diff --git a/doc/Manual.txt b/doc/Manual.txt index f47482fdf2..b0857e6c32 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: // comment + :numbered: Section_intro Section_start @@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` // comment -* :ref:`search` // comment +* :ref:`genindex` +* :ref:`search` END_RST --> diff --git a/doc/Section_example.html b/doc/Section_example.html index 9a94416793..779318d584 100644 --- a/doc/Section_example.html +++ b/doc/Section_example.html @@ -1,17 +1,143 @@ - -
Previous Section - LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - Next Section -
+ + + + + + + + + 7. Example problems — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+ + + - - -
- -

7. Example problems -

-

The LAMMPS distribution includes an examples sub-directory with + +

+
+
+ +
+ + + +
+
+
+ +
+

7. Example problems

+

The LAMMPS distribution includes an examples sub-directory with several sample problems. Each problem is in a sub-directory of its own. Most are 2d models so that they run quickly, requiring at most a couple of minutes to run on a desktop machine. Each problem has an @@ -20,111 +146,256 @@ input script (in.*) and produces a log file (log.*) and dump file coordinates as additional input. A few sample log file outputs on different machines and different numbers of processors are included in the directories to compare your answers to. E.g. a log file like -log.crack.foo.P means it ran on P processors of machine "foo". -

-

For examples that use input data files, many of them were produced by -Pizza.py or setup tools described in the -Additional Tools section of the LAMMPS -documentation and provided with the LAMMPS distribution. -

-

If you uncomment the dump command in the input script, a +log.crack.foo.P means it ran on P processors of machine “foo”.

+

For examples that use input data files, many of them were produced by +Pizza.py or setup tools described in the +Additional Tools section of the LAMMPS +documentation and provided with the LAMMPS distribution.

+

If you uncomment the dump command in the input script, a text dump file will be produced, which can be animated by various -visualization programs. It can -also be animated using the xmovie tool described in the Additional -Tools section of the LAMMPS documentation. -

-

If you uncomment the dump image command in the input +visualization programs. It can +also be animated using the xmovie tool described in the Additional Tools section of the LAMMPS documentation.

+

If you uncomment the dump image command in the input script, and assuming you have built LAMMPS with a JPG library, JPG snapshot images will be produced when the simulation runs. They can be quickly post-processed into a movie using commands described on the -dump image doc page. -

-

Animations of many of these examples can be viewed on the Movies -section of the LAMMPS WWW Site. -

-

These are the sample problems in the examples sub-directories: -

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
balance dynamic load balancing, 2d system
body body particles, 2d system
colloid big colloid particles in a small particle solvent, 2d system
comb models using the COMB potential
crack crack propagation in a 2d solid
cuda use of the USER-CUDA package for GPU acceleration
dipole point dipolar particles, 2d system
dreiding methanol via Dreiding FF
eim NaCl using the EIM potential
ellipse ellipsoidal particles in spherical solvent, 2d system
flow Couette and Poiseuille flow in a 2d channel
friction frictional contact of spherical asperities between 2d surfaces
gpu use of the GPU package for GPU acceleration
hugoniostat Hugoniostat shock dynamics
indent spherical indenter into a 2d solid
intel use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor
kim use of potentials in Knowledge Base for Interatomic Models (KIM)
line line segment particles in 2d rigid bodies
meam MEAM test for SiC and shear (same as shear examples)
melt rapid melt of 3d LJ system
micelle self-assembly of small lipid-like molecules into 2d bilayers
min energy minimization of 2d LJ melt
msst MSST shock dynamics
nb3b use of nonbonded 3-body harmonic pair style
neb nudged elastic band (NEB) calculation for barrier finding
nemd non-equilibrium MD of 2d sheared system
obstacle flow around two voids in a 2d channel
peptide dynamics of a small solvated peptide chain (5-mer)
peri Peridynamic model of cylinder impacted by indenter
pour pouring of granular particles into a 3d box, then chute flow
prd parallel replica dynamics of vacancy diffusion in bulk Si
qeq use of the QEQ pacakge for charge equilibration
reax RDX and TATB models using the ReaxFF
rigid rigid bodies modeled as independent or coupled
shear sideways shear applied to 2d solid, with and without a void
snap NVE dynamics for BCC tantalum crystal using SNAP potential
srd stochastic rotation dynamics (SRD) particles as solvent
tad temperature-accelerated dynamics of vacancy diffusion in bulk Si
tri triangular particles in rigid bodies -
- -

Here is how you might run and visualize one of the sample problems: -

-
cd indent
+dump image doc page.

+
Animations of many of these examples can be viewed on the Movies
+section of the LAMMPS WWW Site.

+
These are the sample problems in the examples sub-directories:

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balancedynamic load balancing, 2d system
bodybody particles, 2d system
colloidbig colloid particles in a small particle solvent, 2d system
combmodels using the COMB potential
crackcrack propagation in a 2d solid
cudause of the USER-CUDA package for GPU acceleration
dipolepoint dipolar particles, 2d system
dreidingmethanol via Dreiding FF
eimNaCl using the EIM potential
ellipseellipsoidal particles in spherical solvent, 2d system
flowCouette and Poiseuille flow in a 2d channel
frictionfrictional contact of spherical asperities between 2d surfaces
gpuuse of the GPU package for GPU acceleration
hugoniostatHugoniostat shock dynamics
indentspherical indenter into a 2d solid
inteluse of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor
kimuse of potentials in Knowledge Base for Interatomic Models (KIM)
lineline segment particles in 2d rigid bodies
meamMEAM test for SiC and shear (same as shear examples)
meltrapid melt of 3d LJ system
micelleself-assembly of small lipid-like molecules into 2d bilayers
minenergy minimization of 2d LJ melt
msstMSST shock dynamics
nb3buse of nonbonded 3-body harmonic pair style
nebnudged elastic band (NEB) calculation for barrier finding
nemdnon-equilibrium MD of 2d sheared system
obstacleflow around two voids in a 2d channel
peptidedynamics of a small solvated peptide chain (5-mer)
periPeridynamic model of cylinder impacted by indenter
pourpouring of granular particles into a 3d box, then chute flow
prdparallel replica dynamics of vacancy diffusion in bulk Si
qequse of the QEQ pacakge for charge equilibration
reaxRDX and TATB models using the ReaxFF
rigidrigid bodies modeled as independent or coupled
shearsideways shear applied to 2d solid, with and without a void
snapNVE dynamics for BCC tantalum crystal using SNAP potential
srdstochastic rotation dynamics (SRD) particles as solvent
tadtemperature-accelerated dynamics of vacancy diffusion in bulk Si
tritriangular particles in rigid bodies

+
vashishta: models using the Vashishta potential

+
Here is how you might run and visualize one of the sample problems:

+
cd indent
 cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
-lmp_linux -in in.indent            # run the problem 
-

-
Running the simulation produces the files dump.indent and
-log.lammps.  You can visualize the dump file as follows:
-

-
../../tools/xmovie/xmovie -scale dump.indent 
-

-
If you uncomment the dump image line(s) in the input
+lmp_linux -in in.indent            # run the problem
+
+
+

Running the simulation produces the files dump.indent and +log.lammps. You can visualize the dump file as follows:

+
../../tools/xmovie/xmovie -scale dump.indent
+
+
+

If you uncomment the dump image line(s) in the input script a series of JPG images will be produced by the run. These can be viewed individually or turned into a movie or animated by tools like ImageMagick or QuickTime or various Windows-based tools. See the -dump image doc page for more details. E.g. this +dump image doc page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a -browser. -

-
% convert -loop 1 *.jpg foo.gif 
-
-
- -

There is also a COUPLE directory with examples of how to use LAMMPS as +browser.

+
% convert -loop 1 *.jpg foo.gif
+
+
+
+

There is also a COUPLE directory with examples of how to use LAMMPS as a library, either by itself or in tandem with another code or library. -See the COUPLE/README file to get started. -

-

There is also an ELASTIC directory with an example script for +See the COUPLE/README file to get started.

+

There is also an ELASTIC directory with an example script for computing elastic constants at zero temperature, using an Si example. See -the ELASTIC/in.elastic file for more info. -

-

There is also an ELASTIC_T directory with an example script for +the ELASTIC/in.elastic file for more info.

+

There is also an ELASTIC_T directory with an example script for computing elastic constants at finite temperature, using an Si example. See -the ELASTIC_T/in.elastic file for more info. -

-

There is also a USER directory which contains subdirectories of +the ELASTIC_T/in.elastic file for more info.

+

There is also a USER directory which contains subdirectories of user-provided examples for user packages. See the README files in those directories for more info. See the -Section_start.html file for more info about user -packages. -

- +Section_start.html file for more info about user +packages.

+
+ + +
+
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/fix_gcmc.html b/doc/fix_gcmc.html index 21864923c1..84b770acfb 100644 --- a/doc/fix_gcmc.html +++ b/doc/fix_gcmc.html @@ -1,369 +1,505 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
+ + + + + + + + + fix gcmc command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+ + + - - -
- -

fix gcmc command -

-

Syntax: -

-
fix ID group-ID gcmc N X M type seed T mu displace keyword values ... 
-
- -

Examples: -

-
fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
+  intra_energy value = intramolecular energy (energy units)
+  tfac_insert value = scale up/down temperature of inserted atoms (unitless)
+
+
+
+

Examples

+
fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
 fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
-fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk 
-
-

Description: -

-

This fix performs grand canonical Monte Carlo (GCMC) exchanges of +fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk +

+
+
+
+

Description

+

This fix performs grand canonical Monte Carlo (GCMC) exchanges of atoms or molecules of the given type with an imaginary ideal gas reservoir at the specified T and chemical potential (mu) as discussed in -(Frenkel). If used with the fix nvt command, +(Frenkel). If used with the fix nvt command, simulations in the grand canonical ensemble (muVT, constant chemical potential, constant volume, and constant temperature) can be performed. Specific uses include computing isotherms in microporous -materials, or computing vapor-liquid coexistence curves. -

-

Every N timesteps the fix attempts a number of GCMC exchanges (insertions +materials, or computing vapor-liquid coexistence curves.

+

Every N timesteps the fix attempts a number of GCMC exchanges (insertions or deletions) of gas atoms or molecules of the given type between the simulation cell and the imaginary reservoir. It also attempts a number of Monte Carlo moves (translations and molecule rotations) of gas of the given type -within the simulation cell or region. The average number of +within the simulation cell or region. The average number of attempted GCMC exchanges is X. The average number of attempted MC moves is M. M should typically be chosen to be approximately equal to the expected number of gas atoms or molecules -of the given type within the simulation cell or region, +of the given type within the simulation cell or region, which will result in roughly one -MC translation per atom or molecule per MC cycle. -

-

For MC moves of molecular gasses, rotations and translations are each +MC translation per atom or molecule per MC cycle.

+

For MC moves of molecular gasses, rotations and translations are each attempted with 50% probability. For MC moves of atomic gasses, translations are attempted 100% of the time. For MC exchanges of either molecular or atomic gasses, deletions and insertions are each -attempted with 50% probability. -

-

All inserted particles are always assigned to two groups: the default group -"all" and the group specified in the fix gcmc command (which can also -be "all"). In addition, particles are also added to any groups specified -by the group and grouptype keywords. +attempted with 50% probability.

+

All inserted particles are always assigned to two groups: the default group +“all” and the group specified in the fix gcmc command (which can also +be “all”). In addition, particles are also added to any groups specified +by the group and grouptype keywords. If inserted particles are individual atoms, they are -assigned the atom type given by the type argument. If they are molecules, -the type argument has no effect and must be set to zero. Instead, -the type of each atom in the inserted molecule is specified -in the file read by the molecule command. -

-

This fix cannot be used to perform MC insertions of gas atoms or +assigned the atom type given by the type argument. If they are molecules, +the type argument has no effect and must be set to zero. Instead, +the type of each atom in the inserted molecule is specified +in the file read by the molecule command.

+

This fix cannot be used to perform MC insertions of gas atoms or molecules other than the exchanged type, but MC deletions, translations, and rotations can be performed on any atom/molecule in the fix group. All atoms in the simulation cell can be moved using regular time integration translations, e.g. via -fix_nvt, resulting in a hybrid GCMC+MD simulation. A +fix_nvt, resulting in a hybrid GCMC+MD simulation. A smaller-than-usual timestep size may be needed when running such a hybrid simulation, especially if the inserted molecules are not well -equilibrated. -

-

This command may optionally use the region keyword to define an -exchange and move volume. The specified region must have been -previously defined with a region command. It must be -defined with side = in. Insertion attempts occur only within the -specified region. For non-rectangular regions, random trial +equilibrated.

+

This command may optionally use the region keyword to define an +exchange and move volume. The specified region must have been +previously defined with a region command. It must be +defined with side = in. Insertion attempts occur only within the +specified region. For non-rectangular regions, random trial points are generated within the rectangular bounding box until a point is found that lies inside the region. If no valid point is generated after 1000 trials, no insertion is performed, but it is counted as an attempted insertion. -Move and deletion attempt candidates are selected +Move and deletion attempt candidates are selected from gas atoms or molecules within the region. If there are no candidates, no move or deletion is performed, but it is counted as an attempt move -or deletion. If an attempted move places the atom or molecule center-of-mass outside -the specified region, a new attempted move is generated. This process is repeated -until the atom or molecule center-of-mass is inside the specified region. -

-

If used with fix_nvt, the temperature of the imaginary +or deletion. If an attempted move places the atom or molecule center-of-mass outside +the specified region, a new attempted move is generated. This process is repeated +until the atom or molecule center-of-mass is inside the specified region.

+

If used with fix_nvt, the temperature of the imaginary reservoir, T, should be set to be equivalent to the target temperature -used in fix_nvt. Otherwise, the imaginary reservoir +used in fix_nvt. Otherwise, the imaginary reservoir will not be in thermal equilibrium with the simulation cell. Also, it is important that the temperature used by fix nvt be dynamic, -which can be achieved as follows: -

-
compute mdtemp mdatoms temp 
+which can be achieved as follows:

+
compute mdtemp mdatoms temp
 compute_modify mdtemp dynamic yes
 fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
-fix_modify mdnvt temp mdtemp 
-

-
Note that neighbor lists are re-built every timestep that this fix is
+fix_modify mdnvt temp mdtemp
+
+ +

Note that neighbor lists are re-built every timestep that this fix is invoked, so you should not set N to be too small. However, periodic rebuilds are necessary in order to avoid dangerous rebuilds and missed interactions. Specifically, avoid performing so many MC translations per timestep that atoms can move beyond the neighbor list skin -distance. See the neighbor command for details. -

-

When an atom or molecule is to be inserted, its +distance. See the neighbor command for details.

+

When an atom or molecule is to be inserted, its coordinates are chosen at a random position within the current simulation cell or region, and new atom velocities are randomly chosen from the specified temperature distribution given by T. The effective temperature for new atom velocities can be increased or decreased -using the optional keyword tfac_insert (see below). Relative +using the optional keyword tfac_insert (see below). Relative coordinates for atoms in a molecule are taken from the template molecule provided by the user. The center of mass of the molecule is placed at the insertion point. The orientation of the molecule -is chosen at random by rotating about this point. -

-

Individual atoms are inserted, unless the mol keyword is used. It -specifies a template-ID previously defined using the -molecule command, which reads a file that defines the +is chosen at random by rotating about this point.

+

Individual atoms are inserted, unless the mol keyword is used. It +specifies a template-ID previously defined using the +molecule command, which reads a file that defines the molecule. The coordinates, atom types, charges, etc, as well as any bond/angle/etc and special neighbor information for the molecule can -be specified in the molecule file. See the molecule +be specified in the molecule file. See the molecule command for details. The only settings required to be in this file -are the coordinates and types of atoms in the molecule. -

-

When not using the mol keyword, you should ensure you do not delete +are the coordinates and types of atoms in the molecule.

+

When not using the mol keyword, you should ensure you do not delete atoms that are bonded to other atoms, or LAMMPS will soon generate an error when it tries to find bonded neighbors. LAMMPS will warn you if any of the atoms eligible for deletion have a non-zero -molecule ID, but does not check for this at the time of deletion. -

-

If you wish to insert molecules via the mol keyword, that will have -their bonds or angles constrained via SHAKE, use the shake keyword, -specifying as its value the ID of a separate fix -shake command which also appears in your input script. -

-

Optionally, users may specify the maximum rotation angle for -molecular rotations using the maxangle keyword and specifying +molecule ID, but does not check for this at the time of deletion.

+

If you wish to insert molecules via the mol keyword, that will have +their bonds or angles constrained via SHAKE, use the shake keyword, +specifying as its value the ID of a separate fix shake command which also appears in your input script.

+

Optionally, users may specify the maximum rotation angle for +molecular rotations using the maxangle keyword and specifying the angle in degrees. Rotations are performed by generating a random point on the unit sphere and a random rotation angle on the range [0,maxangle). The molecule is then rotated by that angle about an -axis passing through the molecule center of mass. The axis is parallel -to the unit vector defined by the point on the unit sphere. +axis passing through the molecule center of mass. The axis is parallel +to the unit vector defined by the point on the unit sphere. The same procedure is used for randomly rotating molecules when they -are inserted, except that the maximum angle is 360 degrees. -

-

Note that fix GCMC does not use configurational bias -MC or any other kind of sampling of intramolecular degrees of freedom. -Inserted molecules can have different orientations, but they will all -have the same intramolecular configuration, -which was specified in the molecule command input. -

-

For atomic gasses, inserted atoms have the specified atom type, but -deleted atoms are any atoms that have been inserted or that belong -to the user-specified fix group. For molecular gasses, exchanged -molecules use the same atom types as in the template molecule +are inserted, except that the maximum angle is 360 degrees.

+

Note that fix GCMC does not use configurational bias +MC or any other kind of sampling of intramolecular degrees of freedom. +Inserted molecules can have different orientations, but they will all +have the same intramolecular configuration, +which was specified in the molecule command input.

+

For atomic gasses, inserted atoms have the specified atom type, but +deleted atoms are any atoms that have been inserted or that belong +to the user-specified fix group. For molecular gasses, exchanged +molecules use the same atom types as in the template molecule supplied by the user. In both cases, exchanged -atoms/molecules are assigned to two groups: the default group "all" -and the group specified in the fix gcmc command (which can also be -"all"). -

-

The gas reservoir pressure can be specified using the pressure -keyword, in which case the user-specified chemical potential is -ignored. For non-ideal gas reservoirs, the user may also specify the -fugacity coefficient using the fugacity_coeff keyword. -

-

The full_energy option means that fix GCMC will compute the total +atoms/molecules are assigned to two groups: the default group “all” +and the group specified in the fix gcmc command (which can also be +“all”).

+

The gas reservoir pressure can be specified using the pressure +keyword, in which case the user-specified chemical potential is +ignored. For non-ideal gas reservoirs, the user may also specify the +fugacity coefficient using the fugacity_coeff keyword.

+

The full_energy option means that fix GCMC will compute the total potential energy of the entire simulated system. The total system energy before and after the proposed GCMC move is then used in the -Metropolis criterion to determine whether or not to accept the +Metropolis criterion to determine whether or not to accept the proposed GCMC move. By default, this option is off, in which case only partial energies are computed to determine the difference in -energy that would be caused by the proposed GCMC move. -

-

The full_energy option is needed for systems with complicated -potential energy calculations, including the following: -

- -

In these cases, LAMMPS will automatically apply the full_energy -keyword and issue a warning message. -

-

When the mol keyword is used, the full_energy option also includes -the intramolecular energy of inserted and deleted molecules. If this -is not desired, the intra_energy keyword can be used to define an +energy that would be caused by the proposed GCMC move.

+

The full_energy option is needed for systems with complicated +potential energy calculations, including the following:

+ +

In these cases, LAMMPS will automatically apply the full_energy +keyword and issue a warning message.

+

When the mol keyword is used, the full_energy option also includes +the intramolecular energy of inserted and deleted molecules. If this +is not desired, the intra_energy keyword can be used to define an amount of energy that is subtracted from the final energy when a molecule is inserted, and added to the initial energy when a molecule is deleted. For molecules that have a non-zero intramolecular energy, this -will ensure roughly the same behavior whether or not the full_energy -option is used. -

-

Inserted atoms and molecules are assigned random velocities based on the +will ensure roughly the same behavior whether or not the full_energy +option is used.

+

Inserted atoms and molecules are assigned random velocities based on the specified temperature T. Because the relative velocity of all atoms in the molecule is zero, this may result in inserted molecules that are systematically too cold. In addition, the intramolecular potential energy of the inserted molecule may cause the kinetic energy -of the molecule to quickly increase or decrease after insertion. -The tfac_insert keyword allows the user to counteract these effects -by changing the temperature used to assign velocities to +of the molecule to quickly increase or decrease after insertion. +The tfac_insert keyword allows the user to counteract these effects +by changing the temperature used to assign velocities to inserted atoms and molecules by a constant factor. For a particular application, some experimentation may be required -to find a value of tfac_insert that results in inserted molecules that -equilibrate quickly to the correct temperature. -

-

Some fixes have an associated potential energy. Examples of such fixes -include: efield, gravity, -addforce, langevin, -restrain, temp/berendsen, -temp/rescale, and wall fixes. -For that energy to be included in the total potential energy of the +to find a value of tfac_insert that results in inserted molecules that +equilibrate quickly to the correct temperature.

+

Some fixes have an associated potential energy. Examples of such fixes +include: efield, gravity, +addforce, langevin, +restrain, temp/berendsen, +temp/rescale, and wall fixes. +For that energy to be included in the total potential energy of the system (the quantity used when performing GCMC moves), -you MUST enable the fix_modify energy option for -that fix. The doc pages for individual fix commands -specify if this should be done. -

-

Use the charge option to insert atoms with a user-specified point -charge. Note that doing so will cause the system to become non-neutral. -LAMMPS issues a warning when using long-range electrostatics (kspace) -with non-neutral systems. See the -compute_group_group documentation for more -details about simulating non-neutral systems with kspace on. -

-

Use of this fix typically will cause the number of atoms to fluctuate, +you MUST enable the fix_modify energy option for +that fix. The doc pages for individual fix commands +specify if this should be done.

+

Use the charge option to insert atoms with a user-specified point +charge. Note that doing so will cause the system to become non-neutral. +LAMMPS issues a warning when using long-range electrostatics (kspace) +with non-neutral systems. See the +compute_group_group documentation for more +details about simulating non-neutral systems with kspace on.

+

Use of this fix typically will cause the number of atoms to fluctuate, therefore, you will want to use the -compute_modify command to insure that the +compute_modify command to insure that the current number of atoms is used as a normalizing factor each time -temperature is computed. Here is the necessary command: -

-
compute_modify thermo_temp dynamic yes 
-
-

If LJ units are used, note that a value of 0.18292026 is used by this -fix as the reduced value for Planck's constant. This value was +temperature is computed. Here is the necessary command:

+
compute_modify thermo_temp dynamic yes
+
+
+

If LJ units are used, note that a value of 0.18292026 is used by this +fix as the reduced value for Planck’s constant. This value was derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 * epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and -mass = 39.948 amu. -

-

The group keyword assigns all inserted atoms to the group -of the group-ID value. The grouptype keyword assigns all -inserted atoms of the specified type to the group -of the group-ID value. -

-

Restart, fix_modify, output, run start/stop, minimize info: -

-

This fix writes the state of the fix to binary restart -files. This includes information about the random +mass = 39.948 amu.

+

The group keyword assigns all inserted atoms to the group +of the group-ID value. The grouptype keyword assigns all +inserted atoms of the specified type to the group +of the group-ID value.

+ +
+

Restart, fix_modify, output, run start/stop, minimize info

+

This fix writes the state of the fix to binary restart files. This includes information about the random number generator seed, the next timestep for MC exchanges, etc. See -the read_restart command for info on how to +the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that -the operation of the fix continues in an uninterrupted fashion. -

-

None of the fix_modify options are relevant to this -fix. -

-

This fix computes a global vector of length 8, which can be accessed -by various output commands. The vector -values are the following global cumulative quantities: -

- -

The vector values calculated by this fix are "extensive". -

-

No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy -minimization. -

-

Restrictions: -

-

This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. -

-

Do not set "neigh_modify once yes" or else this fix will never be -called. Reneighboring is required. -

-

Can be run in parallel, but aspects of the GCMC part will not scale -well in parallel. Only usable for 3D simulations. -

-

Note that very lengthy simulations involving insertions/deletions of +the operation of the fix continues in an uninterrupted fashion.

+

None of the fix_modify options are relevant to this +fix.

+

This fix computes a global vector of length 8, which can be accessed +by various output commands. The vector +values are the following global cumulative quantities:

+ +

The vector values calculated by this fix are “extensive”.

+

No parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy minimization.

+
+
+

Restrictions

+

This fix is part of the MC package. It is only enabled if LAMMPS was +built with that package. See the Making LAMMPS section for more info.

+

Do not set “neigh_modify once yes” or else this fix will never be +called. Reneighboring is required.

+

Can be run in parallel, but aspects of the GCMC part will not scale +well in parallel. Only usable for 3D simulations.

+

Note that very lengthy simulations involving insertions/deletions of billions of gas molecules may run out of atom or molecule IDs and -trigger an error, so it is better to run multiple shorter-duration +trigger an error, so it is better to run multiple shorter-duration simulations. Likewise, very large molecules have not been tested -and may turn out to be problematic. -

-

Use of multiple fix gcmc commands in the same input script can be -problematic if using a template molecule. The issue is that the +and may turn out to be problematic.

+

Use of multiple fix gcmc commands in the same input script can be +problematic if using a template molecule. The issue is that the user-referenced template molecule in the second fix gcmc command may no longer exist since it might have been deleted by the first fix gcmc command. An existing template molecule will need to be -referenced by the user for each subsequent fix gcmc command. -

-

Related commands: -

-

fix atom/swap, -fix nvt, neighbor, -fix deposit, fix evaporate, -delete_atoms -

-

Default: -

-

The option defaults are mol = no, maxangle = 10, full_energy = no, +referenced by the user for each subsequent fix gcmc command.

+
+ +
+

Default

+

The option defaults are mol = no, maxangle = 10, full_energy = no, except for the situations where full_energy is required, as -listed above. -

-
+listed above.

+
+

(Frenkel) Frenkel and Smit, Understanding Molecular Simulation, +Academic Press, London, 2002.

+
+ - -

(Frenkel) Frenkel and Smit, Understanding Molecular Simulation, -Academic Press, London, 2002. -

- + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_reax.html b/doc/pair_reax.html index 3b7aa08940..4e2e02fe93 100644 --- a/doc/pair_reax.html +++ b/doc/pair_reax.html @@ -1,218 +1,384 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
+ + + + + + + + + pair_style reax command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+ + + - - -
- -

pair_style reax command -

-

Syntax: -

-
pair_style reax hbcut hbnewflag tripflag precision 
-
- -

Examples: -

-
pair_style reax
+      
+      

+        

+          

+  
+  

+  
+

+          

+           

+            
+  

+
pair_style reax command

+

+
Syntax

+
pair_style reax hbcut hbnewflag tripflag precision
+

+

+
    
+
  • hbcut = hydrogen-bond cutoff (optional) (distance units)
    • 
+
  • hbnewflag = use old or new hbond function style (0 or 1) (optional)
    • 
+
  • tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
    • 
+
  • precision = precision for charge equilibration (optional)
    • 
+

+

+

+
Examples

+
pair_style reax
 pair_style reax 10.0 0 1 1.0e-5
 pair_coeff * * ffield.reax 3 1 2 2
-pair_coeff * * ffield.reax 3 NULL NULL 3 
-

-
Description:
-

-
Style reax computes the ReaxFF potential of van Duin, Goddard and
+pair_coeff * * ffield.reax 3 NULL NULL 3
+
+ + +
+

Description

+

Style reax computes the ReaxFF potential of van Duin, Goddard and co-workers. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential energy. There is more than one version of ReaxFF. The version implemented in LAMMPS uses the functional forms documented in the supplemental information of the following paper: -(Chenoweth). The version integrated into LAMMPS matches -the most up-to-date version of ReaxFF as of summer 2010. -

-

WARNING: pair style reax is now deprecated and will soon be retired. Users -should switch to pair_style reax/c. The reax style -differs from the reax/c style in the lo-level implementation details. -The reax style is a -Fortran library, linked to LAMMPS. The reax/c style was initially +(Chenoweth). The version integrated into LAMMPS matches +the most up-to-date version of ReaxFF as of summer 2010.

+

WARNING: pair style reax is now deprecated and will soon be retired. Users +should switch to pair_style reax/c. The reax style +differs from the reax/c style in the lo-level implementation details. +The reax style is a +Fortran library, linked to LAMMPS. The reax/c style was initially implemented as stand-alone C code and is now integrated into LAMMPS as -a package. -

-

LAMMPS requires that a file called ffield.reax be provided, containing +a package.

+

LAMMPS requires that a file called ffield.reax be provided, containing the ReaxFF parameters for each atom type, bond type, etc. The format is identical to the ffield file used by van Duin and co-workers. The filename is required as an argument in the pair_coeff command. Any -value other than "ffield.reax" will be rejected (see below). -

-

LAMMPS provides several different versions of ffield.reax in its +value other than “ffield.reax” will be rejected (see below).

+

LAMMPS provides several different versions of ffield.reax in its potentials dir, each called potentials/ffield.reax.label. These are documented in potentials/README.reax. The default ffield.reax -contains parameterizations for the following elements: C, H, O, N, S. -

-

IMPORTANT NOTE: We do not distribute a wide variety of ReaxFF force -field files with LAMMPS. Adri van Duin's group at PSU is the central +contains parameterizations for the following elements: C, H, O, N, S.

+
+

Warning

+

We do not distribute a wide variety of ReaxFF force +field files with LAMMPS. Adri van Duin’s group at PSU is the central repository for this kind of data as they are continuously deriving and updating parameterizations for different classes of materials. You can visit their WWW site at -http://www.engr.psu.edu/adri, register -as a "new user", and then submit a request to their group describing +http://www.engr.psu.edu/adri, register +as a “new user”, and then submit a request to their group describing material(s) you are interested in modeling with ReaxFF. They can tell you what is currently available or what it would take to create a -suitable ReaxFF parameterization. -

-

The format of these files is identical to that used originally by van -Duin. We have tested the accuracy of pair_style reax potential +suitable ReaxFF parameterization.

+
+

The format of these files is identical to that used originally by van +Duin. We have tested the accuracy of pair_style reax potential against the original ReaxFF code for the systems mentioned above. You can use other ffield files for specific chemical systems that may be available elsewhere (but note that their accuracy may not have been -tested). -

-

The hbcut, hbnewflag, tripflag, and precision settings are +tested).

+

The hbcut, hbnewflag, tripflag, and precision settings are optional arguments. If none are provided, default settings are used: -hbcut = 6 (which is Angstroms in real units), hbnewflag = 1 (use -new hbond function style), tripflag = 1 (apply stabilization to all -triple bonds), and precision = 1.0e-6 (one part in 10^6). If you +hbcut = 6 (which is Angstroms in real units), hbnewflag = 1 (use +new hbond function style), tripflag = 1 (apply stabilization to all +triple bonds), and precision = 1.0e-6 (one part in 10^6). If you wish to override any of these defaults, then all of the settings must -be specified. -

-

Two examples using pair_style reax are provided in the examples/reax -sub-directory, along with corresponding examples for -pair_style reax/c. -

-

Use of this pair style requires that a charge be defined for every -atom since the reax pair style performs a charge equilibration (QEq) -calculation. See the atom_style and -read_data commands for details on how to specify -charges. -

-

The thermo variable evdwl stores the sum of all the ReaxFF potential +be specified.

+

Two examples using pair_style reax are provided in the examples/reax +sub-directory, along with corresponding examples for +pair_style reax/c.

+

Use of this pair style requires that a charge be defined for every +atom since the reax pair style performs a charge equilibration (QEq) +calculation. See the atom_style and +read_data commands for details on how to specify +charges.

+

The thermo variable evdwl stores the sum of all the ReaxFF potential energy contributions, with the exception of the Coulombic and charge equilibration contributions which are stored in the thermo variable -ecoul. The output of these quantities is controlled by the -thermo command. -

-

This pair style tallies a breakdown of the total ReaxFF potential -energy into sub-categories, which can be accessed via the compute -pair command as a vector of values of length 14. +ecoul. The output of these quantities is controlled by the +thermo command.

+

This pair style tallies a breakdown of the total ReaxFF potential +energy into sub-categories, which can be accessed via the compute pair command as a vector of values of length 14. The 14 values correspond to the following sub-categories (the variable -names in italics match those used in the ReaxFF FORTRAN library): -

-
  1. eb = bond energy -
  2. ea = atom energy -
  3. elp = lone-pair energy -
  4. emol = molecule energy (always 0.0) -
  5. ev = valence angle energy -
  6. epen = double-bond valence angle penalty -
  7. ecoa = valence angle conjugation energy -
  8. ehb = hydrogen bond energy -
  9. et = torsion energy -
  10. eco = conjugation energy -
  11. ew = van der Waals energy -
  12. ep = Coulomb energy -
  13. efi = electric field energy (always 0.0) -
  14. eqeq = charge equilibration energy -
-

To print these quantities to the log file (with descriptive column -headings) the following commands could be included in an input script: -

-
compute reax all pair reax
-variable eb  	 equal c_reax[1]
-variable ea  	 equal c_reax[2] 
+names in italics match those used in the ReaxFF FORTRAN library):

+
    
+
  1. eb = bond energy
    2. 
+
  2. ea = atom energy
    3. 
+
  3. elp = lone-pair energy
    4. 
+
  4. emol = molecule energy (always 0.0)
    5. 
+
  5. ev = valence angle energy
    6. 
+
  6. epen = double-bond valence angle penalty
    7. 
+
  7. ecoa = valence angle conjugation energy
    8. 
+
  8. ehb = hydrogen bond energy
    9. 
+
  9. et = torsion energy
    10. 
+
  10. eco = conjugation energy
    11. 
+
  11. ew = van der Waals energy
    12. 
+
  12. ep = Coulomb energy
    13. 
+
  13. efi = electric field energy (always 0.0)
    14. 
+
  14. eqeq = charge equilibration energy
    15. 
+

+
To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:

+
compute reax all pair reax
+variable eb           equal c_reax[1]
+variable ea           equal c_reax[2]
 ...
-variable eqeq 	 equal c_reax[14]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq 
-

-
Only a single pair_coeff command is used with the reax style which
+variable eqeq         equal c_reax[14]
+thermo_style custom step temp epair v_eb v_ea ... v_eqeq
+
+ +

Only a single pair_coeff command is used with the reax style which specifies a ReaxFF potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

- -

The specification of the filename and the mapping of LAMMPS atom types +where N is the number of LAMMPS atom types:

+ +

The specification of the filename and the mapping of LAMMPS atom types recognized by the ReaxFF is done differently than for other LAMMPS potentials, due to the non-portable difficulty of passing character -strings (e.g. filename, element names) between C++ and Fortran. -

-

The filename has to be "ffield.reax" and it has to exist in the +strings (e.g. filename, element names) between C++ and Fortran.

+

The filename has to be “ffield.reax” and it has to exist in the directory you are running LAMMPS in. This means you cannot prepend a path to the file in the potentials dir. Rather, you should copy that file into the directory you are running from. If you wish to use -another ReaxFF potential file, then name it "ffield.reax" and put it -in the directory you run from. -

-

In the ReaxFF potential file, near the top, after the general +another ReaxFF potential file, then name it “ffield.reax” and put it +in the directory you run from.

+

In the ReaxFF potential file, near the top, after the general parameters, is the atomic parameters section that contains element names, each with a couple dozen numeric parameters. If there are M -elements specified in the ffield file, think of these as numbered 1 +elements specified in the ffield file, think of these as numbered 1 to M. Each of the N indices you specify for the N atom types of LAMMPS atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will be mapped to whatever element you specify as the first index value, etc. If a mapping value is specified as NULL, the mapping is not performed. This can be used when a ReaxFF potential is used as part -of the hybrid pair style. The NULL values are placeholders for atom -types that will be used with other potentials. -

-

IMPORTANT NOTE: Currently the reax pair style cannot be used as part -of the hybrid pair style. Some additional changes still need to be -made to enable this. -

-

As an example, say your LAMMPS simulation has 4 atom types and the -elements are ordered as C, H, O, N in the ffield file. If you want +of the hybrid pair style. The NULL values are placeholders for atom +types that will be used with other potentials.

+
+

Warning

+

Currently the reax pair style cannot be used as part +of the hybrid pair style. Some additional changes still need to be +made to enable this.

+
+

As an example, say your LAMMPS simulation has 4 atom types and the +elements are ordered as C, H, O, N in the ffield file. If you want the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be -H, you would use the following pair_coeff command: -

-
pair_coeff * * ffield.reax 1 1 4 2 
-
-
- -

Mixing, shift, table, tail correction, restart, rRESPA info: -

-

This pair style does not support the pair_modify -mix, shift, table, and tail options. -

-

This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you +H, you would use the following pair_coeff command:

+
pair_coeff * * ffield.reax 1 1 4 2
+
+
+
+

Mixing, shift, table, tail correction, restart, rRESPA info:

+

This pair style does not support the pair_modify +mix, shift, table, and tail options.

+

This pair style does not write its information to binary restart files, since it is stored in potential files. Thus, you need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

-

This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -

-

Restrictions: -

-

The ReaxFF potential files provided with LAMMPS in the potentials -directory are parameterized for real units. You can use +script that reads a restart file.

+

This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords.

+ +
+

Restrictions

+

The ReaxFF potential files provided with LAMMPS in the potentials +directory are parameterized for real units. You can use the ReaxFF potential with any LAMMPS units, but you would need to create your own potential file with coefficients listed in the -appropriate units if your simulation doesn't use "real" units. -

-

Related commands: -

-

pair_coeff, pair_style reax/c, -fix_reax_bonds -

-

Default: -

-

The keyword defaults are hbcut = 6, hbnewflag = 1, tripflag = 1, -precision = 1.0e-6. -

-
+appropriate units if your simulation doesn’t use “real” units.

+
+ +
+

Default

+

The keyword defaults are hbcut = 6, hbnewflag = 1, tripflag = 1, +precision = 1.0e-6.

+
+

(Chenoweth_2008) Chenoweth, van Duin and Goddard, +Journal of Physical Chemistry A, 112, 1040-1053 (2008).

+
+ - -

(Chenoweth_2008) Chenoweth, van Duin and Goddard, -Journal of Physical Chemistry A, 112, 1040-1053 (2008). -

- + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/searchindex.js b/doc/searchindex.js index b1f3ad6921..38c97ebd12 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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326,330,333,334,339,346,352,353,355,356,358,360,361,362,363,364,368,375,377,384,385,386,387,393,394,395,406,407,408,409,410,411,415,419,421,422,429,439,441,442,443,446,452,454,456,457,458,459,460,462,463,465,467,469,471,474,475,478,482,483,484,485,486,487],afterrun:465,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,147,151,159,188,191,216,231,278,333,346,357,407,408,452,454,455,457,459,464,471,473,483,485],against:[11,12,13,64,217,357,421,422],aggreg:[6,12,65,68,69,79,92,108,115,231,247,290,292,305,452,484],aggress:[231,471],agilio:[9,13],agre:[3,8,185,355,364,395,422],agreement:[5,7],ahd:392,ahead:326,aidan:[0,5,7,9,13,350],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,232],aktulga:[7,9,285,422],al2o3_001:[118,293],al3:164,ala:238,alain:9,alat:[273,409],alb:[419,441,443],albeit:291,albert:9,alchem:[87,159],alcohol:322,alcu:[363,368],alcu_eam:419,alderton:381,alejandr:[251,252],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,191,200,210,213,216,238,240,241,263,275,292,295,314,315,319,322,327,353,354,355,359,362,386,408,426,428,452,454,471],alia:[12,16],alias:[1,348],aliceblu:191,align:[6,12,29,41,71,167,185,206,210,233,350,457,460,478],alkali:386,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,244,246,247,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,303,304,306,307,308,309,310,311,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,337,342,345,346,347,348,349,350,352,355,356,357,358,359,361,362,363,364,365,367,368,369,371,372,373,374,375,377,378,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,452,454,455,456,457,458,459,460,461,462,464,465,466,467,468,469,470,471,472,474,475,476,478,482,483,484,485,486,487],allen:[29,87,381,389],allentildeslei:87,allign:3,allindex:331,alloc:[3,5,6,8,9,11,12,60,225,321,356,358,362,417,422,457,465],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,210,212,213,214,215,216,217,221,222,225,227,228,229,230,232,235,238,241,242,246,248,251,252,273,277,279,280,281,282,286,292,293,295,296,298,299,303,307,314,315,316,317,319,320,321,322,323,324,330,332,334,342,347,348,350,355,356,357,358,361,362,365,368,369,370,371,372,373,378,384,386,390,391,392,393,398,402,407,408,413,419,422,423,426,428,437,447,449,452,455,457,459,460,461,462,463,464,467,469,470,471,474,475,483,484],almost:[2,3,12,60,233,282,319,348,359,362,437],alo:378,alon:[6,7,213,288,421,422,455],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,213,233,238,239,243,248,250,282,292,295,296,300,304,305,314,318,319,325,328,330,350,353,354,355,357,378,381,390,393,396,398,402,409,421,422,440,457,460,467,468,483],alonso:[410,411],alpha:[6,12,51,195,238,274,282,287,355,363,366,369,378,382,384,385,387,392,397,398,409,414,418,442,444,475,478],alpha_:444,alpha_c:406,alpha_i:[429,444],alpha_ialpha_j:444,alpha_lj:406,alphabet:[2,3,22,37,44,55,63,173,184,194,334,342,356,375,438,457],alphanumer:[3,63,194,281,289,332,356,483],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,206,207,210,212,216,242,280,282,307,330,356,357,382,391,393,400,408,437,447,450,453,457,458,462,467,483],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,222,225,226,227,228,229,231,232,235,236,237,238,248,249,251,252,253,254,255,256,257,262,265,266,268,269,270,271,273,274,275,277,278,279,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,300,301,304,305,307,310,311,312,313,314,318,319,320,321,323,325,328,330,332,334,339,342,345,347,348,350,351,352,355,356,357,358,359,361,362,368,372,373,375,379,380,381,382,384,385,3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22,389,423,437,447],cloud:478,clovertown:18,clsuter:72,clump1:[277,292],clump2:[277,292],clump3:[277,292],clump:292,cluster:[],clutter:[3,9],cmap:457,cmatrix:229,cmax:409,cmd:[11,12,275,468],cmin:409,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[393,461],co2:[40,164,295,356],coars:[7,9,29,36,40,54,177,277,292,307,391,424,469],coarser:[348,483],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,333,334,339,375,393,397,413,426,428,430,457,459],coeffcient:457,coeffici:[],coefficienct:382,coefficient0:384,coefficient1:384,coeffieci:[6,366],coeffincientn:384,coexist:[9,227,386],cohes:[6,387,409],coincid:[122,328,373,407,408,452],colberg:189,cold:[6,150,227,231,358,478],coldest:315,coleman8:9,coleman:[9,118,164,293],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,215,241,247,277,287,290,292,330,347,356,358,376,396,457,464,470,476,487],collid:[221,307,329],colliex:164,collinear:[3,277],collis:[3,238,307,325,329,383,390,450],colllis:307,colloid:[],colombo:39,colon:[192,330,458],color1:191,color2:191,color:[3,9,41,188,190,191,210,228,282,287],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,205,206,207,208,241,248,249,282,292,308,309,319,329,388,392,421,422,458,472,474,483],colvar:[],colvarmodul:12,com:[],comamnd:216,comand:[213,459],comannd:362,comb3:[],comb:[],comb_1:284,comb_2:284,combiant:379,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,205,232,241,251,275,281,311,320,328,331,333,347,348,350,354,362,376,378,379,386,387,393,405,406,429,439,441,443,446,449,460,465,470,478,483],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,232,234,235,348,357,362,382,413,418,440],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,236,292,319,356,357,363,384,385,387,397,409,415,422,429,439,440,441,442,443,446,454,455,457,478,483],commerci:7,commmand:[3,6,12,59,107,270,451,452,454,471,486],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,343,391,400,429,441,443,457,460,469],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,210,211,212,214,215,216,232,234,238,240,241,242,251,274,281,283,284,285,292,307,319,330,345,347,358,359,360,362,383,417,454,455,459,466,467,483,485,487],communc:347,comp:[7,189,234,235,295,348,357,386,413,418,423,436,440,442],compact:[63,194,375,438],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,220,283,330,332,347,348,355,357,409,452,471,472,478,482],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,333,334,342,374,438],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,205,206,207,208,210,274,286,311,314,321,324,327,347,362,394,413,440,454,455,483],compens:[6,211,212,290,358,386],compet:318,competit:348,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,232,318,348,362,457,458,462,483],compl:17,complain:[12,17],complement:409,complementari:[7,378,398],complet:[3,6,9,12,15,41,59,71,191,206,210,215,241,275,278,281,307,318,320,332,346,357,362,387,426,428,445,452,457,462,465,469,471,474,478,483],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,238,303,328,345,357,386,440,455,457,460,483],compli:[314,318],complic:[6,7,9,12,13,201,227,455],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,213,214,216,217,222,225,230,234,235,238,241,243,247,248,250,251,252,255,256,257,268,269,271,272,274,275,276,279,290,292,294,295,296,300,301,304,307,310,311,312,314,321,322,327,328,329,347,350,354,355,356,357,362,382,386,390,407,408,426,428,429,457,458,467,475,483,484],componenet:6,composit:[6,201,238,384],compound:[377,386,387,446],compres:[71,114,203],compress:[0,3,6,59,71,114,168,188,190,191,203,216,249,255,279,282],compris:[40,328,396,423,445],compton:[118,164],comptu:[3,6],compuat:348,comput:[],computation:[3,6,211,212,319,368],computational:478,compute_arrai:8,compute_fep:[196,406],compute_group_group:227,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,293],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,486],concav:328,concentr:384,concept:[6,145,155,203,466],conceptu:[3,6,71,153,214,216,357,378,393,409,462],concern:[6,73,87,189,228],concis:[11,318],conclud:12,concret:8,concurr:[9,16,348,483],conden:[319,441,443],condens:[6,147,319,364,380,384,398,446],condit:[],conducit:6,conduct:[],cone:460,confid:[3,471],config:[12,188,454],configfil:215,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,214,215,216,217,221,227,234,235,263,275,283,318,345,355,357,364,368,385,409,439,441,443,446,452,457,459,460,471],confin:[457,471],conflict:[3,12,40,413,455],conform:[3,6,13,59,213,214,250,291,296,318,341,357,386,469],confus:[3,446],conjuct:382,conjug:[7,8,235,354,386,421,422],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,235,238,242,263,278,279,283,284,285,287,292,307,315,322,327,347,348,357,369,371,375,378,382,386,392,398,413,416,424,444,457,460,464,478,487],connect:[3,6,87,150,168,213,232,277,292,295,304,357,379,390,437,443,454,455,461,478],conput:3,consecut:[3,11,12,39,71,165,191,195,196,217,232,233,378,398,402,452,458,460],consequ:[1,6,201,319,397,471],conserv:[3,194,201,213,220,221,228,231,235,237,238,242,247,249,251,263,292,295,310,311,315,322,323,327,357,381,382,390,404,466,471],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,206,210,212,213,217,239,252,274,292,314,315,318,319,322,348,375,386,393,422,423,437,452,453,455,458,459,460,462,465,467,475,478,483],consider:[6,8,235,236,310,311,312,362,466],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,216,217,220,222,225,228,235,236,237,248,251,253,254,255,256,257,258,259,261,262,263,264,266,267,268,269,270,271,279,282,287,289,291,292,310,311,312,313,323,347,348,350,356,357,362,364,368,370,376,378,386,389,393,407,408,409,413,423,426,428,440,447,455,457,458,460,461,462,469,478,483],consistent_fe_initi:200,consit:292,constant:[],constitu:[3,6,241,292,324,328,376,423],constitut:[426,428],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,217,227,228,233,241,245,277,278,290,292,295,305,315,322,355,356,386,462,469,478],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,214,251,274,291,328,358,362,381,413,437,439,440,460,461,476,483],constructor:8,consult:422,consum:[1,287,417,483],consumpt:345,contact:[],contact_stiff:[425,427],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,205,206,207,208,210,215,217,222,229,233,234,235,236,238,249,263,273,274,277,278,280,282,285,289,292,293,297,307,314,318,319,328,329,332,346,348,356,357,360,361,363,364,365,368,377,378,381,384,385,386,393,394,409,415,419,420,421,422,429,439,440,441,442,443,444,446,452,453,454,455,457,458,459,460,462,464,466,469,471,474,475,478,483,485,487],content:[12,18,422,473,475],context:[3,6,8,12,17,117,191,211,212,217,277,289,323,354,449,457,464,473,482,483,484],contibut:70,contigu:454,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,210,213,214,215,216,217,227,228,229,231,232,233,235,236,237,243,248,249,251,253,254,255,256,257,268,269,270,271,276,278,281,282,292,293,296,306,307,309,316,317,319,325,328,332,346,361,362,368,382,383,400,403,421,422,423,426,428,442,452,455,457,459,460,465,471,474,475,483,485],continuum:[6,7,9,200,319,426,428],contour_integr:200,contract:[59,214,216,251,279,292],contradictori:3,contrain:295,contraint:263,contrari:[229,236],contrast:[1,6,42,55,64,150,216,330,426,428,449,486],contrib:319,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,205,206,207,208,214,227,235,238,241,242,246,252,269,270,277,278,286,289,292,293,295,321,347,355,357,365,382,383,384,386,393,407,408,413,421,422,469,475,478],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,210,214,215,216,231,232,235,236,251,253,254,255,256,257,279,284,292,298,299,310,311,312,319,323,345,347,359,386,389,421,422,425,427,439,443,452,454,466,472,473],control_typ:200,controlfil:422,convect:91,conveni:[6,12,29,188,192,208,293,350,429,483],convent:[3,8,9,29,176,183,184,191,291,304,331,384,386,483],converg:[3,6,41,88,188,190,192,197,210,213,214,222,225,255,282,284,287,291,295,353,354,355,357,377,378,398,452,464,471],convers:[3,8,140,190,191,201,204,279,347,378,379,380,386,398,402,406,416,455,471,482],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,208,249,330,333,335,338,341,350,357,363,384,441,443,450,455,457,458,459,464,474,478,482,483,485,487],convex:328,convinc:[7,12],cook:9,cooki:7,cool:[7,155,231,290],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,206,207],coord2:[3,114,203,206,207],coord3:[3,114,203,206,207],coord:[],coordiat:355,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,205,206,207,210,211,212,213,214,215,216,217,220,222,223,225,227,230,231,232,233,234,235,236,248,250,251,253,254,256,257,269,272,273,274,277,278,279,289,290,292,294,295,296,301,304,305,306,307,309,317,318,319,326,327,329,330,350,355,356,357,362,363,364,367,385,452,457,458,460,462,465,467,471,478,483,484],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,319,357,375,421,455],copper:450,coproccesor:16,coprocessor:[1,4,7,9,16,17,362,470],coproprocessor:17,copy_arrai:8,copyright:[7,8,277],coral:191,core:[],core_shel:147,coreshel:[6,9,371,378,380],cornel:[6,171,469],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:[3,6,40,113,190,328,329,350,445,457],cornflowerblu:191,cornsilk:191,corpor:16,corr:377,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,216,227,229,235,251,252,269,277,279,282,318,324,328,347,357,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,448,449,450,457,472,475,478],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,217,222,225,236,245,251,252,285,292,295,304,306,325,328,357,358,362,380,408,454,455,457,467,482,484],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,209,212,214,216,223,225,226,230,235,238,239,247,248,249,251,253,254,255,256,257,258,263,266,268,269,271,274,275,279,284,292,294,295,310,312,314,323,324,325,327,328,329,331,333,334,335,336,337,338,341,343,348,352,354,356,357,363,364,366,369,370,371,372,373,374,375,376,377,378,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,413,414,415,416,418,419,421,422,423,424,429,430,439,440,441,442,443,445,446,448,449,450,452,454,455,457,458,460,470,471,472,474,475,478,483],correspondingli:[407,408,466],cosin:[],cosineshift:27,cosmo:[229,234],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,206,207,210,211,212,224,251,284,319,347,348,360,378,398,402,413,439,454,466],costheta0:[439,441,443,446],costheta:419,costli:[11,88,229,358],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,206,210,216,225,234,281,282,283,287,290,292,294,307,308,314,318,319,320,324,328,330,332,339,344,346,353,355,358,362,365,388,392,393,421,422,453,454,455,457,459,461,464,465,473,478,483,484],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,283,285,320,347,348,355,362,369,371,372,373,374,377,378,379,380,381,386,390,391,393,398,402,406,413,416,421,422,424,438,443,444,446,449,462,469,475,478,482],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,205,206,207,209,210,217,222,224,227,233,251,263,278,295,310,311,328,348,355,356,357,359,362,388,392,413,475,483],counter:[325,452,463,465,471],counteract:227,counterbal:231,counterpart:[188,292,452],counterproduct:18,coupl:[],courant:297,cours:[3,8,126,128,159,188,195,196,228,291,304,318,324,326,327,329,330,348,407,430,454,457,470,478,483,485],courtesi:350,coval:[6,29,386,409,478],covari:229,cover:[6,71,185,191,200,238,386,396,445],coverag:[71,206],cpc:234,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,225,295],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,220,236,320,345,348,362,375,438,452,470,471,474,475,476,483],cpuremain:475,cr2:164,cr3:164,crack:[4,358],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,358,478],craympi:362,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:277,criteria:[3,116,166,190,191,211,212,213,246,355,418,445,459,462,483],criterion:[12,41,121,163,165,168,201,210,213,227,263,284,297,325,330,355,357,377,386,390,462,471,472],criterioni:471,critic:[48,49,249,314,319,355],cross:[3,12,22,71,89,144,173,188,190,202,206,212,216,248,250,269,292,300,304,306,315,322,334,350,357,373,382,383,384,391,392,393,398,400,402,419,424,426,428,441,443,450,457,461,467,485],crossov:1,crossterm:457,crozier:[0,7,13],crucial:282,crystal:[4,6,13,73,273,274,317,350,358,461,475,478],crystallin:[6,274,350,442,478],crystallis:314,crystallogr:[118,164],crystallograph:[350,475],crystallographi:[118,164,350],cs1:164,cs_chunk:6,cs_im:[40,457],cs_re:[40,457],csanyi:[140,420,429],cscl:409,csequ:6,csh:[11,12,375],cshrc:[11,12],csic:[385,439,441,443,446],csinfo:6,csisi:[385,439,441,443,446],csld:[],cst:384,cstherm:6,cstyle:454,csvr:[],ctcm:[363,384],ctemp_cor:220,cterm:296,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:409,cube:[6,41,163,168,210,220,328,350,478],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:368,cummul:[3,6,208,211,212,213,215,224,229,235,237,307,310,311,312,313,315,322,392,475],cumul:[6,201,203,205,206,207,221,227,235,249,251,255,263,292,293,357],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,206,207,208,210,211,212,213,214,215,216,217,221,222,225,227,229,232,233,235,241,248,251,252,256,257,263,268,269,271,277,283,284,286,289,290,291,292,295,296,297,298,299,300,301,303,305,306,307,310,311,312,318,319,322,323,324,325,326,327,329,330,332,345,346,347,348,351,352,354,355,356,357,362,368,375,377,381,384,386,387,390,393,394,397,407,408,409,410,411,413,419,421,422,425,426,427,428,430,441,443,444,447,452,453,454,455,457,458,459,460,461,463,464,465,467,469,471,472,474,475,483,484,485,486,487],curv:[6,165,227,274],curvatur:[389,423,450],custom:[],cut0:455,cut1:466,cut2:466,cut:[],cuthi:[273,285],cutinn:[370,407,408],cutlo:[273,285],cutmax:419,cutoff1:[374,381,398,402,406,416,424],cutoff2:[369,371,372,374,380,381,398,402,406,416,424],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,212,213,218,273,282,283,285,287,289,292,307,320,324,328,330,345,347,348,355,358,359,360,362,363,364,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,455,459,462,466,478,483],cutoffa:385,cutoffc:385,cuu3:384,cval:164,cvd:314,cvel:296,cvff:[],cwiggl:[3,248,324,327,329,483],cyan:[2,190,191],cycl:[3,227,249,251,252,255],cyclic:[3,185],cygwin:12,cylind:[3,4,190,233,278,325,328,460],cylindr:[6,233,304,325],cypress:362,cyrot:368,cyrstal:274,d3q15:238,d3q19:238,d_double_doubl:15,d_e:319,d_flag2:281,d_flag:281,d_name:[113,188,281,309,467],d_single_doubl:15,d_single_singl:15,d_sx:281,d_sy:281,d_sz:281,daan:317,dai:12,daili:12,daivi:269,damag:[],dammak:287,damp:[3,6,194,199,235,236,237,242,251,252,255,279,282,287,292,310,311,323,325,326,354,355,357,369,371,373,378,381,386,390,398,406,416,424,438,444,471,478],damp_com:236,damp_drud:236,dampen:[292,478],dampflag:[325,390],dan:17,danger:[3,12,227,330,382,475],dangl:168,daniel:9,darden:[348,381],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:283,dash:[390,474],dat:[6,91,185,200,453],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,293],dataset:293,datatyp:3,date:[0,6,12,13,421,422,483],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:324,david:[9,19,347,348,441,443],daw:[384,419],dbg:14,dcd:[3,6,7,188,189,190,191,192,275,458,462],ddim:187,deactiv:406,dealt:234,debug:[6,7,11,12,13,14,17,118,122,164,165,275,280,345,347,362,394,413,447,455,456,459,464,467,474,483],deby:[],decai:[378,450],decid:[3,6,12,16,71,248,281,292,320,472],decipher:350,declar:189,declin:307,decod:190,decompos:[87,429],decomposit:[3,5,7,18,62,200,275],decoupl:[6,478],decreas:[3,188,197,198,213,216,222,225,227,235,318,347],decrement:296,deepli:344,deeppink:191,deepskyblu:191,def:[12,13,455],defaul:61,defect:[6,70,163],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,220,221,222,225,226,227,230,233,234,235,236,237,238,246,248,250,251,252,253,254,255,256,257,259,260,261,264,266,267,268,269,270,271,273,274,275,277,278,279,281,283,285,290,292,293,294,295,297,301,305,307,309,310,311,312,313,315,316,317,319,321,322,324,325,326,327,328,329,330,332,333,334,335,336,337,338,341,342,343,345,347,348,350,352,354,355,356,357,358,359,360,361,362,364,365,366,367,369,370,371,372,373,374,375,376,378,379,381,382,383,385,386,388,389,390,391,392,393,394,396,398,399,400,401,402,403,404,405,406,407,408,412,413,414,415,416,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,455,457,458,460,461,462,463,466,467,468,469,471,472,474,475,478,479,480,481,482,483,484],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,216,233,255,293,309,321,324,327,329,331,342,345,356,365,368,376,386,396,419,426,428,429,445,455,457,459,466,468,482,483],defint:475,deform:[],deg2theta:164,deg:478,degener:[3,277],degrad:[8,18,274,348,466],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,213,220,227,229,230,235,236,241,251,252,255,256,257,268,269,271,275,277,291,292,295,310,311,312,317,333,335,338,341,343,355,381,384,392,467,475,478,484],degress:[145,203],del:471,delai:[3,6,12,358,383,475],deleg:393,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,205,206,207,208,211,213,224,227,251,293,310,311,330,332,346,356,358,361,413,457,458,460,468,469,474,479,481,483,484],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[455,483],deloc:[252,386],delr:409,delt_lo:471,delta:[],delta_1:368,delta_3:368,delta_7:368,delta_conf:3,delta_ij:[409,419],delta_mu:3,delta_pi:368,delta_r:419,delta_sigma:368,delx:187,delz:187,demand:287,demo:11,demon:272,demonstr:[282,409],den:278,dendrim:392,denniston:[9,238,240,241,242,274],denomin:[7,170],denot:[118,220,236,274,285,287,378,391,393,422,426,428],dens:[71,213,386],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,206,207,210,216,225,238,241,244,245,274,278,279,283,319,324,350,352,356,363,368,384,409,410,411,419,423,432,434,435,436,457,466,467,475,482],density_continu:428,density_summ:428,depart:[0,7],departur:[249,282],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,208,209,210,212,214,216,222,223,226,229,230,231,233,235,236,238,240,241,248,251,253,254,255,256,257,258,266,268,269,271,273,284,287,289,292,294,295,301,307,310,311,312,314,316,318,319,321,323,324,327,328,329,330,332,333,334,335,336,337,338,341,343,348,350,355,356,358,359,360,362,363,364,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,412,414,415,416,418,419,421,422,423,424,429,430,438,439,440,441,442,443,444,445,446,448,449,450,452,454,457,459,460,463,467,469,471,474,475,477,483,484],dependend:6,depflag:12,dephas:[452,471],depos:217,deposit:[],deprec:[283,421],depth:[51,144,190,319,389,423],dequidt:9,der:[87,107,376,377,406,421,422,449,478],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,214,216,227,235,248,251,253,254,255,256,257,273,279,283,287,316,317,319,324,325,328,354,356,364,368,376,381,386,387,391,400,404,405,409,421,422,438,440,449,478],derjagin:449,derlet:273,descend:191,descent:[7,354],descib:[40,283],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,210,213,214,215,216,217,219,220,228,229,232,233,234,235,236,237,238,240,241,242,246,250,251,252,255,262,270,273,275,280,281,282,283,284,285,292,296,304,307,308,309,310,311,312,313,314,315,316,317,322,324,325,327,332,347,348,350,353,354,355,356,357,361,364,365,367,369,370,371,373,374,375,376,377,378,381,384,386,387,389,390,391,393,398,399,400,401,402,403,404,405,406,407,408,409,412,418,419,420,421,422,423,424,429,430,437,438,439,440,441,442,443,444,446,448,449,450,452,454,455,457,458,460,461,467,470,471,474,483,484,485],descript:[],descriptor:[140,188,394],deserno:348,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,213,219,220,251,252,273,274,293,314,319,365,366,367,370,373,378,380,386,406,407,408,410,411,419,422,440,466],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,208,214,216,225,227,228,235,236,237,241,251,269,277,278,279,280,283,287,292,295,307,310,311,312,313,318,325,339,344,347,348,350,353,355,356,357,382,384,392,407,408,439,441,443,453,454,455,457,461,466,471,472,474,475,483,484,485],desk:7,desktop:[4,6,7,10,12,190],despit:478,destabil:368,destre:341,destroi:[11,39,211,212],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,208,210,212,213,214,215,216,217,225,227,228,229,230,232,233,235,237,238,242,248,249,250,251,252,253,254,255,256,257,261,263,268,269,270,271,274,277,278,279,281,282,284,285,286,292,295,307,310,311,312,313,314,315,317,318,319,320,321,322,323,330,332,334,342,347,348,351,355,356,358,359,362,363,364,365,367,368,370,372,373,374,375,376,377,378,381,382,386,387,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,409,412,413,418,421,422,423,429,430,438,445,448,449,455,457,458,459,460,462,463,466,467,469,472,475,476,483,484,487],detect:[2,3,12,61,63,86,226,278,318,357,377,392,397,452,454,457,468,471,483],determ:362,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,214,216,217,220,222,227,230,231,233,235,236,241,246,248,249,251,256,257,268,269,271,273,275,279,282,289,290,291,292,293,294,297,299,301,307,310,311,312,314,320,321,324,325,326,327,328,329,330,342,347,348,350,356,358,359,362,364,365,372,377,381,383,384,388,390,393,394,402,409,413,422,423,437,440,444,449,454,457,458,460,462,464,467,471,473,474,476,482,483,484],detil:108,devan:[9,424],devanathan:443,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,232,255,277,282,283,286,364,368,386,411,446,459],devemi:9,deviat:[249,255,273,388],deviator:9,devic:[1,3,12,15,17,232,362],device_typ:362,devin:[284,377],devis:411,dfactor:190,dff:478,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,348],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,286],dhi:[59,187,216,278],dhug:[249,282],dhugoniot:[249,282],dia:409,diagnost:[],diagon:[3,6,83,140,141,142,214,251,279,292,322,426,428],diagonalstyl:429,diagram:[41,118,164,184,210,275],diallo:392,diam:[190,191,278,356],diamet:[3,6,40,113,165,188,190,191,195,196,235,278,292,307,323,325,356,376,389,390,396,400,423,445,449,457,458,467],diamond:[350,386,409],diamter:[40,278],dick:6,dicsuss:248,dictat:[201,249],did:[3,12,355,382,383,384,390,413,441,443,465],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,321,347],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,205,210,211,212,213,214,215,216,220,226,227,228,229,230,231,232,235,236,238,248,251,252,253,254,256,257,259,261,264,266,267,268,271,273,275,277,279,282,283,284,287,290,292,295,296,304,305,307,310,311,312,315,316,317,319,322,323,324,325,328,332,333,342,344,346,347,348,350,351,353,354,356,357,359,360,361,362,363,364,368,372,373,375,376,377,382,384,386,389,390,391,393,396,398,399,401,402,409,410,411,412,413,415,419,421,422,423,424,425,426,428,429,430,438,439,440,441,443,445,446,449,451,452,454,455,457,459,460,461,462,465,466,467,469,471,472,474,475,476,478,482,483,484,485],differenti:[1,3,6,29,185,347,378,419,442],difficult:[214,275,362,392,466],difficulti:[295,421],diffract:[],diffus:[],digit:[2,3,191,332],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:212,dihydrid:386,dij:295,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,206,216,233,325,350,409,460,482,483,484],dimdim:483,dimems:274,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,206,250,274,319,350,353,357,419,457,467],dimensionless:[105,121,122,124,127,129,131,136,140,319,348,429,449],dimentionless:135,dimer:[6,292,409],dimgrai:191,dimstr:[41,210],dinola:[279,310],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,309,478],dir1:468,dir2:468,dir:[1,3,4,8,9,11,12,249,273,282,306,419,421,422,455,468,483],dirac:140,direc:419,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,222,229,233,238,274,293,311,323,325,326,327,328,350,354,362,363,364,369,371,372,378,381,384,386,398,402,413,416,424,437,455,467,468,469,475,483],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,215,234,277,283,286,303,307,316,317,357,361,363,364,368,375,377,378,384,385,387,394,395,406,409,410,411,415,419,420,421,422,429,439,441,442,443,446,455,457,458,459,468,483],disabl:[3,12,16,319,397,455,470,483],disadvantag:[6,210],disallow:[188,216,251],disappear:459,discard:[2,3,41,71,206,210,320,328,454,459,460],discontinu:[9,185,355,404],discourag:409,discov:[13,320],discret:[6,8,40,42,190,191,235,238],discuss:[],disk:[6,84,85,158,186,217,227,278,455],disloc:70,disord:[39,70],disp:[],dispar:423,disperion:[381,402],dispers:[3,6,7,9,163,274,347,348,372,381,402,407,413,422,440,446],displac:[],displace_atom:[],displace_box:59,displacemet:460,displai:[11,13,22,37,44,55,173,184,188,190,334,342,375,438],dispters:3,dissip:[6,228,235,274,316,317,370,382,390,407,408,438],dissolut:211,dist:[6,69,91,108,117,188,275,291,383,437,452,484],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,206,207,211,212,213,214,216,217,218,221,227,233,238,248,249,250,251,255,263,273,274,278,282,283,290,291,292,295,296,300,304,305,306,307,314,315,317,318,319,322,324,325,326,327,328,329,333,347,348,350,353,355,357,358,359,362,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,388,389,390,391,392,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,455,457,460,466,467,471,475,478,482,484],distinct:[6,220,289,347,423],distinguish:[6,86,140,241,386,456],distort:363,distrbut:363,distribut:[],distro:[111,375,418,419],ditto:[8,11,12,14,15,16,17,18,115,212,450,455],div:8,divd:117,diverg:[3,12,39,292,317,459,478,485],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,205,210,216,273,315,322,327,347,355,357,387,422,446,466,474,483],divis:[6,238,368,396,406,454,457,475,483],dl_poli:7,dlambda:159,dlammps_async_imd:232,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,318,457,458,462],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:467,dlmp_intel_offload:[12,16],dlo:[59,187,216,278],dlopen:6,dlvo:[7,376,449],dm_lb:238,dmax:[307,353],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,217,227,235,236,246,251,252,256,257,261,268,269,270,271,278,281,292,304,307,310,311,312,321,325,328,330,332,334,342,346,355,356,357,362,363,364,367,375,377,378,384,385,387,392,393,395,396,409,410,411,413,415,418,419,420,429,438,439,441,443,445,446,455,457,458,459,460,462,465,466,467,474,475,483,484,485,486],docuement:423,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,206,209,210,212,213,214,216,220,222,224,227,228,231,233,235,236,238,241,247,251,252,253,254,256,257,268,269,270,271,279,280,281,285,287,290,292,307,310,312,314,315,319,322,323,324,327,328,329,330,335,336,338,339,341,346,347,348,349,350,356,357,358,363,364,365,366,367,368,370,372,373,374,376,377,378,379,381,382,383,384,385,386,388,389,390,391,393,394,395,396,397,400,401,403,404,405,407,408,409,410,411,413,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,446,448,449,450,452,453,454,455,457,458,459,460,461,464,465,467,468,469,470,471,474,475,478,483,487],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,206,207,304,356,358,362,364,377,385,395,421,422,439,441,442,443,446,457,459],dof:[3,8,112,144,145,158,203,292,484],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[356,457],doi:[6,215],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,210,214,216,217,231,234,238,251,252,275,287,292,319,324,325,347,348,357,362,383,413,452,454,457,461,474],domin:[1,386,471],don:[0,8,11,12,13,116,168,197,222,236,281,328,409,455,457],donadio:311,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,210,211,212,213,214,216,217,225,227,232,233,235,236,243,251,256,257,268,269,271,272,274,275,276,281,289,292,293,295,307,310,311,312,314,316,317,330,332,346,347,348,355,357,358,361,362,364,372,384,393,394,395,402,408,409,413,421,437,440,445,452,453,454,455,458,461,462,465,475,476,478,483,484],donor:392,dot:[141,161,197,222,230,250],doti:[368,419],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,216,225,280,328,332,346,348,361,362,368,387,391,421,422,453,457,461,465,470,483,484],dover:200,down:[3,6,7,8,11,39,71,214,227,235,307,323,362,386,413,456,476],downhil:[353,354],download:[5,7,8,9,11,12,13,17,232,394,420],downsid:6,downward:289,dozen:[8,12,107,194,421,422],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:244,dproduct:365,dr_ewald:[118,293],drag:[],dragforc:238,drai:[249,282],drain:[231,323,355],dramat:[59,187,211,212,213,214,216,251,307,310,311,348,362,413,454],drautz:368,draw:190,drawback:281,drawn:[188,190,191,228,452],drayleigh:[249,282],dreid:[],drfourth:105,drho:[113,363,384],drift:[6,103,105,228,229,235,236,247,290,307,466,474,478],drive:[11,12,198,214,216,230,251,273,279,292,326,357],driven:[6,177],driver:[6,12,14,15,194,225,232],drop:[3,191,382],droplet:393,drsquar:105,drude:[],dry:224,dsecriptor:394,dsf:[],dsmc:[],dstyle:278,dt_collis:238,dt_lb:238,dt_md:238,dt_srd:307,dtilt:[59,216],dtneb:471,dtqm:282,dtype:[115,212],dual:[16,17,307,362],dudarev:164,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,126,140,141,143,144,146,148,151,152,153,154,155,157,158,160,164,165,168,169,188,190,194,197,198,205,209,211,212,213,214,215,216,217,222,223,224,225,228,229,232,233,235,236,237,238,241,242,243,247,248,249,250,251,255,263,273,276,278,290,291,292,294,304,306,307,308,310,311,312,313,314,316,317,319,323,324,326,327,328,330,348,353,355,357,358,359,379,382,384,388,389,393,407,408,413,419,421,423,424,437,440,441,443,447,449,450,452,454,457,458,459,466,471,474,475,476,478,483,484],duffi:319,duin:[9,283,288,421,422],duke:348,dummi:[12,29,442],dump1:462,dump2:462,dump2vtk_tri:134,dump:[],dump_atom:8,dump_custom:8,dump_h5md:189,dump_modifi:[],dumpcustom:8,dumptimestep:462,dunbrack:[6,20,171,373,469],dunweg:[235,237],duplic:[2,3,14,15,17,41,42,166,210,229,273,457,482],dupont:[5,7,13],durat:[37,55,143,144,146,147,148,150,151,152,153,154,157,158,184,191,203,227,287,319,342,390,438],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,128,142,147,166,169,185,188,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,218,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,250,251,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,300,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,348,355,357,361,362,382,406,413,422,440,452,453,455,457,460,462,464,465,467,469,471,472,475,476,483,486,487],dvector:8,dvlo:449,dvx:6,dx_lb:238,dy3:164,dyamic:12,dyanam:6,dyanmic:471,dynam:[],dynamo:[5,363,384,409],dyne:482,dyre:403,dysam:460,e28637:29,e_1:368,e_2:368,e_b:387,e_e:386,e_hbond:392,e_i:[6,368,387],e_j:[6,368],e_k:[368,386],e_kl:6,e_lj:[364,381],e_n:[368,386],e_nn:386,e_pr:386,e_rebo:364,e_tors:364,eaa:333,eaat:172,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,93,94,95,96,97,98,99,100,101,102,103,104,105,106,109,110,111,112,113,114,115,116,117,118,119,120,134,140,141,142,144,145,146,147,148,149,152,153,154,155,157,158,159,160,161,162,163,164,165,168,169,171,172,173,174,175,176,177,178,179,180,182,183,184,185,187,188,189,190,191,192,193,194,195,196,197,198,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,241,242,243,244,245,247,248,249,250,251,253,254,255,256,257,258,259,260,261,263,264,265,266,267,268,269,270,271,273,274,275,276,277,278,279,280,281,283,284,285,287,289,292,293,294,295,296,300,301,303,304,305,306,307,308,309,310,311,312,314,317,318,319,320,321,322,323,324,325,327,328,329,330,332,333,335,336,337,338,339,341,342,343,346,347,348,350,354,355,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,418,419,421,422,423,424,425,429,430,431,432,433,434,435,436,437,438,439,440,443,444,445,446,447,448,449,450,451,452,454,455,457,458,459,460,461,462,464,465,466,467,469,471,472,474,475,476,478,482,483,484,485,487],eacn:[41,210],eam0d:274,eam3d:274,eam:[],eam_databas:13,eam_gener:13,eangl:475,earli:[41,203,205,206,207,208,210,286,293],earlier:[7,8,12,59,191,357,390,409,413,471],earliest:471,earth:386,easi:[6,7,8,9,11,13,87,141,188,195,196,197,198,206,209,222,230,231,233,235,236,294,301,310,311,312,324,327,329,356,457,460,465,467,484],easier:[8,9,13,16,188,190,274],easili:[8,11,190,191,323,357,454,464,473,483],eastwood:[347,348],eat:172,eatom:330,eaxmpl:6,eba:21,ebb13:172,ebb:21,ebond:[220,236,474,475],ebt:172,ec_ii:409,ec_ij:409,ec_jj:409,echo:[],eco:[421,422],ecoa:[421,422],ecoul:[107,220,236,421,422,475],ecp:[386,457],edg:[2,3,6,41,59,71,118,163,164,167,168,189,190,199,206,233,294,324,327,328,329,330,350,457,460,467],edge_histo:163,edge_threshold:163,edih:475,edim:315,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,478],editor:13,edu:[7,9,11,13,384,407,418,421,422],edward:[9,17],eebt:172,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,81,89,90,93,103,104,105,106,109,112,141,143,147,152,153,160,163,169,171,172,174,175,176,177,179,180,182,183,184,185,187,188,190,191,195,196,197,200,201,204,207,208,209,211,212,213,214,216,217,223,226,227,228,229,230,231,232,233,235,236,250,251,253,254,255,256,257,258,266,268,269,271,272,273,275,278,279,281,282,283,284,287,291,292,294,295,306,307,310,311,312,314,315,317,319,322,323,324,325,326,327,328,329,330,333,335,336,337,338,341,343,347,348,350,354,355,356,357,358,363,364,366,368,369,370,371,372,373,374,376,377,378,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,413,414,415,416,418,423,424,425,427,430,438,439,440,441,442,443,445,446,448,449,450,452,454,455,459,460,462,466,467,469,475,476,482,483,485],efffect:461,efficaci:39,effici:[0,1,3,6,7,8,10,12,15,17,18,39,58,61,67,112,142,188,189,190,191,214,216,220,229,251,275,277,287,292,295,307,347,348,353,358,362,368,376,378,393,398,402,423,464,487],effort:[5,7,458],efftemp:[96,97,151],efi:[421,422],efield:[],eflux:231,eggebrecht:378,ehb:[421,422],eigensolv:3,eigenvalu:[274,275,347],eigtol:3,eik:159,eim:[],eimp:475,einstein:[287,317],either:[1,2,3,4,6,8,9,11,12,14,15,16,17,22,33,41,44,50,59,63,71,107,113,116,118,140,141,145,147,148,164,165,168,173,178,185,188,189,190,191,194,202,204,205,207,208,210,213,214,215,216,217,227,233,234,238,242,248,249,251,252,255,269,273,289,292,294,295,296,304,307,314,321,325,328,332,334,345,347,348,350,354,355,359,362,368,370,376,384,393,394,396,407,408,409,413,417,419,441,443,445,452,455,457,459,460,461,464,466,469,472,474,483],ejtehadi:[376,389,423],elaplong:[195,196,233,460,475,483],elaps:[3,195,196,197,198,209,216,222,230,231,233,235,236,248,278,294,301,310,311,312,324,325,327,329,430,452,460,462,463,467,471,475,483],elast:[],elastic_t:4,elba:29,electr:[6,194,200,222,236,347,348,387,421,422,450,478,482],electrolyt:[9,449],electron:[3,6,7,9,13,40,96,97,113,118,149,151,156,194,200,219,220,236,237,252,262,270,285,313,319,354,356,363,365,377,381,384,386,387,409,419,420,443,446,450,457,478,482],electron_integr:200,electron_temperatur:200,electron_unit:386,electroneg:[6,283,284,285,377,387],electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,16,18,201,227,283,285,286,320,347,348,376,381,386,398,406,408,422,449],eleftheri:292,elem1:[387,409,429],elem2:[387,409,429],element1:[289,363,384],element2:[289,363,384],element:[3,6,7,8,12,13,63,81,89,103,105,112,117,119,134,140,141,142,143,144,145,146,147,148,152,153,154,155,157,158,161,188,189,190,191,192,194,200,204,205,208,274,289,314,321,363,364,368,377,384,385,386,387,393,394,395,409,410,411,415,419,420,421,422,429,439,441,442,443,446,478,483,486],elementn:[363,384],elementset:200,elev:471,elif:[140,332],elig:[3,201,211,212,224,227,392],elimin:[3,6,71,228,235,236,292,295,316,317,452],elj:381,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,82,144,186],ellipsoid:[3,4,6,7,13,40,42,82,113,130,144,165,186,188,235,253,256,259,260,268,292,307,352,355,389,408,423,438,457,467,485],ellipsoidflag:457,elong:[220,236,475],elp:[421,422],els:[3,7,8,12,71,107,116,117,119,189,190,202,203,204,205,206,207,208,227,251,292,307,319,320,321,330,332,347,393,456,468,483,486],elsewher:[8,248,307,409,420,421,422,469,475,483],elt:409,emac:[],email:[0,3,5,7,8,11,387],emb:[3,9,328],emb_lin_neg:409,embed:[3,5,7,11,12,13,29,88,142,163,319,363,384,387,406,409,410,411,419,438,447,455],embt:172,emi:[7,9],emol:[421,422,475],emphas:390,empir:[200,311,364,386],emploi:[9,274,287,442],empti:[3,57,71,167,292,347,358,397,457,468,469,483],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,83,87,96,97,98,99,100,101,105,109,111,112,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,147,149,151,152,156,157,159,163,171,172,174,175,176,177,178,179,180,182,183,184,185,188,189,191,192,194,195,196,197,198,199,201,207,209,211,212,213,215,216,217,222,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,244,245,247,249,251,252,253,254,255,256,257,258,259,260,261,262,264,266,267,268,269,270,271,273,274,275,277,278,282,283,284,285,286,287,288,289,291,292,294,295,296,297,298,299,300,301,303,304,306,307,310,312,313,314,315,316,317,319,320,322,323,324,325,326,327,328,331,333,335,336,337,338,339,341,342,343,348,355,357,361,362,363,364,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,455,458,459,464,466,476,483,487],enclos:[2,6,12,167,188,280,332,409,453,455,465,483],encod:[13,39,42,188,190,191,281,393],encompass:[3,6,40,57,59,116,166,303,321,438,460],encount:[3,8,12,59,205,361,462,483],encourag:[7,8,286,305],end12i:113,end12x:113,end12z:113,end1i:113,end1x:113,end1z:113,end2i:113,end2x:113,end2z:113,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,57,59,71,113,168,169,172,187,188,190,191,192,195,196,204,205,207,208,213,216,220,228,233,235,236,237,250,251,252,263,279,291,292,296,307,310,311,312,313,315,318,319,322,326,329,330,346,347,356,357,361,362,382,384,389,423,426,428,429,430,444,447,452,455,457,458,459,460,462,464,465,469,473,475,478,483,487],end_of_step:8,endbondtors:[3,172,178,457],endif:8,energet:[213,364,422],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,123,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,188,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,333,335,336,337,338,341,343,347,348,353,354,355,357,358,362,363,364,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,421,422,423,424,429,430,431,432,437,438,439,440,441,442,443,445,446,447,448,449,450,452,455,457,462,466,467,469,471,473,474,475,478,482,483,486],energy_update_freq:422,enforc:[6,57,58,104,187,188,189,190,192,194,201,213,216,251,272,274,284,292,295,332,347,398,454,483,484],enforce2d:[],eng:[11,65,69,108,188,225,330,332,377,411],eng_previ:332,engin:[200,216,277,296,316,384,410],engr:[421,422],enhanc:[196,200,452],enlarg:[59,190],enough:[3,40,61,86,165,166,168,210,236,278,282,287,292,320,324,325,328,358,362,378,417,457,461,462],enpub:384,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,214,227,228,251,297,318,348,368,383,406,437,439,446],enter:[57,155,387,446,471],enthalpi:[123,253,254,384,474,475,483],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,206,207,210,213,215,224,227,228,231,235,236,247,251,253,254,255,256,257,273,275,277,290,292,305,319,321,332,362,381,402,413,440,457,465,466],entireti:[396,445],entiti:[6,8,40,42,188,292],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,205,206,207,215,282,330,356,368,385,409,415,422,429,439,440,441,442,443,446,483],entropi:471,entry1:[38,56,191,375,440],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:362,environ:[1,3,6,11,12,16,17,18,190,229,234,273,362,363,368,375,377,385,386,419,441,454,468,483],epair:[107,191,388,392,421,422,475],epen:[421,422],epfl:[229,234],epp:381,epq:381,eps0:449,eps14:406,epsilon0:443,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,227,292,307,324,328,353,355,367,373,374,376,378,379,380,381,389,391,392,393,396,397,398,399,400,401,402,403,404,405,406,412,416,423,424,433,439,445,448,449,466,478,482],epsilon_0:450,epsilon_14:373,epsilon_:423,epsilon_d:379,epsilon_i:[389,413,423],epsilon_i_:423,epsilon_i_a:[389,423],epsilon_i_b:[389,423],epsilon_i_c:[389,423],epsilon_ij:413,epsilon_j:[389,413,423],epsilon_j_:423,epsilon_j_a:[389,423],epsilon_j_b:[389,423],epsilon_j_c:[389,423],epsilon_lj:423,epton:418,eqch:160,eqeq:[421,422],eqp:381,eqq:381,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,208,209,210,214,216,217,222,227,228,230,231,233,235,236,238,241,242,248,249,255,265,273,275,278,280,282,283,284,287,289,291,292,294,296,301,303,310,311,312,315,316,317,319,321,322,324,327,329,330,332,346,350,355,357,358,359,361,362,377,382,388,389,392,407,412,419,421,422,423,425,426,427,429,430,440,445,446,450,453,454,455,457,459,460,464,465,468,471,473,475,483,484],equat:[3,6,7,8,9,91,112,118,164,173,184,194,214,220,221,229,235,236,238,241,249,250,251,252,255,269,273,275,282,283,287,295,307,315,319,322,324,325,327,329,341,347,348,376,381,382,386,387,390,395,407,408,409,413,423,426,428,432,433,435,436,444,450,478],equi:252,equidist:250,equil:[3,283,351,464,487],equilater:467,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,213,214,227,249,251,252,269,270,282,283,284,285,315,316,317,322,377,378,421,422,453,467],equilibria:322,equilibribum:[211,212],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,214,216,227,228,229,236,238,251,255,269,282,287,291,295,296,304,307,314,315,317,322,333,335,338,341,377,409,415,478],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,205,208,214,216,227,235,251,269,279,291,292,327,382,386,441,443,457,460,465,466,475,478],equlibrium:6,equliibr:[283,285],er3:164,eradiu:[40,113,386,457],eras:[294,316],erat:[216,408],erc:378,erfc:[378,398,413],erforc:113,erg:482,erhart:[201,384,441,443],ermscal:365,ernst:9,eror:3,eros:409,erose_form:409,erot:[],errata:[441,443],erratum:324,erron:3,error:[],erta:390,ervel:[113,457],escap:[217,478],especi:[8,11,16,153,165,194,201,210,227,282,287,290,291,362,454],espresso:[9,286],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,255,274,323,348,364,378,398,443,462,475],essex:29,establish:[87,231],estim:[1,3,6,10,12,38,41,56,91,141,200,210,221,249,307,314,347,348,353,413,422,440,471,475],esu:482,esub:409,eta:[6,238,251,282,283,285,323,385,387,389,419,442,446,482],eta_dot:251,eta_ij:419,eta_ji:387,etag:[40,457],etail:475,etap:251,etap_dot:251,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,200,201,202,203,205,206,207,208,211,212,216,217,225,227,228,235,251,278,289,293,319,320,328,332,346,347,355,356,357,358,360,384,385,393,406,408,417,421,422,439,441,443,446,452,455,457,458,459,464,466,467,471,473,474,475,476,478,482,483,485,487],ethernet:18,etol:[355,357,452,471],etot0:282,etot:[6,94,96,97,110,141,151,191,220,236,249,282,474,475],eu2:164,eu3:164,euler:[355,357],eulerian:200,euqat:431,europhi:238,ev_tal:8,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,216,222,228,230,231,233,234,235,236,274,280,283,294,297,301,310,311,312,321,324,327,329,330,332,347,348,353,355,362,413,419,425,427,440,452,453,455,459,460,462,464,465,466,467,471,473,475,483,484],evalut:[332,455],evan:[153,269],evanseck:[6,20,171,373,469],evapor:[],evaul:[8,355],evdwl:[107,421,422,475],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,205,206,207,208,210,211,212,214,216,217,220,233,236,249,251,252,274,287,289,292,293,303,307,315,319,322,324,328,330,340,347,353,355,357,362,367,386,387,390,393,413,423,446,447,457,458,460,462,463,464,466,467,469,472,474,475,476,478,487],evenli:[3,41,141,185,210,238,396,447,457],event:[],eventu:[3,6,12,15,167,283,471],ever:[54,56,234,307],evera:[376,389,423,438],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,221,224,225,227,229,231,232,233,238,239,247,251,252,255,272,273,274,278,279,280,281,282,283,284,285,287,289,290,292,293,295,296,307,309,310,311,312,313,314,315,318,319,320,321,322,330,332,346,348,357,358,359,362,382,383,393,406,421,422,434,451,452,453,457,459,461,462,464,465,466,471,472,473,475,483,487],everyth:[8,107],everywher:[116,400],eviri:386,evolut:[229,238,275,452],evolv:[238,275,320],ewald:[2,3,5,6,7,8,12,88,110,118,141,320,347,348,355,369,371,372,378,381,386,398,402,416,424,438,440,459],ewald_disp:381,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,210,213,228,229,235,236,237,278,287,288,307,319,334,347,375,459,464,471,483,485,487],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,205,210,216,221,228,235,236,237,252,262,263,270,274,282,307,312,313,326,362,375,382,384,390,393,396,407,413,440,459,460,467,471,483],exager:478,examin:[6,8,9,17,213,274],examp:[455,483],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,206,207,210,214,216,221,224,251,274,298,299,307,355,362,457,483],exceed:[3,41,59,210,216,251,307,465],excel:386,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,205,209,210,214,216,223,226,227,230,233,235,237,251,252,253,254,255,256,257,258,262,263,266,268,269,270,271,275,284,285,292,294,295,304,307,310,312,313,319,323,327,330,332,333,334,335,336,337,338,341,342,343,347,348,350,352,356,357,358,360,361,362,363,364,366,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,410,414,415,416,418,421,422,423,424,430,438,439,440,441,442,443,445,446,448,449,450,452,454,455,457,459,460,462,465,466,467,468,469,471,475,478,482,483,484,486],excess:386,exchang:[2,3,6,8,9,61,62,194,200,201,227,235,284,292,315,319,322,347,362,386,472],exchange:347,excit:[9,386],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,206,211,212,239,247,277,290,292,314,325,330,355,356,358,370,390,393,407,408,413,437,469],exclus:[1,3,9,12,16,87,362,377,413,466,476],excurs:452,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,232,286,332,346,349,361,453,455,465,468,471,483],exemplari:228,exemplifi:386,exert:[6,233,236,287,326,327,328,348],exhaust:[200,361,483],exhibit:[251,354,386,466],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,209,212,214,217,227,277,278,280,330,333,335,336,338,342,351,356,362,393,421,447,453,455,457,458,459,468,469,470,483,484,485],exit:[2,3,11,12,41,57,188,210,346,361,455,456,465,474,483],exlanatori:3,exp:[],expand:[],expans:[12,140,188,468,483],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,210,222,227,229,248,273,279,281,282,287,292,330,348,358,375,409,413,452,455,457,459,462,466,471,483],expens:[6,10,71,191,273,277,292,319,330,347,348,358,362,455],experi:[6,13,15,17,209,217,232,241,250,279,291,292,353,357,382,413,466,471],experienc:[6,12,240,241],experiment:[227,347,362,471],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,208,210,212,214,216,251,273,281,292,304,330,332,346,347,350,356,357,361,367,384,396,430,445,455,458,459,462,464,467,478,483,487],explan:[3,6,59,113,140,188,203,250,273,393,451,454,455,457,466],explanatori:[3,8,117,188,202,203,205,206,207,292,356,454,483],explantori:[3,288],explic:412,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,216,298,299,334,352,364,365,368,373,375,384,386,397,407,444,451,454,458,461],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,206,209,216,223,226,228,230,235,251,253,254,255,256,257,258,266,268,269,271,281,282,284,292,294,295,310,312,313,319,323,327,333,335,336,337,338,341,343,356,362,363,364,366,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,410,413,414,415,416,418,423,424,430,431,432,433,434,435,436,438,439,440,441,442,443,444,445,446,448,449,450,457,459,466,467,469,470,476,478],explictli:[16,470],exploit:[9,15,17,275],explor:[118,164],expon:[3,283,285,384,389,392,406,412,424],exponenti:[87,419,439,446,450,471,483],expos:11,exposit:[200,382,383],express:[6,140,151,165,195,196,214,248,273,283,319,325,332,368,384,386,400,409,429,438,483],expressiont:368,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,208,209,215,218,222,225,226,227,229,230,231,233,235,237,249,251,255,263,273,274,290,291,292,294,296,301,304,306,310,311,312,313,314,316,317,319,321,324,328,329,389,409,422,423,429,474,475],extent:[1,3,41,45,57,71,163,167,188,199,206,210,233,326,329,347,350,364,425,427,440,454,457,460],exterior:[3,6,328],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,205,210,212,251,280,281,282,292,307,355,356,359,360,381,390,393,396,409,413,454,455,457,460,469,478,483],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,285,357,378,387,409,429,455,462,474],extract_atom:11,extract_comput:[11,455],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,214,216,251,317,386,442,478],extrema:406,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,321],f_a:[441,442,443],f_ave:117,f_c:442,f_f:443,f_fix_id:282,f_harm:317,f_i:419,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,246,309,321,475,483],f_ij:419,f_indent:208,f_int:316,f_jj:91,f_k:419,f_langevin:319,f_max:[282,287],f_msst:249,f_r:[236,441,442,443],f_sigma:368,f_solid:317,f_ss:6,f_temp:236,face:[3,6,57,59,71,153,163,167,199,206,207,324,326,327,328,329,350,389,409,423,457,460],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,229,307,317,390,469],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,210,214,216,217,227,232,235,237,238,249,251,252,255,275,279,291,295,297,299,307,311,315,322,323,324,328,338,348,350,362,364,365,368,369,371,373,378,379,380,382,386,390,393,397,398,409,413,415,416,422,424,430,439,444,454,457,460,461,466,469,471,472,475,478,482,483],factori:[3,455],factoriz:347,fail:[3,11,12,59,169,214,217,347,355,357,380,422,455],failur:[121,426,456,483],fairli:[11,413,466,471],faken:73,falcon:232,fall:[3,6,191,205,278,455,483],fals:[86,330,332,483],fame:8,famili:[446,454],familiar:[0,11],fan:419,far:[3,6,12,17,57,59,61,86,188,191,192,210,211,212,214,217,251,273,291,292,307,324,335,338,353,357,358,445,455,457,462,475],farago:235,farrel:[441,443],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,206,210,212,217,227,229,233,248,249,251,253,254,255,256,257,265,268,269,270,271,281,282,284,292,296,300,306,309,317,319,323,324,325,327,329,357,393,407,460,469,483,486],fasolino:395,fast:[6,7,9,12,13,17,39,188,260,282,320,347,348,370,407,408,438,440,459,464,466,475,484,487],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,209,210,216,223,226,230,234,235,251,253,254,255,256,257,258,266,268,269,271,279,283,284,292,294,295,307,310,312,314,316,319,323,327,333,335,336,337,338,341,343,347,348,359,360,362,363,364,366,368,369,370,371,372,373,374,375,376,377,378,381,382,384,385,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,414,415,416,418,423,424,430,438,439,440,441,442,443,445,446,448,449,450,452,466,470,478],fastest:[1,6,14,17,153,206,319,320,362,454],fatal:[3,474],fault:[70,422],faulti:12,fava:389,favor:213,favorit:7,fbmc:314,fcc:[],fcm:[265,483],fdirect:220,fdotr:394,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:384,feedback:[7,232],feel:[7,232,233,241,273,328,330,357,413],felling:411,felt:328,femtosecond:482,fene:[],fennel:[378,398],fep:[],ferguson:[6,171,469],fermi:[1,12,15,151,362,443],fermion:[9,386],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,205,206,207,208,236,251,278,281,283,295,321,347,355,356,357,364,454,457,462,466,468,476,483,485],fewer:[1,3,11,15,16,61,241,466],fewest:3,fextern:225,feynman:275,fff:455,ffield:[377,387,421,422],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,274,347,348,466],fft_inc:[12,348],fft_lib:12,fft_path:12,fftbench:[347,476],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,197,198,222,225,229,275,291,378,398,402,437],field1:[458,462],field2:458,field:[],fifth:[304,415],figur:[1,3,8,11,12,282,454,455],fij:381,file0:273,file1:[11,13,273,318,332,356,462,464,468],file2:[11,13,318,332,356,462,464,468],file:[],file_from:189,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,210,215,273,277,280,283,284,285,288,289,292,293,318,319,344,345,346,357,363,364,368,378,384,385,387,395,409,410,411,415,419,420,421,422,429,439,440,441,442,443,446,453,454,455,458,459,464,468,475,483,485,486,487],filennam:464,filep:[3,188,191,459,464,487],filepo:289,fill:[7,165,190,278,319,350,358,368,422,460],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,380],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,213,214,224,227,250,273,279,287,291,353,355,357,358,378,393,398,402,409,438,440,478,483],find_custom:8,fine:[16,17,169,197,222,317,358,362,483],finer:[140,165,483],finest:347,finger:[165,187,248,460],finish:[6,11,41,210,332,344,346,347,359,361,362,445,462,483,484],finit:[],finni:[7,384,438],finvers:220,fiorin:[9,215],fire:[353,354,355,357,471],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,203,204,205,206,207,208,210,213,216,227,228,233,238,248,249,250,251,273,275,280,281,282,284,289,292,295,296,304,305,307,308,309,316,317,318,319,321,325,330,332,333,339,350,355,356,357,358,361,362,363,364,367,368,369,371,373,375,377,378,384,386,387,390,391,393,394,395,397,398,402,407,408,409,411,413,415,419,421,422,429,437,439,440,441,442,443,446,450,452,453,454,455,457,458,459,462,464,466,469,470,471,474,475,478,483,484,485,487],fischer:[6,9,19,20,171,373,469],fit:[3,6,9,12,38,56,185,291,307,364,368,395,409,413,433,440,442,465,483],five:[73,151,282,356,368,410,457,471],fix:[],fix_adapt:[159,196,406],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,278],fix_evapor:201,fix_flux:200,fix_gcmc:[201,356],fix_gl:229,fix_gld:229,fix_grav:278,fix_id:[3,214,249,251,253,254,255,256,257,279,282],fix_modifi:[],fix_mov:[187,325],fix_nh:8,fix_npt:229,fix_nvt:[201,227],fix_poem:[3,6],fix_pour:[3,217],fix_qbmsst:9,fix_qeq:[3,377],fix_rattl:295,fix_reax_bond:421,fix_rigid:[241,367],fix_saed_vtk:293,fix_setforc:8,fix_shak:295,fix_srd:3,fix_styl:255,fix_temp_rescal:313,fixedpoint:[214,251],fixextern:225,fixid:200,fji:381,flag1:[219,360],flag2:[219,360],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,208,213,215,219,232,235,239,241,247,248,274,281,292,304,306,307,314,318,327,330,345,348,356,360,361,362,364,392,397,409,437,452,454,455,457,458,459,461,462,463,467,483],flag_buck:372,flag_coul:[372,381,402],flag_lj:[381,402],flagfld:[370,407,408],flaghi:[3,370,407,408],flaglog:[370,407,408],flagn:219,flagvf:[370,407,408],flat:[6,319,324,325,329],flavor:[2,7,12],fld:[9,324,370,407,408],flen:365,flex_press:365,flexibl:[3,6,8,166,190,203,206,215,229,252,315,322,386,442,475],flip:[3,6,216,251,326,327],floor:483,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,214,227,228,235,238,251,255,273,274,317,319,341],fluid:[],fluid_veloc:242,flush:[3,191,474],flux:[],flv:190,fly:[7,9,12,41,190,194,200,217,220,292,295,320,368,475,478],fmackai:9,fmag:218,fmass:275,fmax:[355,475],fmomentum:220,fmsec:[2,191,235,236,248,251,279,292,310,311,466,477,482,484],fname:346,fno:[12,16],fnorm:[355,475],fnpt:220,fnvt:220,foce:393,fock:365,focu:295,fogarti:[9,285,422],foil:[140,273,429],fold:[305,466],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,210,215,216,217,220,221,225,227,228,229,232,234,235,236,238,241,249,251,255,256,257,268,269,271,274,275,277,280,281,282,283,285,287,289,291,292,293,295,309,310,311,312,315,316,317,318,319,321,322,330,331,335,336,337,338,341,343,345,350,352,355,356,357,362,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,426,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,446,448,449,450,452,454,455,457,458,459,460,462,464,465,466,469,471,472,473,478,483,484,486],foo:[4,8,11,12,188,190,225,455,468,483],foot:6,footprint:[12,362],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:241,forcefield:[291,392],forcegroup:238,forcezero:353,ford:381,forestgreen:191,forev:71,forget:[236,478],forgiv:251,fork:[12,188],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,9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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 force/tally 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_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":211,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,206,207,208,211,212,214,215,216,217,221,224,227,228,233,235,236,237,238,239,241,246,249,251,252,255,269,270,274,275,278,279,280,281,282,284,287,289,290,292,293,307,309,314,315,316,317,320,322,324,326,330,342,345,347,348,350,351,353,354,356,358,359,360,362,365,368,370,386,407,408,413,421,422,437,438,452,453,454,457,458,460,462,464,465,466,469,471,473,474,475,476,477,482,484,485,486],"function":483,"long":[369,371,372,373,374,378,380,381,398,402,406,416,424],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:297,adp:363,airebo:364,alloi:384,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:199,arrai:6,aspher:[6,82,144,253,256,259,260,268],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,281,483],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:209,awpmd:[9,365],balanc:[41,210],barostat:6,basal:67,beck:366,berendsen:[279,310],between:6,binary2txt:13,bodi:[6,8,42,68,261,367],bond:[8,13,69,211,212,213,288],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:368,born:[369,380],boundari:[7,57],box:[6,58,214],brownian:370,buck:[371,372,380],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,373,406],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,333,374],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[324,376,449],colvar:[9,13,215],com:[74,75,146],comb3:377,comb:[284,377],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,483],compute_modifi:102,condit:7,conduct:[6,315],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:204,cosin:[23,24,25,26,27,28,174],cossq:335,coul:[369,371,372,373,374,378,379,380,391,398,402,406,416,424],coupl:6,creat:212,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:311,csvr:311,cubic:400,cuda:[9,14,109,112,143,152,197,209,223,226,230,251,258,294,295,310,312,323,369,371,373,374,384,390,391,398,399,401,404,414,439,441],custom:8,cut:[49,365,371,374,378,381,386,388,398,399,406,412,416],cvff:336,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[378,398],deform:[148,149,216],delete_atom:168,delete_bond:169,delta:24,deposit:217,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],diagnost:7,diel:379,dielectr:170,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:173,dihedral_styl:[2,171,172,174,175,176,177,178,179,180,181,182,183,184,185],dilat:80,dimens:186,dipol:[6,29,381],direct:220,discuss:6,disp:6,displac:[81,86],displace_atom:187,distribut:[7,12],document:0,dpd:382,drag:218,dreid:[6,392],drude:[6,9,150,219,220,236],dsf:[378,398],dsmc:383,dump:[6,8,188,189,190,192],dump_modifi:191,dynam:283,eam:[13,384],echo:193,edip:385,eff:[9,13,96,97,149,151,156,237,252,262,270,313,386],efield:222,eim:387,elast:6,emac:13,enforce2d:223,ensembl:7,erot:[82,83,84,85],error:3,evapor:224,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],exp:[27,174],expand:[46,401],extend:[8,11],extern:225,fcc:273,featur:[7,8,483],fene:[45,46],fep:[9,13,87,196],field:[6,7],file:6,finit:6,fix:[2,6,8,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,483],fix_modifi:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],flow:6,fluid:238,flux:[91,142],forc:[6,7,142,308],fourier:[30,31,175,337],freez:226,from:[6,11],futur:5,gauss:388,gaybern:389,gcmc:227,gener:[1,6,7,13],get:12,gld:228,gle:229,global:6,gpu:[9,15,366,369,371,373,374,376,378,381,382,384,388,389,391,398,399,400,401,412,414,423,424,430,439,440,441,448,449,450],gran:[325,390],granular:6,graviti:230,gromac:391,group2ndx:331,group:[88,330,483],gyrat:[89,90],h5md:[9,188,189],harmon:[32,47,48,49,176,179,324,338,415],hbond:392,heat:[91,142,231],heatconduct:431,helix:177,hertz:[390,425],histo:205,histori:[5,390],hook:390,hourglass_error:122,how:6,hybrid:[33,50,178,339,393],idealga:432,imag:[188,190],imd:232,implicit:373,improp:[8,92],improper_coeff:334,improper_styl:[2,333,335,336,337,338,339,340,341,342,343],includ:344,inclus:8,indent:233,indic:0,individu:2,induc:6,inertia:93,info:[0,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,345],input:[2,6,8],instal:11,instruct:9,integr:[6,7],integrate_tlsph:298,integrate_ulsph:299,intel:[9,16,373,389,398,439],interfac:[6,11],internal_energi:123,introduct:7,invers:220,ipi:234,ipp:13,jul:[],jump:346,kate:13,keyword:413,kim:[9,394],kokko:[9,17],kspace:[2,8,9,320],kspace_modifi:347,kspace_styl:[6,348],label:349,lammp:[0,1,2,6,7,8,11,12],langevin:[235,236,237],lattic:350,lcbop:395,librari:[6,11,12],limit:[263,312],line:[12,264,396],linear:405,lineforc:243,list:[2,397],lj1043:324,lj126:324,lj93:324,lj96:399,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:351,lubric:407,lubricateu:408,make:12,mass:352,math:483,matlab:13,meam:[9,409,410,411],measur:1,meso:[244,245],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:412,min_modifi:353,min_styl:354,minim:[8,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,355],misc:9,mod:[319,442],model:[6,7],modifi:8,molecul:356,molfil:[9,188,192],moltempl:13,momentum:[239,247],morri:436,mors:[51,392,414],move:248,move_tri_surf:300,movi:[188,190],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[369,371,373,378,398],msst:249,multi:[6,7,179],multipl:6,nb3b:415,neb:[250,357],neigh_modifi:358,neighbor:359,nemd:6,newton:360,next:361,nharmon:180,noforc:[260,265],non:[6,7],none:[34,52,181,340,417],nongauss:105,nonlinear:53,nph:[251,252,253,254,292],nphug:255,npt:[251,252,256,257,292],nve:[258,259,260,261,262,263,264,265,266,267,292],nvt:[251,252,268,269,270,271,292],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,171,172,174,175,176,177,179,180,182,183,185,230,251,253,254,255,256,257,258,266,268,269,271,284,333,335,336,337,338,341,343,363,364,366,369,370,371,372,373,374,376,377,378,379,381,382,384,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,411,414,415,416,418,423,424,430,439,440,441,442,443,445,446,448,449,450],onewai:272,open:7,oper:483,opl:182,opt:[19,373,384,398,402,414],optim:1,option:[6,8,12],orient:273,orthogon:6,other:6,output:[6,7,8,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],overlai:393,overview:11,packag:[1,9,12,14,15,16,17,18,19,362],pair:[6,107,108],pair_coeff:375,pair_modifi:413,pair_styl:[2,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450],pair_writ:447,pairwis:8,parallel:11,paramet:6,pars:2,partial:152,particl:[6,7,42],partit:451,past:5,per:6,perform:[1,10],peri:418,period:25,phonon:[9,13,274],pimd:275,piston:326,planeforc:276,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:418,poem:[9,277],point:283,polariz:6,poli:[370,407,408],polym:13,polymorph:419,post:7,potenti:[2,6,8],pour:278,pppm:6,prd:452,pre:7,press:279,pressur:112,previou:12,print:[280,453],problem:[3,4],process:[6,7],processor:454,profil:153,properti:[6,113,114,115,281],pymol_aspher:13,python:[9,11,13,455],qbmsst:282,qeq:[283,284,285],qmmm:[9,286],qtb:[9,287],quadrat:183,quantiti:6,quartic:[35,54],quip:420,quit:456,ramp:154,rattl:295,rdf:116,read_data:457,read_dump:458,read_restart:459,reax:[9,13,285,288,289,421,422],reaxc:9,rebo:364,recent:290,reduc:117,refer:483,reflect:327,region:[8,117,155,156,328,460,483],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,226,227,228,229,230,231,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,287,288,289,290,292,293,294,296,297,298,299,300,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,341,342,343,344,345,346,347,348,350,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,469,470,471,472,473,474,475,476,477,479,480,481,483,484,485,486,487],relax:214,replic:461,replica:[6,7],report:3,requir:12,rerun:462,rescal:[312,313],reset:221,reset_timestep:463,resquar:423,restart2data:13,restart:[6,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,464],restrain:291,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],rho:126,rhosum:434,rigid:[6,83,98,241,292],ring:341,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,465],run_styl:466,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,424],self:306,serial:11,set:[6,467],setforc:294,setvel:301,shake:295,share:[11,12],shell:[6,468],shield:283,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:283,slice:119,sllod:[269,270],small:292,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,296,297,298,299,300,301,303,425,426,427,428],smooth:[404,405],sna:140,snad:140,snap:429,snapshot:6,snav:140,soft:[406,430],solver:2,sourc:7,spatial:[206,207],spc:6,speci:289,special:[7,413,483],special_bond:469,sph:[9,431,432,433,434,435,436],sphere:[84,85,158,207,241,254,257,266,271],spheric:6,spline:[410,411],spring:[304,305,306,317],squar:28,srd:[307,329],srp:437,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],state:309,stationari:245,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],store:[308,309],strategi:1,streitz:378,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:470,summari:6,swap:[201,213],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],system:6,tabl:[0,6,38,56,185,440,441],tad:471,taitwat:[435,436],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,310,311,312,313],temper:472,temperatur:6,tersoff:[441,442,443],test:11,tfmc:314,thermal:[6,315],thermo:[6,473],thermo_modifi:474,thermo_styl:475,thermodynam:[6,8],thermostat:6,thole:444,time:[6,208],timer:476,timestep:477,tip3p:6,tip4p:[6,378,398,402,406],tip:12,tlsph:426,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:318,tool:[12,13],torqu:160,transform:220,tri:[267,445],tri_surfac:427,triangle_mesh_vertic:134,triclin:6,tstat:382,ttm:319,tune:320,type:7,ulsph:428,ulsph_num_neigh:135,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\ No newline at end of file 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_serial":12,"abstract":17,"boolean":[3,330,332],"break":[],"byte":[3,12,474],"case":[1,2,3,6,8,9,11,12,13,15,16,17,18,39,40,41,45,46,59,61,63,71,73,104,108,114,116,117,143,144,145,146,148,151,152,153,154,155,157,158,159,163,165,167,168,169,171,188,189,190,191,197,198,202,203,204,205,206,207,208,209,210,212,214,216,220,222,224,227,230,231,233,234,235,236,238,249,251,252,253,254,255,256,257,268,269,271,273,274,279,281,282,283,284,291,292,294,296,298,299,301,304,307,310,311,312,314,315,319,321,322,324,325,327,328,329,330,332,346,347,348,350,352,354,355,356,357,359,361,362,364,373,376,378,380,384,386,389,390,392,393,394,396,406,407,408,409,413,415,419,422,425,427,430,440,441,443,450,452,455,457,459,460,464,465,467,469,471,473,474,475,476,478,482,483,484,486,487],"catch":[1,3,455],"char":[6,8],"class":[1,3,5,6,7,8,9,11,12,13,22,37,44,55,173,184,225,281,334,342,374,393,421,422,438,446,455,457],"default":[],"export":[190,375],"final":[3,5,6,7,8,11,12,17,41,59,87,141,191,202,203,204,205,206,207,208,210,214,216,227,250,251,255,282,286,292,293,296,316,318,319,326,332,355,357,363,364,368,384,387,394,406,409,415,419,420,439,440,441,443,446,452,465,471,478,483,485],"float":[3,6,8,12,40,42,71,113,188,191,203,208,232,281,293,309,386,426,428,455,457,467,474,483],"function":[],"import":[1,2,3,6,11,17,18,71,87,105,165,176,194,203,206,214,227,230,235,236,251,287,292,310,311,312,314,319,329,331,357,393,406,455,457,466,474,478],"int":[3,6,8,11,101,225,227,235,237,287,319,474],"long":[],"new":[],"null":[3,6,91,112,141,165,194,209,215,218,221,248,281,290,294,296,300,301,304,305,325,363,364,377,384,387,390,393,394,395,409,410,411,415,419,421,422,429,439,441,442,443,446,457,460,465,467,484],"public":[0,7,8,12,225,234,387,420],"return":[2,3,6,8,11,14,15,16,17,18,19,41,71,108,117,134,135,139,163,165,191,203,206,207,216,225,332,344,346,390,454,455,456,464,467,473,483],"short":[1,3,6,7,13,16,163,251,292,307,320,348,358,359,362,364,368,369,371,372,373,377,378,380,386,393,398,402,406,409,413,416,424,440,444,452,455,465,467,471,478],"static":[],"switch":[1,3,6,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,91,109,112,140,143,152,164,171,172,174,175,176,177,179,180,182,183,185,190,193,197,201,209,216,223,226,230,234,235,238,251,253,254,255,256,257,258,266,268,269,271,284,292,294,295,310,312,316,317,323,327,333,335,336,337,338,341,343,344,346,348,351,357,361,362,363,364,366,369,370,371,372,373,374,376,377,378,381,382,384,385,387,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,414,415,416,418,421,423,424,430,439,440,441,442,443,445,446,448,449,450,451,452,454,457,459,464,466,470,472,483,485,487],"throw":474,"true":[6,12,13,17,108,115,188,210,212,216,251,252,273,274,275,279,292,314,318,330,332,362,386,390,439,455,459,467,483],"try":[1,3,8,12,17,19,203,232,238,315,316,317,322,455,483],"var":[3,11,12,165,330,346,468,483],"void":[4,6,7,8,41,168,210,225,460],"while":[1,3,9,10,11,12,13,14,18,71,105,140,148,163,176,188,192,201,207,214,216,220,228,229,234,235,236,238,251,269,282,287,289,320,348,355,362,368,379,384,422,441,443,446,452,455,466,471,478],a10:332,a123:332,a12:423,a2m:[6,91],a_0:[238,319,368],a_0_real:238,a_1:319,a_2:319,a_3:319,a_4:319,a_c:376,a_cc:376,a_f:443,a_i:444,a_ij:368,a_j:444,a_pi:368,a_sigma:368,a_ss:376,aacut:274,aat:172,aatom1:115,aatom2:115,aatom3:115,ab_23_cd:332,abbrevi:12,abc:[3,12,332,455,483],abf:215,abf_integr:13,abi:192,abil:[3,9,214,251,279,292,386],abl:[3,8,11,12,39,86,188,192,213,222,226,315,322,362,455,483,486],ablat:319,about:[0,1,3,4,6,8,9,10,11,12,13,17,39,41,42,61,63,78,108,115,116,118,159,165,188,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,218,220,221,222,223,224,225,226,227,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,250,255,258,259,260,261,262,263,264,265,266,267,272,273,274,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,294,295,304,305,307,308,310,311,312,313,314,315,316,317,318,319,321,322,323,324,326,327,328,329,330,345,348,354,355,357,362,367,373,378,393,418,422,449,455,458,459,464,465,467,472,476,483,485,487],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,57,63,64,68,70,71,72,73,76,77,86,87,89,90,91,93,94,96,97,112,114,116,118,140,141,143,144,145,146,147,148,151,152,153,154,155,157,158,159,163,164,165,167,168,171,172,173,174,175,176,177,178,179,180,182,183,185,188,189,190,191,194,195,196,197,198,203,204,205,206,207,208,210,213,214,216,217,222,225,227,231,233,235,236,237,241,250,251,255,275,278,280,285,291,292,296,304,307,310,311,312,313,330,332,333,334,335,336,337,338,339,341,343,348,350,352,356,357,361,362,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,416,418,419,421,422,423,424,429,430,431,432,433,434,435,436,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326,330,333,334,339,346,352,353,355,356,358,360,361,362,363,364,368,375,377,384,385,386,387,393,394,395,406,407,408,409,410,411,415,419,421,422,429,439,441,442,443,446,452,454,456,457,458,459,460,462,463,465,467,469,471,474,475,478,482,483,484,485,486,487],afterrun:465,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,147,151,159,188,191,216,231,278,333,346,357,407,408,452,454,455,457,459,464,471,473,483,485],against:[11,12,13,64,217,357,421,422],aggreg:[6,12,65,68,69,79,92,108,115,231,247,290,292,305,452,484],aggress:[231,471],agilio:[9,13],agre:[3,8,185,355,364,395,422],agreement:[5,7],ahd:392,ahead:326,aidan:[0,5,7,9,13,350],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,232],aktulga:[7,9,285,422],al2o3_001:[118,293],al3:164,ala:238,alain:9,alat:[273,409],alb:[419,441,443],albeit:291,albert:9,alchem:[87,159],alcohol:322,alcu:[363,368],alcu_eam:419,alderton:381,alejandr:[251,252],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,191,200,210,213,216,238,240,241,263,275,292,295,314,315,319,322,327,353,354,355,359,362,386,408,426,428,452,454,471],alia:[12,16],alias:[1,348],aliceblu:191,align:[6,12,29,41,71,167,185,206,210,233,350,457,460,478],alkali:386,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,244,246,247,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,303,304,306,307,308,309,310,311,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,337,342,345,346,347,348,349,350,352,355,356,357,358,359,361,362,363,364,365,367,368,369,371,372,373,374,375,377,378,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,452,454,455,456,457,458,459,460,461,462,464,465,466,467,468,469,470,471,472,474,475,476,478,482,483,484,485,486,487],allen:[29,87,381,389],allentildeslei:87,allign:3,allindex:331,alloc:[3,5,6,8,9,11,12,60,225,321,356,358,362,417,422,457,465],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,210,212,213,214,215,216,217,221,222,225,227,228,229,230,232,235,238,241,242,246,248,251,252,273,277,279,280,281,282,286,292,293,295,296,298,299,303,307,314,315,316,317,319,320,321,322,323,324,330,332,334,342,347,348,350,355,356,357,358,361,362,365,368,369,370,371,372,373,378,384,386,390,391,392,393,398,402,407,408,413,419,422,423,426,428,437,447,449,452,455,457,459,460,461,462,463,464,467,469,470,471,474,475,483,484],almost:[2,3,12,60,233,282,319,348,359,362,437],alo:378,alon:[6,7,213,288,421,422,455],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,213,233,238,239,243,248,250,282,292,295,296,300,304,305,314,318,319,325,328,330,350,353,354,355,357,378,381,390,393,396,398,402,409,421,422,440,457,460,467,468,483],alonso:[410,411],alpha:[6,12,51,195,238,274,282,287,355,363,366,369,378,382,384,385,387,392,397,398,409,414,418,442,444,475,478],alpha_:444,alpha_c:406,alpha_i:[429,444],alpha_ialpha_j:444,alpha_lj:406,alphabet:[2,3,22,37,44,55,63,173,184,194,334,342,356,375,438,457],alphanumer:[3,63,194,281,289,332,356,483],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,206,207,210,212,216,242,280,282,307,330,356,357,382,391,393,400,408,437,447,450,453,457,458,462,467,483],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,222,225,226,227,228,229,231,232,235,236,237,238,248,249,251,252,253,254,255,256,257,262,265,266,268,269,270,271,273,274,275,277,278,279,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,300,301,304,305,307,310,311,312,313,314,318,319,320,321,323,325,328,330,332,334,339,342,345,347,348,350,351,352,355,356,357,358,359,361,362,368,372,373,375,379,380,381,382,384,385,3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22,389,423,437,447],cloud:478,clovertown:18,clsuter:72,clump1:[277,292],clump2:[277,292],clump3:[277,292],clump:292,cluster:[],clutter:[3,9],cmap:457,cmatrix:229,cmax:409,cmd:[11,12,275,468],cmin:409,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[393,461],co2:[40,164,295,356],coars:[7,9,29,36,40,54,177,277,292,307,391,424,469],coarser:[348,483],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,333,334,339,375,393,397,413,426,428,430,457,459],coeffcient:457,coeffici:[],coefficienct:382,coefficient0:384,coefficient1:384,coeffieci:[6,366],coeffincientn:384,coexist:[9,227,386],cohes:[6,387,409],coincid:[122,328,373,407,408,452],colberg:189,cold:[6,150,227,231,358,478],coldest:315,coleman8:9,coleman:[9,118,164,293],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,215,241,247,277,287,290,292,330,347,356,358,376,396,457,464,470,476,487],collid:[221,307,329],colliex:164,collinear:[3,277],collis:[3,238,307,325,329,383,390,450],colllis:307,colloid:[],colombo:39,colon:[192,330,458],color1:191,color2:191,color:[3,9,41,188,190,191,210,228,282,287],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,205,206,207,208,241,248,249,282,292,308,309,319,329,388,392,421,422,458,472,474,483],colvar:[],colvarmodul:12,com:[],comamnd:216,comand:[213,459],comannd:362,comb3:[],comb:[],comb_1:284,comb_2:284,combiant:379,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,205,232,241,251,275,281,311,320,328,331,333,347,348,350,354,362,376,378,379,386,387,393,405,406,429,439,441,443,446,449,460,465,470,478,483],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,232,234,235,348,357,362,382,413,418,440],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,236,292,319,356,357,363,384,385,387,397,409,415,422,429,439,440,441,442,443,446,454,455,457,478,483],commerci:7,commmand:[3,6,12,59,107,270,451,452,454,471,486],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,343,391,400,429,441,443,457,460,469],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,210,211,212,214,215,216,232,234,238,240,241,242,251,274,281,283,284,285,292,307,319,330,345,347,358,359,360,362,383,417,454,455,459,466,467,483,485,487],communc:347,comp:[7,189,234,235,295,348,357,386,413,418,423,436,440,442],compact:[63,194,375,438],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,220,283,330,332,347,348,355,357,409,452,471,472,478,482],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,333,334,342,374,438],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,205,206,207,208,210,274,286,311,314,321,324,327,347,362,394,413,440,454,455,483],compens:[6,211,212,290,358,386],compet:318,competit:348,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,232,318,348,362,457,458,462,483],compl:17,complain:[12,17],complement:409,complementari:[7,378,398],complet:[3,6,9,12,15,41,59,71,191,206,210,215,241,275,278,281,307,318,320,332,346,357,362,387,426,428,445,452,457,462,465,469,471,474,478,483],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,238,303,328,345,357,386,440,455,457,460,483],compli:[314,318],complic:[6,7,9,12,13,201,227,455],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,213,214,216,217,222,225,230,234,235,238,241,243,247,248,250,251,252,255,256,257,268,269,271,272,274,275,276,279,290,292,294,295,296,300,301,304,307,310,311,312,314,321,322,327,328,329,347,350,354,355,356,357,362,382,386,390,407,408,426,428,429,457,458,467,475,483,484],componenet:6,composit:[6,201,238,384],compound:[377,386,387,446],compres:[71,114,203],compress:[3,6,59,71,114,168,188,190,191,203,216,249,255,279,282],compris:[40,328,396,423,445],compton:[118,164],comptu:[3,6],compuat:348,comput:[],computation:[3,6,211,212,319,368],computational:478,compute_arrai:8,compute_fep:[196,406],compute_group_group:227,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,293],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,486],concav:328,concentr:384,concept:[6,145,155,203,466],conceptu:[3,6,71,153,214,216,357,378,393,409,462],concern:[6,73,87,189,228],concis:[11,318],conclud:12,concret:8,concurr:[9,16,348,483],conden:[319,441,443],condens:[6,147,319,364,380,384,398,446],condit:[],conducit:6,conduct:[],cone:460,confid:[3,471],config:[12,188,454],configfil:215,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,214,215,216,217,221,227,234,235,263,275,283,318,345,355,357,364,368,385,409,439,441,443,446,452,457,459,460,471],confin:[457,471],conflict:[3,12,40,413,455],conform:[3,6,13,59,213,214,250,291,296,318,341,357,386,469],confus:[3,446],conjuct:382,conjug:[7,8,235,354,386,421,422],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,235,238,242,263,278,279,283,284,285,287,292,307,315,322,327,347,348,357,369,371,375,378,382,386,392,398,413,416,424,444,457,460,464,478,487],connect:[3,6,87,150,168,213,232,277,292,295,304,357,379,390,437,443,454,455,461,478],conput:3,consecut:[3,11,12,39,71,165,191,195,196,217,232,233,378,398,402,452,458,460],consequ:[1,6,201,319,397,471],conserv:[3,194,201,213,220,221,228,231,235,237,238,242,247,249,251,263,292,295,310,311,315,322,323,327,357,381,382,390,404,466,471],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,206,210,212,213,217,239,252,274,292,314,315,318,319,322,348,375,386,393,422,423,437,452,453,455,458,459,460,462,465,467,475,478,483],consider:[6,8,235,236,310,311,312,362,466],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,216,217,220,222,225,228,235,236,237,248,251,253,254,255,256,257,258,259,261,262,263,264,266,267,268,269,270,271,279,282,287,289,291,292,310,311,312,313,323,347,348,350,356,357,362,364,368,370,376,378,386,389,393,407,408,409,413,423,426,428,440,447,455,457,458,460,461,462,469,478,483],consistent_fe_initi:200,consit:292,constant:[],constitu:[3,6,241,292,324,328,376,423],constitut:[426,428],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,217,227,228,233,241,245,277,278,290,292,295,305,315,322,355,356,386,462,469,478],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,214,251,274,291,328,358,362,381,413,437,439,440,460,461,476,483],constructor:8,consult:422,consum:[1,287,417,483],consumpt:345,contact:[],contact_stiff:[425,427],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,205,206,207,208,210,215,217,222,229,233,234,235,236,238,249,263,273,274,277,278,280,282,285,289,292,293,297,307,314,318,319,328,329,332,346,348,356,357,360,361,363,364,365,368,377,378,381,384,385,386,393,394,409,415,419,420,421,422,429,439,440,441,442,443,444,446,452,453,454,455,457,458,459,460,462,464,466,469,471,474,475,478,483,485,487],content:[12,18,422,473,475],context:[3,6,8,12,17,117,191,211,212,217,277,289,323,354,449,457,464,473,482,483,484],contibut:70,contigu:454,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,210,213,214,215,216,217,227,228,229,231,232,233,235,236,237,243,248,249,251,253,254,255,256,257,268,269,270,271,276,278,281,282,292,293,296,306,307,309,316,317,319,325,328,332,346,361,362,368,382,383,400,403,421,422,423,426,428,442,452,455,457,459,460,465,471,474,475,483,485],continuum:[6,7,9,200,319,426,428],contour_integr:200,contract:[59,214,216,251,279,292],contradictori:3,contrain:295,contraint:263,contrari:[229,236],contrast:[1,6,42,55,64,150,216,330,426,428,449,486],contrib:319,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,205,206,207,208,214,227,235,238,241,242,246,252,269,270,277,278,286,289,292,293,295,321,347,355,357,365,382,383,384,386,393,407,408,413,421,422,469,475,478],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,210,214,215,216,231,232,235,236,251,253,254,255,256,257,279,284,292,298,299,310,311,312,319,323,345,347,359,386,389,421,422,425,427,439,443,452,454,466,472,473],control_typ:200,controlfil:422,convect:91,conveni:[6,12,29,188,192,208,293,350,429,483],convent:[3,8,9,29,176,183,184,191,291,304,331,384,386,483],converg:[3,6,41,88,188,190,192,197,210,213,214,222,225,255,282,284,287,291,295,353,354,355,357,377,378,398,452,464,471],convers:[3,8,140,190,191,201,204,279,347,378,379,380,386,398,402,406,416,455,471,482],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,208,249,330,333,335,338,341,350,357,363,384,441,443,450,455,457,458,459,464,474,478,482,483,485,487],convex:328,convinc:[7,12],cook:9,cooki:7,cool:[7,155,231,290],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,206,207],coord2:[3,114,203,206,207],coord3:[3,114,203,206,207],coord:[],coordiat:355,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,205,206,207,210,211,212,213,214,215,216,217,220,222,223,225,227,230,231,232,233,234,235,236,248,250,251,253,254,256,257,269,272,273,274,277,278,279,289,290,292,294,295,296,301,304,305,306,307,309,317,318,319,326,327,329,330,350,355,356,357,362,363,364,367,385,452,457,458,460,462,465,467,471,478,483,484],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,319,357,375,421,455],copper:450,coproccesor:16,coprocessor:[1,4,7,9,16,17,362,470],coproprocessor:17,copy_arrai:8,copyright:[7,8,277],coral:191,core:[],core_shel:147,coreshel:[6,9,371,378,380],cornel:[6,171,469],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:[3,6,40,113,190,328,329,350,445,457],cornflowerblu:191,cornsilk:191,corpor:16,corr:377,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,216,227,229,235,251,252,269,277,279,282,318,324,328,347,357,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,448,449,450,457,472,475,478],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,217,222,225,236,245,251,252,285,292,295,304,306,325,328,357,358,362,380,408,454,455,457,467,482,484],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,209,212,214,216,223,225,226,230,235,238,239,247,248,249,251,253,254,255,256,257,258,263,266,268,269,271,274,275,279,284,292,294,295,310,312,314,323,324,325,327,328,329,331,333,334,335,336,337,338,341,343,348,352,354,356,357,363,364,366,369,370,371,372,373,374,375,376,377,378,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,413,414,415,416,418,419,421,422,423,424,429,430,439,440,441,442,443,445,446,448,449,450,452,454,455,457,458,460,470,471,472,474,475,478,483],correspondingli:[407,408,466],cosin:[],cosineshift:27,cosmo:[229,234],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,206,207,210,211,212,224,251,284,319,347,348,360,378,398,402,413,439,454,466],costheta0:[439,441,443,446],costheta:419,costli:[11,88,229,358],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,206,210,216,225,234,281,282,283,287,290,292,294,307,308,314,318,319,320,324,328,330,332,339,344,346,353,355,358,362,365,388,392,393,421,422,453,454,455,457,459,461,464,465,473,478,483,484],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,283,285,320,347,348,355,362,369,371,372,373,374,377,378,379,380,381,386,390,391,393,398,402,406,413,416,421,422,424,438,443,444,446,449,462,469,475,478,482],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,205,206,207,209,210,217,222,224,227,233,251,263,278,295,310,311,328,348,355,356,357,359,362,388,392,413,475,483],counter:[325,452,463,465,471],counteract:227,counterbal:231,counterpart:[188,292,452],counterproduct:18,coupl:[],courant:297,cours:[3,8,126,128,159,188,195,196,228,291,304,318,324,326,327,329,330,348,407,430,454,457,470,478,483,485],courtesi:350,coval:[6,29,386,409,478],covari:229,cover:[6,71,185,191,200,238,386,396,445],coverag:[71,206],cpc:234,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,225,295],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,220,236,320,345,348,362,375,438,452,470,471,474,475,476,483],cpuremain:475,cr2:164,cr3:164,crack:[4,358],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,358,478],craympi:362,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:277,criteria:[3,116,166,190,191,211,212,213,246,355,418,445,459,462,483],criterion:[12,41,121,163,165,168,201,210,213,227,263,284,297,325,330,355,357,377,386,390,462,471,472],criterioni:471,critic:[48,49,249,314,319,355],cross:[3,12,22,71,89,144,173,188,190,202,206,212,216,248,250,269,292,300,304,306,315,322,334,350,357,373,382,383,384,391,392,393,398,400,402,419,424,426,428,441,443,450,457,461,467,485],crossov:1,crossterm:457,crozier:[0,7,13],crucial:282,crystal:[4,6,13,73,273,274,317,350,358,461,475,478],crystallin:[6,274,350,442,478],crystallis:314,crystallogr:[118,164],crystallograph:[350,475],crystallographi:[118,164,350],cs1:164,cs_chunk:6,cs_im:[40,457],cs_re:[40,457],csanyi:[140,420,429],cscl:409,csequ:6,csh:[11,12,375],cshrc:[11,12],csic:[385,439,441,443,446],csinfo:6,csisi:[385,439,441,443,446],csld:[],cst:384,cstherm:6,cstyle:454,csvr:[],ctcm:[363,384],ctemp_cor:220,cterm:296,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:409,cube:[6,41,163,168,210,220,328,350,478],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:368,cummul:[3,6,208,211,212,213,215,224,229,235,237,307,310,311,312,313,315,322,392,475],cumul:[6,201,203,205,206,207,221,227,235,249,251,255,263,292,293,357],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,206,207,208,210,211,212,213,214,215,216,217,221,222,225,227,229,232,233,235,241,248,251,252,256,257,263,268,269,271,277,283,284,286,289,290,291,292,295,296,297,298,299,300,301,303,305,306,307,310,311,312,318,319,322,323,324,325,326,327,329,330,332,345,346,347,348,351,352,354,355,356,357,362,368,375,377,381,384,386,387,390,393,394,397,407,408,409,410,411,413,419,421,422,425,426,427,428,430,441,443,444,447,452,453,454,455,457,458,459,460,461,463,464,465,467,469,471,472,474,475,483,484,485,486,487],curv:[6,165,227,274],curvatur:[389,423,450],custom:[],cut0:455,cut1:466,cut2:466,cut:[],cuthi:[273,285],cutinn:[370,407,408],cutlo:[273,285],cutmax:419,cutoff1:[374,381,398,402,406,416,424],cutoff2:[369,371,372,374,380,381,398,402,406,416,424],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,212,213,218,273,282,283,285,287,289,292,307,320,324,328,330,345,347,348,355,358,359,360,362,363,364,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,455,459,462,466,478,483],cutoffa:385,cutoffc:385,cuu3:384,cval:164,cvd:314,cvel:296,cvff:[],cwiggl:[3,248,324,327,329,483],cyan:[2,190,191],cycl:[3,227,249,251,252,255],cyclic:[3,185],cygwin:12,cylind:[3,4,190,233,278,325,328,460],cylindr:[6,233,304,325],cypress:362,cyrot:368,cyrstal:274,d3q15:238,d3q19:238,d_double_doubl:15,d_e:319,d_flag2:281,d_flag:281,d_name:[113,188,281,309,467],d_single_doubl:15,d_single_singl:15,d_sx:281,d_sy:281,d_sz:281,daan:317,dai:12,daili:12,daivi:269,damag:[],dammak:287,damp:[3,6,194,199,235,236,237,242,251,252,255,279,282,287,292,310,311,323,325,326,354,355,357,369,371,373,378,381,386,390,398,406,416,424,438,444,471,478],damp_com:236,damp_drud:236,dampen:[292,478],dampflag:[325,390],dan:17,danger:[3,12,227,330,382,475],dangl:168,daniel:9,darden:[348,381],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:283,dash:[390,474],dat:[6,91,185,200,453],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,293],dataset:293,datatyp:3,date:[0,6,12,13,421,422,483],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:324,david:[9,19,347,348,441,443],daw:[384,419],dbg:14,dcd:[3,6,7,188,189,190,191,192,275,458,462],ddim:187,deactiv:406,dealt:234,debug:[6,7,11,12,13,14,17,118,122,164,165,275,280,345,347,362,394,413,447,455,456,459,464,467,474,483],deby:[],decai:[378,450],decid:[3,6,12,16,71,248,281,292,320,472],decipher:350,declar:189,declin:307,decod:190,decompos:[87,429],decomposit:[3,5,7,18,62,200,275],decoupl:[6,478],decreas:[3,188,197,198,213,216,222,225,227,235,318,347],decrement:296,deepli:344,deeppink:191,deepskyblu:191,def:[12,13,455],defaul:61,defect:[6,70,163],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,220,221,222,225,226,227,230,233,234,235,236,237,238,246,248,250,251,252,253,254,255,256,257,259,260,261,264,266,267,268,269,270,271,273,274,275,277,278,279,281,283,285,290,292,293,294,295,297,301,305,307,309,310,311,312,313,315,316,317,319,321,322,324,325,326,327,328,329,330,332,333,334,335,336,337,338,341,342,343,345,347,348,350,352,354,355,356,357,358,359,360,361,362,364,365,366,367,369,370,371,372,373,374,375,376,378,379,381,382,383,385,386,388,389,390,391,392,393,394,396,398,399,400,401,402,403,404,405,406,407,408,412,413,414,415,416,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,455,457,458,460,461,462,463,466,467,468,469,471,472,474,475,478,479,480,481,482,483,484],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,216,233,255,293,309,321,324,327,329,331,342,345,356,365,368,376,386,396,419,426,428,429,445,455,457,459,466,468,482,483],defint:475,deform:[],deg2theta:164,deg:478,degener:[3,277],degrad:[8,18,274,348,466],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,213,220,227,229,230,235,236,241,251,252,255,256,257,268,269,271,275,277,291,292,295,310,311,312,317,333,335,338,341,343,355,381,384,392,467,475,478,484],degress:[145,203],del:471,delai:[3,6,12,358,383,475],deleg:393,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,205,206,207,208,211,213,224,227,251,293,310,311,330,332,346,356,358,361,413,457,458,460,468,469,474,479,481,483,484],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[455,483],deloc:[252,386],delr:409,delt_lo:471,delta:[],delta_1:368,delta_3:368,delta_7:368,delta_conf:3,delta_ij:[409,419],delta_mu:3,delta_pi:368,delta_r:419,delta_sigma:368,delx:187,delz:187,demand:287,demo:11,demon:272,demonstr:[282,409],den:278,dendrim:392,denniston:[9,238,240,241,242,274],denomin:[7,170],denot:[118,220,236,274,285,287,378,391,393,422,426,428],dens:[71,213,386],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,206,207,210,216,225,238,241,244,245,274,278,279,283,319,324,350,352,356,363,368,384,409,410,411,419,423,432,434,435,436,457,466,467,475,482],density_continu:428,density_summ:428,depart:[0,7],departur:[249,282],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,208,209,210,212,214,216,222,223,226,229,230,231,233,235,236,238,240,241,248,251,253,254,255,256,257,258,266,268,269,271,273,284,287,289,292,294,295,301,307,310,311,312,314,316,318,319,321,323,324,327,328,329,330,332,333,334,335,336,337,338,341,343,348,350,355,356,358,359,360,362,363,364,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,412,414,415,416,418,419,421,422,423,424,429,430,438,439,440,441,442,443,444,445,446,448,449,450,452,454,457,459,460,463,467,469,471,474,475,477,483,484],dependend:6,depflag:12,dephas:[452,471],depos:217,deposit:[],deprec:[283,421],depth:[51,144,190,319,389,423],dequidt:9,der:[87,107,376,377,406,421,422,449,478],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,214,216,227,235,248,251,253,254,255,256,257,273,279,283,287,316,317,319,324,325,328,354,356,364,368,376,381,386,387,391,400,404,405,409,421,422,438,440,449,478],derjagin:449,derlet:273,descend:191,descent:[7,354],descib:[40,283],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,210,213,214,215,216,217,219,220,228,229,232,233,234,235,236,237,238,240,241,242,246,250,251,252,255,262,270,273,275,280,281,282,283,284,285,292,296,304,307,308,309,310,311,312,313,314,315,316,317,322,324,325,327,332,347,348,350,353,354,355,356,357,361,364,365,367,369,370,371,373,374,375,376,377,378,381,384,386,387,389,390,391,393,398,399,400,401,402,403,404,405,406,407,408,409,412,418,419,420,421,422,423,424,429,430,437,438,439,440,441,442,443,444,446,448,449,450,452,454,455,457,458,460,461,467,470,471,474,483,484,485],descript:[],descriptor:[140,188,394],deserno:348,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,213,219,220,251,252,273,274,293,314,319,365,366,367,370,373,378,380,386,406,407,408,410,411,419,422,440,466],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,208,214,216,225,227,228,235,236,237,241,251,269,277,278,279,280,283,287,292,295,307,310,311,312,313,318,325,339,344,347,348,350,353,355,356,357,382,384,392,407,408,439,441,443,453,454,455,457,461,466,471,472,474,475,483,484,485],desk:7,desktop:[4,6,7,10,12,190],despit:478,destabil:368,destre:341,destroi:[11,39,211,212],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,208,210,212,213,214,215,216,217,225,227,228,229,230,232,233,235,237,238,242,248,249,250,251,252,253,254,255,256,257,261,263,268,269,270,271,274,277,278,279,281,282,284,285,286,292,295,307,310,311,312,313,314,315,317,318,319,320,321,322,323,330,332,334,342,347,348,351,355,356,358,359,362,363,364,365,367,368,370,372,373,374,375,376,377,378,381,382,386,387,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,409,412,413,418,421,422,423,429,430,438,445,448,449,455,457,458,459,460,462,463,466,467,469,472,475,476,483,484,487],detect:[2,3,12,61,63,86,226,278,318,357,377,392,397,452,454,457,468,471,483],determ:362,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,214,216,217,220,222,227,230,231,233,235,236,241,246,248,249,251,256,257,268,269,271,273,275,279,282,289,290,291,292,293,294,297,299,301,307,310,311,312,314,320,321,324,325,326,327,328,329,330,342,347,348,350,356,358,359,362,364,365,372,377,381,383,384,388,390,393,394,402,409,413,422,423,437,440,444,449,454,457,458,460,462,464,467,471,473,474,476,482,483,484],detil:108,devan:[9,424],devanathan:443,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,232,255,277,282,283,286,364,368,386,411,446,459],devemi:9,deviat:[249,255,273,388],deviator:9,devic:[1,3,12,15,17,232,362],device_typ:362,devin:[284,377],devis:411,dfactor:190,dff:478,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,348],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,286],dhi:[59,187,216,278],dhug:[249,282],dhugoniot:[249,282],dia:409,diagnost:[],diagon:[3,6,83,140,141,142,214,251,279,292,322,426,428],diagonalstyl:429,diagram:[41,118,164,184,210,275],diallo:392,diam:[190,191,278,356],diamet:[3,6,40,113,165,188,190,191,195,196,235,278,292,307,323,325,356,376,389,390,396,400,423,445,449,457,458,467],diamond:[350,386,409],diamter:[40,278],dick:6,dicsuss:248,dictat:[201,249],did:[3,12,355,382,383,384,390,413,441,443,465],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,321,347],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,205,210,211,212,213,214,215,216,220,226,227,228,229,230,231,232,235,236,238,248,251,252,253,254,256,257,259,261,264,266,267,268,271,273,275,277,279,282,283,284,287,290,292,295,296,304,305,307,310,311,312,315,316,317,319,322,323,324,325,328,332,333,342,344,346,347,348,350,351,353,354,356,357,359,360,361,362,363,364,368,372,373,375,376,377,382,384,386,389,390,391,393,396,398,399,401,402,409,410,411,412,413,415,419,421,422,423,424,425,426,428,429,430,438,439,440,441,443,445,446,449,451,452,454,455,457,459,460,461,462,465,466,467,469,471,472,474,475,476,478,482,483,484,485],differenti:[1,3,6,29,185,347,378,419,442],difficult:[214,275,362,392,466],difficulti:[295,421],diffract:[],diffus:[],digit:[2,3,191,332],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:212,dihydrid:386,dij:295,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,206,216,233,325,350,409,460,482,483,484],dimdim:483,dimems:274,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,206,250,274,319,350,353,357,419,457,467],dimensionless:[105,121,122,124,127,129,131,136,140,319,348,429,449],dimentionless:135,dimer:[6,292,409],dimgrai:191,dimstr:[41,210],dinola:[279,310],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,309,478],dir1:468,dir2:468,dir:[1,3,4,8,9,11,12,249,273,282,306,419,421,422,455,468,483],dirac:140,direc:419,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,222,229,233,238,274,293,311,323,325,326,327,328,350,354,362,363,364,369,371,372,378,381,384,386,398,402,413,416,424,437,455,467,468,469,475,483],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,215,234,277,283,286,303,307,316,317,357,361,363,364,368,375,377,378,384,385,387,394,395,406,409,410,411,415,419,420,421,422,429,439,441,442,443,446,455,457,458,459,468,483],disabl:[3,12,16,319,397,455,470,483],disadvantag:[6,210],disallow:[188,216,251],disappear:459,discard:[2,3,41,71,206,210,320,328,454,459,460],discontinu:[9,185,355,404],discourag:409,discov:[13,320],discret:[6,8,40,42,190,191,235,238],discuss:[],disk:[6,84,85,158,186,217,227,278,455],disloc:70,disord:[39,70],disp:[],dispar:423,disperion:[381,402],dispers:[3,6,7,9,163,274,347,348,372,381,402,407,413,422,440,446],displac:[],displace_atom:[],displace_box:59,displacemet:460,displai:[11,13,22,37,44,55,173,184,188,190,334,342,375,438],dispters:3,dissip:[6,228,235,274,316,317,370,382,390,407,408,438],dissolut:211,dist:[6,69,91,108,117,188,275,291,383,437,452,484],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,206,207,211,212,213,214,216,217,218,221,227,233,238,248,249,250,251,255,263,273,274,278,282,283,290,291,292,295,296,300,304,305,306,307,314,315,317,318,319,322,324,325,326,327,328,329,333,347,348,350,353,355,357,358,359,362,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,388,389,390,391,392,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,455,457,460,466,467,471,475,478,482,484],distinct:[6,220,289,347,423],distinguish:[6,86,140,241,386,456],distort:363,distrbut:363,distribut:[],distro:[111,375,418,419],ditto:[8,11,12,14,15,16,17,18,115,212,450,455],div:8,divd:117,diverg:[3,12,39,292,317,459,478,485],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,205,210,216,273,315,322,327,347,355,357,387,422,446,466,474,483],divis:[6,238,368,396,406,454,457,475,483],dl_poli:7,dlambda:159,dlammps_async_imd:232,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,318,457,458,462],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:467,dlmp_intel_offload:[12,16],dlo:[59,187,216,278],dlopen:6,dlvo:[7,376,449],dm_lb:238,dmax:[307,353],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,217,227,235,236,246,251,252,256,257,261,268,269,270,271,278,281,292,304,307,310,311,312,321,325,328,330,332,334,342,346,355,356,357,362,363,364,367,375,377,378,384,385,387,392,393,395,396,409,410,411,413,415,418,419,420,429,438,439,441,443,445,446,455,457,458,459,460,462,465,466,467,474,475,483,484,485,486],docuement:423,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,206,209,210,212,213,214,216,220,222,224,227,228,231,233,235,236,238,241,247,251,252,253,254,256,257,268,269,270,271,279,280,281,285,287,290,292,307,310,312,314,315,319,322,323,324,327,328,329,330,335,336,338,339,341,346,347,348,349,350,356,357,358,363,364,365,366,367,368,370,372,373,374,376,377,378,379,381,382,383,384,385,386,388,389,390,391,393,394,395,396,397,400,401,403,404,405,407,408,409,410,411,413,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,446,448,449,450,452,453,454,455,457,458,459,460,461,464,465,467,468,469,470,471,474,475,478,483,487],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,206,207,304,356,358,362,364,377,385,395,421,422,439,441,442,443,446,457,459],dof:[3,8,112,144,145,158,203,292,484],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[356,457],doi:[6,215],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,210,214,216,217,231,234,238,251,252,275,287,292,319,324,325,347,348,357,362,383,413,452,454,457,461,474],domin:[1,386,471],don:[0,8,11,12,13,116,168,197,222,236,281,328,409,455,457],donadio:311,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,210,211,212,213,214,216,217,225,227,232,233,235,236,243,251,256,257,268,269,271,272,274,275,276,281,289,292,293,295,307,310,311,312,314,316,317,330,332,346,347,348,355,357,358,361,362,364,372,384,393,394,395,402,408,409,413,421,437,440,445,452,453,454,455,458,461,462,465,475,476,478,483,484],donor:392,dot:[141,161,197,222,230,250],doti:[368,419],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,216,225,280,328,332,346,348,361,362,368,387,391,421,422,453,457,461,465,470,483,484],dover:200,down:[3,6,7,8,11,39,71,214,227,235,307,323,362,386,413,456,476],downhil:[353,354],download:[5,7,8,9,11,12,13,17,232,394,420],downsid:6,downward:289,dozen:[8,12,107,194,421,422],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:244,dproduct:365,dr_ewald:[118,293],drag:[],dragforc:238,drai:[249,282],drain:[231,323,355],dramat:[59,187,211,212,213,214,216,251,307,310,311,348,362,413,454],drautz:368,draw:190,drawback:281,drawn:[188,190,191,228,452],drayleigh:[249,282],dreid:[],drfourth:105,drho:[113,363,384],drift:[6,103,105,228,229,235,236,247,290,307,466,474,478],drive:[11,12,198,214,216,230,251,273,279,292,326,357],driven:[6,177],driver:[6,12,14,15,194,225,232],drop:[3,191,382],droplet:393,drsquar:105,drude:[],dry:224,dsecriptor:394,dsf:[],dsmc:[],dstyle:278,dt_collis:238,dt_lb:238,dt_md:238,dt_srd:307,dtilt:[59,216],dtneb:471,dtqm:282,dtype:[115,212],dual:[16,17,307,362],dudarev:164,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,126,140,141,143,144,146,148,151,152,153,154,155,157,158,160,164,165,168,169,188,190,194,197,198,205,209,211,212,213,214,215,216,217,222,223,224,225,228,229,232,233,235,236,237,238,241,242,243,247,248,249,250,251,255,263,273,276,278,290,291,292,294,304,306,307,308,310,311,312,313,314,316,317,319,323,324,326,327,328,330,348,353,355,357,358,359,379,382,384,388,389,393,407,408,413,419,421,423,424,437,440,441,443,447,449,450,452,454,457,458,459,466,471,474,475,476,478,483,484],duffi:319,duin:[9,283,288,421,422],duke:348,dummi:[12,29,442],dump1:462,dump2:462,dump2vtk_tri:134,dump:[],dump_atom:8,dump_custom:8,dump_h5md:189,dump_modifi:[],dumpcustom:8,dumptimestep:462,dunbrack:[6,20,171,373,469],dunweg:[235,237],duplic:[2,3,14,15,17,41,42,166,210,229,273,457,482],dupont:[5,7,13],durat:[37,55,143,144,146,147,148,150,151,152,153,154,157,158,184,191,203,227,287,319,342,390,438],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,128,142,147,166,169,185,188,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,218,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,250,251,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,300,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,348,355,357,361,362,382,406,413,422,440,452,453,455,457,460,462,464,465,467,469,471,472,475,476,483,486,487],dvector:8,dvlo:449,dvx:6,dx_lb:238,dy3:164,dyamic:12,dyanam:6,dyanmic:471,dynam:[],dynamo:[5,363,384,409],dyne:482,dyre:403,dysam:460,e28637:29,e_1:368,e_2:368,e_b:387,e_e:386,e_hbond:392,e_i:[6,368,387],e_j:[6,368],e_k:[368,386],e_kl:6,e_lj:[364,381],e_n:[368,386],e_nn:386,e_pr:386,e_rebo:364,e_tors:364,eaa:333,eaat:172,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,93,94,95,96,97,98,99,100,101,102,103,104,105,106,109,110,111,112,113,114,115,116,117,118,119,120,134,140,141,142,144,145,146,147,148,149,152,153,154,155,157,158,159,160,161,162,163,164,165,168,169,171,172,173,174,175,176,177,178,179,180,182,183,184,185,187,188,189,190,191,192,193,194,195,196,197,198,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,241,242,243,244,245,247,248,249,250,251,253,254,255,256,257,258,259,260,261,263,264,265,266,267,268,269,270,271,273,274,275,276,277,278,279,280,281,283,284,285,287,289,292,293,294,295,296,300,301,303,304,305,306,307,308,309,310,311,312,314,317,318,319,320,321,322,323,324,325,327,328,329,330,332,333,335,336,337,338,339,341,342,343,346,347,348,350,354,355,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,418,419,421,422,423,424,425,429,430,431,432,433,434,435,436,437,438,439,440,443,444,445,446,447,448,449,450,451,452,454,455,457,458,459,460,461,462,464,465,466,467,469,471,472,474,475,476,478,482,483,484,485,487],eacn:[41,210],eam0d:274,eam3d:274,eam:[],eam_databas:13,eam_gener:13,eangl:475,earli:[41,203,205,206,207,208,210,286,293],earlier:[7,8,12,59,191,357,390,409,413,471],earliest:471,earth:386,easi:[6,7,8,9,11,13,87,141,188,195,196,197,198,206,209,222,230,231,233,235,236,294,301,310,311,312,324,327,329,356,457,460,465,467,484],easier:[8,9,13,16,188,190,274],easili:[8,11,190,191,323,357,454,464,473,483],eastwood:[347,348],eat:172,eatom:330,eaxmpl:6,eba:21,ebb13:172,ebb:21,ebond:[220,236,474,475],ebt:172,ec_ii:409,ec_ij:409,ec_jj:409,echo:[],eco:[421,422],ecoa:[421,422],ecoul:[107,220,236,421,422,475],ecp:[386,457],edg:[2,3,6,41,59,71,118,163,164,167,168,189,190,199,206,233,294,324,327,328,329,330,350,457,460,467],edge_histo:163,edge_threshold:163,edih:475,edim:315,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,478],editor:13,edu:[7,9,11,13,384,407,418,421,422],edward:[9,17],eebt:172,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,81,89,90,93,103,104,105,106,109,112,141,143,147,152,153,160,163,169,171,172,174,175,176,177,179,180,182,183,184,185,187,188,190,191,195,196,197,200,201,204,207,208,209,211,212,213,214,216,217,223,226,227,228,229,230,231,232,233,235,236,250,251,253,254,255,256,257,258,266,268,269,271,272,273,275,278,279,281,282,283,284,287,291,292,294,295,306,307,310,311,312,314,315,317,319,322,323,324,325,326,327,328,329,330,333,335,336,337,338,341,343,347,348,350,354,355,356,357,358,363,364,366,368,369,370,371,372,373,374,376,377,378,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,413,414,415,416,418,423,424,425,427,430,438,439,440,441,442,443,445,446,448,449,450,452,454,455,459,460,462,466,467,469,475,476,482,483,485],efffect:461,efficaci:39,effici:[0,1,3,6,7,8,10,12,15,17,18,39,58,61,67,112,142,188,189,190,191,214,216,220,229,251,275,277,287,292,295,307,347,348,353,358,362,368,376,378,393,398,402,423,464,487],effort:[5,7,458],efftemp:[96,97,151],efi:[421,422],efield:[],eflux:231,eggebrecht:378,ehb:[421,422],eigensolv:3,eigenvalu:[274,275,347],eigtol:3,eik:159,eim:[],eimp:475,einstein:[287,317],either:[1,2,3,4,6,8,9,11,12,14,15,16,17,22,33,41,44,50,59,63,71,107,113,116,118,140,141,145,147,148,164,165,168,173,178,185,188,189,190,191,194,202,204,205,207,208,210,213,214,215,216,217,227,233,234,238,242,248,249,251,252,255,269,273,289,292,294,295,296,304,307,314,321,325,328,332,334,345,347,348,350,354,355,359,362,368,370,376,384,393,394,396,407,408,409,413,417,419,441,443,445,452,455,457,459,460,461,464,466,469,472,474,483],ejtehadi:[376,389,423],elaplong:[195,196,233,460,475,483],elaps:[3,195,196,197,198,209,216,222,230,231,233,235,236,248,278,294,301,310,311,312,324,325,327,329,430,452,460,462,463,467,471,475,483],elast:[],elastic_t:4,elba:29,electr:[6,194,200,222,236,347,348,387,421,422,450,478,482],electrolyt:[9,449],electron:[3,6,7,9,13,40,96,97,113,118,149,151,156,194,200,219,220,236,237,252,262,270,285,313,319,354,356,363,365,377,381,384,386,387,409,419,420,443,446,450,457,478,482],electron_integr:200,electron_temperatur:200,electron_unit:386,electroneg:[6,283,284,285,377,387],electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,16,18,201,227,283,285,286,320,347,348,376,381,386,398,406,408,422,449],eleftheri:292,elem1:[387,409,429],elem2:[387,409,429],element1:[289,363,384],element2:[289,363,384],element:[3,6,7,8,12,13,63,81,89,103,105,112,117,119,134,140,141,142,143,144,145,146,147,148,152,153,154,155,157,158,161,188,189,190,191,192,194,200,204,205,208,274,289,314,321,363,364,368,377,384,385,386,387,393,394,395,409,410,411,415,419,420,421,422,429,439,441,442,443,446,478,483,486],elementn:[363,384],elementset:200,elev:471,elif:[140,332],elig:[3,201,211,212,224,227,392],elimin:[3,6,71,228,235,236,292,295,316,317,452],elj:381,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,82,144,186],ellipsoid:[3,4,6,7,13,40,42,82,113,130,144,165,186,188,235,253,256,259,260,268,292,307,352,355,389,408,423,438,457,467,485],ellipsoidflag:457,elong:[220,236,475],elp:[421,422],els:[3,7,8,12,71,107,116,117,119,189,190,202,203,204,205,206,207,208,227,251,292,307,319,320,321,330,332,347,393,456,468,483,486],elsewher:[8,248,307,409,420,421,422,469,475,483],elt:409,emac:[],email:[0,3,5,7,8,11,387],emb:[3,9,328],emb_lin_neg:409,embed:[3,5,7,11,12,13,29,88,142,163,319,363,384,387,406,409,410,411,419,438,447,455],embt:172,emi:[7,9],emol:[421,422,475],emphas:390,empir:[200,311,364,386],emploi:[9,274,287,442],empti:[3,57,71,167,292,347,358,397,457,468,469,483],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,83,87,96,97,98,99,100,101,105,109,111,112,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,147,149,151,152,156,157,159,163,171,172,174,175,176,177,178,179,180,182,183,184,185,188,189,191,192,194,195,196,197,198,199,201,207,209,211,212,213,215,216,217,222,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,244,245,247,249,251,252,253,254,255,256,257,258,259,260,261,262,264,266,267,268,269,270,271,273,274,275,277,278,282,283,284,285,286,287,288,289,291,292,294,295,296,297,298,299,300,301,303,304,306,307,310,312,313,314,315,316,317,319,320,322,323,324,325,326,327,328,331,333,335,336,337,338,339,341,342,343,348,355,357,361,362,363,364,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,455,458,459,464,466,476,483,487],enclos:[2,6,12,167,188,280,332,409,453,455,465,483],encod:[13,39,42,188,190,191,281,393],encompass:[3,6,40,57,59,116,166,303,321,438,460],encount:[3,8,12,59,205,361,462,483],encourag:[7,8,286,305],end12i:113,end12x:113,end12z:113,end1i:113,end1x:113,end1z:113,end2i:113,end2x:113,end2z:113,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,57,59,71,113,168,169,172,187,188,190,191,192,195,196,204,205,207,208,213,216,220,228,233,235,236,237,250,251,252,263,279,291,292,296,307,310,311,312,313,315,318,319,322,326,329,330,346,347,356,357,361,362,382,384,389,423,426,428,429,430,444,447,452,455,457,458,459,460,462,464,465,469,473,475,478,483,487],end_of_step:8,endbondtors:[3,172,178,457],endif:8,energet:[213,364,422],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,123,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,188,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,333,335,336,337,338,341,343,347,348,353,354,355,357,358,362,363,364,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,421,422,423,424,429,430,431,432,437,438,439,440,441,442,443,445,446,447,448,449,450,452,455,457,462,466,467,469,471,473,474,475,478,482,483,486],energy_update_freq:422,enforc:[6,57,58,104,187,188,189,190,192,194,201,213,216,251,272,274,284,292,295,332,347,398,454,483,484],enforce2d:[],eng:[11,65,69,108,188,225,330,332,377,411],eng_previ:332,engin:[200,216,277,296,316,384,410],engr:[421,422],enhanc:[196,200,452],enlarg:[59,190],enough:[3,40,61,86,165,166,168,210,236,278,282,287,292,320,324,325,328,358,362,378,417,457,461,462],enpub:384,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,214,227,228,251,297,318,348,368,383,406,437,439,446],enter:[57,155,387,446,471],enthalpi:[123,253,254,384,474,475,483],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,206,207,210,213,215,224,227,228,231,235,236,247,251,253,254,255,256,257,273,275,277,290,292,305,319,321,332,362,381,402,413,440,457,465,466],entireti:[396,445],entiti:[6,8,40,42,188,292],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,205,206,207,215,282,330,356,368,385,409,415,422,429,439,440,441,442,443,446,483],entropi:471,entry1:[38,56,191,375,440],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:362,environ:[1,3,6,11,12,16,17,18,190,229,234,273,362,363,368,375,377,385,386,419,441,454,468,483],epair:[107,191,388,392,421,422,475],epen:[421,422],epfl:[229,234],epp:381,epq:381,eps0:449,eps14:406,epsilon0:443,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,227,292,307,324,328,353,355,367,373,374,376,378,379,380,381,389,391,392,393,396,397,398,399,400,401,402,403,404,405,406,412,416,423,424,433,439,445,448,449,466,478,482],epsilon_0:450,epsilon_14:373,epsilon_:423,epsilon_d:379,epsilon_i:[389,413,423],epsilon_i_:423,epsilon_i_a:[389,423],epsilon_i_b:[389,423],epsilon_i_c:[389,423],epsilon_ij:413,epsilon_j:[389,413,423],epsilon_j_:423,epsilon_j_a:[389,423],epsilon_j_b:[389,423],epsilon_j_c:[389,423],epsilon_lj:423,epton:418,eqch:160,eqeq:[421,422],eqp:381,eqq:381,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,208,209,210,214,216,217,222,227,228,230,231,233,235,236,238,241,242,248,249,255,265,273,275,278,280,282,283,284,287,289,291,292,294,296,301,303,310,311,312,315,316,317,319,321,322,324,327,329,330,332,346,350,355,357,358,359,361,362,377,382,388,389,392,407,412,419,421,422,423,425,426,427,429,430,440,445,446,450,453,454,455,457,459,460,464,465,468,471,473,475,483,484],equat:[3,6,7,8,9,91,112,118,164,173,184,194,214,220,221,229,235,236,238,241,249,250,251,252,255,269,273,275,282,283,287,295,307,315,319,322,324,325,327,329,341,347,348,376,381,382,386,387,390,395,407,408,409,413,423,426,428,432,433,435,436,444,450,478],equi:252,equidist:250,equil:[3,283,351,464,487],equilater:467,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,213,214,227,249,251,252,269,270,282,283,284,285,315,316,317,322,377,378,421,422,453,467],equilibria:322,equilibribum:[211,212],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,214,216,227,228,229,236,238,251,255,269,282,287,291,295,296,304,307,314,315,317,322,333,335,338,341,377,409,415,478],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,205,208,214,216,227,235,251,269,279,291,292,327,382,386,441,443,457,460,465,466,475,478],equlibrium:6,equliibr:[283,285],er3:164,eradiu:[40,113,386,457],eras:[294,316],erat:[216,408],erc:378,erfc:[378,398,413],erforc:113,erg:482,erhart:[201,384,441,443],ermscal:365,ernst:9,eror:3,eros:409,erose_form:409,erot:[],errata:[441,443],erratum:324,erron:3,error:[],erta:390,ervel:[113,457],escap:[217,478],especi:[8,11,16,153,165,194,201,210,227,282,287,290,291,362,454],espresso:[9,286],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,255,274,323,348,364,378,398,443,462,475],essex:29,establish:[87,231],estim:[1,3,6,10,12,38,41,56,91,141,200,210,221,249,307,314,347,348,353,413,422,440,471,475],esu:482,esub:409,eta:[6,238,251,282,283,285,323,385,387,389,419,442,446,482],eta_dot:251,eta_ij:419,eta_ji:387,etag:[40,457],etail:475,etap:251,etap_dot:251,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,200,201,202,203,205,206,207,208,211,212,216,217,225,227,228,235,251,278,289,293,319,320,328,332,346,347,355,356,357,358,360,384,385,393,406,408,417,421,422,439,441,443,446,452,455,457,458,459,464,466,467,471,473,474,475,476,478,482,483,485,487],ethernet:18,etol:[355,357,452,471],etot0:282,etot:[6,94,96,97,110,141,151,191,220,236,249,282,474,475],eu2:164,eu3:164,euler:[355,357],eulerian:200,euqat:431,europhi:238,ev_tal:8,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,216,222,228,230,231,233,234,235,236,274,280,283,294,297,301,310,311,312,321,324,327,329,330,332,347,348,353,355,362,413,419,425,427,440,452,453,455,459,460,462,464,465,466,467,471,473,475,483,484],evalut:[332,455],evan:[153,269],evanseck:[6,20,171,373,469],evapor:[],evaul:[8,355],evdwl:[107,421,422,475],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,205,206,207,208,210,211,212,214,216,217,220,233,236,249,251,252,274,287,289,292,293,303,307,315,319,322,324,328,330,340,347,353,355,357,362,367,386,387,390,393,413,423,446,447,457,458,460,462,463,464,466,467,469,472,474,475,476,478,487],evenli:[3,41,141,185,210,238,396,447,457],event:[],eventu:[3,6,12,15,167,283,471],ever:[54,56,234,307],evera:[376,389,423,438],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,221,224,225,227,229,231,232,233,238,239,247,251,252,255,272,273,274,278,279,280,281,282,283,284,285,287,289,290,292,293,295,296,307,309,310,311,312,313,314,315,318,319,320,321,322,330,332,346,348,357,358,359,362,382,383,393,406,421,422,434,451,452,453,457,459,461,462,464,465,466,471,472,473,475,483,487],everyth:[8,107],everywher:[116,400],eviri:386,evolut:[229,238,275,452],evolv:[238,275,320],ewald:[2,3,5,6,7,8,12,88,110,118,141,320,347,348,355,369,371,372,378,381,386,398,402,416,424,438,440,459],ewald_disp:381,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,210,213,228,229,235,236,237,278,287,288,307,319,334,347,375,459,464,471,483,485,487],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,205,210,216,221,228,235,236,237,252,262,263,270,274,282,307,312,313,326,362,375,382,384,390,393,396,407,413,440,459,460,467,471,483],exager:478,examin:[6,8,9,17,213,274],examp:[455,483],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,206,207,210,214,216,221,224,251,274,298,299,307,355,362,457,483],exceed:[3,41,59,210,216,251,307,465],excel:386,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,205,209,210,214,216,223,226,227,230,233,235,237,251,252,253,254,255,256,257,258,262,263,266,268,269,270,271,275,284,285,292,294,295,304,307,310,312,313,319,323,327,330,332,333,334,335,336,337,338,341,342,343,347,348,350,352,356,357,358,360,361,362,363,364,366,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,410,414,415,416,418,421,422,423,424,430,438,439,440,441,442,443,445,446,448,449,450,452,454,455,457,459,460,462,465,466,467,468,469,471,475,478,482,483,484,486],excess:386,exchang:[2,3,6,8,9,61,62,194,200,201,227,235,284,292,315,319,322,347,362,386,472],exchange:347,excit:[9,386],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,206,211,212,239,247,277,290,292,314,325,330,355,356,358,370,390,393,407,408,413,437,469],exclus:[1,3,9,12,16,87,362,377,413,466,476],excurs:452,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,232,286,332,346,349,361,453,455,465,468,471,483],exemplari:228,exemplifi:386,exert:[6,233,236,287,326,327,328,348],exhaust:[200,361,483],exhibit:[251,354,386,466],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,209,212,214,217,227,277,278,280,330,333,335,336,338,342,351,356,362,393,421,447,453,455,457,458,459,468,469,470,483,484,485],exit:[2,3,11,12,41,57,188,210,346,361,455,456,465,474,483],exlanatori:3,exp:[],expand:[],expans:[12,140,188,468,483],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,210,222,227,229,248,273,279,281,282,287,292,330,348,358,375,409,413,452,455,457,459,462,466,471,483],expens:[6,10,71,191,273,277,292,319,330,347,348,358,362,455],experi:[6,13,15,17,209,217,232,241,250,279,291,292,353,357,382,413,466,471],experienc:[6,12,240,241],experiment:[227,347,362,471],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,208,210,212,214,216,251,273,281,292,304,330,332,346,347,350,356,357,361,367,384,396,430,445,455,458,459,462,464,467,478,483,487],explan:[3,6,59,113,140,188,203,250,273,393,451,454,455,457,466],explanatori:[3,8,117,188,202,203,205,206,207,292,356,454,483],explantori:[3,288],explic:412,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,216,298,299,334,352,364,365,368,373,375,384,386,397,407,444,451,454,458,461],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,206,209,216,223,226,228,230,235,251,253,254,255,256,257,258,266,268,269,271,281,282,284,292,294,295,310,312,313,319,323,327,333,335,336,337,338,341,343,356,362,363,364,366,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,410,413,414,415,416,418,423,424,430,431,432,433,434,435,436,438,439,440,441,442,443,444,445,446,448,449,450,457,459,466,467,469,470,476,478],explictli:[16,470],exploit:[9,15,17,275],explor:[118,164],expon:[3,283,285,384,389,392,406,412,424],exponenti:[87,419,439,446,450,471,483],expos:11,exposit:[200,382,383],express:[6,140,151,165,195,196,214,248,273,283,319,325,332,368,384,386,400,409,429,438,483],expressiont:368,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,208,209,215,218,222,225,226,227,229,230,231,233,235,237,249,251,255,263,273,274,290,291,292,294,296,301,304,306,310,311,312,313,314,316,317,319,321,324,328,329,389,409,422,423,429,474,475],extent:[1,3,41,45,57,71,163,167,188,199,206,210,233,326,329,347,350,364,425,427,440,454,457,460],exterior:[3,6,328],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,205,210,212,251,280,281,282,292,307,355,356,359,360,381,390,393,396,409,413,454,455,457,460,469,478,483],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,285,357,378,387,409,429,455,462,474],extract_atom:11,extract_comput:[11,455],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,214,216,251,317,386,442,478],extrema:406,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,321],f_a:[441,442,443],f_ave:117,f_c:442,f_f:443,f_fix_id:282,f_harm:317,f_i:419,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,246,309,321,475,483],f_ij:419,f_indent:208,f_int:316,f_jj:91,f_k:419,f_langevin:319,f_max:[282,287],f_msst:249,f_r:[236,441,442,443],f_sigma:368,f_solid:317,f_ss:6,f_temp:236,face:[3,6,57,59,71,153,163,167,199,206,207,324,326,327,328,329,350,389,409,423,457,460],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,229,307,317,390,469],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,210,214,216,217,227,232,235,237,238,249,251,252,255,275,279,291,295,297,299,307,311,315,322,323,324,328,338,348,350,362,364,365,368,369,371,373,378,379,380,382,386,390,393,397,398,409,413,415,416,422,424,430,439,444,454,457,460,461,466,469,471,472,475,478,482,483],factori:[3,455],factoriz:347,fail:[3,11,12,59,169,214,217,347,355,357,380,422,455],failur:[121,426,456,483],fairli:[11,413,466,471],faken:73,falcon:232,fall:[3,6,191,205,278,455,483],fals:[86,330,332,483],fame:8,famili:[446,454],familiar:[0,11],fan:419,far:[3,6,12,17,57,59,61,86,188,191,192,210,211,212,214,217,251,273,291,292,307,324,335,338,353,357,358,445,455,457,462,475],farago:235,farrel:[441,443],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,206,210,212,217,227,229,233,248,249,251,253,254,255,256,257,265,268,269,270,271,281,282,284,292,296,300,306,309,317,319,323,324,325,327,329,357,393,407,460,469,483,486],fasolino:395,fast:[6,7,9,12,13,17,39,188,260,282,320,347,348,370,407,408,438,440,459,464,466,475,484,487],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,209,210,216,223,226,230,234,235,251,253,254,255,256,257,258,266,268,269,271,279,283,284,292,294,295,307,310,312,314,316,319,323,327,333,335,336,337,338,341,343,347,348,359,360,362,363,364,366,368,369,370,371,372,373,374,375,376,377,378,381,382,384,385,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,414,415,416,418,423,424,430,438,439,440,441,442,443,445,446,448,449,450,452,466,470,478],fastest:[1,6,14,17,153,206,319,320,362,454],fatal:[3,474],fault:[70,422],faulti:12,fava:389,favor:213,favorit:7,fbmc:314,fcc:[],fcm:[265,483],fdirect:220,fdotr:394,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:384,feedback:[7,232],feel:[7,232,233,241,273,328,330,357,413],felling:411,felt:328,femtosecond:482,fene:[],fennel:[378,398],fep:[],ferguson:[6,171,469],fermi:[1,12,15,151,362,443],fermion:[9,386],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,205,206,207,208,236,251,278,281,283,295,321,347,355,356,357,364,454,457,462,466,468,476,483,485],fewer:[1,3,11,15,16,61,241,466],fewest:3,fextern:225,feynman:275,fff:455,ffield:[377,387,421,422],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,274,347,348,466],fft_inc:[12,348],fft_lib:12,fft_path:12,fftbench:[347,476],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,197,198,222,225,229,275,291,378,398,402,437],field1:[458,462],field2:458,field:[],fifth:[304,415],figur:[1,3,8,11,12,282,454,455],fij:381,file0:273,file1:[11,13,273,318,332,356,462,464,468],file2:[11,13,318,332,356,462,464,468],file:[],file_from:189,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,210,215,273,277,280,283,284,285,288,289,292,293,318,319,344,345,346,357,363,364,368,378,384,385,387,395,409,410,411,415,419,420,421,422,429,439,440,441,442,443,446,453,454,455,458,459,464,468,475,483,485,486,487],filennam:464,filep:[3,188,191,459,464,487],filepo:289,fill:[7,165,190,278,319,350,358,368,422,460],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,380],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,213,214,224,227,250,273,279,287,291,353,355,357,358,378,393,398,402,409,438,440,478,483],find_custom:8,fine:[16,17,169,197,222,317,358,362,483],finer:[140,165,483],finest:347,finger:[165,187,248,460],finish:[6,11,41,210,332,344,346,347,359,361,362,445,462,483,484],finit:[],finni:[7,384,438],finvers:220,fiorin:[9,215],fire:[353,354,355,357,471],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,203,204,205,206,207,208,210,213,216,227,228,233,238,248,249,250,251,273,275,280,281,282,284,289,292,295,296,304,305,307,308,309,316,317,318,319,321,325,330,332,333,339,350,355,356,357,358,361,362,363,364,367,368,369,371,373,375,377,378,384,386,387,390,391,393,394,395,397,398,402,407,408,409,411,413,415,419,421,422,429,437,439,440,441,442,443,446,450,452,453,454,455,457,458,459,462,464,466,469,470,471,474,475,478,483,484,485,487],fischer:[6,9,19,20,171,373,469],fit:[3,6,9,12,38,56,185,291,307,364,368,395,409,413,433,440,442,465,483],five:[73,151,282,356,368,410,457,471],fix:[],fix_adapt:[159,196,406],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,278],fix_evapor:201,fix_flux:200,fix_gcmc:[201,356],fix_gl:229,fix_gld:229,fix_grav:278,fix_id:[3,214,249,251,253,254,255,256,257,279,282],fix_modifi:[],fix_mov:[187,325],fix_nh:8,fix_npt:229,fix_nvt:[201,227],fix_poem:[3,6],fix_pour:[3,217],fix_qbmsst:9,fix_qeq:[3,377],fix_rattl:295,fix_reax_bond:421,fix_rigid:[241,367],fix_saed_vtk:293,fix_setforc:8,fix_shak:295,fix_srd:3,fix_styl:255,fix_temp_rescal:313,fixedpoint:[214,251],fixextern:225,fixid:200,fji:381,flag1:[219,360],flag2:[219,360],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,208,213,215,219,232,235,239,241,247,248,274,281,292,304,306,307,314,318,327,330,345,348,356,360,361,362,364,392,397,409,437,452,454,455,457,458,459,461,462,463,467,483],flag_buck:372,flag_coul:[372,381,402],flag_lj:[381,402],flagfld:[370,407,408],flaghi:[3,370,407,408],flaglog:[370,407,408],flagn:219,flagvf:[370,407,408],flat:[6,319,324,325,329],flavor:[2,7,12],fld:[9,324,370,407,408],flen:365,flex_press:365,flexibl:[3,6,8,166,190,203,206,215,229,252,315,322,386,442,475],flip:[3,6,216,251,326,327],floor:483,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,214,227,228,235,238,251,255,273,274,317,319,341],fluid:[],fluid_veloc:242,flush:[3,191,474],flux:[],flv:190,fly:[7,9,12,41,190,194,200,217,220,292,295,320,368,475,478],fmackai:9,fmag:218,fmass:275,fmax:[355,475],fmomentum:220,fmsec:[2,191,235,236,248,251,279,292,310,311,466,477,482,484],fname:346,fno:[12,16],fnorm:[355,475],fnpt:220,fnvt:220,foce:393,fock:365,focu:295,fogarti:[9,285,422],foil:[140,273,429],fold:[305,466],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,210,215,216,217,220,221,225,227,228,229,232,234,235,236,238,241,249,251,255,256,257,268,269,271,274,275,277,280,281,282,283,285,287,289,291,292,293,295,309,310,311,312,315,316,317,318,319,321,322,330,331,335,336,337,338,341,343,345,350,352,355,356,357,362,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,426,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,446,448,449,450,452,454,455,457,458,459,460,462,464,465,466,469,471,472,473,478,483,484,486],foo:[4,8,11,12,188,190,225,455,468,483],foot:6,footprint:[12,362],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:241,forcefield:[291,392],forcegroup:238,forcezero:353,ford:381,forestgreen:191,forev:71,forget:[236,478],forgiv:251,fork:[12,188],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,93,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:[6,9,12,29,91,134,140,141,163,203,204,205,206,207,208,228,289,304,305,319,377,387,409,415,444,446,452,453,455,457,460],thirumalai:177,thistl:191,tho:385,thole:[],thompson:[0,5,7,9,13,112,140,141,350,429],thoroughli:9,those:[1,2,3,4,5,6,7,8,12,13,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,43,45,46,47,48,49,50,51,53,54,56,61,71,77,87,91,108,109,110,112,116,140,141,143,145,152,155,165,169,171,172,174,175,176,177,178,179,180,182,183,185,187,188,190,191,201,202,203,204,206,207,208,214,216,217,224,230,232,233,234,235,241,250,251,253,254,255,256,257,258,266,268,269,271,278,281,284,292,309,316,317,321,325,326,327,330,331,333,335,336,337,338,339,341,343,347,348,355,357,358,362,363,364,366,369,370,371,372,373,374,375,376,377,378,381,382,384,385,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,413,414,415,416,418,421,422,423,424,429,430,438,439,440,441,442,443,445,446,448,449,450,452,454,455,457,459,460,461,462,464,466,467,469,471,474,475,476,478,483,486,487],though:[6,8,12,39,40,63,71,91,104,165,188,191,201,206,211,212,214,216,221,252,290,292,294,303,315,322,332,347,350,357,382,383,384,386,387,389,390,406,407,413,446,452,457,459,460,465,469,476,483],thought:[148,235,269,292,323,324,354,390,397,478],thread:[1,3,9,12,16,17,18,232,320,345,362,470,476],threads_per_atom:3,three:[1,3,6,54,63,74,87,91,105,117,118,119,130,140,144,164,165,177,194,213,214,219,239,251,255,274,279,292,307,314,316,319,337,341,347,348,356,362,363,364,368,384,385,387,389,390,394,397,409,410,411,415,419,422,423,429,439,441,442,443,446,455,457,460,483],threebodi:439,thresh:[41,188,190,191,210,455],threshhold:[3,41,190,210,330,455],threshold:[3,41,86,191,210,273,358,422,452,471],thrid:455,through:[3,6,7,9,11,12,63,165,188,192,214,225,227,232,233,238,240,241,242,251,252,275,283,300,314,319,324,346,353,364,385,386,390,398,424,430,437,444,452,455,458,468,474,478],throughout:[6,16,116,118,320,362,457],thru:[3,6,7,11,12,66,74,75,81,89,90,93,103,104,105,106,160,187,188,191,205,248,307,327,332,346,355,361,460],thrust:1,thu:[1,2,3,6,8,9,11,12,18,33,38,39,41,42,50,59,61,63,64,66,67,70,71,72,73,75,77,81,88,90,91,93,103,104,106,108,109,113,114,115,116,117,140,141,142,145,148,153,155,160,161,162,165,167,168,169,173,178,184,185,187,188,190,191,192,194,195,196,197,198,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,220,222,224,228,229,230,231,232,233,235,236,241,246,251,255,265,273,279,281,283,287,290,292,293,294,295,296,300,301,304,305,306,307,308,310,311,312,314,315,318,319,321,322,323,324,327,328,329,330,332,333,339,347,348,350,353,355,356,357,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,382,383,384,385,386,387,388,389,390,393,394,395,396,398,402,406,407,408,409,410,411,413,414,416,418,419,420,421,422,423,429,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,450,452,454,455,457,458,459,460,461,462,464,465,466,467,469,471,472,473,474,475,476,478,482,483,484,485,486],thumb:[8,10,17,165,187,248,292,362,376,460,466],thz:287,ti2:164,ti3:164,ti4:164,tight:368,tightli:281,tij:381,tildeslei:[29,87,381],tile:[3,6,41,62,165,210,396,445,454,483],tilt:[3,6,57,58,59,71,153,167,188,191,206,214,216,217,230,249,251,252,273,282,348,350,446,457,460,475],time:[],time_integr:200,timedelta:204,timelin:5,timer:14,timescal:[3,202,203,204,205,206,207,208,249,282,287,386,452,466],timespan:[235,236,251,279,292,310,311],timestamp:[3,462],timestep:[],timesteppnig:295,tin:[377,378],tine:204,tinfoil:348,tini:[116,165,355,368,484],tinker:7,tip3p:[],tip4:6,tip4p:[],tip:[],tirrel:324,titan:15,titer:292,titl:[203,204,205,206,207,208,280,422],title1:[203,204,205,206,207,208],title2:[203,204,205,206,207,208],title3:[203,204,205,206,207,208],tji:381,tl1:164,tl3:164,tlbr_msw:419,tlo:471,tloop:[251,252,255],tlsph:122,tlsph_defgrad:122,tlsph_strain:[124,125],tlsph_strain_rat:[124,125,131],tlsph_stress:[121,131,132],tm3:164,tmax:[3,221,471],tmd:[],tmd_dump_fil:318,tmdatom:318,tmin:221,tmp1:[205,208,468],tmp2:[205,208,468],tmp3:468,tmp:[6,12,41,66,68,69,75,90,93,104,106,114,116,145,160,162,188,190,191,210,281,292,315,322,361,464,468,483],tobia:[251,252,292],todd:269,toe:159,toff:[356,457],togeth:[2,3,6,11,12,17,39,41,71,115,141,145,159,166,188,195,196,203,205,210,214,220,229,236,251,279,292,296,301,304,307,325,329,330,388,393,455,460,465,478,486],toggl:[59,169,464],togheth:3,togther:3,tol:[295,307,347,439],toler:[3,214,283,284,285,295,307,355,357,439,452,471],tomato:191,tong:[9,13],too:[1,3,6,7,39,41,64,67,70,72,73,77,88,140,153,166,168,190,210,211,212,214,217,224,227,231,251,274,279,283,287,289,295,307,314,315,319,322,348,357,358,362,382,452,460,471,474,478,483],took:[71,430],tool:[],toolkit:[6,7,13,14,15],top:[0,3,8,9,11,12,13,59,148,187,194,209,216,231,238,250,269,293,326,327,329,357,362,421,422,429,457,461,467],top_group:301,top_veloc:301,topic:[483,486],toplog:[3,454],topolgi:40,topolog:[2,3,6,7,8,12,13,39,40,87,108,115,168,169,191,211,212,232,277,356,393,413,454,457,458,459,461,462,469],topwal:209,torder:292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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 force/tally 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_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":211,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,206,207,208,211,212,214,215,216,217,221,224,227,228,233,235,236,237,238,239,241,246,249,251,252,255,269,270,274,275,278,279,280,281,282,284,287,289,290,292,293,307,309,314,315,316,317,320,322,324,326,330,342,345,347,348,350,351,353,354,356,358,359,360,362,365,368,370,386,407,408,413,421,422,437,438,452,453,454,457,458,460,462,464,465,466,469,471,473,474,475,476,477,482,484,485,486],"function":483,"long":[369,371,372,373,374,378,380,381,398,402,406,416,424],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:297,adp:363,airebo:364,alloi:384,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:199,arrai:6,aspher:[6,82,144,253,256,259,260,268],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,281,483],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:209,awpmd:[9,365],balanc:[41,210],barostat:6,basal:67,beck:366,berendsen:[279,310],between:6,binary2txt:13,bodi:[6,8,42,68,261,367],bond:[8,13,69,211,212,213,288],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:368,born:[369,380],boundari:[7,57],box:[6,58,214],brownian:370,buck:[371,372,380],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,373,406],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,333,374],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[324,376,449],colvar:[9,13,215],com:[74,75,146],comb3:377,comb:[284,377],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,483],compute_modifi:102,condit:7,conduct:[6,315],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:204,cosin:[23,24,25,26,27,28,174],cossq:335,coul:[369,371,372,373,374,378,379,380,391,398,402,406,416,424],coupl:6,creat:212,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:311,csvr:311,cubic:400,cuda:[9,14,109,112,143,152,197,209,223,226,230,251,258,294,295,310,312,323,369,371,373,374,384,390,391,398,399,401,404,414,439,441],custom:8,cut:[49,365,371,374,378,381,386,388,398,399,406,412,416],cvff:336,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[378,398],deform:[148,149,216],delete_atom:168,delete_bond:169,delta:24,deposit:217,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],diagnost:7,diel:379,dielectr:170,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:173,dihedral_styl:[2,171,172,174,175,176,177,178,179,180,181,182,183,184,185],dilat:80,dimens:186,dipol:[6,29,381],direct:220,discuss:6,disp:6,displac:[81,86],displace_atom:187,distribut:[7,12],document:0,dpd:382,drag:218,dreid:[6,392],drude:[6,9,150,219,220,236],dsf:[378,398],dsmc:383,dump:[6,8,188,189,190,192],dump_modifi:191,dynam:283,eam:[13,384],echo:193,edip:385,eff:[9,13,96,97,149,151,156,237,252,262,270,313,386],efield:222,eim:387,elast:6,emac:13,enforce2d:223,ensembl:7,erot:[82,83,84,85],error:3,evapor:224,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],exp:[27,174],expand:[46,401],extend:[8,11],extern:225,fcc:273,featur:[7,8,483],fene:[45,46],fep:[9,13,87,196],field:[6,7],file:6,finit:6,fix:[2,6,8,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,483],fix_modifi:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],flow:6,fluid:238,flux:[91,142],forc:[6,7,142,308],fourier:[30,31,175,337],freez:226,from:[6,11],futur:5,gauss:388,gaybern:389,gcmc:227,gener:[1,6,7,13],get:12,gld:228,gle:229,global:6,gpu:[9,15,366,369,371,373,374,376,378,381,382,384,388,389,391,398,399,400,401,412,414,423,424,430,439,440,441,448,449,450],gran:[325,390],granular:6,graviti:230,gromac:391,group2ndx:331,group:[88,330,483],gyrat:[89,90],h5md:[9,188,189],harmon:[32,47,48,49,176,179,324,338,415],hbond:392,heat:[91,142,231],heatconduct:431,helix:177,hertz:[390,425],histo:205,histori:[5,390],hook:390,hourglass_error:122,how:6,hybrid:[33,50,178,339,393],idealga:432,imag:[188,190],imd:232,implicit:373,improp:[8,92],improper_coeff:334,improper_styl:[2,333,335,336,337,338,339,340,341,342,343],includ:344,inclus:8,indent:233,indic:0,individu:2,induc:6,inertia:93,info:[0,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,345],input:[2,6,8],instal:11,instruct:9,integr:[6,7],integrate_tlsph:298,integrate_ulsph:299,intel:[9,16,373,389,398,439],interfac:[6,11],internal_energi:123,introduct:7,invers:220,ipi:234,ipp:13,jul:[],jump:346,kate:13,keyword:413,kim:[9,394],kokko:[9,17],kspace:[2,8,9,320],kspace_modifi:347,kspace_styl:[6,348],label:349,lammp:[0,1,2,6,7,8,11,12],langevin:[235,236,237],lattic:350,lcbop:395,librari:[6,11,12],limit:[263,312],line:[12,264,396],linear:405,lineforc:243,list:[2,397],lj1043:324,lj126:324,lj93:324,lj96:399,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:351,lubric:407,lubricateu:408,make:12,mass:352,math:483,matlab:13,meam:[9,409,410,411],measur:1,meso:[244,245],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:412,min_modifi:353,min_styl:354,minim:[8,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,355],misc:9,mod:[319,442],model:[6,7],modifi:8,molecul:356,molfil:[9,188,192],moltempl:13,momentum:[239,247],morri:436,mors:[51,392,414],move:248,move_tri_surf:300,movi:[188,190],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[369,371,373,378,398],msst:249,multi:[6,7,179],multipl:6,nb3b:415,neb:[250,357],neigh_modifi:358,neighbor:359,nemd:6,newton:360,next:361,nharmon:180,noforc:[260,265],non:[6,7],none:[34,52,181,340,417],nongauss:105,nonlinear:53,nph:[251,252,253,254,292],nphug:255,npt:[251,252,256,257,292],nve:[258,259,260,261,262,263,264,265,266,267,292],nvt:[251,252,268,269,270,271,292],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,171,172,174,175,176,177,179,180,182,183,185,230,251,253,254,255,256,257,258,266,268,269,271,284,333,335,336,337,338,341,343,363,364,366,369,370,371,372,373,374,376,377,378,379,381,382,384,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,411,414,415,416,418,423,424,430,439,440,441,442,443,445,446,448,449,450],onewai:272,open:7,oper:483,opl:182,opt:[19,373,384,398,402,414],optim:1,option:[6,8,12],orient:273,orthogon:6,other:6,output:[6,7,8,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],overlai:393,overview:11,packag:[1,9,12,14,15,16,17,18,19,362],pair:[6,107,108],pair_coeff:375,pair_modifi:413,pair_styl:[2,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450],pair_writ:447,pairwis:8,parallel:11,paramet:6,pars:2,partial:152,particl:[6,7,42],partit:451,past:5,per:6,perform:[1,10],peri:418,period:25,phonon:[9,13,274],pimd:275,piston:326,planeforc:276,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:418,poem:[9,277],point:283,polariz:6,poli:[370,407,408],polym:13,polymorph:419,post:7,potenti:[2,6,8],pour:278,pppm:6,prd:452,pre:7,press:279,pressur:112,previou:12,print:[280,453],problem:[3,4],process:[6,7],processor:454,profil:153,properti:[6,113,114,115,281],pymol_aspher:13,python:[9,11,13,455],qbmsst:282,qeq:[283,284,285],qmmm:[9,286],qtb:[9,287],quadrat:183,quantiti:6,quartic:[35,54],quip:420,quit:456,ramp:154,rattl:295,rdf:116,read_data:457,read_dump:458,read_restart:459,reax:[9,13,285,288,289,421,422],reaxc:9,rebo:364,recent:290,reduc:117,refer:483,reflect:327,region:[8,117,155,156,328,460,483],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,226,227,228,229,230,231,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,287,288,289,290,292,293,294,296,297,298,299,300,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,341,342,343,344,345,346,347,348,350,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,469,470,471,472,473,474,475,476,477,479,480,481,483,484,485,486,487],relax:214,replic:461,replica:[6,7],report:3,requir:12,rerun:462,rescal:[312,313],reset:221,reset_timestep:463,resquar:423,restart2data:13,restart:[6,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,464],restrain:291,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],rho:126,rhosum:434,rigid:[6,83,98,241,292],ring:341,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,465],run_styl:466,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,424],self:306,serial:11,set:[6,467],setforc:294,setvel:301,shake:295,share:[11,12],shell:[6,468],shield:283,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:283,slice:119,sllod:[269,270],small:292,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,296,297,298,299,300,301,303,425,426,427,428],smooth:[404,405],sna:140,snad:140,snap:429,snapshot:6,snav:140,soft:[406,430],solver:2,sourc:7,spatial:[206,207],spc:6,speci:289,special:[7,413,483],special_bond:469,sph:[9,431,432,433,434,435,436],sphere:[84,85,158,207,241,254,257,266,271],spheric:6,spline:[410,411],spring:[304,305,306,317],squar:28,srd:[307,329],srp:437,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],state:309,stationari:245,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],store:[308,309],strategi:1,streitz:378,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:470,summari:6,swap:[201,213],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],system:6,tabl:[0,6,38,56,185,440,441],tad:471,taitwat:[435,436],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,310,311,312,313],temper:472,temperatur:6,tersoff:[441,442,443],test:11,tfmc:314,thermal:[6,315],thermo:[6,473],thermo_modifi:474,thermo_styl:475,thermodynam:[6,8],thermostat:6,thole:444,time:[6,208],timer:476,timestep:477,tip3p:6,tip4p:[6,378,398,402,406],tip:12,tlsph:426,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:318,tool:[12,13],torqu:160,transform:220,tri:[267,445],tri_surfac:427,triangle_mesh_vertic:134,triclin:6,tstat:382,ttm:319,tune:320,type:7,ulsph:428,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:343,uncomput:479,undump:480,unfix:481,unit:482,user:[9,12,14,16,18],vacf:161,valu:[6,483],variabl:[6,8,483],variou:1,vashishta:446,vcm:162,vector:[6,321,483],veloc:484,version:[0,5,12],via:12,vim:13,viscos:[6,322],viscou:[242,323],visual:6,vol:139,voronoi:[9,163],vtk:293,wall:[6,324,325,326,327,328,329],wall_surfac:303,warn:3,water:6,weight:205,what:[7,12],wolf:[369,378],wrapper:11,write:6,write_data:485,write_dump:486,write_restart:487,xmgrace:13,xmovi:13,xrd:164,xtc:9,yukawa:[448,449],zbl:[443,450]}}) 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