,247,323,326,328,481],cyan:[2,189,190],cycl:[3,226,248,250,251,254],cyclic:[3,184],cygwin:12,cylind:[3,4,189,232,277,324,327,458],cylindr:[6,232,303,324],cypress:361,cyrot:367,cyrstal:273,d3q15:237,d3q19:237,d_double_doubl:15,d_e:318,d_flag2:280,d_flag:280,d_name:[113,187,280,308,465],d_single_doubl:15,d_single_singl:15,d_sx:280,d_sy:280,d_sz:280,daan:316,dai:12,daili:12,daivi:268,damag:[],dammak:286,damp:[3,6,193,198,234,235,236,241,250,251,254,278,281,286,291,309,310,322,324,325,353,354,356,368,370,372,377,380,385,389,397,405,415,423,437,443,469,476],damp_com:235,damp_drud:235,dampen:[291,476],dampflag:[324,389],dan:17,danger:[3,12,226,329,381,473],dangl:167,daniel:9,darden:[347,380],darkblu:190,darkcyan:190,darken:189,darkgoldenrod:190,darkgrai:190,darkgreen:190,darkkhaki:190,darkmagenta:190,darkolivegreen:190,darkorang:190,darkorchid:190,darkr:190,darksalmon:190,darkseagreen:190,darkslateblu:190,darkslategrai:190,darkturquois:190,darkviolet:190,dasgupta:282,dash:[389,472],dat:[6,91,184,199,451],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,292],dataset:292,datatyp:3,date:[0,6,12,13,420,421,481],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,187,203],davi:323,david:[9,19,346,347,440,442],daw:[383,418],dbg:14,dcd:[3,6,7,187,188,189,190,191,274,456,460],ddim:186,deactiv:405,dealt:233,debug:[6,7,11,12,13,14,17,118,122,163,164,274,279,344,346,361,393,412,445,453,454,457,462,465,472,481],deby:[],decai:[377,448],decid:[3,6,12,16,71,247,280,291,319,470],decipher:349,declar:188,declin:306,decod:189,decompos:[87,428],decomposit:[3,5,7,18,62,199,274],decoupl:[6,476],decreas:[3,187,196,197,212,215,221,224,234,317,346],decrement:295,deepli:343,deeppink:190,deepskyblu:190,def:[12,13,453],defaul:61,defect:[6,70,162],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,170,171,172,173,174,175,176,178,179,181,182,183,184,185,186,187,188,189,190,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,219,220,221,224,225,226,229,232,233,234,235,236,237,245,247,249,250,251,252,253,254,255,256,258,259,260,263,265,266,267,268,269,270,272,273,274,276,277,278,280,282,284,289,291,292,293,294,296,300,304,306,308,309,310,311,312,314,315,316,318,320,321,323,324,325,326,327,328,329,331,332,333,334,335,336,337,340,341,342,344,346,347,349,351,353,354,355,356,357,358,359,360,361,363,364,365,366,368,369,370,371,372,373,374,375,377,378,380,381,382,384,385,387,388,389,390,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,411,412,413,414,415,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,455,456,458,459,460,461,464,465,466,467,469,470,472,473,476,477,478,479,480,481,482],definit:[2,3,6,8,12,13,78,80,116,140,190,202,203,204,205,206,207,215,232,254,292,308,320,323,326,328,330,341,344,355,364,367,375,385,395,418,425,427,428,444,453,455,457,464,466,480,481],defint:473,deform:[],deg2theta:163,deg:476,degener:[3,276],degrad:[8,18,273,347,464],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,163,164,170,171,174,175,182,184,186,189,202,212,219,226,228,229,234,235,240,250,251,254,255,256,267,268,270,274,276,290,291,294,309,310,311,316,332,334,337,340,342,354,380,383,391,465,473,476,482],degress:[144,202],del:469,delai:[3,6,12,357,382,473],deleg:392,delet:[2,3,7,8,12,54,57,60,63,162,167,168,193,202,203,204,205,206,207,210,212,223,226,250,292,309,310,329,331,345,355,357,360,412,455,456,458,466,467,472,477,479,481,482],delete_atom:[],delete_bond:[],delete_el:199,deli:186,delimit:[453,481],deloc:[251,385],delr:408,delt_lo:469,delta:[],delta_1:367,delta_3:367,delta_7:367,delta_conf:3,delta_ij:[408,418],delta_mu:[3,200],delta_pi:367,delta_r:418,delta_sigma:367,delx:186,delz:186,demand:286,demo:11,demon:271,demonstr:[281,408],den:277,dendrim:391,denniston:[9,237,239,240,241,273],denomin:[7,169],denot:[118,219,235,273,284,286,377,390,392,421,425,427],dens:[71,212,385],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,150,162,164,194,195,199,202,205,206,209,215,224,237,240,243,244,273,277,278,282,318,323,349,351,355,362,367,383,408,409,410,418,422,431,433,434,435,455,464,465,473,480],density_continu:427,density_summ:427,depart:[0,7],departur:[248,281],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,142,147,151,152,158,164,165,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,189,190,193,194,195,196,197,200,202,204,205,207,208,209,211,213,221,222,225,228,229,230,232,234,235,237,239,240,247,250,252,253,254,255,256,257,265,267,268,270,272,283,286,288,291,293,294,300,306,309,310,311,313,315,317,318,320,322,323,326,327,328,329,331,332,333,334,335,336,337,340,342,347,349,354,355,357,358,359,361,362,363,365,366,367,368,369,370,371,372,373,374,375,376,377,378,380,381,383,384,385,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,408,409,411,413,414,415,417,418,420,421,422,423,428,429,437,438,439,440,441,442,443,444,446,447,448,450,452,455,457,458,461,465,467,469,472,473,475,481,482],dependend:6,depflag:12,dephas:[450,469],depos:216,deposit:[],deprec:282,depth:[51,143,189,318,388,422],dequidt:9,der:[87,107,375,376,405,420,421,447,476],deriv:[6,7,8,38,56,63,87,140,158,184,203,213,215,226,234,247,250,252,253,254,255,256,272,278,282,286,315,316,318,323,324,327,353,355,363,367,375,380,385,386,390,399,403,404,408,420,421,437,439,447,476],derjagin:447,derlet:272,descend:190,descent:[7,353],descib:[40,282],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,143,144,148,149,152,155,157,158,162,163,164,166,167,176,181,184,187,188,193,194,195,202,203,204,205,206,207,209,212,213,214,215,216,218,219,227,228,231,232,233,234,235,236,237,239,240,241,245,249,250,251,254,261,269,272,274,279,280,281,282,283,284,291,295,303,306,307,308,309,310,311,312,313,314,315,316,321,323,324,326,331,346,347,349,352,353,354,355,356,360,363,364,366,368,369,370,372,373,374,375,376,377,380,383,385,386,388,389,390,392,397,398,399,400,401,402,403,404,405,406,407,408,411,417,418,419,420,421,422,423,428,429,436,437,438,439,440,441,442,443,446,447,448,450,452,453,455,456,458,459,465,468,469,472,481,482,483],descript:[],descriptor:[140,187,393],deserno:347,design:[0,3,6,7,8,9,11,13,14,15,17,118,146,149,163,199,212,218,219,250,251,272,273,292,313,318,364,365,366,369,372,377,379,385,405,406,407,409,410,418,421,439,464],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,146,164,177,186,200,202,207,213,215,224,226,227,234,235,236,240,250,268,276,277,278,279,282,286,291,294,306,309,310,311,312,317,324,338,343,346,347,349,352,354,355,356,381,383,391,406,407,438,440,442,451,452,453,455,459,464,469,470,472,473,481,482,483],desk:7,desktop:[4,6,7,10,12,17,189],despit:476,destabil:367,destre:340,destroi:[11,39,210,211],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,142,143,144,147,157,158,159,161,164,165,168,169,172,183,187,189,190,193,194,195,199,202,203,204,205,207,209,211,212,213,214,215,216,224,226,227,228,229,231,232,234,236,237,241,247,248,249,250,251,252,253,254,255,256,260,262,267,268,269,270,273,276,277,278,280,281,283,284,285,291,294,306,309,310,311,312,313,314,316,317,318,319,320,321,322,329,331,333,341,346,347,350,354,355,357,358,361,362,363,364,366,367,369,371,372,373,374,375,376,377,380,381,385,386,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,407,408,411,412,417,420,421,422,428,429,437,444,446,447,453,455,456,457,458,460,461,464,465,467,470,473,474,481,482,485],detect:[2,3,12,61,63,86,225,277,317,356,376,391,396,450,452,455,466,469,481],determ:361,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,152,153,162,163,164,186,187,189,190,191,192,196,197,198,201,202,203,204,205,206,207,208,209,213,215,216,219,221,226,229,230,232,234,235,240,245,247,248,250,255,256,267,268,270,272,274,278,281,288,289,290,291,292,293,296,298,300,306,309,310,311,313,319,320,323,324,325,326,327,328,329,341,346,347,349,355,357,358,361,363,364,371,376,380,382,383,387,389,392,393,401,408,412,421,422,436,439,443,447,452,455,456,458,460,462,465,469,471,472,474,480,481,482],detil:108,devan:[9,423],devanathan:442,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,231,254,276,281,282,285,363,367,385,410,457],devemi:9,deviat:[248,254,272,387],deviator:9,devic:[1,3,12,15,17,231,361],device_typ:361,devin:[283,376],devis:410,dfactor:189,dff:476,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,347],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,285],dhi:[59,186,215,277],dhug:[248,281],dhugoniot:[248,281],dia:408,diagnost:[],diagon:[3,6,83,140,141,213,250,278,291,321,425,427],diagonalstyl:428,diagram:[41,118,163,183,209,274],diallo:391,diam:[189,190,277,355],diamet:[3,6,40,113,164,187,189,190,194,195,234,277,291,306,322,324,355,375,388,389,395,399,422,444,447,455,456,465],diamond:[349,385,408],diamter:[40,277],dick:6,dicsuss:247,dictat:[200,248],did:[3,12,354,381,382,383,389,412,440,442,463],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,160,320,346],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,142,143,144,145,147,150,151,152,153,154,156,157,158,164,165,167,172,183,184,186,187,189,190,193,195,198,200,202,204,209,210,211,212,213,214,215,219,225,226,227,228,229,230,231,234,235,237,247,250,251,252,253,255,256,258,260,263,265,266,267,270,272,274,276,278,281,282,283,286,289,291,294,295,303,304,306,309,310,311,314,315,316,318,321,322,323,324,327,331,332,341,343,345,346,347,349,350,352,353,355,356,358,359,360,361,362,363,367,371,372,374,375,376,381,383,385,388,389,390,392,395,397,398,400,401,408,409,410,411,412,414,418,420,421,422,423,424,425,427,428,429,437,438,439,440,442,444,447,448,449,450,452,453,455,457,458,459,460,463,464,465,467,469,470,472,473,474,476,480,481,482,483],differenti:[1,3,6,29,184,346,377,418,441],difficult:[213,274,361,391,464],difficulti:[294,420],diffract:[],diffus:[],digit:[2,3,190,331],dih_table1:184,dih_table2:184,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:211,dihydrid:385,dij:294,dilat:[],dim1:3,dim2:3,dim:[3,59,71,142,145,146,147,150,151,152,153,154,156,164,186,205,215,232,324,349,408,458,480,481,482],dimdim:481,dimems:273,dimens:[],dimension:[3,39,112,118,140,142,144,145,146,147,150,151,152,153,154,156,163,185,202,205,249,273,318,349,352,356,418,455,465],dimensionless:[105,121,122,124,127,129,131,136,140,318,347,428,447],dimentionless:135,dimer:[6,291,408],dimgrai:190,dimstr:[41,209],dinola:[278,309],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,187,308,476],dir1:466,dir2:466,dir:[1,3,4,8,11,12,248,272,281,305,418,420,421,453,466,481],dirac:140,direc:418,direct:[],directli:[3,6,8,9,11,12,87,113,140,187,188,189,196,221,228,232,237,273,292,310,322,324,325,326,327,349,353,361,362,363,368,370,371,377,380,383,385,397,401,412,415,423,436,453,465,466,467,473,481],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,191,214,233,276,282,285,302,306,315,316,356,360,362,363,367,374,376,377,383,384,386,393,394,405,408,409,410,414,418,419,420,421,428,438,440,441,442,453,455,456,457,466,481],disabl:[3,12,16,318,396,453,468],disadvantag:[6,209],disallow:[187,215,250],disappear:457,discard:[2,3,41,71,205,209,319,327,452,457,458],discontinu:[9,184,354,403],discourag:408,discov:[13,319],discret:[6,8,40,42,189,190,234,237],discuss:[],disk:[6,84,85,157,185,216,226,277,453],disloc:70,disord:[39,70],disp:[],dispar:422,disperion:[380,401],dispers:[3,6,7,9,162,273,346,347,371,380,401,406,412,421,439],displac:[],displace_atom:[],displace_box:59,displacemet:458,displai:[11,13,22,37,44,55,172,183,187,189,333,341,374,437],dispters:3,dissip:[6,227,234,273,315,316,369,381,389,406,407,437],dissolut:210,dist:[6,69,91,108,117,187,274,290,382,436,450,482],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,153,159,162,164,165,166,167,171,186,187,189,190,198,202,205,206,210,211,212,213,215,216,217,220,226,232,237,247,248,249,250,254,262,272,273,277,281,282,289,290,291,294,295,299,303,304,305,306,313,314,316,317,318,321,323,324,325,326,327,328,332,346,347,349,352,354,356,357,358,361,364,365,366,367,368,369,370,371,372,373,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,395,396,397,398,399,400,401,402,403,404,405,406,407,408,411,412,413,414,415,416,417,418,420,421,422,423,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,453,455,458,464,465,469,473,476,480,482],distinct:[6,219,288,346,422],distinguish:[6,86,140,240,385],distort:362,distrbut:362,distribut:[],distro:[111,374,417,418],ditto:[8,11,12,14,15,16,17,18,115,211,453],div:8,divd:117,diverg:[3,12,39,291,316,457,476,483],divid:[3,6,16,41,91,112,117,126,128,141,161,162,172,183,190,202,203,204,209,215,272,314,321,326,346,354,356,386,421,464,472,481],divis:[6,237,367,395,405,452,455,473,481],dl_poli:7,dlambda:158,dlammps_async_imd:231,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,189],dlammps_gzip:[3,12,187,189,317,455,456,460],dlammps_jpeg:[3,12,189],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,189],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,187],dlen:465,dlmp_intel_offload:[12,16],dlo:[59,186,215,277],dlvo:[7,375,447],dm_lb:237,dmax:[306,352],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,143,144,157,159,161,164,165,166,172,183,187,188,189,190,191,193,194,195,200,201,202,203,204,205,206,207,216,226,234,235,245,250,251,255,256,260,267,268,269,270,277,280,291,303,306,309,310,311,320,324,327,329,331,333,341,345,354,355,356,361,362,363,366,374,376,377,383,384,386,391,392,394,395,408,409,410,412,414,417,418,419,428,437,438,440,442,444,453,455,456,457,458,460,463,464,465,472,473,481,482,483,484],docuement:422,dodgerblu:190,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,143,144,147,152,154,158,163,164,165,166,168,170,172,177,183,184,186,187,188,189,190,193,199,200,202,205,208,209,211,212,213,215,219,221,223,226,227,230,232,234,235,237,240,246,250,251,252,253,255,256,267,268,269,270,278,279,280,284,286,289,291,306,309,311,313,314,318,321,322,323,326,327,328,329,334,335,337,338,340,345,346,347,348,349,355,356,357,362,363,364,365,366,367,369,371,372,373,375,376,377,378,380,381,382,383,384,385,387,388,389,390,392,393,394,395,396,399,400,402,403,404,406,407,408,409,410,412,418,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,442,443,444,446,447,448,450,451,452,453,455,456,457,458,459,462,463,465,466,467,468,469,472,473,476,481,485],doegenomestolif:7,doesn:[3,7,8,12,164,187,200,205,206,303,355,357,361,363,376,384,394,420,421,438,440,441,442,455,457],dof:[3,8,112,143,144,157,202,291,482],dof_per_atom:[144,202],dof_per_chunk:[144,202],doff:[355,455],doi:[6,214],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,153,163,166,186,188,189,190,193,200,209,213,215,216,230,233,237,250,251,274,286,291,318,323,324,346,347,356,361,382,412,450,452,455,459,472],domin:[1,385,469],don:[0,8,11,12,13,116,167,196,221,235,280,327,408,453,455],donadio:310,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,158,161,164,167,184,187,189,190,199,200,202,204,205,206,207,209,210,211,212,213,215,216,224,226,231,232,234,235,242,250,255,256,267,268,270,271,273,274,275,280,288,291,292,294,306,309,310,311,313,315,316,329,331,345,346,347,354,356,357,360,361,363,371,383,392,393,394,401,407,408,412,420,436,439,444,450,451,452,453,456,459,460,463,473,474,476,481,482],donor:391,dot:[141,160,196,221,229,249],doti:[367,418],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,215,224,279,327,331,345,347,360,361,367,386,390,420,421,451,455,459,463,468,481,482],dover:199,down:[3,6,7,8,11,39,71,213,234,306,322,361,385,412,454,474],downhil:[352,353],download:[5,7,8,9,11,12,13,17,231,393,419],downsid:6,downward:288,dozen:[8,12,107,193,420,421],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:243,dproduct:364,dr_ewald:[118,292],drag:[],dragforc:237,drai:[248,281],drain:[230,322,354],dramat:[59,186,210,211,212,213,215,250,306,309,310,347,361,412,452],drautz:367,draw:189,drawback:280,drawn:[187,189,190,227,450],drayleigh:[248,281],dreid:[],drfourth:105,drho:[113,362,383],drift:[6,103,105,227,228,234,235,246,289,306,464,472,476],drive:[11,12,197,213,215,229,250,272,278,291,325,356],driven:[6,176],driver:[6,12,14,15,193,224,231],drop:[3,190,381],droplet:392,drsquar:105,drude:[],dry:223,dsecriptor:393,dsf:[],dsmc:[],dstyle:277,dt_collis:237,dt_lb:237,dt_md:237,dt_srd:306,dtilt:[59,215],dtneb:469,dtqm:281,dtype:[115,211],dual:[17,306,361],dudarev:163,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,126,140,141,142,143,145,147,150,151,152,153,154,156,157,159,163,164,167,168,187,189,193,196,197,204,208,210,211,212,213,214,215,216,221,222,223,224,227,228,231,232,234,235,236,237,240,241,242,246,247,248,249,250,254,262,272,275,277,289,290,291,293,303,305,306,307,309,310,311,312,313,315,316,318,322,323,325,326,327,329,347,352,354,356,357,358,378,381,383,387,388,392,406,407,412,418,420,422,423,436,439,440,442,445,447,448,450,452,455,456,457,464,469,472,473,474,476,481,482],duffi:318,duin:[9,282,287,420,421],duke:347,dummi:[12,29,441],dump1:460,dump2:460,dump2vtk_tri:134,dump:[],dump_atom:8,dump_custom:8,dump_h5md:188,dump_modifi:[],dumpcustom:8,dumptimestep:460,dunbrack:[6,20,170,372,467],dunweg:[234,236],duplic:[2,3,14,15,16,17,18,19,41,42,165,209,228,272,455,480],dupont:[5,7,13],durat:[37,55,142,143,145,146,147,149,150,151,152,153,156,157,183,190,202,226,286,318,341,389,437],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,128,146,165,168,184,187,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,246,247,249,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,299,303,304,305,306,307,308,309,310,311,312,313,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1,286,291,319,323,324,327,357,361,377,416,455,459,460],enpub:383,enrti:12,ensembl:[],ensight:6,ensur:[3,6,140,187,200,213,226,227,250,296,317,347,367,382,405,436,438],enter:[57,154,386,469],enthalpi:[123,252,253,383,472,473,481],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,144,163,164,190,193,194,195,202,205,206,209,212,214,223,226,227,230,234,235,246,250,252,253,254,255,256,272,274,276,289,291,304,318,320,331,361,380,401,412,439,455,463,464],entireti:[395,444],entiti:[6,8,40,42,187,291],entri:[3,8,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,162,184,190,204,205,206,214,281,329,355,367,384,408,414,421,428,438,439,440,441,442],entropi:469,entry1:[38,56,190,374,439],entry2:190,entryn:190,enumer:[165,187],enumuer:6,env:361,environ:[1,3,6,11,12,16,17,18,189,228,233,272,361,362,367,374,376,384,385,418,440,452,466,481],epair:[107,190,387,391,420,421,473],epen:[420,421],epfl:[228,233],epp:380,epq:380,eps0:447,eps14:405,epsilon0:442,epsilon:[3,6,36,45,46,50,53,54,87,170,194,195,226,291,306,323,327,352,354,366,372,373,375,377,378,379,380,388,390,391,392,395,396,397,398,399,400,401,402,403,404,405,411,415,422,423,432,438,444,446,447,464,476,480],epsilon_0:448,epsilon_14:372,epsilon_:422,epsilon_d:378,epsilon_i:[388,412,422],epsilon_i_:422,epsilon_i_a:[388,422],epsilon_i_b:[388,422],epsilon_i_c:[388,422],epsilon_ij:412,epsilon_j:[388,412,422],epsilon_j_:422,epsilon_j_a:[388,422],epsilon_j_b:[388,422],epsilon_j_c:[388,422],epsilon_lj:422,epton:417,eqch:159,eqeq:[420,421],eqp:380,eqq:380,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,143,158,160,164,189,190,193,194,195,196,197,200,203,204,207,208,209,213,215,216,221,226,227,229,230,232,234,235,237,240,241,247,248,254,264,272,274,277,279,281,282,283,286,288,290,291,293,295,300,302,309,310,311,314,315,316,318,320,321,323,326,328,329,331,345,354,356,357,358,360,361,376,381,387,388,391,406,411,418,420,421,422,424,425,426,428,429,439,444,448,451,452,453,455,457,458,462,463,466,469,471,473,481,482],equat:[3,6,7,8,9,91,112,118,163,172,183,193,213,219,220,228,234,235,237,240,248,249,250,251,254,268,272,274,281,282,286,294,306,314,318,321,323,324,326,328,340,346,347,375,380,381,385,386,389,394,406,407,408,412,422,425,427,431,432,434,435,443,448,476],equi:251,equidist:249,equil:[3,282,350,462,485],equilater:465,equilibr:[3,4,5,6,7,9,59,91,164,193,200,203,212,213,226,248,250,251,268,269,281,282,283,284,314,315,316,321,376,377,420,421,451,465],equilibria:321,equilibribum:[210,211],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,147,148,171,173,213,215,226,227,228,235,237,250,254,268,281,286,290,294,295,303,306,313,314,316,321,332,334,337,340,376,408,414,476],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:199,equival:[6,12,13,59,124,125,133,138,162,166,190,204,207,213,215,226,234,250,268,278,290,291,326,381,385,440,442,455,458,463,464,473,476],equlibrium:6,equliibr:[282,284],er3:163,eradiu:[40,113,385,455],eras:[293,315],erat:[215,407],erc:377,erfc:[377,397,412],erforc:113,erg:480,erhart:[200,383,440,442],ermscal:364,ernst:9,eror:3,eros:408,erose_form:408,erot:[],errata:[440,442],erratum:323,erron:3,error:[],erta:389,ervel:[113,455],escap:[216,476],especi:[8,11,16,152,164,193,200,209,226,281,286,289,290,361,452],espresso:[9,285],essenti:[8,11,12,27,88,128,145,146,147,150,151,152,153,154,156,173,203,254,273,322,347,363,377,397,442,460,473],essex:29,establish:[87,230],estim:[1,3,6,10,12,38,41,56,91,141,199,209,220,248,306,313,346,347,352,412,421,439,469,473],esu:480,esub:408,eta:[6,237,250,281,282,284,322,384,386,388,418,441,480],eta_dot:250,eta_ij:418,eta_ji:386,etag:[40,455],etail:473,etap:250,etap_dot:250,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,142,144,145,146,147,148,150,151,152,153,154,156,158,164,166,167,168,177,187,189,190,193,199,200,201,202,204,205,206,207,210,211,215,216,224,226,227,234,250,277,288,292,318,319,327,331,345,346,354,355,356,357,359,383,384,392,405,407,416,420,421,438,440,442,450,453,455,456,457,462,464,465,469,471,472,473,476,480,481,483,485],ethernet:18,etol:[354,356,450,469],etot0:281,etot:[6,94,96,97,110,141,150,190,219,235,248,281,472,473],eu2:163,eu3:163,euler:[354,356],eulerian:199,euqat:430,europhi:237,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,144,154,162,164,187,189,190,194,195,196,197,199,201,202,203,204,205,206,207,208,215,221,227,229,230,232,233,234,235,273,279,282,293,296,300,309,310,311,320,323,326,328,329,331,346,347,352,354,361,412,418,424,426,439,450,451,453,457,458,460,462,463,464,465,469,471,473,481,482],evalut:[331,453],evan:[152,268],evanseck:[6,20,170,372,467],evapor:[],evaul:[8,354],evdwl:[107,420,421,473],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,165,166,180,184,187,190,193,194,195,200,201,202,204,205,206,207,209,210,211,213,215,216,219,232,235,248,250,251,273,286,288,291,292,302,306,314,318,321,323,327,329,339,346,352,354,356,361,366,385,386,389,392,412,422,445,455,456,458,460,461,462,464,465,467,470,472,473,474,476,485],evenli:[3,41,141,184,209,237,395,445,455],event:[],eventu:[3,6,12,15,166,282,469],ever:[54,56,233,306],evera:[375,388,422,437],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,128,152,167,187,188,189,190,191,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,220,223,224,226,228,230,231,232,237,238,246,250,251,254,271,272,273,277,278,279,280,281,282,283,284,286,288,289,291,292,294,295,306,308,309,310,311,312,313,314,317,318,319,320,321,329,331,345,347,356,357,358,361,381,382,392,405,420,421,433,449,450,451,455,457,459,460,462,463,464,469,470,471,473,481,485],everyth:[8,107],everywher:[116,399],eviri:385,evolut:[228,237,274,450],evolv:[237,274,319],ewald:[2,3,5,6,7,8,12,88,110,118,141,319,346,347,354,368,370,371,377,380,385,397,401,415,423,437,439,457],ewald_disp:380,ewalddisp:3,exact:[22,41,44,71,122,158,167,172,209,212,227,228,234,235,236,277,286,287,306,318,333,346,374,457,462,469,483,485],exactli:[3,6,12,14,17,38,41,56,59,71,91,143,148,155,164,184,194,195,204,209,215,220,227,234,235,236,251,261,262,269,273,281,306,311,312,325,361,374,381,383,389,392,395,406,412,439,457,458,465,469,481],exager:476,examin:[6,8,9,212,273],examp:[453,481],exampl:[],exce:[3,6,16,17,18,41,58,71,166,202,205,206,209,213,215,220,223,250,273,297,298,306,354,361,455,481],exceed:[3,41,59,209,215,250,306,463],excel:385,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,164,168,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,190,193,196,202,203,204,208,209,213,215,222,225,226,229,232,234,236,250,251,252,253,254,255,256,257,261,262,265,267,268,269,270,274,283,284,291,293,294,303,306,309,311,312,318,322,329,331,332,333,334,335,336,337,340,341,342,346,347,349,351,355,356,357,359,360,361,362,363,365,368,369,370,371,372,373,374,375,376,377,379,380,381,383,384,385,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,407,409,413,414,415,417,420,421,422,423,429,437,438,439,440,441,442,444,446,447,448,450,452,453,455,457,458,460,463,464,465,466,467,469,473,476,480,481,482,484],excess:385,exchang:[2,3,6,8,9,61,62,193,199,200,226,234,283,291,314,318,321,346,361,385,470],exchange:346,excit:[9,385],exclud:[3,6,9,12,16,17,63,71,112,140,144,151,152,168,187,202,205,210,211,238,246,276,289,291,313,324,329,354,355,357,369,389,392,406,407,412,436,467],exclus:[1,3,9,12,16,87,361,376,412,464,474],excurs:450,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,165,189,231,285,331,345,348,360,451,453,463,466,469,481],exemplari:227,exemplifi:385,exert:[6,232,235,286,325,326,327,347],exhaust:[199,360,481],exhibit:[250,353,385,464],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,164,165,183,188,189,190,193,198,208,211,213,216,226,276,277,279,329,332,334,335,337,341,350,355,361,392,420,445,451,453,455,456,457,466,467,468,481,482,483],exit:[2,3,11,12,41,57,187,209,345,360,453,454,463,472,481],exlanatori:3,exp:[],expand:[],expans:[12,140,187,466],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,145,156,162,184,209,221,226,228,247,272,278,280,281,286,291,329,347,357,374,408,412,450,453,455,457,460,464,469,481],expens:[6,10,71,190,272,276,291,318,329,346,347,357,361,453],experi:[6,13,15,17,208,216,231,240,249,278,290,291,352,356,381,412,464,469],experienc:[6,12,239,240],experiment:[346,361,469],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,144,152,184,187,189,190,193,202,203,207,209,211,213,215,250,272,280,291,303,329,331,345,346,349,355,356,360,366,383,395,429,444,448,453,456,457,460,462,465,476,481,485],explan:[3,6,59,113,140,187,202,249,272,392,449,452,453,455,464],explanatori:[3,8,117,187,201,202,204,205,206,291,355,452,481],explantori:[3,287],explic:411,explicit:[6,9,11,22,44,77,87,113,116,158,172,194,195,215,297,298,333,351,363,364,367,372,374,383,385,396,406,443,449,452,456,459],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,142,151,154,162,164,170,171,173,174,175,176,178,179,181,182,184,187,190,196,205,208,215,222,225,227,229,234,250,252,253,254,255,256,257,265,267,268,270,280,281,283,291,293,294,309,311,312,318,322,332,334,335,336,337,340,342,355,361,362,363,365,368,369,370,371,372,373,374,375,376,377,378,380,381,382,383,384,386,387,388,389,390,391,392,395,396,397,398,399,400,401,402,403,404,405,406,409,412,413,414,415,417,422,423,429,430,431,432,433,434,435,437,438,439,440,441,442,443,444,446,447,448,455,457,464,465,467,468,474,476],explictli:[16,468],exploit:[9,15,17,274],explor:[118,163],expon:[3,282,284,383,388,391,405,411,423],exponenti:[87,418,438,448,469,481],expos:11,exposit:[199,381,382],express:[6,140,150,164,194,195,213,247,272,282,318,324,331,367,383,385,399,408,428,437,481],expressiont:367,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,193,196,197,200,207,208,214,217,221,224,225,226,228,229,230,232,234,236,248,250,254,262,272,273,289,290,291,293,295,300,303,305,309,310,311,312,313,315,316,318,320,323,327,328,388,408,421,422,428,472,473],extent:[1,3,41,45,57,71,162,166,187,198,205,209,232,325,328,346,349,363,424,426,439,452,455,458],exterior:[3,6,327],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,142,143,145,147,150,151,152,153,154,156,157,163,164,165,166,170,190,204,209,211,250,279,280,281,291,306,354,355,358,359,380,389,392,395,408,412,452,453,455,458,467,476,481],extract:[3,6,11,13,36,63,87,107,115,117,119,194,195,284,356,377,386,408,428,453,460,472],extract_atom:11,extract_comput:[11,453],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,189,213,215,250,316,385,441,476],extrema:405,extrins:199,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[160,320],f_a:[440,441,442],f_ave:117,f_c:441,f_f:442,f_fix_id:281,f_harm:316,f_i:418,f_id:[6,71,117,119,187,193,201,202,203,204,205,206,207,245,308,320,473,481],f_ij:418,f_indent:207,f_int:315,f_jj:91,f_k:418,f_langevin:318,f_max:[281,286],f_msst:248,f_r:[235,440,441,442],f_sigma:367,f_solid:316,f_ss:6,f_temp:235,face:[3,6,57,59,71,152,162,166,198,205,206,323,325,326,327,328,349,388,408,422,455,458],face_threshold:162,facet:162,facil:[0,12],facilit:[6,13],fact:[6,8,16,228,306,316,389,467],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,140,158,163,166,170,181,187,189,190,194,195,203,209,213,215,216,226,231,234,236,237,248,250,251,254,274,278,290,294,296,298,306,310,314,321,322,323,327,337,347,349,361,363,364,367,368,370,372,377,378,379,381,385,389,392,396,397,408,412,414,415,421,423,429,438,443,452,455,458,459,464,467,469,470,473,476,480,481],factori:[3,453],factoriz:346,fail:[3,11,12,59,168,213,216,346,354,356,379,421,453],failur:[121,425],fairli:[11,412,464,469],faken:73,falcon:231,fall:[3,6,190,204,277,453],fals:[86,329,331,481],fame:8,famili:452,familiar:[0,11],fan:418,far:[3,6,12,17,57,59,61,86,187,190,191,209,210,211,213,216,250,272,290,291,306,323,334,337,352,356,357,444,453,455,460,473],farago:234,farrel:[440,442],farther:187,fashion:[6,8,41,71,164,190,193,194,195,200,205,209,211,216,226,228,232,247,248,250,252,253,254,255,256,264,267,268,269,270,280,281,283,291,295,299,305,308,316,318,322,323,324,326,328,356,392,406,458,467,481,484],fasolino:394,fast:[6,7,9,12,13,17,39,187,259,281,319,346,347,369,406,407,437,439,457,462,464,473,482,485],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,142,151,170,171,173,174,175,176,178,179,181,182,184,187,190,193,196,208,209,222,225,229,233,234,250,252,253,254,255,256,257,265,267,268,270,278,282,283,291,293,294,306,309,311,313,315,318,322,332,334,335,336,337,340,342,346,347,358,359,361,362,363,365,367,368,369,370,371,372,373,374,375,376,377,380,381,383,384,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,409,413,414,415,417,422,423,429,437,438,439,440,441,442,444,446,447,448,450,464,468,476],fastest:[6,14,17,152,205,318,319,361,452],fatal:[3,472],fault:[70,421],faulti:12,fava:388,favor:212,favorit:7,fbmc:313,fcc:[],fcm:[264,481],fdirect:219,fdotr:393,fdti:87,fe2:163,fe3:163,fe_md_boundari:199,featu:8,featur:[],fecr:383,feedback:[7,231],feel:[7,231,232,240,272,327,329,356,412],felling:410,felt:327,femtosecond:480,fene:[],fennel:[377,397],fep:[],ferguson:[6,170,467],fermi:[1,12,15,150,361,442],fermion:[9,385],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,191,201,202,203,204,205,206,207,235,250,277,280,282,294,320,346,354,355,356,363,452,455,460,464,466,474,481,483],fewer:[1,3,11,15,16,61,240,464],fewest:3,fextern:224,feynman:274,fff:453,ffield:[376,386,420,421],ffmpeg:[3,12,189],ffplai:189,fft:[1,3,7,12,14,15,88,109,110,141,273,346,347,464],fft_inc:[12,347],fft_lib:12,fft_path:12,fftbench:[346,474],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,196,197,221,224,228,274,290,377,397,401,436],field1:[456,460],field2:456,field:[],fifth:[303,414],figur:[1,3,8,11,12,281,452,453],fij:380,file0:272,file1:[11,13,272,317,331,355,460,462,466],file2:[11,13,317,331,355,460,462,466],file:[],file_from:188,filenam:[3,12,13,38,41,56,184,187,189,190,191,199,202,203,204,205,206,207,209,214,272,276,279,282,283,284,287,288,291,292,317,318,343,344,345,356,362,363,367,377,383,384,386,394,408,409,410,414,418,419,420,421,428,438,439,440,441,442,451,452,453,456,457,462,466,473,481,483,484,485],filennam:462,filep:[3,187,190,457,462,485],filepo:288,fill:[7,164,189,277,318,349,357,367,421,458],filter:[190,199],final_integr:8,final_integrate_respa:8,finchham:[6,146,379],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,167,184,191,200,212,213,223,226,249,272,278,286,290,352,354,356,357,377,392,397,401,408,437,439,476,481],find_custom:8,fine:[16,17,168,196,221,316,357,361,481],finer:[140,164,481],finest:346,finger:[164,186,247,458],finish:[6,11,41,209,331,343,345,346,358,360,361,444,460,481,482],finit:[],finni:[7,383,437],finvers:219,fiorin:[9,214],fire:[352,353,354,356,469],firebrick:190,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,149,152,158,160,162,163,165,166,167,171,184,187,188,189,190,191,193,200,202,203,204,205,206,207,209,212,215,226,227,232,237,247,248,249,250,272,274,279,280,281,283,288,291,294,295,303,304,306,307,308,315,316,317,318,320,324,329,331,332,338,349,354,355,356,357,360,361,362,363,366,367,368,370,372,374,376,377,383,385,386,389,390,393,394,396,397,401,406,407,408,410,412,414,418,420,421,428,436,438,439,440,441,442,450,451,452,453,455,456,457,460,462,464,467,468,469,472,473,476,481,482,483,485],fischer:[6,9,19,20,170,372,467],fit:[3,6,9,12,38,56,184,290,306,363,367,394,408,412,432,439,441,463,481],five:[73,150,281,355,367,409,455,469],fix:[],fix_adapt:[158,195,405],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,200,277],fix_evapor:200,fix_flux:199,fix_gcmc:[200,355],fix_gl:228,fix_gld:228,fix_grav:277,fix_id:[3,213,248,250,252,253,254,255,256,278,281],fix_modifi:[],fix_mov:[186,324],fix_nh:8,fix_npt:228,fix_nvt:[200,226],fix_poem:[3,6],fix_pour:[3,216],fix_qbmsst:9,fix_qeq:[3,376],fix_rattl:294,fix_reax_bond:420,fix_rigid:[240,366],fix_saed_vtk:292,fix_setforc:8,fix_shak:294,fix_srd:3,fix_styl:254,fix_temp_rescal:312,fixedpoint:[213,250],fixextern:224,fixid:199,fji:380,flag1:[218,359],flag2:[218,359],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,159,163,167,187,189,190,191,207,212,214,218,231,234,238,240,246,247,273,280,291,303,305,306,313,317,326,329,344,347,355,359,360,361,363,391,396,408,436,450,452,453,455,456,457,459,460,461,465,481],flag_buck:371,flag_coul:[371,380,401],flag_lj:[380,401],flagfld:[369,406,407],flaghi:[3,369,406,407],flaglog:[369,406,407],flagn:218,flagvf:[369,406,407],flat:[6,318,323,324,328],flavor:[2,7,12],fld:[9,323,369,406,407],flen:364,flex_press:364,flexibl:[3,6,8,165,189,202,205,214,228,251,314,321,385,441,473],flip:[3,6,215,250,325,326],floor:481,flop:12,floralwhit:190,flow:[],fluctuat:[6,64,87,213,226,227,234,237,250,254,272,273,316,318,340],fluid:[],fluid_veloc:241,flush:[3,190,472],flux:[],flv:189,fly:[7,9,12,41,189,193,199,216,219,291,294,319,367,473,476],fmackai:9,fmag:217,fmass:274,fmax:[354,473],fmomentum:219,fmsec:[2,190,234,235,247,250,278,291,309,310,464,475,480,482],fname:345,fno:12,fnorm:[354,473],fnpt:219,fnvt:219,foce:392,fock:364,focu:294,fogarti:[9,284,421],foil:[140,272,428],fold:[304,464],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,143,144,150,152,157,160,162,164,165,170,173,174,175,176,178,179,181,182,184,187,188,189,190,193,199,200,201,202,203,204,205,206,207,209,214,215,216,219,220,224,226,227,228,231,233,234,235,237,240,248,250,254,255,256,267,268,270,273,274,276,279,280,281,282,284,286,288,290,291,292,294,308,309,310,311,314,315,316,317,318,320,321,329,330,334,335,336,337,340,342,344,349,351,354,355,356,361,362,363,364,365,366,367,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,425,427,428,429,430,431,432,433,434,435,436,438,439,440,441,442,443,444,446,447,448,450,452,453,455,456,457,458,460,462,463,464,467,469,470,471,476,481,482,484],foo:[4,8,11,12,187,189,224,453,466,481],foot:6,footprint:[12,361],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:240,forcefield:[290,391],forcegroup:237,forcezero:352,ford:380,forestgreen:190,forev:71,forget:[235,476],forgiv:250,fork:[12,187],form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,158,159,168,172,190,193,194,195,211,227,228,234,236,240,247,268,273,284,286,290,291,318,323,327,332,333,340,351,353,355,356,363,364,367,374,383,385,387,391,392,396,408,410,414,415,418,420,421,422,428,429,437,439,440,441,442,447,449,452,453,455,460,465,472,476,481],formal:[6,78,80,91,227,228,234,250,274,306,314],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,172,184,187,188,189,190,191,202,204,205,206,207,209,211,273,276,280,282,284,287,291,292,302,317,318,329,330,333,351,355,356,362,363,367,374,383,386,396,408,410,419,420,421,423,428,439,445,452,453,455,456,457,460,471,472,473,481,483],former:[6,12,16,39,41,190,209,318,322,367,369,461,467,481],formerli:[7,13],formul:[1,40,64,141,196,221,234,250,268,282,284,290,294,317,346,363,367,383,385,388,408,417],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,163,164,169,171,172,183,187,194,195,196,197,202,203,204,207,208,215,221,229,230,232,234,235,247,272,273,279,288,293,300,304,306,309,310,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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 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 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 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 temp command","compute temp/asphere 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/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 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/sphere command","fix nphug command","fix npt/asphere 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/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 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 fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style 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 meam command","pair_style meam/spline","pair_style meam/sw/spline","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 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_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":210,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,144,152,153,157,163,164,167,169,183,185,186,187,189,190,191,192,194,195,196,198,199,200,202,205,206,207,210,211,213,214,215,216,220,223,226,227,232,234,235,236,237,238,240,245,248,250,251,254,268,269,273,274,277,278,279,280,281,283,286,288,289,291,292,306,308,313,314,315,316,319,321,323,325,329,341,344,346,347,349,350,352,353,355,357,358,359,361,364,367,369,385,406,407,412,420,421,436,437,450,451,452,455,456,458,460,462,463,464,467,469,471,472,473,474,475,480,482,483,484],"function":481,"long":[368,370,371,372,373,377,379,380,397,401,405,415,423],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[194,195],addforc:196,addit:[12,13],addtorqu:197,adiabat:6,adjust_dt:296,adp:362,airebo:363,alloi:383,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:198,arrai:6,aspher:[6,82,143,252,255,258,259,267],atc:[9,199],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,162,198,200,201,280,481],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:208,awpmd:[9,364],balanc:[41,209],barostat:6,basal:67,beck:365,berendsen:[278,309],between:6,binary2txt:13,bodi:[6,8,42,68,260,366],bond:[8,13,69,210,211,212,287],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:367,born:[368,379],boundari:[7,57],box:[6,58,213],brownian:369,buck:[370,371,379],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,170,372,405],chunk:[6,66,71,75,90,93,104,106,114,144,159,161,202],citat:7,class2:[21,43,171,332,373],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[323,375,447],colvar:[9,13,214],com:[74,75,145],comb3:376,comb:[283,376],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,481],compute_modifi:102,condit:7,conduct:[6,314],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:203,cosin:[23,24,25,26,27,28,173],cossq:334,coul:[368,370,371,372,373,377,378,379,390,397,401,405,415,423],coupl:6,creat:211,create_atom:164,create_bond:165,create_box:166,createatom:13,creation:7,csld:310,csvr:310,cubic:399,cuda:[9,14,109,112,142,151,196,208,222,225,229,250,257,293,294,309,311,322,368,370,372,373,383,389,390,397,398,400,403,413,438,440],custom:8,cut:[49,364,370,373,377,380,385,387,397,398,405,411,415],cvff:335,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[377,397],deform:[147,148,215],delete_atom:167,delete_bond:168,delta:24,deposit:216,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,9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06,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,463],run_styl:464,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,423],self:305,serial:11,set:[6,465],setforc:293,setvel:300,shake:294,share:[11,12],shell:[6,466],shield:282,shift:[26,27,48,49,173],simpl:31,simul:6,size:6,slater:282,slice:119,sllod:[268,269],small:291,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,295,296,297,298,299,300,302,424,425,426,427],smooth:[403,404],sna:140,snad:140,snap:428,snapshot:6,snav:140,soft:[405,429],solver:2,sourc:7,spatial:[205,206],spc:6,speci:288,special:[7,412,481],special_bond:467,sph:[9,430,431,432,433,434,435],sphere:[84,85,157,206,240,253,256,265,270],spheric:6,spline:[409,410],spring:[303,304,305,316],squar:28,srd:[306,328],srp:436,standard:9,start:[12,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328],state:308,stationari:244,stop:[194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328],store:[307,308],strategi:1,streitz:377,stress:141,structur:2,style:[1,2,6,8],submit:8,suffix:468,summari:6,swap:[200,212],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485],system:6,tabl:[0,6,38,56,184,439,440],tad:469,taitwat:[434,435],temp:[142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,309,310,311,312],temper:470,temperatur:6,tersoff:[440,441,442],test:11,tfmc:313,thermal:[6,314],thermo:[6,471],thermo_modifi:472,thermo_styl:473,thermodynam:[6,8],thermostat:6,thole:443,time:[6,207],timer:474,timestep:475,tip3p:6,tip4p:[6,377,397,401,405],tip:12,tlsph:425,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:317,tool:13,torqu:159,transform:219,tri:[266,444],tri_surfac:426,triangle_mesh_vertic:134,triclin:6,tstat:381,ttm:318,tune:319,type:7,ulsph:427,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:342,uncomput:477,undump:478,unfix:479,unit:480,user:[9,12,14,16,18],vacf:160,valu:[6,481],variabl:[6,8,481],variou:1,vcm:161,vector:[6,320,481],veloc:482,version:[0,5,12],via:12,vim:13,viscos:[6,321],viscou:[241,322],visual:6,vol:139,voronoi:162,vtk:292,wall:[6,323,324,325,326,327,328],wall_surfac:302,warn:3,water:6,weight:204,what:[7,12],wolf:[368,377],wrapper:11,write:6,write_data:483,write_dump:484,write_restart:485,xmgrace:13,xmovi:13,xrd:163,yukawa:[446,447],zbl:[442,448]}})
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