diff --git a/doc/Eqs/angle_dipole_couple.jpg b/doc/Eqs/angle_dipole_couple.jpg new file mode 100644 index 0000000000..f16849b2f9 Binary files /dev/null and b/doc/Eqs/angle_dipole_couple.jpg differ diff --git a/doc/Eqs/angle_dipole_couple.tex b/doc/Eqs/angle_dipole_couple.tex new file mode 100644 index 0000000000..a857d83d7a --- /dev/null +++ b/doc/Eqs/angle_dipole_couple.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} + +\begin{eqnarray*} +-\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\ +\vec{F_j} & = & -\vec{F_i} \\ +\end{eqnarray*} + +\end{document} diff --git a/doc/angle_dipole.html b/doc/angle_dipole.html index 5367f273fc..6c78a4e535 100644 --- a/doc/angle_dipole.html +++ b/doc/angle_dipole.html @@ -159,15 +159,17 @@ and the reference (bond) vector r_ij:

angle.

The torque on the dipole can be obtained by differentiating the potential using the ‘chain rule’ as in appendix C.3 of -(Allen):

+(Allen):

_images/angle_dipole_torque.jpg

Example: if gamma0 is set to 0 degrees, the torque generated by the potential will tend to align the dipole along the reference direction defined by the (bond) vector r_ij (in other words, mu_j is restrained to point towards atom ‘i’).

-

Note that the angle dipole potential does not give rise to any force, -because it does not depend on the distance between i and j (it only -depends on the angle between mu_j and r_ij).

+

The dipolar torque T_j must be counterbalanced in order to conserve +the local angular momentum. This is achieved via an additional force +couple generating a torque equivalent to the opposite of T_j:

+_images/angle_dipole_couple.jpg +

where F_i and F_j are applied on atoms i and j, respectively.

The following coefficients must be defined for each angle type via the angle_coeff command as in the example above, or in the data file or restart files read by the read_data diff --git a/doc/angle_dipole.txt b/doc/angle_dipole.txt index 7585c82658..6ca68c5942 100644 --- a/doc/angle_dipole.txt +++ b/doc/angle_dipole.txt @@ -50,9 +50,13 @@ the potential will tend to align the dipole along the reference direction defined by the (bond) vector r_ij (in other words, mu_j is restrained to point towards atom 'i'). -Note that the angle dipole potential does not give rise to any force, -because it does not depend on the distance between i and j (it only -depends on the angle between mu_j and r_ij). +The dipolar torque T_j must be counterbalanced in order to conserve +the local angular momentum. This is achieved via an additional force +couple generating a torque equivalent to the opposite of T_j: + +:c,image(Eqs/angle_dipole_couple.jpg) + +where F_i and F_j are applied on atoms i and j, respectively. The following coefficients must be defined for each angle type via the "angle_coeff"_angle_coeff.html command as in the example above, or in diff --git a/doc/fix_ave_chunk.html b/doc/fix_ave_chunk.html index eb6f9b5939..e90cb69a0c 100644 --- a/doc/fix_ave_chunk.html +++ b/doc/fix_ave_chunk.html @@ -159,7 +159,7 @@ v_name = per-atom vector calculated by an atom-style variable with name norm arg = all or sample or none = how output on Nfreq steps is normalized all = output is sum of atoms across all Nrepeat samples, divided by atom count sample = output is sum of Nrepeat sample averages, divided by Nrepeat - none = output is sum of Nrepeat sums, divided by Nrepeat + none = output is sum of Nrepeat sample sums, divided by Nrepeat ave args = one or running or window M one = output new average value every Nfreq steps running = output cumulative average of all previous Nfreq steps @@ -260,8 +260,8 @@ that are a multiples of Nfreq. The average is over Nrepeat quantities, computed in the preceding portion of the simulation every Nevery timesteps. Nfreq must be a multiple of Nevery and Nevery must be non-zero even if Nrepeat is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq.

+contributing to the average value cannot overlap, i.e. Nrepeat*Nevery +can not exceed Nfreq.

For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on timesteps 90,92,94,96,98,100 will be used to compute the final average on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on @@ -363,7 +363,7 @@ atoms in the chunk. The averaged output value for the chunk on the average over atoms across the entire Nfreq timescale.

If the norm setting is sample, the chunk value is summed over atoms for each sample, as is the count, and an “average sample value” is -computed for each sample, i.e. Sample-sum / Sample-count. The outuput +computed for each sample, i.e. Sample-sum / Sample-count. The output value for the chunk on the Nfreq timesteps is the average of the Nrepeat “average sample values”, i.e. the sum of Nrepeat “average sample values” divided by Nrepeat. In other words it is an average @@ -372,7 +372,7 @@ of an average.

sample seting is done, except the individual “average sample values” are “summed sample values”. A summed sample value is simply the chunk value summed over atoms in the sample, without dividing by the number -of atoms in the sample. The outuput value for the chunk on the +of atoms in the sample. The output value for the chunk on the Nfreq timesteps is the average of the Nrepeat “summed sample values”, i.e. the sum of Nrepeat “summed sample values” divided by Nrepeat.

diff --git a/doc/fix_ave_chunk.txt b/doc/fix_ave_chunk.txt index e1d23477c8..4a53a6915f 100644 --- a/doc/fix_ave_chunk.txt +++ b/doc/fix_ave_chunk.txt @@ -34,7 +34,7 @@ keyword = {norm} or {ave} or {bias} or {adof} or {cdof} or {file} or {overwrite} {norm} arg = {all} or {sample} or {none} = how output on {Nfreq} steps is normalized all = output is sum of atoms across all {Nrepeat} samples, divided by atom count sample = output is sum of {Nrepeat} sample averages, divided by {Nrepeat} - none = output is sum of {Nrepeat} sums, divided by {Nrepeat} + none = output is sum of {Nrepeat} sample sums, divided by {Nrepeat} {ave} args = {one} or {running} or {window M} one = output new average value every Nfreq steps running = output cumulative average of all previous Nfreq steps @@ -147,8 +147,8 @@ that are a multiples of {Nfreq}. The average is over {Nrepeat} quantities, computed in the preceding portion of the simulation every {Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. +contributing to the average value cannot overlap, i.e. Nrepeat*Nevery +can not exceed Nfreq. For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on timesteps 90,92,94,96,98,100 will be used to compute the final average @@ -270,7 +270,7 @@ average over atoms across the entire {Nfreq} timescale. If the {norm} setting is {sample}, the chunk value is summed over atoms for each sample, as is the count, and an "average sample value" is -computed for each sample, i.e. Sample-sum / Sample-count. The outuput +computed for each sample, i.e. Sample-sum / Sample-count. The output value for the chunk on the {Nfreq} timesteps is the average of the {Nrepeat} "average sample values", i.e. the sum of {Nrepeat} "average sample values" divided by {Nrepeat}. In other words it is an average @@ -280,7 +280,7 @@ If the {norm} setting is {none}, a similar computation as for the {sample} seting is done, except the individual "average sample values" are "summed sample values". A summed sample value is simply the chunk value summed over atoms in the sample, without dividing by the number -of atoms in the sample. The outuput value for the chunk on the +of atoms in the sample. The output value for the chunk on the {Nfreq} timesteps is the average of the {Nrepeat} "summed sample values", i.e. the sum of {Nrepeat} "summed sample values" divided by {Nrepeat}. diff --git a/doc/pair_srp.html b/doc/pair_srp.html index 38b3f4f567..a59ff37536 100644 --- a/doc/pair_srp.html +++ b/doc/pair_srp.html @@ -137,6 +137,7 @@
  • keyword = exclude
    • +bptype value = atom type for bond particles
 exclude value = yes or no
    @@ -196,18 +197,23 @@ or read_restart< is used.

    Warning

    -

    Pair style srp considers each bond of type btype to -be a fictitious “particle” of type bptype, where bptype is the -largest atom type in the system. There cannot be any actual particles -assigned to this atom type. This means you must specify the number of -types in your system to be one larger would normally be the case, -e.g. via the create_box or -read_data commands. These ficitious “bond particles” -are inserted at the beginning of the run, and serve as placeholders -that define the position of the bonds. This allows neighbor lists to -be constructed and pairwise interactions to be computed in almost the -same way as is done for actual particles. Because bonds interact only -with other bonds, pair_style hybrid should be used +

    Pair style srp considers each bond of type btype to +be a fictitious “particle” of type bptype, where bptype is either +the largest atom type in the system, or the type set by the bptype +flag. Any actual existing particles with this atom type will be deleted +at the beginning of a run. This means you must specify the number of +types in your system accordingly; usually to be one larger than what +would normally be the case, e.g. via the create_box +or by changing the header in your data file. +The ficitious “bond particles” are inserted at the beginning of the +run, and serve as placeholders that define the position of the bonds.

    +
    +
    This allows neighbor lists to be constructed and pairwise interactions
    +
    +
    to be computed in almost the same way as is done for actual particles.
    +
    Because bonds interact only with other bonds,
    +
    +

    pair_style hybrid should be used to turn off interactions between atom type bptype and all other types of atoms. An error will be flagged if pair_style hybrid is not used.

    diff --git a/doc/pair_srp.txt b/doc/pair_srp.txt index 02e3f8383e..2c1c054f96 100644 --- a/doc/pair_srp.txt +++ b/doc/pair_srp.txt @@ -17,6 +17,7 @@ btype = bond type to apply SRP interactions to (can be wildcard, see below) :l distance = {min} or {mid} :l zero or more keyword/value pairs may be appended :l keyword = {exclude} :l + {bptype} value = atom type for bond particles {exclude} value = {yes} or {no} :pre :ule @@ -78,17 +79,19 @@ The last coefficient is optional. If not specified, the global cutoff is used. IMPORTANT NOTE: Pair style srp considers each bond of type {btype} to -be a fictitious "particle" of type {bptype}, where {bptype} is the -largest atom type in the system. There cannot be any actual particles -assigned to this atom type. This means you must specify the number of -types in your system to be one larger would normally be the case, -e.g. via the "create_box"_create_box.html or -"read_data"_read_data.html commands. These ficitious "bond particles" -are inserted at the beginning of the run, and serve as placeholders -that define the position of the bonds. This allows neighbor lists to -be constructed and pairwise interactions to be computed in almost the -same way as is done for actual particles. Because bonds interact only -with other bonds, "pair_style hybrid"_pair_hybrid.html should be used +be a fictitious "particle" of type {bptype}, where {bptype} is either +the largest atom type in the system, or the type set by the {bptype} +flag. Any actual existing particles with this atom type will be deleted +at the beginning of a run. This means you must specify the number of +types in your system accordingly; usually to be one larger than what +would normally be the case, e.g. via the "create_box"_create_box.html +or by changing the header in your "data file"_read_data.html. +The ficitious "bond particles" are inserted at the beginning of the +run, and serve as placeholders that define the position of the bonds. + This allows neighbor lists to be constructed and pairwise interactions +to be computed in almost the same way as is done for actual particles. + Because bonds interact only with other bonds, +"pair_style hybrid"_pair_hybrid.html should be used to turn off interactions between atom type {bptype} and all other types of atoms. An error will be flagged if "pair_style hybrid"_pair_hybrid.html is not used. diff --git a/doc/read_restart.html b/doc/read_restart.html index 5b3bcb2a46..dd2222866b 100644 --- a/doc/read_restart.html +++ b/doc/read_restart.html @@ -242,65 +242,90 @@ does not have to end in ”.mpiio”, just contain those characters. Unlike MPI-IO dump files, a particular restart file must be both written and read using MPI-IO.

    -

    A restart file stores the following information about a simulation: -units, atom style and atom style related settings (id, map, -sort), communication settings (mode, cutoff, vel), timestep, -simulation box size and shape and boundary settings, group -definitions, per-type atom settings such as mass, per-atom attributes -including their group assignments and molecular topology attributes, -force field styles and - in most cases - force field coefficients, and -special_bonds settings. This means that commands -for these quantities do not need to be re-specified in the input -script that reads the restart file, though you can redefine settings -after the restart file is read.

    -

    One exception is that some force styles (pair, bond, angle, etc) do -not store their coefficient info in restart files. Typically these -are many-body or tabulated potentials which read their parameters from -separate files; you may need to re-specify the pair style and pair coeff commands in -your restart input script. The doc pages for individual pair styles -mention if this is the case. This is also true of bond_style hybrid -(and angle_style, dihedral_style, improper_style hybrid).

    -

    All settings made by the pair_modify command, such -as the shift and tail settings, are stored in the restart file with -the pair style. The one exception is the pair_modify compute setting is not stored, since it is typically -only used for debugging purposes.

    -

    Information about kspace_style settings are not -stored in the restart file. Hence if you wish to use an Ewald or PPPM -solver, these commands must be re-issued after the restart file is -read.

    -

    The list of fixes used for a simulation is not stored in -the restart file. This means the new input script should specify all -fixes it will use. Note that some fixes store an internal “state” -which is written to the restart file. This allows the fix to continue -on with its calculations in a restarted simulation. To re-enable such -a fix, the fix command in the new input script must use the same -fix-ID and group-ID as was used in the input script that wrote the -restart file. If a match is found, LAMMPS prints a message indicating -that the fix is being re-enabled. If no match is found before the -first run or minimization is performed by the new script, the “state” -information for the saved fix is discarded. See the doc pages for -individual fixes for info on which ones can be restarted in this -manner.

    -

    Bond interactions (angle, etc) that have been turned off by the fix shake or delete_bonds command will -be written to a restart file as if they are turned on. This means -they will need to be turned off again in a new run after the restart -file is read.

    +

    Here is the list of information included in a restart file, which +means these quantities do not need to be re-specified in the input +script that reads the restart file, though you can redefine many of +these settings after the restart file is read.

    + +

    Here is a list of information not stored in a restart file, which +means you must re-issue these commands in your input script, after +reading the restart file.

    + +

    Note that some force field styles (pair, bond, angle, etc) do not +store their coefficient info in restart files. Typically these are +many-body or tabulated potentials which read their parameters from +separate files. In these cases you will need to re-specify the “pair +pair_coeff, bond_coeff, etc +commands in your restart input script. The doc pages for individual +force field styles mention if this is the case. This is also true of +pair_style hybrid (bond hybrid, angle hybrid, etc) +commands; they do not store coefficient info.

    +

    As indicated in the above list, the fixes used for a +simulation are not stored in the restart file. This means the new +input script should specify all fixes it will use. However, note that +some fixes store an internal “state” which is written to the restart +file. This allows the fix to continue on with its calculations in a +restarted simulation. To re-enable such a fix, the fix command in the +new input script must use the same fix-ID and group-ID as was used in +the input script that wrote the restart file. If a match is found, +LAMMPS prints a message indicating that the fix is being re-enabled. +If no match is found before the first run or minimization is performed +by the new script, the “state” information for the saved fix is +discarded. See the doc pages for individual fixes for info on which +ones can be restarted in this manner.

    +

    Likewise, the computes used for a simulation are not stored +in the restart file. This means the new input script should specify +all computes it will use. However, some computes create a fix +internally to store “state” information that persists from timestep to +timestep. An example is the compute msd command +which uses a fix to store a reference coordinate for each atom, so +that a displacement can be calculated at any later time. If the +compute command in the new input script uses the same compute-ID and +group-ID as was used in the input script that wrote the restart file, +then it will create the same fix in the restarted run. This means the +re-created fix will be re-enabled with the stored state information as +described in the previous paragraph, so that the compute can continue +its calculations in a consistent manner.

    +

    Some pair styles, like the granular pair styles, also +use a fix to store “state” information that persists from timestep to +timestep. In the case of granular potentials, it is contact +information between pairs of touching particles. This info will also +be re-enabled in the restart script, assuming you re-use the same +granular pair style.

    +

    LAMMPS allow bond interactions (angle, etc) to be turned off or deleted +in various ways, which can affect how their info is stored in a +restart file.

    +

    If bonds (angles, etc) have been turned off by the fix shake or delete_bonds command, +their info will be written to a restart file as if they are turned on. +This means they will need to be turned off again in a new run after +the restart file is read.

    Bonds that are broken (e.g. by a bond-breaking potential) are written to the restart file as broken bonds with a type of 0. Thus these bonds will still be broken when the restart file is read.

    Bonds that have been broken by the fix bond/break command have disappeared from the system. No information about these bonds is written to the restart file.

    -
    -

    Warning

    -

    No other information is stored in the restart file. -This means that an input script that reads a restart file should -specify settings for quantities like timestep size, -thermodynamic, neighbor list -criteria including settings made via the -neigh_modify comand, dump file -output, geometric regions, etc.

    -
    diff --git a/doc/read_restart.txt b/doc/read_restart.txt index 7c086a5978..bc1349419a 100644 --- a/doc/read_restart.txt +++ b/doc/read_restart.txt @@ -134,57 +134,90 @@ written and read using MPI-IO. :line -A restart file stores the following information about a simulation: -units, atom style and atom style related settings ({id}, {map}, -{sort}), communication settings ({mode}, {cutoff}, {vel}), timestep, -simulation box size and shape and boundary settings, group -definitions, per-type atom settings such as mass, per-atom attributes -including their group assignments and molecular topology attributes, -force field styles and - in most cases - force field coefficients, and -"special_bonds"_special_bonds.html settings. This means that commands -for these quantities do not need to be re-specified in the input -script that reads the restart file, though you can redefine settings -after the restart file is read. +Here is the list of information included in a restart file, which +means these quantities do not need to be re-specified in the input +script that reads the restart file, though you can redefine many of +these settings after the restart file is read. -One exception is that some force styles (pair, bond, angle, etc) do -not store their coefficient info in restart files. Typically these -are many-body or tabulated potentials which read their parameters from -separate files; you may need to re-specify the "pair -style"_pair_style.html and "pair coeff"_pair_coeff.html commands in -your restart input script. The doc pages for individual pair styles -mention if this is the case. This is also true of bond_style hybrid -(and angle_style, dihedral_style, improper_style hybrid). +"units"_units.html +"atom style"_atom_style.html and "atom_modify"_atom_modify.html settings id, map, sort +"comm style"_comm_style.html and "comm_modify"_comm_modify settings mode, cutoff, vel +"timestep"_timestep.html +simulation box size and shape and "boundary"_boundary.html settings +atom "group"_group.html definitions +per-type atom settings such as "mass"_mass.thml +per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc) +force field styles ("pair"_pair_style.html, "bond"_bond_style.html, "angle"_angle_style.html, etc) +force field coefficients ("pair"_pair_coeff.html, "bond"_bond_coeff.html, "angle"_angle_coeff.html, etc) in some cases (see below) +"pair_modify"_pair_modify.html settings, except the compute option +"special_bonds"_special_bonds.html settings :ul -All settings made by the "pair_modify"_pair_modify.html command, such -as the shift and tail settings, are stored in the restart file with -the pair style. The one exception is the "pair_modify -compute"_pair_modify.html setting is not stored, since it is typically -only used for debugging purposes. +Here is a list of information not stored in a restart file, which +means you must re-issue these commands in your input script, after +reading the restart file. -Information about "kspace_style"_kspace_style.html settings are not -stored in the restart file. Hence if you wish to use an Ewald or PPPM -solver, these commands must be re-issued after the restart file is -read. +"fix"_fix.html commands (see below) +"compute"_compute.html commands (see below) +"variable"_variable.html commands +"region"_region.html commands +"neighbor list"_neighbor.html criteria including "neigh_modify"_neigh_modify.html settings +"kspace_style"_kspace_style.html and "kspace_modify"_kspace_modify.html settings +info for "thermodynamic"_thermo_style.html, "dump"_dump.html, or "restart"_restart.html output :ul -The list of "fixes"_fix.html used for a simulation is not stored in -the restart file. This means the new input script should specify all -fixes it will use. Note that some fixes store an internal "state" -which is written to the restart file. This allows the fix to continue -on with its calculations in a restarted simulation. To re-enable such -a fix, the fix command in the new input script must use the same -fix-ID and group-ID as was used in the input script that wrote the -restart file. If a match is found, LAMMPS prints a message indicating -that the fix is being re-enabled. If no match is found before the -first run or minimization is performed by the new script, the "state" -information for the saved fix is discarded. See the doc pages for -individual fixes for info on which ones can be restarted in this -manner. +Note that some force field styles (pair, bond, angle, etc) do not +store their coefficient info in restart files. Typically these are +many-body or tabulated potentials which read their parameters from +separate files. In these cases you will need to re-specify the "pair +"pair_coeff"_pair_coeff.html, "bond_coeff"_bond_coeff.html, etc +commands in your restart input script. The doc pages for individual +force field styles mention if this is the case. This is also true of +"pair_style hybrid"_pair_hybrid.html (bond hybrid, angle hybrid, etc) +commands; they do not store coefficient info. -Bond interactions (angle, etc) that have been turned off by the "fix -shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command will -be written to a restart file as if they are turned on. This means -they will need to be turned off again in a new run after the restart -file is read. +As indicated in the above list, the "fixes"_fix.html used for a +simulation are not stored in the restart file. This means the new +input script should specify all fixes it will use. However, note that +some fixes store an internal "state" which is written to the restart +file. This allows the fix to continue on with its calculations in a +restarted simulation. To re-enable such a fix, the fix command in the +new input script must use the same fix-ID and group-ID as was used in +the input script that wrote the restart file. If a match is found, +LAMMPS prints a message indicating that the fix is being re-enabled. +If no match is found before the first run or minimization is performed +by the new script, the "state" information for the saved fix is +discarded. See the doc pages for individual fixes for info on which +ones can be restarted in this manner. + +Likewise, the "computes"_fix.html used for a simulation are not stored +in the restart file. This means the new input script should specify +all computes it will use. However, some computes create a fix +internally to store "state" information that persists from timestep to +timestep. An example is the "compute msd"_compute_msd.html command +which uses a fix to store a reference coordinate for each atom, so +that a displacement can be calculated at any later time. If the +compute command in the new input script uses the same compute-ID and +group-ID as was used in the input script that wrote the restart file, +then it will create the same fix in the restarted run. This means the +re-created fix will be re-enabled with the stored state information as +described in the previous paragraph, so that the compute can continue +its calculations in a consistent manner. + +Some pair styles, like the "granular pair styles"_pair_gran.html, also +use a fix to store "state" information that persists from timestep to +timestep. In the case of granular potentials, it is contact +information between pairs of touching particles. This info will also +be re-enabled in the restart script, assuming you re-use the same +granular pair style. + +LAMMPS allow bond interactions (angle, etc) to be turned off or deleted +in various ways, which can affect how their info is stored in a +restart file. + +If bonds (angles, etc) have been turned off by the "fix +shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command, +their info will be written to a restart file as if they are turned on. +This means they will need to be turned off again in a new run after +the restart file is read. Bonds that are broken (e.g. by a bond-breaking potential) are written to the restart file as broken bonds with a type of 0. Thus these @@ -195,14 +228,6 @@ bond/break"_fix_bond_break.html command have disappeared from the system. No information about these bonds is written to the restart file. -IMPORTANT NOTE: No other information is stored in the restart file. -This means that an input script that reads a restart file should -specify settings for quantities like "timestep size"_timestep.html, -"thermodynamic"_thermo_style.html, "neighbor list"_neighbor.html -criteria including settings made via the -"neigh_modify"_neigh_modify.html comand, "dump"_dump.html file -output, "geometric regions"_region.html, etc. - :line [Restrictions:] diff --git a/doc/searchindex.js b/doc/searchindex.js index 9e008e990f..fcd01ae84f 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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9,61,63,71,146,147,148,149,150,151,154,155,156,157,159,160,167,168,170,171,174,175,180,189,190,191,192,193,194,196,197,198,202,203,205,206,213,214,215,216,217,219,223,230,241,242,243,244,245,250,251,252,254,259,260,266,271,272,274,277,281,285,293,295,298,306,311,313,314,315,317,318,319,320,321,325,327,329,333,336,337,342,349,355,356,358,359,361,363,364,365,366,367,371,378,380,387,388,389,390,396,397,398,409,410,411,412,413,414,415,419,423,425,426,433,434,444,446,447,448,451,457,459,461,462,463,464,465,467,468,470,472,474,476,479,480,483,487,488,489,490,491,492],afterrun:470,afterward:3,afterword:41,ag1:166,ag2:166,again:[6,11,12,16,17,62,142,147,153,161,190,193,219,234,281,336,349,360,410,411,457,459,460,462,464,469,476,478,488,490],against:[11,12,13,64,220,360,425,426],aggreg:[6,12,65,68,69,79,93,110,117,234,250,293,295,308,457,489],aggress:[234,476],agilio:[9,13],agre:[3,8,187,358,367,398,426],agreement:[5,7],ahd:395,ahead:329,aidan:[0,5,7,9,13,353],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:192,akohlmei:[7,9,13,194,235],aktulga:[7,9,288,426],al2o3:433,al2o3_001:[120,296],al3:166,ala:[241,433],alain:9,alat:[276,412],alb:[423,446,448],albeit:294,albert:9,alchem:[87,161],alcohol:325,alcu:[366,371],alcu_eam:423,alderton:384,alejandr:[254,255],alessandro:13,algebra:415,algorithm:[0,1,6,7,8,9,41,61,193,202,213,216,219,241,243,244,266,278,295,298,317,318,322,325,330,356,357,358,362,365,389,411,415,430,432,457,459,476],alia:[12,16],alias:[1,351],aliceblu:193,align:[6,12,29,41,71,169,187,209,213,236,353,462,465,483],alkali:389,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,155,160,161,162,163,164,165,166,167,168,169,170,171,173,175,180,186,187,190,191,192,193,194,196,197,198,199,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,247,249,250,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,290,291,292,293,294,295,296,297,298,299,300,301,302,306,307,309,310,311,312,313,314,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,340,345,348,349,350,351,352,353,355,358,359,360,361,362,364,365,366,367,368,370,371,372,374,375,376,377,378,380,381,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,405,409,410,411,412,413,414,415,416,417,418,419,420,422,423,424,425,426,427,428,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,455,456,457,459,460,461,462,463,464,465,466,467,469,470,471,472,473,474,475,476,477,479,480,481,483,487,488,489,490,491,492],allen:[29,87,384,392],allentildeslei:87,allign:3,allindex:334,alloc:[3,5,6,8,9,11,12,60,228,324,359,361,365,421,426,462,470],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,92,108,110,144,146,147,160,165,166,167,169,175,186,187,190,192,193,194,196,197,199,201,202,203,205,206,207,208,209,210,211,213,215,216,217,218,219,220,224,225,228,230,231,232,233,235,238,241,244,245,249,251,254,255,276,280,282,283,284,285,289,295,296,298,299,301,302,306,310,317,318,319,320,322,323,324,325,326,327,333,335,337,345,350,351,353,358,359,360,361,364,365,368,371,372,373,374,375,376,381,387,389,393,394,395,396,401,405,410,411,415,417,423,426,427,430,432,433,442,452,454,457,460,462,464,465,466,467,468,469,472,474,475,476,479,480,488,489],almost:[2,3,12,60,236,285,322,351,362,365,442],alo:381,alon:[6,7,216,291,425,426,460],alond:13,along:[6,8,9,12,29,40,87,120,166,167,189,190,192,216,236,241,242,246,251,253,285,295,298,299,303,307,308,317,321,322,328,331,333,353,356,357,358,360,381,384,393,396,399,401,405,412,425,426,445,462,465,472,473,488],alonso:[413,414],alpha:[6,12,51,197,241,277,285,290,358,366,369,372,381,385,387,388,390,395,400,401,412,418,422,447,449,480,483],alpha_:449,alpha_c:409,alpha_i:[434,449],alpha_ialpha_j:449,alpha_lj:409,alphabet:[2,3,22,37,44,55,63,175,186,196,337,345,359,378,443,462],alphanumer:[3,63,196,284,292,335,359,488],alreadi:[3,7,8,9,12,16,17,18,42,167,168,170,191,201,205,209,210,213,215,219,245,283,285,310,333,359,360,385,394,396,403,411,442,452,455,458,462,463,467,472,488],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,72,73,75,77,81,87,89,90,92,94,104,105,106,107,108,109,114,116,118,119,121,142,143,144,145,146,147,148,149,150,151,153,154,155,156,157,159,160,161,162,163,164,165,167,168,169,170,171,173,175,186,187,188,189,190,191,192,193,194,196,197,198,199,201,204,205,206,207,208,209,210,211,212,213,214,2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209,210,214,215,220,232,237,241,254,281,295,317,370,460,462,465,466,471,472],carefulli:[11,12,54,292,333,396,398,467],carlo:[6,7,9,196,203,216,230,295,317,386,443],caro:[203,387],carpent:[7,13],carri:[16,247,284,322,393,426],cart:[3,459],carter:[9,17],cartesian:[3,62,366,459],carv:170,cascad:[224,322],cash:7,cast:[232,488],cat:[15,192],catastroph:286,cate:241,categori:[],cation:[390,433],cauchi:[135,140],caus:[1,2,3,6,8,12,16,17,167,169,170,171,190,193,201,217,224,230,266,276,293,295,298,327,329,330,331,332,335,349,351,358,360,364,395,401,407,410,411,417,456,460,461,462,463,466,467,469,470,488,492],caution:[1,351],cautiou:[214,215],cautious:367,caveat:[367,471],cbecker:[366,387],cc1:[6,14,66,75,90,94,105,107,116,147,162,164,205,209],cc2:14,ccc:[388,444,446,448,451],ccflag:[12,16,17,18,19,190],ccm6:387,ccsi:[388,444,446,448,451],ccu:371,cd2:166,cdeam:387,cdennist:9,cdll:11,cdof:[6,147,205],cdte:371,cdte_bop:371,cdtese:371,cdzn:371,cdznte:371,ce3:166,ce4:166,ceas:357,ceil:488,cell:[3,6,59,88,118,120,165,166,167,190,201,217,218,230,235,252,254,255,258,277,285,288,322,350,351,353,386,389,415,480],cella:[6,480],cellalpha:[6,480],cellb:[6,480],cellbeta:[6,480],cellc:[6,480],cellgamma:[6,480],center:[3,6,25,42,63,66,71,74,75,86,89,90,99,104,105,106,116,118,120,147,148,149,152,155,159,162,164,167,192,193,196,197,198,200,205,208,209,210,217,219,220,221,223,230,231,236,238,239,244,250,254,259,260,271,272,274,277,281,286,292,293,295,296,299,307,308,310,312,313,314,315,317,318,320,327,331,336,353,359,370,388,389,392,393,399,410,411,412,413,414,444,446,447,448,450,451,465,472,483,488],centimet:487,central:[3,61,70,76,77,92,108,118,124,142,244,276,298,308,359,415,419,425,426,451,462],centro:[],centroid:[3,278,450,472],cerda:350,ceriotti2:232,ceriotti:[13,232,237],certain:[1,2,3,6,8,12,17,39,71,115,119,121,171,190,192,204,205,206,208,209,210,211,216,228,229,295,297,311,324,335,342,349,361,396,417,426,449,464,468,483,488],certainli:236,cerutti:351,cfg:[3,6,7,13,190,191,192,193,194],cfile:426,cfl:[130,300],cfor:299,cg_type:428,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:298,ch2lmp:[],ch3:298,ch5md:191,chain3:361,chain:[],challeng:[6,299],chalopin:290,champaign:[235,350,351,410],chan:415,chandler:[366,387],chandrasekhar:[6,401],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,104,118,128,130,149,150,151,167,168,169,171,187,189,190,191,192,193,194,196,197,198,199,200,202,203,209,210,212,213,214,215,216,217,218,219,220,224,225,227,229,230,232,234,235,236,238,240,241,242,244,250,251,252,254,255,256,257,258,259,260,266,271,272,273,274,276,277,281,282,284,285,289,292,293,294,295,297,298,299,310,313,314,315,316,318,319,320,321,322,323,325,328,331,333,351,356,358,360,363,365,385,389,393,396,410,411,412,415,417,425,426,433,443,457,458,459,460,462,463,464,465,466,467,468,470,471,472,473,474,477,480,484,486,487,488,489,490],change_box:[],changeabl:190,channel:[4,199],chapter:[278,351],charact:[2,3,6,12,38,41,56,63,187,190,192,193,194,196,213,284,292,335,359,364,389,400,423,425,426,433,445,459,460,464,469,470,488,490,491,492],character:[6,67,70,108,118,142,434,457,476],characterist:[239,310,319],charg:[1,3,4,5,6,7,9,11,15,40,87,88,115,120,166,167,190,194,196,197,198,203,220,225,230,284,286,287,288,292,312,325,350,351,359,372,374,380,381,383,384,387,389,390,396,401,405,409,420,425,426,433,443,448,449,451,452,454,455,462,463,467,472,474,483,487,488],charmm2lammp:13,charmm:[],chartreus:193,cheap:310,cheaper:[224,392,427],check:[3,6,8,11,12,15,17,39,41,71,91,187,203,209,213,214,215,220,227,230,236,237,294,298,310,318,320,325,333,335,349,358,359,360,361,362,365,386,397,400,417,426,457,459,460,462,470,476,479,480,488],checkf:187,checkqeq:426,checku:187,chem:[6,13,20,21,25,39,40,43,45,46,87,88,108,114,143,173,174,184,207,218,223,231,232,239,241,253,254,255,272,273,278,282,285,287,295,299,310,313,314,317,318,319,320,327,336,344,346,350,351,357,360,367,372,376,377,380,381,382,384,385,389,391,392,394,395,401,405,406,409,412,416,417,420,433,442,449,471,474,476,483],chemic:[9,120,161,166,190,202,203,230,286,291,292,317,351,425,426,438],chemistri:[9,285,286,288,371,389,425,426],chen:322,cheng:380,chenoweth:[425,426],chenoweth_2008:[425,426],chi:[93,156,189,276,286,288,390,392,489],chiefli:424,child:8,chip:[7,12,17,18,365,475],chipot:218,chiral:344,chmod:[11,12],cho:412,chocol:[7,193],choic:[3,6,12,15,16,18,40,41,54,87,143,146,160,171,187,205,209,210,213,216,219,220,232,238,241,252,254,278,286,295,317,345,351,356,357,360,362,365,396,409,417,421,462,471,472,475,476,482,483,487],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,119,157,158,192,214,215,216,217,220,227,238,241,252,254,256,257,258,259,260,282,310,314,328,350,351,357,452,457,459,471,477],chose:[446,448],chosen:[2,3,6,12,17,142,167,170,179,187,192,198,203,217,220,227,230,231,239,241,252,254,258,278,281,292,310,314,317,318,323,325,326,332,351,352,357,365,389,393,399,400,403,428,446,457,471,476,483],chri:165,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,9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:[3,59,71,116,170,190,192,193,219,252,258,282,285],compris:[40,331,399,427,450],compton:[120,166],comptu:3,compuat:351,comput:[],computation:[3,6,214,215,322,371],computational:483,compute_arrai:8,compute_fep:[198,409],compute_group_group:230,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[120,296],compute_scalar:8,compute_temp:8,compute_ti:198,compute_vector:8,compute_xrd:166,concaten:[2,3,491],concav:331,concentr:387,concept:[6,147,157,205,471],conceptu:[3,6,71,155,217,219,360,381,396,412,467],concern:[6,73,87,191,231],concis:[11,321],conclud:12,concret:8,concurr:[9,16,351,488],conden:[322,446,448],condens:[6,149,322,367,383,387,401,451],condit:[],conducit:6,conduct:[],cone:465,confer:415,confid:[3,476],config:[12,190,459],configfil:218,configur:[1,2,6,12,15,17,38,59,124,169,187,189,190,192,196,217,218,219,220,224,230,237,238,266,278,286,321,348,358,360,367,371,388,412,415,444,446,448,451,457,462,464,465,476],confin:[462,476],conflict:[3,12,40,417,460],conform:[3,6,13,59,216,217,253,294,299,321,344,360,389,474],confus:[3,451],conjuct:385,conjug:[7,8,238,357,389,425,426],conjunct:[6,7,71,86,87,116,150,155,161,167,171,193,197,198,238,241,245,266,281,282,286,287,288,290,295,310,318,325,330,350,351,360,372,374,378,381,385,389,395,401,417,420,428,449,462,465,469,483,492],connect:[3,6,87,152,170,216,235,280,295,298,307,360,382,393,442,448,459,460,466,483],conput:3,consecut:[3,11,12,39,71,167,193,197,198,220,235,236,381,401,405,457,463,465],consequ:[1,6,203,322,400,476],conserv:[3,196,203,216,223,224,231,234,238,240,241,245,250,252,254,266,295,298,313,314,318,325,326,330,360,384,385,393,407,433,471,476],consid:[6,9,70,71,78,87,117,149,152,153,170,190,193,197,198,204,206,209,213,215,216,220,242,255,277,295,317,318,321,322,325,351,378,389,396,426,427,433,442,457,458,460,463,464,465,467,470,472,480,483,488],consider:[6,8,238,239,313,314,315,365,471],consist:[3,6,8,9,11,12,40,42,65,69,79,93,105,110,113,114,117,147,150,152,167,179,189,194,199,200,205,219,220,223,225,228,231,238,239,240,251,254,256,257,258,259,260,261,262,264,265,266,267,269,270,271,272,273,274,282,285,290,292,294,295,313,314,315,316,326,350,351,353,359,360,365,367,371,373,379,381,389,392,396,410,411,412,415,417,427,430,432,433,445,452,460,462,463,465,466,467,474,483,488],consistent_fe_initi:202,consit:295,constant:[],constitu:[3,6,244,295,327,331,379,427],constitut:[430,432],constrain:[3,6,8,145,146,147,148,150,153,154,155,156,157,159,160,196,205,220,230,231,236,244,248,280,281,293,295,298,308,318,325,358,359,389,467,474,483],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,92,108,120,142,166,217,254,277,294,331,361,365,384,415,417,442,444,445,465,466,481,488],constructor:8,consult:426,consum:[1,290,421,488],consumpt:348,contact:[],contact_stiff:[429,431],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,118,120,142,147,155,165,166,167,169,173,175,186,187,190,192,193,194,196,197,198,202,204,205,206,208,209,210,211,213,218,220,225,232,236,237,238,239,241,252,266,276,277,280,281,283,285,288,292,295,296,300,310,317,321,322,331,332,335,349,351,359,360,363,364,366,367,368,371,380,381,384,387,388,389,396,397,412,415,419,423,424,425,426,434,444,445,446,447,448,449,451,457,458,459,460,462,463,464,465,467,469,471,474,476,479,480,483,488,490,492],content:[12,18,426,478,480],context:[3,6,8,12,17,118,119,193,214,215,220,280,292,326,357,454,462,469,478,487,488,489],contibut:70,contigu:459,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,104,105,163,193,196,197,198,203,205,206,207,208,209,210,211,213,216,217,218,219,220,230,231,232,234,235,236,238,239,240,246,251,252,254,256,257,258,259,260,271,272,273,274,279,281,284,285,295,296,299,309,310,312,319,320,322,328,331,335,349,364,365,371,385,386,403,406,425,426,427,430,432,447,457,460,462,464,465,470,476,479,480,488,490],continuum:[6,7,9,202,322,430,432],contour_integr:202,contract:[59,217,219,254,282,295],contradictori:3,contrain:298,contraint:266,contrari:[232,239],contrast:[1,6,42,55,64,149,152,219,333,430,432,454,491],contrib:322,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,94,103,105,107,109,110,111,112,114,116,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,198,203,204,205,206,208,209,210,211,217,230,238,241,244,245,249,255,272,273,280,281,289,292,295,296,298,324,350,358,360,368,385,386,387,389,396,410,411,415,417,425,426,433,474,480,483],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,124,142,176,190,192,196,202,203,213,217,218,219,234,235,238,239,254,256,257,258,259,260,282,287,295,301,302,313,314,315,322,326,348,350,362,389,392,415,425,426,429,431,444,448,457,459,471,477,478],control_typ:202,controlfil:426,convect:91,conveni:[6,12,29,190,194,211,296,353,434,488],convent:[3,8,9,29,178,185,186,193,294,307,334,387,389,488],converg:[3,6,41,88,190,192,194,199,213,216,217,225,228,258,285,287,290,294,298,356,357,358,360,380,381,401,433,457,469,476],convers:[3,8,142,192,193,203,206,282,350,381,382,383,389,401,405,409,420,460,476,487],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,167,174,190,192,193,211,252,333,336,338,341,344,353,360,366,387,415,446,448,455,460,462,463,464,469,479,483,487,488,490,492],convex:331,convinc:[7,12],cook:9,cooki:7,cool:[7,157,234,293],cooordin:190,cooper:[5,7],coord123:116,coord1:[3,116,205,209,210],coord2:[3,116,205,209,210],coord3:[3,116,205,209,210],coord:[],coordb:433,coordbb:433,coordiat:358,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,94,104,105,107,115,116,118,136,142,150,156,162,164,165,167,171,189,190,191,192,193,194,196,199,204,205,208,209,210,213,214,215,216,217,218,219,220,223,225,226,228,230,233,234,235,236,237,238,239,251,253,254,256,257,259,260,272,275,276,277,280,281,282,292,293,295,297,298,299,304,307,308,309,310,312,320,321,322,329,330,332,333,353,358,359,360,365,366,367,370,388,433,457,462,463,465,467,470,472,476,483,488,489],coordn:[116,205],coorind:105,copi:[0,3,4,8,11,12,15,17,40,121,192,322,360,378,425,460],copper:455,coproccesor:16,coprocessor:[1,4,7,9,16,17,365,475],coproprocessor:17,copy_arrai:8,copyright:[7,8,280],coral:193,core:[],core_shel:149,coreshel:[6,9,374,381,383],cornel:[6,173,474],corner123i:115,corner123x:115,corner123z:115,corner1i:115,corner1x:115,corner1z:115,corner2i:115,corner2x:115,corner2z:115,corner3i:115,corner3x:115,corner3z:115,corner:[3,6,40,115,192,331,332,353,450,462],cornflowerblu:193,cornsilk:193,corpor:16,corr:380,correct:[3,6,9,11,12,16,17,59,87,88,103,104,112,118,149,154,161,192,219,230,232,238,254,255,272,280,282,285,321,327,331,350,360,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,453,454,455,462,477,480,483],correction_max_iter:202,correctli:[3,8,9,11,17,71,81,103,104,145,146,148,150,152,153,154,155,156,159,160,163,190,193,199,220,225,228,239,248,254,255,288,295,298,307,309,328,331,360,361,365,383,411,415,459,460,462,472,487,489],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,97,98,111,114,115,116,117,120,121,129,132,133,134,135,136,138,139,140,142,145,146,154,161,166,173,174,175,176,177,178,179,181,182,184,185,187,190,192,193,197,198,199,205,207,208,209,210,212,215,217,219,226,228,229,233,238,241,242,250,251,252,254,256,257,258,259,260,261,266,269,271,272,274,277,278,282,287,295,297,298,313,315,317,326,327,328,330,331,332,334,336,337,338,339,340,341,344,346,351,355,357,359,360,366,367,369,372,373,374,375,376,377,378,379,380,381,384,385,387,388,389,390,391,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,412,413,415,417,418,419,420,422,423,425,426,427,428,433,434,435,444,445,446,447,448,450,451,453,454,455,457,459,460,462,463,465,475,476,477,479,480,483,488],correspondingli:[410,411,471],cosin:[],cosineshift:27,cosmo:[232,237],cossq:[],cost:[1,6,10,11,12,17,39,41,71,111,120,143,166,192,193,205,209,210,213,214,215,227,254,287,322,350,351,363,381,401,405,415,417,444,459,471],costheta0:[444,446,448,451],costheta:423,costli:[11,88,232,361],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,94,105,107,111,114,116,147,157,162,164,180,190,192,193,197,198,205,206,209,213,219,228,237,284,285,286,290,293,295,297,310,311,317,321,322,323,327,331,333,335,342,347,349,356,358,361,365,368,391,395,396,425,426,458,459,460,462,464,466,469,470,478,483,488,489],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,88,109,110,118,143,168,172,286,288,323,350,351,358,365,372,374,375,376,377,380,381,382,383,384,389,393,394,396,401,405,409,417,420,425,426,428,433,443,448,449,451,454,467,474,480,483,487],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,116,118,119,155,165,171,199,200,203,205,208,209,210,212,213,220,225,227,230,236,254,266,281,298,313,314,331,351,358,359,360,362,365,391,395,417,480,488],counter:[328,457,468,470,476],counteract:230,counterbal:234,counterpart:[190,295,457],counterproduct:18,coupl:[],courant:300,cours:[3,8,128,130,161,190,197,198,231,294,307,321,327,329,330,332,333,351,410,435,459,462,475,483,488,490],courtesi:353,cov:433,coval:[6,29,389,412,433,483],covari:232,cover:[6,71,187,193,202,241,389,399,450],coverag:[71,209],cpc:237,cpp:[1,3,6,8,9,11,12,13,87,190,197,198,228,298],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,193,207,223,239,323,348,351,365,378,443,457,475,476,479,480,481,488],cpuremain:480,cr2:166,cr3:166,crack:[4,361],crada:[5,7],crai:[5,7,13,18,190],crash:[3,12,361,483],craympi:365,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:202,create_faceset:202,create_group:191,create_nodeset:202,createatom:[],creation:[],crimson:193,critchlei:280,criteria:[3,118,168,192,193,214,215,216,249,358,422,450,464,467,488],criterion:[12,41,123,165,167,170,203,213,216,230,266,287,300,328,333,358,360,380,389,393,433,467,476,477],criterioni:476,critic:[6,48,49,252,317,322,358],cross:[3,12,22,71,89,146,175,190,192,204,209,215,219,251,253,272,295,303,307,309,318,325,337,353,360,376,385,386,387,394,395,396,401,403,405,423,428,430,432,446,448,455,462,466,472,490],crossov:1,crossterm:462,crozier:[0,7,13],crucial:285,crystal:[4,6,13,73,108,276,277,320,353,361,466,480,483],crystallin:[6,104,277,353,447,483],crystallis:317,crystallogr:[120,166],crystallograph:[353,480],crystallographi:[120,166,353],cs1:166,cs_chunk:6,cs_im:[40,462],cs_re:[40,462],csanyi:[142,424,434],cscl:412,csequ:6,csh:[11,12,378],cshrc:[11,12],csic:[388,444,446,448,451],csinfo:6,csisi:[388,444,446,448,451],csld:[],cst:387,cstherm:6,cstyle:459,csvr:[],ctcm:[366,387],ctemp_cor:223,cterm:299,ctr:9,ctype:11,cu1:166,cu2:166,cu3au:412,cube:[6,41,165,170,213,223,331,353,483],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:371,cummul:[3,6,211,214,215,216,218,227,232,238,240,310,313,314,315,316,318,325,395,480],cumul:[6,203,205,208,209,210,224,230,238,252,254,258,266,295,296,360],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,103,104,110,118,119,132,143,147,155,157,163,165,168,171,189,190,191,192,193,194,197,198,202,205,209,210,211,213,214,215,216,217,218,219,220,224,225,228,230,232,235,236,238,244,251,254,255,259,260,266,271,272,274,280,286,287,289,292,293,294,295,298,299,300,301,302,303,304,306,308,309,310,313,314,315,321,322,325,326,327,328,329,330,332,333,335,348,349,350,351,354,355,357,358,359,360,365,371,378,380,384,387,389,390,393,396,397,400,410,411,412,413,414,417,423,425,426,429,430,431,432,435,446,448,449,452,457,458,459,460,462,463,464,465,466,468,469,470,472,474,476,477,479,480,488,489,490,491,492],curv:[6,167,230,277],curvatur:[392,427,455],custom:[],cut0:460,cut1:471,cut2:471,cut:[],cuthi:[276,288],cutinn:[373,410,411],cutlo:[276,288],cutmax:423,cutoff1:[377,384,401,405,409,420,428],cutoff2:[372,374,375,377,383,384,401,405,409,420,428],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,92,108,110,117,118,142,165,168,170,215,216,221,276,285,286,288,290,292,295,310,323,327,331,333,348,350,351,358,361,362,363,365,366,367,368,369,370,371,372,373,374,375,376,377,379,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,426,427,428,433,434,435,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,460,464,467,471,483,488],cutoffa:388,cutoffc:388,cuu3:387,cval:166,cvd:317,cvel:299,cvff:[],cwiggl:[3,251,327,330,332,488],cyan:[2,192,193],cycl:[3,230,252,254,255,258],cyclic:[3,187],cygwin:12,cylind:[3,4,192,236,281,328,331,465],cylindr:[6,236,307,328],cypress:365,cyrot:371,cyrstal:277,d3q15:241,d3q19:241,d_double_doubl:15,d_e:322,d_flag2:284,d_flag:284,d_name:[115,190,284,312,472],d_single_doubl:15,d_single_singl:15,d_sx:284,d_sy:284,d_sz:284,daan:320,dai:12,daili:12,daivi:272,damag:[],dammak:290,damp:[3,6,196,201,238,239,240,245,254,255,258,282,285,290,295,313,314,326,328,329,357,358,360,372,374,376,381,384,389,393,401,409,420,428,443,449,476,483],damp_com:239,damp_drud:239,dampen:[295,483],dampflag:[328,393],dan:17,danger:[3,12,230,333,385,480],dangl:170,daniel:9,darden:[351,384],darkblu:193,darkcyan:193,darken:192,darkgoldenrod:193,darkgrai:193,darkgreen:193,darkkhaki:193,darkmagenta:193,darkolivegreen:193,darkorang:193,darkorchid:193,darkr:193,darksalmon:193,darkseagreen:193,darkslateblu:193,darkslategrai:193,darkturquois:193,darkviolet:193,dasgupta:286,dash:[393,479],dat:[6,91,187,202,458],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,296],dataset:296,datatyp:3,date:[0,6,12,13,189,425,426,488],datom1:117,datom2:117,datom3:117,datom4:117,datum:[3,6,42,65,68,69,79,93,110,117,190,206],davi:327,david:[9,19,350,351,446,448],daw:[387,423],dbg:14,dcd:[3,6,7,190,191,192,193,194,278,463,467],ddim:189,deactiv:409,dealt:237,debug:[6,7,11,12,13,14,17,120,124,166,167,278,283,348,350,365,397,417,452,460,461,464,469,472,479,488],deby:[],decai:[92,381,455],decid:[3,6,12,16,71,251,284,295,323,477],decipher:353,declar:191,declin:310,decod:192,decompos:[87,434],decomposit:[3,5,7,18,62,202,278],decoupl:[6,483],decreas:[3,190,199,200,207,216,219,225,228,230,238,321,350],decrement:299,deepli:347,deeppink:193,deepskyblu:193,def:[12,13,460],defaul:61,defect:[6,70,165,415],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,173,174,175,176,177,178,179,181,182,184,185,186,187,188,189,190,191,192,193,196,197,198,199,200,201,202,203,204,205,206,208,209,210,211,212,213,214,215,216,217,219,220,223,224,225,228,229,230,233,236,237,238,239,240,241,249,251,253,254,255,256,257,258,259,260,262,263,264,267,269,270,271,272,273,274,276,277,278,280,281,282,284,286,288,293,295,296,297,298,300,304,308,310,312,313,314,315,316,318,319,320,322,324,325,327,328,329,330,331,332,333,335,336,337,338,339,340,341,344,345,346,348,350,351,353,355,357,358,359,360,361,362,363,364,365,367,368,369,370,372,373,374,375,376,377,378,379,381,382,384,385,386,388,389,391,392,393,394,395,396,397,399,401,402,403,404,405,406,407,408,409,410,411,415,416,417,418,419,420,422,423,425,426,427,428,429,430,431,432,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,459,460,462,463,465,466,467,468,471,472,473,474,476,477,479,480,483,484,485,486,487,488,489],definit:[2,3,6,8,12,13,78,80,118,142,193,205,206,207,208,209,210,211,219,236,258,296,312,324,327,330,332,334,345,348,359,368,371,379,389,399,423,430,432,434,450,460,462,464,471,473,487,488],defint:480,deform:[],deg2theta:166,deg:483,degener:[3,280],degrad:[8,18,277,351,471],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,93,95,97,98,100,102,103,108,114,145,146,147,148,149,150,151,152,153,154,155,156,157,159,160,166,167,173,174,177,178,185,187,189,192,205,216,223,230,232,233,238,239,244,254,255,258,259,260,271,272,274,278,280,294,295,298,313,314,315,320,336,338,341,344,346,358,384,387,395,472,480,483,489],degress:[147,205],del:476,delai:[3,6,12,361,386,480],deleg:396,delet:[2,3,7,8,12,54,57,60,63,165,170,171,196,205,206,208,209,210,211,214,216,227,230,254,296,313,314,333,335,349,359,361,364,417,462,463,465,473,474,479,484,486,488,489],delete_atom:[],delete_bond:[],delete_el:202,deli:189,delimit:[460,488],deloc:[255,389,433],delr:412,delt_lo:476,delta:[],delta_1:371,delta_3:371,delta_7:371,delta_conf:3,delta_ij:[412,423],delta_mu:3,delta_pi:371,delta_r:423,delta_sigma:371,delx:189,delz:189,demand:290,demo:11,demon:275,demonstr:[285,412],den:281,dendrim:395,denniston:[9,241,243,244,245,277],denomin:[7,172],denot:[120,223,239,277,288,290,381,394,396,426,430,432],dens:[71,216,389],densiti:[3,6,7,9,18,40,41,59,101,118,128,142,153,165,167,197,198,202,205,209,210,213,219,228,241,244,247,248,277,281,282,286,322,327,353,355,359,366,371,387,412,413,414,423,427,433,437,439,440,441,462,471,472,480,487],density_continu:432,density_summ:432,depart:[0,7],departur:[252,285],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,93,104,110,111,114,115,116,117,121,142,145,150,154,155,161,167,168,173,174,175,176,177,178,179,181,182,184,185,186,187,189,190,192,193,196,197,198,199,200,203,205,207,208,209,211,212,213,215,217,219,225,226,229,232,233,234,236,238,239,241,243,244,251,254,256,257,258,259,260,261,269,271,272,274,276,287,290,292,295,297,298,304,310,313,314,315,317,319,321,322,324,326,327,330,331,332,333,335,336,337,338,339,340,341,344,346,351,353,358,359,361,362,363,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,387,388,389,390,391,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,412,413,415,416,418,419,420,422,423,425,426,427,428,433,434,435,443,444,445,446,447,448,449,450,451,453,454,455,457,459,462,464,465,468,472,474,476,479,480,482,488,489],dependend:6,depflag:12,dephas:[457,476],depos:220,deposit:[],deprec:[286,425],depth:[51,146,192,322,392,427],dequidt:9,der:[87,109,379,380,409,425,426,454,483],deriv:[6,7,8,9,38,56,63,87,142,161,187,206,217,219,230,238,251,254,256,257,258,259,260,276,282,286,290,319,320,322,327,328,331,357,359,367,371,379,384,389,390,394,403,407,408,412,415,425,426,443,445,454,483],derjagin:454,derlet:276,descend:193,descent:[7,357],descib:[40,286],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,112,115,118,120,132,142,143,146,147,151,152,155,158,160,161,165,166,167,169,170,179,184,187,190,191,196,197,198,205,206,207,208,209,210,211,213,216,217,218,219,220,222,223,231,232,235,236,237,238,239,240,241,243,244,245,249,253,254,255,258,265,273,276,278,283,284,285,286,287,288,295,299,307,310,311,312,313,314,315,316,317,318,319,320,325,327,328,330,335,350,351,353,356,357,358,359,360,364,367,368,370,372,373,374,376,377,378,379,380,381,384,387,389,390,392,393,394,396,401,402,403,404,405,406,407,408,409,410,411,412,415,416,422,423,424,425,426,427,428,433,434,435,442,443,444,445,446,447,448,449,451,453,454,455,457,459,460,462,463,465,466,472,475,476,479,488,489,490],descript:[],descriptor:[142,190,397],deserno:351,design:[0,3,6,7,8,9,11,13,14,15,17,120,149,152,166,202,216,222,223,254,255,276,277,296,317,322,368,369,370,373,376,381,383,389,409,410,411,413,414,423,426,445,471],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,114,119,143,149,167,180,189,205,211,217,219,228,230,231,238,239,240,244,254,272,280,281,282,283,286,290,295,298,310,313,314,315,316,321,328,342,347,350,351,353,356,358,359,360,385,387,395,410,411,444,446,448,458,459,460,462,466,471,476,477,479,480,488,489,490],desk:7,desktop:[4,6,7,10,12,192],despit:483,destabil:371,destre:344,destroi:[11,39,214,215],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,94,103,105,107,109,111,113,114,116,119,121,142,143,145,146,147,150,160,161,162,164,167,168,171,172,175,186,189,190,192,193,196,197,198,202,205,206,207,208,209,211,213,215,216,217,218,219,220,228,230,231,232,233,235,236,238,240,241,245,251,252,253,254,255,256,257,258,259,260,264,266,271,272,273,274,277,280,281,282,284,285,287,288,289,295,298,310,313,314,315,316,317,318,320,321,322,323,324,325,326,333,335,337,345,350,351,354,358,359,361,362,365,366,367,368,370,371,373,375,376,377,378,379,380,381,384,385,389,390,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,411,412,416,417,422,425,426,427,433,434,435,443,450,453,454,460,462,463,464,465,467,468,471,472,474,477,480,481,488,489,492],detect:[2,3,12,61,63,86,92,229,281,321,360,380,395,400,457,459,462,473,476,488],determ:365,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,103,109,111,114,120,121,129,143,155,156,165,166,167,189,190,192,193,194,195,199,200,201,204,205,206,207,208,209,210,211,212,213,217,219,220,223,225,230,233,234,236,238,239,244,249,251,252,254,259,260,271,272,274,276,278,282,285,292,293,294,295,296,297,300,302,304,310,313,314,315,317,323,324,327,328,329,330,331,332,333,345,350,351,353,359,361,362,365,367,368,375,380,384,386,387,391,393,396,397,405,412,415,417,426,427,433,442,445,449,454,459,462,463,465,467,469,472,476,478,479,481,487,488,489],detil:110,devan:[9,428],devanathan:448,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,235,258,280,285,286,289,367,371,389,414,415,433,451,464],devemi:9,deviat:[252,258,276,391],deviator:9,devic:[1,3,12,15,17,235,365],device_typ:365,devin:[287,380],devis:414,dfactor:192,dff:483,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,351],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,289,415],dhi:[59,189,219,281],dhug:[252,285],dhugoniot:[252,285],dia:412,diagnost:[],diagon:[3,6,83,142,143,144,217,254,282,295,325,430,432],diagonalstyl:434,diagram:[41,120,166,186,213,278],diallo:395,diam:[192,193,281,359],diamet:[3,6,40,115,167,190,192,193,197,198,238,281,295,310,326,328,359,379,392,393,399,403,427,450,454,462,463,472],diamond:[353,389,412],diamter:[40,281],dick:6,dicsuss:251,dictat:[203,252],did:[3,12,358,385,386,387,393,417,446,448,470],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,163,324,350],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,92,95,97,98,122,142,145,146,147,148,150,153,154,155,156,157,159,160,161,167,168,170,175,186,187,189,190,192,193,196,198,201,203,205,208,213,214,215,216,217,218,219,223,229,230,231,232,233,234,235,238,239,241,251,254,255,256,257,259,260,262,264,267,269,270,271,274,276,278,280,282,285,286,287,290,293,295,298,299,307,308,310,313,314,315,318,319,320,322,325,326,327,328,331,335,336,345,347,349,350,351,353,354,356,357,359,360,362,363,364,365,366,367,371,375,376,378,379,380,385,387,389,392,393,394,396,399,401,402,404,405,412,413,414,416,417,419,423,425,426,427,428,429,430,432,433,434,435,443,444,445,446,448,450,451,454,456,457,459,460,462,464,465,466,467,470,471,472,474,476,477,479,480,481,483,487,488,489,490],differenti:[1,3,6,29,187,350,381,423,447],difficult:[217,278,365,395,471],difficulti:[92,108,298,425],diffract:[],diffus:[],digit:[2,3,193,335,415],dih_table1:187,dih_table2:187,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:215,dihydrid:389,dij:298,dilat:[],dim1:3,dim2:3,dim:[3,59,71,145,148,149,150,153,154,155,156,157,159,167,189,209,219,236,328,353,412,465,487,488,489],dimdim:488,dimems:277,dimens:[],dimension:[3,39,92,114,120,142,145,147,148,149,150,153,154,155,156,157,159,166,188,205,209,253,277,322,353,356,360,423,462,472],dimensionless:[106,123,124,126,129,131,133,138,142,322,351,434,454],dimentionless:137,dimer:[6,295,412],dimgrai:193,dimstr:[41,213],dinola:[282,313],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,190,312,483],dir1:473,dir2:473,dir:[1,3,4,8,9,11,12,252,276,285,309,423,425,426,460,473,488],dirac:142,direc:423,direct:[],directli:[3,6,8,9,11,12,87,115,142,144,190,191,192,199,225,232,236,241,277,296,314,326,328,329,330,331,353,357,365,366,367,372,374,375,381,384,387,389,401,405,417,420,428,442,460,472,473,474,480,488],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,194,218,237,280,286,289,306,310,319,320,360,364,366,367,371,378,380,381,387,388,390,397,398,409,412,413,414,415,419,423,424,425,426,433,434,444,446,447,448,451,460,462,463,464,473,488],disabl:[3,12,16,322,400,460,475,488],disadvantag:[6,213],disallow:[190,219,254],disappear:464,discard:[2,3,41,71,207,209,213,323,331,459,464,465],discontinu:[9,187,358,407],discourag:412,discov:[13,323],discret:[6,8,40,42,192,193,238,241],discuss:[],disk:[6,84,85,92,160,188,220,230,281,460],disloc:[70,415],disord:[39,70,415],disp:[],dispar:427,disperion:[384,405],dispers:[3,6,7,9,165,277,350,351,375,384,405,410,417,426,445,451],displac:[],displace_atom:[],displace_box:59,displacemet:465,displai:[11,13,22,37,44,55,175,186,190,192,337,345,378,443],dispters:3,disregard:415,dissip:[6,231,238,277,319,320,373,385,393,410,411,443],dissolut:214,dist:[6,69,91,110,119,190,278,294,386,442,457,489],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,92,94,104,105,106,107,108,110,116,117,118,119,120,122,136,142,156,162,165,167,168,169,170,174,189,190,192,193,201,205,209,210,214,215,216,217,219,220,221,224,230,236,241,251,252,253,254,258,266,276,277,281,285,286,293,294,295,298,299,303,307,308,309,310,317,318,320,321,322,325,327,328,329,330,331,332,336,350,351,353,356,358,360,361,362,365,368,369,370,371,372,373,374,375,376,377,379,381,382,383,384,385,386,387,388,389,391,392,393,394,395,399,400,401,402,403,404,405,406,407,408,409,410,411,412,415,416,417,418,419,420,421,422,423,425,426,427,428,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,460,462,465,471,472,476,480,483,487,489],distinct:[6,223,292,350,427],distinguish:[6,86,142,244,389,461],distort:366,distrbut:366,distribut:[],distro:[113,378,422,423],ditto:[8,11,12,14,15,16,17,18,117,215,455,460],div:8,divd:119,diverg:[3,12,39,295,320,464,483,490],divid:[3,6,16,41,91,114,119,128,130,143,164,165,175,186,193,205,206,208,213,219,276,318,325,330,350,358,360,390,426,433,451,471,479,488],divis:[6,241,371,399,409,459,462,480,488],dl_poli:[6,7],dlambda:161,dlammps_async_imd:235,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,192],dlammps_gzip:[3,12,190,192,321,462,463,467],dlammps_jpeg:[3,12,192],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,192],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,190],dlen:472,dlmp_intel_offload:[12,16],dlo:[59,189,219,281],dlopen:6,dlvo:[7,379,454],dm_lb:241,dmax:[310,356],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,94,103,105,106,107,109,111,113,114,116,119,121,143,146,147,160,162,164,167,168,169,175,186,189,190,191,192,193,194,196,197,198,203,204,205,206,207,208,209,210,211,220,230,238,239,249,254,255,259,260,264,271,272,273,274,281,284,295,307,310,313,314,315,324,328,331,333,335,337,345,349,358,359,360,365,366,367,370,378,380,381,387,388,390,395,396,398,399,412,413,414,417,419,422,423,424,434,443,444,446,448,450,451,460,462,463,464,465,467,470,471,472,479,480,488,489,490,491],docuement:427,dodgerblu:193,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,72,87,88,91,105,112,118,119,120,144,146,147,149,150,155,157,161,166,167,168,169,171,173,175,180,186,187,189,190,191,192,193,196,202,203,205,209,212,213,215,216,217,219,223,225,227,230,231,234,236,238,239,241,244,250,254,255,256,257,259,260,271,272,273,274,282,283,284,288,290,293,295,310,313,315,317,318,322,325,326,327,330,331,332,333,338,339,341,342,344,349,350,351,352,353,359,360,361,366,367,368,369,370,371,373,375,376,377,379,380,381,382,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,403,404,406,407,408,410,411,412,413,414,415,417,423,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,453,454,455,457,458,459,460,462,463,464,465,466,469,470,472,473,474,475,476,479,480,483,488,492],doegenomestolif:7,doesn:[3,7,8,12,167,190,203,209,210,307,359,361,365,367,380,388,398,425,426,444,446,447,448,451,462,464],dof:[3,8,114,146,147,160,205,295,489],dof_per_atom:[147,205],dof_per_chunk:[147,205],doff:[359,462],doi:[6,218],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,120,156,166,169,189,191,192,193,196,203,213,217,219,220,234,237,241,254,255,278,290,295,322,327,328,350,351,360,365,386,417,457,459,462,466,479],domin:[1,389,476],don:[0,8,11,12,13,118,170,199,225,239,284,331,412,433,460,462],donadio:314,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,161,164,167,170,187,190,192,193,202,203,205,207,208,209,210,211,213,214,215,216,217,219,220,228,230,235,236,238,239,246,254,259,260,271,272,274,275,277,278,279,284,292,295,296,298,310,313,314,315,317,319,320,333,335,349,350,351,358,360,361,364,365,367,375,387,396,397,398,405,411,412,417,425,442,445,450,457,458,459,460,463,466,467,470,480,481,483,488,489],donor:395,dot:[143,163,199,225,233,253],doti:[371,423],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,219,228,283,331,335,349,351,364,365,371,390,394,415,425,426,458,462,466,470,475,488,489],dover:202,down:[3,6,7,8,11,39,71,217,230,238,310,326,365,389,417,433,461,481],downhil:[356,357],download:[5,7,8,9,11,12,13,17,235,397,424],downsid:6,downward:292,dozen:[8,12,109,196,425,426],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:247,dproduct:368,dr_ewald:[120,296],drag:[],dragforc:241,drai:[252,285],drain:[234,326,358],dramat:[59,189,214,215,216,217,219,254,310,313,314,351,365,417,433,459],drautz:371,draw:192,drawback:284,drawn:[190,192,193,231,457],drayleigh:[252,285],dreid:[],drfourth:106,drho:[115,366,387],drift:[6,104,106,231,232,238,239,250,293,310,471,479,483],drive:[11,12,200,217,219,233,254,276,282,295,329,360],driven:[6,179],driver:[6,12,14,15,196,228,235],drop:[3,193,385],droplet:396,drsquar:106,drude:[],dry:227,dsecriptor:397,dsf:[],dsmc:[],dstyle:281,dt_collis:241,dt_lb:241,dt_md:241,dt_srd:310,dtilt:[59,219],dtneb:476,dtqm:285,dtype:[117,215],dual:[16,17,310,365],dudarev:166,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,94,103,104,105,106,107,112,118,120,128,142,143,145,146,148,150,153,154,155,156,157,159,160,162,166,167,170,171,190,192,196,199,200,208,212,214,215,216,217,218,219,220,225,226,227,228,231,232,235,236,238,239,240,241,244,245,246,250,251,252,253,254,258,266,276,279,281,293,294,295,297,307,309,310,311,313,314,315,316,317,319,320,322,326,327,329,330,331,333,351,356,358,360,361,362,382,385,387,391,392,396,410,411,417,423,425,427,428,442,445,446,448,452,454,455,457,459,462,463,464,471,476,479,480,481,483,488,489],duffi:322,duin:[9,286,291,425,426],duke:351,dummi:[12,29,447],dump1:467,dump2:467,dump2vtk_tri:136,dump:[],dump_atom:8,dump_custom:8,dump_h5md:191,dump_modifi:[],dumpcustom:8,dumptimestep:467,dunbrack:[6,20,173,376,474],dunweg:[238,240],duplic:[2,3,14,15,17,41,42,168,213,232,276,462,487],dupont:[5,7,13],durat:[37,55,145,146,148,149,150,152,153,154,155,156,159,160,186,193,205,230,290,322,345,393,443],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,128,130,144,149,168,171,187,190,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,224,225,226,227,228,229,230,231,232,233,234,235,236,238,239,240,241,242,243,244,245,246,247,248,250,251,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,303,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,351,358,360,364,365,385,409,415,417,426,445,457,458,460,462,465,467,469,470,472,474,476,477,480,481,488,491,492],dvector:8,dvlo:454,dvx:6,dx_lb:241,dy3:166,dyamic:12,dyanam:6,dyanmic:476,dynam:[],dynamo:[5,366,387,412],dyne:487,dyre:406,dysam:465,e28637:29,e_1:371,e_2:371,e_b:390,e_e:389,e_hbond:395,e_i:[6,371,390],e_j:[6,371],e_k:[371,389],e_kl:6,e_lj:[367,384],e_n:[371,389],e_nn:389,e_pr:389,e_rebo:367,e_tors:367,e_tot:415,e_vol:415,eaa:336,eaat:174,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,92,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,111,112,113,114,115,116,117,118,119,120,121,122,136,142,143,144,146,147,148,149,150,151,154,155,156,157,159,160,161,162,163,164,165,166,167,170,171,173,174,175,176,177,178,179,180,181,182,184,185,186,187,189,190,191,192,193,194,195,196,197,198,199,200,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,244,245,246,247,248,250,251,252,253,254,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,286,287,288,290,292,295,296,297,298,299,303,304,306,307,308,309,310,311,312,313,314,315,317,320,321,322,323,324,325,326,327,328,330,331,332,333,335,336,338,339,340,341,342,344,345,346,349,350,351,353,357,358,359,360,361,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,415,416,417,418,419,420,422,423,425,426,427,428,429,433,434,435,436,437,438,439,440,441,442,443,444,445,448,449,450,451,452,453,454,455,456,457,459,460,462,463,464,465,466,467,469,470,471,472,474,476,477,479,480,481,482,483,487,488,489,490,492],eacn:[41,213],eam0d:277,eam3d:277,eam:[],eam_databas:13,eam_gener:13,eangl:480,earli:[41,205,208,209,210,211,213,289,296],earlier:[7,8,12,59,193,360,393,412,417,476],earliest:476,earth:389,easi:[6,7,8,9,11,13,87,143,190,197,198,199,200,209,212,225,233,234,236,238,239,297,304,313,314,315,327,330,332,359,462,465,470,472,489],easier:[8,9,13,16,190,192,277],easili:[8,11,192,193,326,360,459,469,478,488],eastwood:[350,351],eat:174,eatom:333,eaxmpl:6,eba:21,ebb13:174,ebb:21,ebond:[223,239,479,480],ebt:174,ec_ii:412,ec_ij:412,ec_jj:412,echo:[],eco:[425,426],ecoa:[425,426],ecoul:[109,223,239,425,426,480],ecp:[389,462],edg:[2,3,6,41,59,71,120,165,166,169,170,191,192,201,209,236,297,327,330,331,332,333,353,462,465,472],edge_histo:165,edge_threshold:165,edih:480,edim:318,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,483],editor:13,edu:[7,9,11,13,387,410,422,425,426],edward:[9,17],eebt:174,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,81,89,90,94,104,105,106,107,111,114,143,145,149,154,155,162,165,171,173,174,176,177,178,179,181,182,184,185,186,187,189,190,192,193,197,198,199,202,203,206,210,211,212,214,215,216,217,219,220,226,229,230,231,232,233,234,235,236,238,239,253,254,256,257,258,259,260,261,269,271,272,274,275,276,278,281,282,284,285,286,287,290,294,295,297,298,309,310,313,314,315,317,318,320,322,325,326,327,328,329,330,331,332,333,336,338,339,340,341,344,346,350,351,353,357,358,359,360,361,366,367,369,371,372,373,374,375,376,377,379,380,381,384,385,387,388,389,390,391,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,413,415,417,418,419,420,422,427,428,429,431,433,435,443,444,445,446,447,448,450,451,453,454,455,457,459,460,464,465,467,471,472,474,480,481,487,488,490],efffect:466,efficaci:39,effici:[0,1,3,6,7,8,10,12,15,17,18,39,58,61,67,114,144,190,191,192,193,206,207,217,219,223,232,254,278,280,290,295,298,310,350,351,356,361,365,371,379,381,396,401,405,415,427,469,492],effort:[5,7,463],efftemp:[97,98,153],efi:[425,426],efield:[],eflux:234,eggebrecht:[381,433],ehb:[425,426],eigensolv:3,eigenvalu:[277,278,350],eigtol:3,eik:161,eim:[],eimp:480,einstein:[290,320],either:[1,2,3,4,6,8,9,11,12,14,15,16,17,22,33,41,44,50,59,63,71,104,109,115,118,120,142,143,147,149,150,166,167,170,175,180,187,190,191,192,193,196,204,206,208,210,211,213,216,217,218,219,220,230,236,237,241,245,251,252,254,255,258,272,276,292,295,297,298,299,307,310,317,324,328,331,335,337,348,350,351,353,357,358,362,365,371,373,379,387,396,397,399,410,411,412,415,417,421,423,446,448,450,457,460,462,464,465,466,469,471,474,477,479,488],ejtehadi:[379,392,427],elaplong:[197,198,236,465,480,488],elaps:[3,189,197,198,199,200,212,219,225,233,234,236,238,239,251,281,297,304,313,314,315,327,328,330,332,435,457,465,467,468,472,476,480,488],elast:[],elastic_t:4,elba:29,electr:[6,196,202,225,239,350,351,390,425,426,455,483,487],electrolyt:[9,454],electron:[3,6,7,9,13,40,97,98,115,120,151,153,158,196,202,222,223,239,240,255,265,273,288,316,322,357,359,366,368,380,384,387,389,390,412,415,423,424,433,448,451,455,462,482,483,487],electron_integr:202,electron_temperatur:202,electron_unit:389,electroneg:[6,286,287,288,380,390,433],electroneg_compon:433,electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,16,18,203,230,286,288,289,323,350,351,379,384,389,401,409,411,426,433,454],eleftheri:295,elem1:[390,412,434],elem2:[390,412,434],elem:433,element1:[292,366,387,433],element2:[292,366,387,433],element:[3,6,7,8,12,13,63,81,89,104,106,114,119,121,136,142,143,144,145,146,147,148,149,150,154,155,156,157,159,160,163,190,191,192,193,194,196,202,206,208,211,277,292,317,324,366,367,371,380,387,388,389,390,396,397,398,412,413,414,415,419,423,424,425,426,433,434,444,446,447,448,451,483,488,491],elementn:[366,387],elementset:202,elev:476,elif:[142,335],elig:[3,203,214,215,227,230,395],elimin:[3,6,71,231,238,239,295,298,319,320,457],elj:384,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,82,146,188],ellipsoid:[3,4,6,7,13,40,42,82,115,132,146,167,188,190,238,256,259,262,263,271,295,310,355,358,392,411,427,443,462,472,490],ellipsoidflag:462,elong:[223,239,480],elp:[425,426],els:[3,7,8,12,71,109,118,119,121,191,192,204,205,206,208,209,210,211,230,254,295,310,322,323,324,333,335,350,396,461,473,488,491],elsewher:[8,251,310,412,424,425,426,474,480,488],elt:412,emac:[],email:[0,3,5,7,8,9,11,390],emb:[3,9,331],emb_lin_neg:412,embed:[3,5,7,11,12,13,29,88,144,165,322,366,387,390,409,412,413,414,423,443,452,460],embt:174,emi:[7,9],emil:9,emol:[425,426,480],emphas:393,empir:[202,314,367,389],emploi:[9,277,290,447],empti:[3,57,71,169,295,350,361,400,462,473,474,488],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,83,87,97,98,99,100,101,102,106,111,113,114,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,149,151,153,154,158,159,161,165,173,174,176,177,178,179,180,181,182,184,185,186,187,190,191,193,194,196,197,198,199,200,201,203,207,210,212,214,215,216,218,219,220,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,250,252,254,255,256,257,258,259,260,261,262,263,264,265,267,269,270,271,272,273,274,276,277,278,280,281,285,286,287,288,289,290,291,292,294,295,297,298,299,300,301,302,303,304,306,307,309,310,313,315,316,317,318,319,320,322,323,325,326,327,328,329,330,331,334,336,338,339,340,341,342,344,345,346,351,358,360,364,365,366,367,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,422,423,42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,287,288,318,319,320,325,380,381,425,426,458,472],equilibria:325,equilibribum:[214,215],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,150,151,174,176,217,219,230,231,232,239,241,254,258,272,285,290,294,298,299,307,310,317,318,320,325,336,338,341,344,380,412,419,433,483],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:202,equival:[6,12,13,59,61,126,127,135,140,165,169,193,208,211,217,219,230,238,254,272,282,294,295,330,385,389,433,446,448,462,465,470,471,480,483],equlibrium:6,equliibr:[286,288],er3:166,eradiu:[40,115,389,462],eras:[297,319],erat:[219,411],erc:381,erfc:[381,401,417],erforc:115,erg:487,erhart:[203,387,446,448],ermscal:368,ernst:9,eror:3,eros:412,erose_form:412,erot:[],errata:[446,448],erratum:327,erron:3,error:[],erta:393,ervel:[115,462],escap:[220,483],especi:[8,11,16,155,167,196,203,213,230,285,290,293,294,365,459],espresso:[9,289],essenti:[8,11,12,27,88,130,148,149,150,153,154,155,156,157,159,176,206,258,277,326,351,367,381,401,448,467,480],essex:29,establish:[87,234],estim:[1,3,6,10,12,38,41,56,91,143,202,213,224,252,310,317,350,351,356,417,426,445,476,480],esu:487,esub:412,eta:[6,241,254,285,286,288,326,388,390,392,423,447,451,487],eta_dot:254,eta_ij:423,eta_ji:390,etag:[40,462],etail:480,etap:254,etap_dot:254,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,95,111,112,115,117,143,145,147,148,149,150,151,153,154,155,156,157,159,161,167,169,170,171,180,190,192,193,196,197,202,203,204,205,208,209,210,211,214,215,219,220,228,230,231,238,254,281,292,296,322,323,331,335,349,350,358,359,360,361,363,387,388,396,409,411,415,421,425,426,444,446,448,451,457,460,462,463,464,469,471,472,476,478,479,480,481,483,487,488,490,492],ethernet:18,etol:[358,360,457,476],etot0:285,etot:[6,95,97,98,112,143,153,193,223,239,252,285,479,480],eu2:166,eu3:166,euler:[358,360],eulerian:202,euqat:436,europhi:241,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,109,119,142,144,147,157,165,167,189,190,192,193,197,198,199,200,202,204,205,206,207,208,209,210,211,212,219,225,231,233,234,236,237,238,239,277,283,286,297,300,304,313,314,315,324,327,330,332,333,335,350,351,356,358,365,415,417,423,429,431,433,445,457,458,460,464,465,467,469,470,471,472,476,478,480,488,489],evalut:[335,460],evan:[155,272],evanseck:[6,20,173,376,474],evapor:[],evaul:[8,358],evdwl:[109,425,426,480],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,121,168,169,183,187,190,193,196,197,198,203,204,205,208,209,210,211,213,214,215,217,219,220,223,236,239,252,254,255,277,290,292,295,296,306,310,318,322,325,327,331,333,343,350,356,358,360,365,370,389,390,393,396,417,427,451,452,462,463,465,467,468,469,471,472,474,477,479,480,481,483,492],evenli:[3,41,143,187,213,241,399,452,462],event:[],eventu:[3,6,12,15,169,286,476],ever:[54,56,237,310],evera:[379,392,427,443],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,115,121,130,155,170,190,191,192,193,194,196,197,198,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,224,227,228,230,232,234,235,236,241,242,250,254,255,258,275,276,277,281,282,283,284,285,286,287,288,290,292,293,295,296,298,299,310,312,313,314,315,316,317,318,321,322,323,324,325,333,335,349,351,360,361,362,365,385,386,396,409,425,426,433,439,456,457,458,462,464,466,467,469,470,471,476,477,478,480,488,492],everyth:[8,109],everywher:[118,403],eviri:389,evolut:[232,241,278,457],evolv:[241,278,323],ewald:[2,3,5,6,7,8,12,88,112,120,143,323,350,351,358,372,374,375,381,384,389,401,405,420,428,443,445,464],ewald_disp:384,ewalddisp:3,exact:[22,41,44,71,124,161,170,175,213,216,231,232,238,239,240,281,290,291,310,322,337,350,378,464,469,476,488,490,492],exactli:[3,6,12,14,17,38,41,56,59,71,72,91,118,146,151,158,167,187,197,198,208,213,219,224,231,238,239,240,255,265,266,273,277,285,310,315,316,329,365,378,385,387,393,396,399,410,417,445,464,465,472,476,488],exager:483,examin:[6,8,9,17,216,277],examp:[460,488],exampl:[],exce:[3,6,16,17,18,41,58,71,169,204,205,208,209,210,211,213,217,219,224,227,254,277,292,296,301,302,310,358,365,462,488],exceed:[3,41,59,213,219,254,310,470],excel:389,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,110,111,114,119,143,145,146,147,148,149,150,151,153,154,155,156,157,158,159,160,167,171,173,174,175,176,177,178,179,181,182,184,185,186,187,189,190,193,196,199,205,206,208,212,213,217,219,226,229,230,233,236,238,240,254,255,256,257,258,259,260,261,265,266,269,271,272,273,274,278,287,288,295,297,298,307,310,313,315,316,322,326,330,333,335,336,337,338,339,340,341,344,345,346,350,351,353,355,359,360,361,363,364,365,366,367,369,372,373,374,375,376,377,378,379,380,381,383,384,385,387,388,389,390,391,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,411,413,418,419,420,422,425,426,427,428,435,443,444,445,446,447,448,450,451,453,454,455,457,459,460,462,464,465,467,470,471,472,473,474,476,480,483,487,488,489,491],excess:[207,389],exchang:[2,3,6,8,9,61,62,196,202,203,230,238,287,295,318,322,325,350,365,389,477],exchange:350,excit:[9,389],exclud:[3,6,9,12,16,17,63,71,114,142,147,154,155,171,190,205,209,214,215,242,250,280,293,295,317,328,333,358,359,361,373,393,396,410,411,417,442,474],exclus:[1,3,9,12,16,87,365,380,415,417,471,481],excurs:457,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,168,192,235,289,335,349,352,364,458,460,470,473,476,488],exempl:433,exemplari:231,exemplifi:389,exert:[6,236,239,290,329,330,331,351],exhaust:[202,364,488],exhibit:[92,254,357,389,471],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,124,167,168,186,191,192,193,196,201,212,215,217,220,230,280,281,283,333,336,338,339,341,345,354,359,365,396,425,452,458,460,462,463,464,473,474,475,488,489,490],exit:[2,3,11,12,41,57,190,213,349,364,460,461,470,479,488],exlanatori:3,exp:[],expand:[],expans:[12,142,190,473,488],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,103,148,159,165,187,213,225,230,232,251,276,282,284,285,290,295,333,351,361,378,412,415,417,457,460,462,464,467,471,476,488],expens:[6,10,71,193,276,280,295,322,333,350,351,361,365,460],experi:[6,13,15,17,212,220,235,244,253,282,294,295,356,360,385,417,471,476],experienc:[6,12,243,244],experiment:[230,350,365,476],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,93,147,155,187,190,192,193,196,205,206,211,213,215,217,219,254,276,284,295,307,333,335,349,350,353,359,360,364,370,387,399,433,435,450,460,463,464,467,469,472,483,488,492],explan:[3,6,59,115,142,190,205,253,276,396,456,459,460,462,471],explanatori:[3,8,119,190,204,205,208,209,210,295,359,459,488],explantori:[3,291],explic:416,explicit:[6,9,11,22,44,77,87,115,118,161,175,197,198,219,301,302,337,355,367,368,371,376,378,387,389,400,410,449,456,459,463,466],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,111,114,145,154,157,165,167,173,174,176,177,178,179,181,182,184,185,187,190,193,199,209,212,219,226,229,231,233,238,254,256,257,258,259,260,261,269,271,272,274,284,285,287,295,297,298,313,315,316,322,326,330,336,338,339,340,341,344,346,359,365,366,367,369,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,413,415,417,418,419,420,422,427,428,435,436,437,438,439,440,441,443,444,445,446,447,448,449,450,451,453,454,455,462,464,471,472,474,475,481,483],explictli:[16,475],exploit:[9,15,17,278],explor:[120,166],expon:[3,286,288,387,392,395,409,416,428],exponenti:[87,423,444,451,455,476,488],expos:11,exposit:[202,385,386],express:[6,142,153,167,197,198,217,251,276,286,322,328,335,371,387,389,403,412,433,434,443,488],expressiont:371,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,95,98,99,109,111,119,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,196,199,200,203,211,212,218,221,225,228,229,230,232,233,234,236,238,240,252,254,258,266,276,277,293,294,295,297,299,304,307,309,313,314,315,316,317,319,320,322,324,327,331,332,392,412,415,426,427,434,479,480],extent:[1,3,41,45,57,71,165,169,190,201,209,213,236,329,332,350,353,367,429,431,445,459,462,465],exterior:[3,6,331],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,103,111,112,114,120,143,145,146,148,150,153,154,155,156,157,159,160,166,167,168,169,173,193,208,213,215,254,283,284,285,295,310,358,359,362,363,384,393,396,399,412,417,459,460,462,465,474,483,488],extract:[3,6,11,13,36,63,87,109,117,119,121,197,198,288,360,381,390,412,434,460,467,479],extract_atom:11,extract_comput:[11,460],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,192,207,217,219,254,320,389,447,483],extrema:409,extrins:202,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[163,324],f_a:[446,447,448],f_ave:119,f_c:447,f_f:448,f_fix_id:285,f_harm:320,f_i:423,f_id:[6,71,119,121,190,196,204,205,206,207,208,209,210,211,249,312,324,480,488],f_ij:423,f_indent:211,f_int:319,f_jj:91,f_k:423,f_langevin:322,f_max:[285,290],f_msst:252,f_r:[239,446,447,448],f_sigma:371,f_solid:320,f_ss:6,f_temp:239,face:[3,6,57,59,71,155,165,169,201,209,210,327,329,330,331,332,353,392,412,427,462,465],face_threshold:165,facet:165,facil:[0,12],facilit:[6,13],fact:[6,8,16,232,310,320,393,433,474],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,87,91,103,110,117,118,120,142,161,166,169,173,184,189,190,192,193,197,198,206,213,217,219,220,230,235,238,240,241,252,254,255,258,278,282,294,298,300,302,310,314,318,325,326,327,331,341,351,353,359,365,367,368,371,372,374,376,381,382,383,385,389,393,396,400,401,412,415,417,419,420,426,428,435,444,449,459,462,465,466,471,474,476,477,480,483,487,488],factori:[3,460],factoriz:350,fail:[3,11,12,59,171,217,220,350,358,360,383,426,460],failur:[123,430,461,488],fairli:[11,417,471,476],faken:73,falcon:235,fall:[3,6,193,208,281,460,488],fals:[86,333,335,433,488],fame:8,famili:[451,459],familiar:[0,11],fan:423,far:[3,6,12,17,57,59,61,86,190,193,194,213,214,215,217,220,254,276,294,295,310,327,338,341,356,360,361,450,460,462,467,480],farago:238,farrel:[446,448],farther:190,fashion:[6,8,41,71,167,193,196,197,198,203,209,213,215,220,230,232,236,251,252,254,256,257,258,259,260,268,271,272,273,274,284,285,287,295,299,303,309,312,320,322,326,327,328,330,332,360,396,410,465,474,488,491],fasolino:398,fast:[6,7,9,12,13,17,39,190,263,285,323,350,351,373,410,411,415,443,445,464,469,471,480,489,492],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,106,111,114,145,154,173,174,176,177,178,179,181,182,184,185,187,190,193,199,212,213,219,226,229,233,237,238,254,256,257,258,259,260,261,269,271,272,274,282,286,287,295,297,298,310,313,315,317,319,322,326,330,336,338,339,340,341,344,346,350,351,362,363,365,366,367,369,371,372,373,374,375,376,377,378,379,380,381,384,385,387,388,390,391,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,413,418,419,420,422,427,428,435,443,444,445,446,447,448,450,451,453,454,455,457,471,475,483],fastest:[1,6,14,17,155,209,322,323,365,459],fatal:[3,479],fault:[70,426],faulti:12,fava:392,favor:216,favorit:7,fbmc:317,fcc:[],fcm:[268,488],fdirect:223,fdotr:397,fdti:87,fe2:166,fe3:166,fe_md_boundari:202,featu:8,featur:[],fecr:387,feedback:[7,235],feel:[7,235,236,244,276,331,333,360,417],felling:414,felt:331,femtosecond:487,fene:[],fennel:[381,401],fep:[],ferguson:[6,173,474],fermi:[1,12,15,153,365,448],fermion:[9,389],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,194,204,205,206,208,209,210,211,239,254,281,284,286,298,324,350,358,359,360,367,433,459,462,467,471,473,481,488,490],fewer:[1,3,11,15,16,61,244,471],fewest:3,fextern:228,feynman:278,fff:460,ffield:[380,390,425,426,433],ffmpeg:[3,12,192],ffplai:192,fft:[1,3,7,12,14,15,88,111,112,143,277,350,351,471],fft_inc:[12,351],fft_lib:12,fft_path:12,fftbench:[350,481],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:442,fictiti:[6,199,200,225,228,232,278,294,381,401,405,442],field1:[463,467],field2:463,field:[],fifth:[307,419],figur:[1,3,8,11,12,285,459,460],fij:384,file0:276,file1:[11,13,276,321,335,359,467,469,473],file2:[11,13,321,335,359,467,469,473],file:[],file_from:191,filen:359,filenam:[3,12,13,38,41,56,187,190,192,193,194,202,205,206,207,208,209,210,211,213,218,276,280,283,286,287,288,291,292,295,296,321,322,347,348,349,359,360,366,367,371,381,387,388,390,398,412,413,414,419,423,424,425,426,433,434,444,445,446,447,448,451,458,459,460,463,464,469,473,480,488,490,491,492],filennam:469,filep:[3,190,193,464,469,492],filepo:292,fill:[7,9,167,192,281,322,353,361,371,415,426,465],filter:[193,202],final_integr:8,final_integrate_respa:8,finchham:[6,149,383],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,119,170,187,194,203,216,217,227,230,253,276,282,290,294,356,358,360,361,381,396,401,405,412,433,443,445,483,488],find_custom:8,fine:[16,17,171,199,225,320,361,365,488],finer:[142,167,488],finest:350,finger:[167,189,251,465],finish:[6,11,41,213,335,347,349,350,362,364,365,450,467,488,489],finit:[],finni:[7,387,443],finvers:223,fiorin:[9,218],fire:[356,357,358,360,476],firebrick:193,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,104,105,106,108,114,118,119,129,132,135,136,140,143,152,155,161,163,165,166,168,169,170,174,187,190,191,192,193,194,196,197,205,206,208,209,210,211,213,216,219,230,231,236,241,251,252,253,254,276,278,283,284,285,287,292,295,298,299,307,308,310,311,312,319,320,321,322,324,328,333,335,336,342,353,358,359,360,361,364,365,366,367,370,371,372,374,376,378,380,381,387,389,390,393,394,396,397,398,400,401,405,410,411,412,414,415,417,419,423,425,426,433,434,442,444,445,446,447,448,451,455,457,458,459,460,462,463,464,467,469,471,474,475,476,479,480,483,488,489,490,492],fischer:[6,9,19,20,173,376,474],fit:[3,6,9,12,38,56,187,294,310,367,371,398,412,417,438,445,447,470,488],five:[73,153,285,359,371,413,462,476],fix:[],fix_adapt:[161,198,409],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,203,281],fix_evapor:203,fix_flux:202,fix_gcmc:[203,359],fix_gl:232,fix_gld:232,fix_grav:281,fix_id:[3,217,252,254,256,257,258,259,260,282,285],fix_modifi:[],fix_mov:[189,328],fix_nh:8,fix_npt:232,fix_nvt:[203,230],fix_poem:[3,6],fix_pour:[3,220],fix_qbmsst:9,fix_qeq:[3,380],fix_rattl:298,fix_reax_bond:425,fix_rigid:[244,370],fix_saed_vtk:296,fix_setforc:8,fix_shak:298,fix_srd:3,fix_styl:258,fix_temp_rescal:316,fixedpoint:[217,254],fixextern:228,fixid:202,fji:384,flag1:[222,363],flag2:[222,363],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,94,104,105,107,120,162,166,170,190,192,193,194,211,216,218,222,235,238,242,244,250,251,277,284,295,307,309,310,317,321,330,333,348,351,359,363,364,365,367,395,400,412,415,442,457,459,460,462,463,464,466,467,468,472,488],flag_buck:375,flag_coul:[375,384,405],flag_lj:[384,405],flagfld:[373,410,411],flaghi:[3,373,410,411],flaglog:[373,410,411],flagn:222,flagvf:[373,410,411],flat:[6,322,327,328,332],flavor:[2,7,12],fld:[9,327,373,410,411],flen:368,flex_press:368,flexibl:[3,6,8,168,192,205,209,218,232,255,318,325,389,447,480],flip:[3,6,219,254,329,330],floor:488,flop:12,floralwhit:193,flow:[],fluctuat:[6,64,87,217,230,231,238,241,254,258,276,277,320,322,344],fluid:[],fluid_veloc:245,flush:[3,193,479],flux:[],flv:192,fly:[7,9,12,41,192,196,202,207,220,223,295,298,323,371,415,480,483],fmackai:9,fmag:221,fmass:278,fmax:[358,480],fmomentum:223,fmsec:[2,193,238,239,251,254,282,295,313,314,471,482,487,489],fname:349,fno:[12,16],fnorm:[358,480],fnpt:223,fnvt:223,foce:396,fock:368,focu:298,fogarti:[9,288,426],foil:[142,276,434],fold:[308,471],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,92,97,98,108,115,118,119,121,142,143,146,147,153,155,160,163,165,167,168,173,176,177,178,179,181,182,184,185,187,190,191,192,193,196,202,203,204,205,206,207,208,209,210,211,213,218,219,220,223,224,228,230,231,232,235,237,238,239,241,244,252,254,258,259,260,271,272,274,277,278,280,283,284,285,286,288,290,292,294,295,296,298,312,313,314,315,318,319,320,321,322,324,325,333,334,338,339,340,341,344,346,348,353,355,358,359,360,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,422,423,424,425,426,427,428,430,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,453,454,455,457,459,460,462,463,464,465,467,469,470,471,474,476,477,478,483,488,489,491],foo:[4,8,11,12,190,192,228,460,473,488],foot:6,footprint:[12,365],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:244,forcefield:[294,395],forcegroup:241,forcezero:356,ford:384,forestgreen:193,forev:71,forget:[239,483],forgiv:254,fork:[12,190],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,92,94,104,105,107,118,142,143,161,162,171,175,193,196,197,198,215,231,232,238,240,244,251,272,277,288,290,294,295,322,327,331,336,337,344,355,357,359,360,367,368,371,378,387,389,391,395,396,400,412,414,415,419,420,423,425,426,427,433,434,435,443,445,446,447,448,454,456,459,460,462,467,472,479,483,488],formal:[6,78,80,91,231,232,238,254,278,310,318,433],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,175,187,190,191,192,193,194,205,208,209,210,211,213,215,277,280,284,286,288,291,295,296,306,321,322,333,334,337,355,359,360,366,367,371,378,387,390,400,412,414,424,425,426,428,434,445,451,452,459,460,462,463,464,467,478,479,480,488,490],former:[6,12,16,39,41,193,213,322,326,371,373,468,474,488],formerli:[7,13],formul:[1,40,64,143,199,225,238,254,272,286,288,294,298,321,350,367,371,387,389,392,412,422],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,95,97,98,107,114,120,143,145,146,147,148,149,150,151,153,154,155,156,157,158,159,160,166,167,172,174,175,186,189,190,197,198,199,200,205,206,207,208,211,212,219,225,233,234,236,238,239,251,276,277,283,292,297,304,308,310,313,314,315,324,327,330,332,333,335,336,337,339,345,353,359,367,368,370,371,376,377,378,379,384,385,387,388,392,393,394,395,397,400,401,403,404,405,407,408,410,411,412,416,417,418,427,428,435,443,444,446,447,448,451,453,454,458,462,465,472,479,480,487,488,489],forth:[1,6,11,12,13,14,15,364,460,465,469],fortran:[3,6,9,11,12,13,228,387,396,412,425,426],fortun:8,forward:[3,8,87,349,360,365],foster:[371,422,423],foul:170,found:[3,6,9,12,73,161,190,216,218,230,235,241,277,317,323,335,349,361,378,381,384,457,463,464,479],four:[6,11,54,81,104,105,142,163,252,322,344,359,360,415,457],fourier:[],fourth:[6,106,294,307,317,376,419,433],fox:[6,120,173,441,474],fphi:[38,56,445],fpic:12,fplo:[38,56,445],fprime:445,fqdn:237,fqq:384,frac:[223,239,449,483],fraction:[1,3,6,8,12,16,39,41,80,111,143,170,189,192,193,203,214,215,216,217,252,281,285,292,293,310,315,316,353,360,365,371,373,393,410,411,467,472],fragment:[42,235,292],frame:[83,142,193,202,252,285,329,392],framer:[192,193],framework:[5,232,366,434],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,161,198,276,310,319,320,321,322,357,360,368,389,409,415,423,454,459],freedom:[3,6,8,95,97,98,100,102,103,114,145,146,147,148,149,150,151,152,153,154,155,156,157,159,160,205,216,223,230,232,238,239,244,254,255,258,259,260,271,272,274,278,280,295,298,313,314,315,320,358,384,480,483,489],freeli:[0,6,7,12,146,160,165,192],freez:[],frenkel:[230,320],freq:201,frequenc:[3,6,16,39,104,193,207,266,277,278,285,290,348,385,389,426,433,457,471,476,488,491],frequent:[3,64,67,70,72,73,77,88,92,108,142,193,214,215,227,318,325,417,469],fri:[252,285],friction:[4,5,6,10,42,196,232,238,285,290,295,322,326,328,393,472],friedrich:300,from:[],front:[252,285,329],frontend:[192,289],frozen:[6,114,171,229,231,239,361,391],fs2:[6,91],fscale:235,fstr:488,fstring:460,ftol:[358,360,457,476],fuchsia:193,fuction:381,fudg:298,fugac:230,fugacity_coeff:230,fulfil:6,full:[1,2,6,9,12,17,38,39,40,91,192,206,207,218,241,276,350,351,365,371,387,389,390,392,449,462,464,469,470,474,476,481,483,491],full_energi:[3,230],fuller:358,fulli:[3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improp:[],improper_coeff:[],improper_styl:[],impropercoeff:3,impropertyp:215,imprort:98,improt:[197,198],improv:[0,1,9,16,39,41,193,213,254,277,365,395,401,415,417,426,444,447],in3:166,inaccur:[1,3,6,170,252,350],inaccuraci:331,inact:395,inappropri:167,incid:[120,166,220],includ:[],includig:[335,349],inclus:[],incom:235,incompat:[3,11,397],incomplet:[3,11,462],incompress:[255,389],inconsist:[3,171,216,463],inconveni:353,incorpor:[285,371,382],incorrect:[3,150,238,412],incorrectli:[3,353,393,488],increas:[1,3,6,10,18,38,56,57,59,111,120,143,187,190,192,193,207,214,215,216,219,230,238,282,293,294,295,318,321,325,350,351,360,365,389,392,426,445,447,460,471,476,488],increasingli:389,increment:[3,11,130,199,200,212,213,220,225,227,254,299,300,333,349,364,399,433,457,460,474,476,488],incur:[14,17,205,209,210,227,322,459],inde:150,indefatig:7,indefinit:319,indent:[],independ:[4,6,9,11,12,16,17,41,59,63,91,119,121,153,167,189,196,204,205,206,208,209,210,211,213,216,217,218,219,220,231,233,238,239,241,244,254,277,282,286,290,295,296,299,309,320,322,353,393,415,457,460,479,489],indetermin:[190,193],index:[0,3,6,8,11,12,38,39,40,56,68,69,119,121,187,190,193,204,206,235,237,278,296,322,333,334,335,355,364,417,425,426,445,452,462,477,488],indianr:193,indigo:193,indirectli:[6,488],indistinguish:238,indium:434,individu:[],induc:[],industri:7,ineffici:[3,6,40,64,67,70,72,73,77,92,108,142,155,192,219,254,277,350,362],inelig:203,inerti:411,inertia:[],inexpens:[232,471],inf:[2,3,12,325,465],infer:[3,95,97,98,161,199,200,213,214,215,225,235,280,310,318,325,353,378,390,462,474,480],infil:[3,13,295,459],infin:[3,358,467,480],infininti:192,infinit:[3,220,229,236,238,241,277,310,322,328,329,351,353,389,466,487],infinitesim:6,inflect:[382,403],influenc:[3,9,41,80,149,251,281,350,351,417,446,447,448],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,39,41,42,59,61,62,63,68,88,117,119,120,166,167,173,190,191,192,193,194,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,225,226,227,228,229,230,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,253,261,262,263,264,265,266,267,268,269,270,275,276,277,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,300,307,308,310,311,313,314,315,316,317,318,319,321,324,325,326,327,329,330,331,332,334,348,350,351,354,357,358,359,360,361,363,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,422,423,424,425,426,427,428,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,453,454,455,459,460,462,463,464,466,467,469,474,476,477,479,481,488,490,491,492],infrequ:[6,385,457,476],infti:[382,410,411],ingtegr:371,inher:[350,358,417],inherit:[6,449],inhomogen:[18,322,417],inidividu:358,init:[3,8,293,433],init_fil:322,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,39,40,41,56,57,59,62,71,80,81,86,87,104,105,132,163,168,169,187,189,190,192,193,194,197,198,201,202,206,213,215,216,217,219,226,230,231,235,236,237,238,239,241,246,250,251,252,253,254,258,266,277,278,279,284,285,290,293,294,295,297,309,310,312,317,319,320,321,322,323,324,327,328,329,330,332,333,335,350,354,357,358,360,367,368,384,385,386,415,424,425,426,433,445,457,459,460,462,464,465,467,469,470,472,476,477,480,483,488,489,490,492],initial_integr:8,initial_integrate_respa:8,initialis:424,initialt:322,inlclud:11,inlcud:488,inlin:460,inner2:[376,394],inner:[3,8,16,190,236,335,349,356,357,358,360,364,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,384,385,386,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,422,424,425,426,427,428,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,450,451,452,453,454,455,471,476,488],inner_distance_cutoff:395,innergroup:244,innermost:[38,56,363,445,471],innernod:244,innner:407,inordin:323,inorgan:[6,451],inp:[218,335,434,451],input1:[65,68,69,79,93,110,115,116,117,119,121,312],input2:[65,68,69,79,93,110,115,116,117,119,121,312],input:[],input_doubl:3,inquir:300,insensit:12,insert:[3,5,7,8,12,59,167,196,220,230,236,281,350,434,442,460,466,483],insid:[2,3,6,8,11,71,131,137,167,190,193,204,209,210,220,221,227,230,236,241,244,281,295,310,327,329,330,331,332,333,348,353,403,460,461,462,464,465,472,476,488],insight:[6,13],instabl:[241,384,432],instal:[],instanc:[6,11,197,218,232,329,391,396,417,423,460,483],instantan:[6,63,216,217,231,232,254,258,277,282,285,290,292,295,317,468,480],instanti:[6,11,12,202,396,459],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,90,104,119,146,149,171,187,190,198,205,208,209,210,211,213,217,218,230,238,241,244,245,277,283,293,295,312,330,348,350,351,354,361,365,374,375,387,400,402,409,412,415,457,465,469,476,478,483,488],institut:[9,235,280],instruct:[3,8,11,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,111,114,145,154,165,173,174,176,177,178,179,181,182,184,185,187,188,192,199,212,219,226,229,233,238,256,257,258,259,260,269,271,272,274,287,295,297,298,313,315,326,330,336,338,339,340,341,344,346,351,366,367,369,372,373,374,375,376,377,379,380,381,384,385,387,388,390,391,392,393,394,395,399,401,402,403,404,405,406,407,408,409,410,413,418,419,420,422,427,428,435,444,445,446,447,448,450,453,454,455,471,483],insuffici:[3,6,12],insult:254,insur:[3,6,11,12,17,39,40,61,73,103,105,167,168,187,190,192,193,199,214,215,220,225,226,227,228,230,233,238,250,283,284,293,295,310,322,327,331,332,333,335,349,359,361,365,379,392,396,421,427,445,459,460,462,463,467,470,471,479,480,488,489],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,108,115,117,119,121,142,165,167,170,171,173,177,178,182,187,189,190,192,193,203,205,209,210,214,215,216,220,222,228,230,231,232,235,238,239,240,241,277,280,281,284,285,290,295,310,312,314,317,321,322,340,350,353,373,385,386,399,412,425,426,430,432,434,457,459,460,461,462,470,471,472,476,479,488,489],integr:[],integrate_ulsph:301,intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,207,231,424,462],intens:[1,3,6,9,63,66,74,75,86,89,90,91,94,104,105,106,107,114,116,118,119,120,121,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,164,166,196,205,206,208,209,210,211,213,214,215,216,224,227,234,244,252,254,258,292,295,296,310,318,322,324,325,479,480],intepol:488,inter:[14,18,42,61,62,147,170,171,190,216,238,240,253,287,295,350,360,371,472,483,488,490,492],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,72,77,79,87,88,92,93,108,109,110,112,114,117,118,124,125,126,127,129,130,131,132,133,134,135,137,138,139,140,142,143,144,146,160,161,165,168,169,170,171,172,173,175,179,180,186,190,196,197,198,214,215,216,229,230,235,236,238,240,244,266,276,278,280,286,288,294,295,301,302,310,311,317,322,326,327,328,331,332,337,338,339,341,345,350,351,358,359,360,361,362,363,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,422,423,426,427,428,430,432,433,434,435,442,443,444,446,447,448,449,450,451,452,453,454,455,457,460,462,464,466,467,471,472,474,479,480,483,490],interatom:[3,4,7,167,190,253,319,320,366,371,387,389,397,412,415,433,447,488],intercept:120,interchang:6,interconnect:18,interconvert:389,intereract:39,interesect:331,interest:[1,5,7,8,9,11,13,71,166,278,317,320,351,388,411,425,426,460,488],interf:365,interfac:[],interfer:[12,254,367],interg:[6,483],intergr:[471,475],interi:411,interior:[3,6,41,331,465],interlac:412,interleav:[6,167,470],intermedi:[6,12,59,192,253,276,344,360,460,461,470,474],intermix:457,intermolecular:367,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,100,102,120,143,147,149,166,174,187,192,193,196,197,198,202,215,219,223,235,247,248,252,254,258,277,295,299,336,338,341,344,348,358,359,436,437,445,460,462,464,467,476,479,480,487,488,489,490],internal_element_set:202,internal_quadratur:202,internet:237,interpenetr:412,interpentr:[437,438,440],interpol:[6,15,38,56,101,187,192,193,202,241,276,350,351,360,371,417,426,439,445,446],interpret:[2,6,11,192,208,393,435,457,460,476,488],interrupt:285,intersect:[3,6,120,193,331,333,465],intersert:331,interspers:358,interstiti:[165,415],intertia:[3,94],interv:[3,6,91,191,206,238,285,290,291,302,433,439,457,476,488],intestieti:120,intial:[6,365,367],intiial:[41,467],intiti:[3,309],intra:295,intra_energi:230,intramolecular:[29,230],introduc:[6,9,92,108,192,254,285,290,295,344,350,366,381,389,401,405,409,444,476,488],introduct:[],intsal:[],intuit:353,inv:[120,166,296],invalid:[3,12,71,89,170,266,360,410,411,464],invari:[108,135,140,142],invent:298,invers:[],invert:[1,6,171,277],invis:331,invoc:[165,216,365,430,432,460],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,94,104,105,107,111,112,113,114,119,145,154,161,162,165,167,168,170,171,173,174,176,177,178,179,181,182,184,185,187,190,192,193,194,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,238,239,240,241,242,243,244,245,246,247,248,250,251,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,279,280,281,282,283,284,286,287,288,289,290,291,292,293,295,296,297,298,299,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,336,338,339,340,341,344,346,349,350,351,352,353,358,360,365,366,367,369,372,373,374,375,376,377,379,380,381,384,385,387,388,390,391,392,393,394,395,396,397,399,401,402,403,404,405,406,407,408,409,410,411,413,417,418,419,420,422,427,428,430,432,434,435,444,445,446,447,448,450,451,452,453,454,455,456,459,460,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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 hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix 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 mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":214,"default":[37,39,40,55,57,58,59,61,62,71,87,88,92,103,104,106,108,109,120,124,125,142,147,155,156,160,166,167,170,172,186,188,189,190,192,193,194,195,197,198,199,201,202,203,205,209,210,211,214,215,217,218,219,220,224,227,230,231,236,238,239,240,241,242,244,249,252,254,255,258,272,273,277,278,281,282,283,284,285,287,290,292,293,295,296,310,312,317,318,319,320,323,325,327,329,333,345,348,350,351,353,354,356,357,359,361,362,363,365,368,371,373,389,410,411,415,417,425,426,442,443,457,458,459,462,463,465,467,469,470,471,474,476,478,479,480,481,482,487,489,490,491],"function":488,"long":[207,372,374,375,376,377,381,383,384,401,405,409,420,428],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[197,198],addforc:199,addit:[12,13],addtorqu:200,adiabat:6,adjust_dt:300,adp:366,airebo:367,alloi:387,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:201,arrai:6,aspher:[6,82,146,256,259,262,263,271],atc:[9,202],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,92,96,97,100,101,102,108,112,113,115,142,143,165,201,203,204,284,488],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:212,awpmd:[9,368],balanc:[41,213],barostat:6,basal:67,beck:369,berendsen:[282,313],between:6,binary2txt:13,bodi:[6,8,42,68,264,370],bond:[8,13,69,214,215,216,291],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:371,born:[372,383],boundari:[7,57],box:[6,58,217],brownian:373,buck:[374,375,383],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,173,376,409],chunk:[6,66,71,75,90,94,105,107,116,147,162,164,205],citat:7,class2:[21,43,174,336,377],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[327,379,454],colvar:[9,13,218],com:[74,75,148],comb3:380,comb:[287,380],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,488],compute_modifi:103,condit:7,conduct:[6,318],constant:6,constraint:7,contact:76,contact_radiu:122,coord:77,core:6,correl:[206,207],cosin:[23,24,25,26,27,28,176],cossq:338,coul:[372,374,375,376,377,381,382,383,394,401,405,409,420,428],coupl:6,creat:215,create_atom:167,create_bond:168,create_box:169,createatom:13,creation:7,csld:314,csvr:314,cubic:403,cuda:[9,14,111,114,145,154,199,212,226,229,233,254,261,297,298,313,315,326,372,374,376,377,387,393,394,401,402,404,407,418,444,446],custom:8,cut:[49,368,374,377,381,384,389,391,401,402,409,416,420],cvff:339,damag:[78,123],data2xmovi:13,data:6,databas:13,deby:[381,401],dec:0,deform:[150,151,219],delete_atom:170,delete_bond:171,delta:24,deposit:220,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],diagnost:7,diel:382,dielectr:172,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:175,dihedral_styl:[2,173,174,176,177,178,179,180,181,182,183,184,185,186,187],dilat:80,dimens:188,dipol:[6,29,384],direct:223,discuss:6,disp:6,displac:[81,86],displace_atom:189,distribut:[7,12],document:0,dpd:385,drag:221,dreid:[6,395],drude:[6,9,152,222,223,239],dsf:[381,401],dsmc:386,dump:[6,8,190,191,192,194],dump_modifi:193,dynam:286,eam:[13,387],echo:195,edip:388,eff:[9,13,97,98,151,153,158,240,255,265,273,316,389],efield:225,eim:390,elast:6,emac:13,enforce2d:226,ensembl:7,erot:[82,83,84,85],error:3,evapor:227,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],exp:[27,176],expand:[46,404],extend:[8,11],extern:228,fcc:276,featur:[7,8,488],fene:[45,46],fep:[9,13,87,198],field:[6,7],file:6,finit:6,fix:[2,6,8,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,488],fix_modifi:[197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,25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442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],rho:128,rhosum:439,rigid:[6,83,99,244,295],ring:344,rotat:159,rule:2,run:[6,11,12,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,470],run_styl:471,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,428],self:309,serial:11,set:[6,472],setforc:297,setvel:304,shake:298,share:[11,12],shell:[6,473],shield:286,shift:[26,27,48,49,176],simpl:31,simul:6,size:6,slater:286,slice:121,sllod:[272,273],small:295,smd:[9,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,299,300,301,302,303,304,306,429,430,431,432],smooth:[407,408],smtbq:[9,433],sna:142,snad:142,snap:434,snapshot:6,snav:142,soft:[409,435],solver:2,sourc:7,spatial:[209,210],spc:6,speci:292,special:[7,417,488],special_bond:474,sph:[9,436,437,438,439,440,441],sphere:[84,85,160,210,244,257,260,269,274],spheric:6,spline:[413,414],spring:[307,308,309,320],squar:28,srd:[310,332],srp:442,standard:9,start:[12,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332],state:312,stationari:248,stop:[197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332],store:[311,312],strategi:1,streitz:381,stress:[143,144],structur:2,style:[1,2,6,8],submit:8,suffix:475,summari:6,swap:[203,216],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],system:6,tabl:[0,6,38,56,187,445,446],tad:476,taitwat:[440,441],talli:144,temp:[145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,313,314,315,316],temper:477,temperatur:6,tersoff:[446,447,448],test:11,tfmc:317,thermal:[6,318],thermo:[6,478],thermo_modifi:479,thermo_styl:480,thermodynam:[6,8],thermostat:6,thole:449,time:[6,211],timer:481,timestep:482,tip3p:6,tip4p:[6,381,401,405,409],tip:12,tlsph:430,tlsph_defgrad:129,tlsph_dt:130,tl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\ No newline at end of file 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,50,57,58,59,61,63,71,146,147,148,149,150,151,154,155,156,157,159,160,167,168,170,171,174,175,180,189,190,191,192,193,194,196,197,198,202,203,205,206,213,214,215,216,217,219,223,230,241,242,243,244,245,250,251,252,254,259,260,266,271,272,274,277,281,285,293,295,298,306,311,313,314,315,317,318,319,320,321,325,327,329,333,336,337,342,349,355,356,358,359,361,363,364,365,366,367,371,378,380,387,388,389,390,396,397,398,409,410,411,412,413,414,415,419,423,425,426,433,434,444,446,447,448,451,457,459,461,462,463,464,465,467,468,470,472,474,476,479,480,483,487,488,489,490,491,492],afterrun:470,afterward:3,afterword:41,ag1:166,ag2:166,again:[6,11,12,16,17,62,142,147,153,161,190,193,219,234,281,336,349,360,410,411,457,459,460,462,464,469,476,478,488,490],against:[11,12,13,64,220,360,425,426],aggreg:[6,12,65,68,69,79,93,110,117,234,250,293,295,308,457,489],aggress:[234,476],agilio:[9,13],agre:[3,8,187,358,367,398,426],agreement:[5,7],ahd:395,ahead:329,aidan:[0,5,7,9,13,353],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:192,akohlmei:[7,9,13,194,235],aktulga:[7,9,288,426],al2o3:433,al2o3_001:[120,296],al3:166,ala:[241,433],alain:9,alat:[276,412],alb:[423,446,448],albeit:294,albert:9,alchem:[87,161],alcohol:325,alcu:[366,371],alcu_eam:423,alderton:384,alejandr:[254,255],alessandro:13,algebra:415,algorithm:[0,1,6,7,8,9,41,61,193,202,213,216,219,241,243,244,266,278,295,298,317,318,322,325,330,356,357,358,362,365,389,411,415,430,432,457,459,476],alia:[12,16],alias:[1,351],aliceblu:193,align:[6,12,29,41,71,169,187,209,213,236,353,462,465,483],alkali:389,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,155,160,161,162,163,164,165,166,167,168,169,170,171,173,175,180,186,187,190,191,192,193,194,196,197,198,199,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,247,249,250,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,290,291,292,293,294,295,296,297,298,299,300,301,302,306,307,309,310,311,312,313,314,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,340,345,348,349,350,351,352,353,355,358,359,360,361,362,364,365,366,367,368,370,371,372,374,375,376,377,378,380,381,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,405,409,410,411,412,413,414,415,416,417,418,419,420,422,423,424,425,426,427,428,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,455,456,457,459,460,461,462,463,464,465,466,467,469,470,471,472,473,474,475,476,477,479,480,481,483,487,488,489,490,491,492],allen:[29,87,384,392],allentildeslei:87,allign:3,allindex:334,alloc:[3,5,6,8,9,11,12,60,228,324,359,361,365,421,426,462,470],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,92,108,110,144,146,147,160,165,166,167,169,175,186,187,190,192,193,194,196,197,199,201,202,203,205,206,207,208,209,210,211,213,215,216,217,218,219,220,224,225,228,230,231,232,233,235,238,241,244,245,249,251,254,255,276,280,282,283,284,285,289,295,296,298,299,301,302,306,310,317,318,319,320,322,323,324,325,326,327,333,335,337,345,350,351,353,358,359,360,361,364,365,368,371,372,373,374,375,376,381,387,389,393,394,395,396,401,405,410,411,415,417,423,426,427,430,432,433,442,452,454,457,460,462,464,465,466,467,468,469,472,474,475,476,479,480,488,489],almost:[2,3,12,60,236,285,322,351,362,365,442],alo:381,alon:[6,7,216,291,425,426,460],alond:13,along:[6,8,9,12,29,40,87,120,166,167,189,190,192,216,236,241,242,246,251,253,285,295,298,299,303,307,308,317,321,322,328,331,333,353,356,357,358,360,381,384,393,396,399,401,405,412,425,426,445,462,465,472,473,488],alonso:[413,414],alpha:[6,12,51,197,241,277,285,290,358,366,369,372,381,385,387,388,390,395,400,401,412,418,422,447,449,480,483],alpha_:449,alpha_c:409,alpha_i:[434,449],alpha_ialpha_j:449,alpha_lj:409,alphabet:[2,3,22,37,44,55,63,175,186,196,337,345,359,378,443,462],alphanumer:[3,63,196,284,292,335,359,488],alreadi:[3,7,8,9,12,16,17,18,42,167,168,170,191,201,205,209,210,213,215,219,245,283,285,310,333,359,360,385,394,396,403,411,442,452,455,458,462,463,467,472,488],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,72,73,75,77,81,87,89,90,92,94,104,105,106,107,108,109,114,116,118,119,121,142,143,144,145,146,147,148,149,150,151,153,154,155,156,157,159,160,161,162,163,164,165,167,168,169,170,171,173,175,186,187,188,189,190,191,192,193,194,196,197,198,199,201,204,205,206,207,208,209,210,211,21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compress:[3,59,71,116,170,190,192,193,219,252,258,282,285],compris:[40,331,399,427,450],compton:[120,166],comptu:3,compuat:351,comput:[],computation:[3,6,214,215,322,371],computational:483,compute_arrai:8,compute_fep:[198,409],compute_group_group:230,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[120,296],compute_scalar:8,compute_temp:8,compute_ti:198,compute_vector:8,compute_xrd:166,concaten:[2,3,491],concav:331,concentr:387,concept:[6,147,157,205,471],conceptu:[3,6,71,155,217,219,360,381,396,412,467],concern:[6,73,87,191,231],concis:[11,321],conclud:12,concret:8,concurr:[9,16,351,488],conden:[322,446,448],condens:[6,149,322,367,383,387,401,451],condit:[],conducit:6,conduct:[],cone:465,confer:415,confid:[3,476],config:[12,190,459],configfil:218,configur:[1,2,6,12,15,17,38,59,124,169,187,189,190,192,196,217,218,219,220,224,230,237,238,266,278,286,321,348,358,360,367,371,388,412,415,444,446,448,451,457,462,464,465,476],confin:[462,476],conflict:[3,12,40,417,460],conform:[3,6,13,59,216,217,253,294,299,321,344,360,389,474],confus:[3,451],conjuct:385,conjug:[7,8,238,357,389,425,426],conjunct:[6,7,71,86,87,116,150,155,161,167,171,193,197,198,238,241,245,266,281,282,286,287,288,290,295,310,318,325,330,350,351,360,372,374,378,381,385,389,395,401,417,420,428,449,462,465,469,483,492],connect:[3,6,87,152,170,216,235,280,295,298,307,360,382,393,442,448,459,460,466,483],conput:3,consecut:[3,11,12,39,71,167,193,197,198,220,235,236,381,401,405,457,463,465],consequ:[1,6,203,322,400,476],conserv:[3,29,196,203,216,223,224,231,234,238,240,241,245,250,252,254,266,295,298,313,314,318,325,326,330,360,384,385,393,407,433,471,476],consid:[6,9,70,71,78,87,117,149,152,153,170,190,193,197,198,204,206,209,213,215,216,220,242,255,277,295,317,318,321,322,325,351,378,389,396,426,427,433,442,457,458,460,463,464,465,467,470,472,480,483,488],consider:[6,8,238,239,313,314,315,365,471],consist:[3,6,8,9,11,12,40,42,65,69,79,93,105,110,113,114,117,147,150,152,167,179,189,194,199,200,205,219,220,223,225,228,231,238,239,240,251,254,256,257,258,259,260,261,262,264,265,266,267,269,270,271,272,273,274,282,285,290,292,294,295,313,314,315,316,326,350,351,353,359,360,365,367,371,373,379,381,389,392,396,410,411,412,415,417,427,430,432,433,445,452,460,462,463,464,465,466,467,474,483,488],consistent_fe_initi:202,consit:295,constant:[],constitu:[3,6,244,295,327,331,379,427],constitut:[430,432],constrain:[3,6,8,145,146,147,148,150,153,154,155,156,157,159,160,196,205,220,230,231,236,244,248,280,281,293,295,298,308,318,325,358,359,389,467,474,483],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,92,108,120,142,166,217,254,277,294,331,361,365,384,415,417,442,444,445,465,466,481,488],constructor:8,consult:426,consum:[1,290,421,488],consumpt:348,contact:[],contact_stiff:[429,431],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,118,120,142,147,155,165,166,167,169,173,175,186,187,190,192,193,194,196,197,198,202,204,205,206,208,209,210,211,213,218,220,225,232,236,237,238,239,241,252,266,276,277,280,281,283,285,288,292,295,296,300,310,317,321,322,331,332,335,349,351,359,360,363,364,366,367,368,371,380,381,384,387,388,389,396,397,412,415,419,423,424,425,426,434,444,445,446,447,448,449,451,457,458,459,460,462,463,464,465,467,469,471,474,476,479,480,483,488,490,492],content:[12,18,426,478,480],context:[3,6,8,12,17,118,119,193,214,215,220,280,292,326,357,454,462,469,478,487,488,489],contibut:70,contigu:459,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,104,105,163,193,196,197,198,203,205,206,207,208,209,210,211,213,216,217,218,219,220,230,231,232,234,235,236,238,239,240,246,251,252,254,256,257,258,259,260,271,272,273,274,279,281,284,285,295,296,299,309,310,312,319,320,322,328,331,335,349,364,365,371,385,386,403,406,425,426,427,430,432,447,457,460,462,464,465,470,476,479,480,488,490],continuum:[6,7,9,202,322,430,432],contour_integr:202,contract:[59,217,219,254,282,295],contradictori:3,contrain:298,contraint:266,contrari:[232,239],contrast:[1,6,42,55,64,149,152,219,333,430,432,454,491],contrib:322,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,94,103,105,107,109,110,111,112,114,116,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,198,203,204,205,206,208,209,210,211,217,230,238,241,244,245,249,255,272,273,280,281,289,292,295,296,298,324,350,358,360,368,385,386,387,389,396,410,411,415,417,425,426,433,474,480,483],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,124,142,176,190,192,196,202,203,213,217,218,219,234,235,238,239,254,256,257,258,259,260,282,287,295,301,302,313,314,315,322,326,348,350,362,389,392,415,425,426,429,431,444,448,457,459,471,477,478],control_typ:202,controlfil:426,convect:91,conveni:[6,12,29,190,194,211,296,353,434,488],convent:[3,8,9,29,178,185,186,193,294,307,334,387,389,488],converg:[3,6,41,88,190,192,194,199,213,216,217,225,228,258,285,287,290,294,298,356,357,358,360,380,381,401,433,457,469,476],convers:[3,8,142,192,193,203,206,282,350,381,382,383,389,401,405,409,420,460,476,487],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,167,174,190,192,193,211,252,333,336,338,341,344,353,360,366,387,415,446,448,455,460,462,463,464,469,479,483,487,488,490,492],convex:331,convinc:[7,12],cook:9,cooki:7,cool:[7,157,234,293],cooordin:190,cooper:[5,7],coord123:116,coord1:[3,116,205,209,210],coord2:[3,116,205,209,210],coord3:[3,116,205,209,210],coord:[],coordb:433,coordbb:433,coordiat:358,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,94,104,105,107,115,116,118,136,142,150,156,162,164,165,167,171,189,190,191,192,193,194,196,199,204,205,208,209,210,213,214,215,216,217,218,219,220,223,225,226,228,230,233,234,235,236,237,238,239,251,253,254,256,257,259,260,272,275,276,277,280,281,282,292,293,295,297,298,299,304,307,308,309,310,312,320,321,322,329,330,332,333,353,358,359,360,365,366,367,370,388,433,457,462,463,464,465,467,470,472,476,483,488,489],coordn:[116,205],coorind:105,copi:[0,3,4,8,11,12,15,17,40,121,192,322,360,378,425,460],copper:455,coproccesor:16,coprocessor:[1,4,7,9,16,17,365,475],coproprocessor:17,copy_arrai:8,copyright:[7,8,280],coral:193,core:[],core_shel:149,coreshel:[6,9,374,381,383],cornel:[6,173,474],corner123i:115,corner123x:115,corner123z:115,corner1i:115,corner1x:115,corner1z:115,corner2i:115,corner2x:115,corner2z:115,corner3i:115,corner3x:115,corner3z:115,corner:[3,6,40,115,192,331,332,353,450,462],cornflowerblu:193,cornsilk:193,corpor:16,corr:380,correct:[3,6,9,11,12,16,17,59,87,88,103,104,112,118,149,154,161,192,219,230,232,238,254,255,272,280,282,285,321,327,331,350,360,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,453,454,455,462,477,480,483],correction_max_iter:202,correctli:[3,8,9,11,17,71,81,103,104,145,146,148,150,152,153,154,155,156,159,160,163,190,193,199,220,225,228,239,248,254,255,288,295,298,307,309,328,331,360,361,365,383,411,415,459,460,462,472,487,489],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,97,98,111,114,115,116,117,120,121,129,132,133,134,135,136,138,139,140,142,145,146,154,161,166,173,174,175,176,177,178,179,181,182,184,185,187,190,192,193,197,198,199,205,207,208,209,210,212,215,217,219,226,228,229,233,238,241,242,250,251,252,254,256,257,258,259,260,261,266,269,271,272,274,277,278,282,287,295,297,298,313,315,317,326,327,328,330,331,332,334,336,337,338,339,340,341,344,346,351,355,357,359,360,366,367,369,372,373,374,375,376,377,378,379,380,381,384,385,387,388,389,390,391,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,412,413,415,417,418,419,420,422,423,425,426,427,428,433,434,435,444,445,446,447,448,450,451,453,454,455,457,459,460,462,463,465,475,476,477,479,480,483,488],correspondingli:[410,411,471],cosin:[],cosineshift:27,cosmo:[232,237],cossq:[],cost:[1,6,10,11,12,17,39,41,71,111,120,143,166,192,193,205,209,210,213,214,215,227,254,287,322,350,351,363,381,401,405,415,417,444,459,471],costheta0:[444,446,448,451],costheta:423,costli:[11,88,232,361],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,94,105,107,111,114,116,147,157,162,164,180,190,192,193,197,198,205,206,209,213,219,228,237,284,285,286,290,293,295,297,310,311,317,321,322,323,327,331,333,335,342,347,349,356,358,361,365,368,391,395,396,425,426,458,459,460,462,464,466,469,470,478,483,488,489],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,88,109,110,118,143,168,172,286,288,323,350,351,358,365,372,374,375,376,377,380,381,382,383,384,389,393,394,396,401,405,409,417,420,425,426,428,433,443,448,449,451,454,467,474,480,483,487],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,116,118,119,155,165,171,199,200,203,205,208,209,210,212,213,220,225,227,230,236,254,266,281,298,313,314,331,351,358,359,360,362,365,391,395,417,480,488],counter:[328,457,468,470,476],counteract:230,counterbal:234,counterbalanc:29,counterpart:[190,295,457],counterproduct:18,coupl:[],courant:300,cours:[3,8,128,130,161,190,197,198,231,294,307,321,327,329,330,332,333,351,410,435,459,462,475,483,488,490],courtesi:353,cov:433,coval:[6,29,389,412,433,483],covari:232,cover:[6,71,187,193,202,241,389,399,450],coverag:[71,209],cpc:237,cpp:[1,3,6,8,9,11,12,13,87,190,197,198,228,298],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,193,207,223,239,323,348,351,365,378,443,457,475,476,479,480,481,488],cpuremain:480,cr2:166,cr3:166,crack:[4,361],crada:[5,7],crai:[5,7,13,18,190],crash:[3,12,361,483],craympi:365,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:202,create_faceset:202,create_group:191,create_nodeset:202,createatom:[],creation:[],crimson:193,critchlei:280,criteria:[3,118,168,192,193,214,215,216,249,358,422,450,464,467,488],criterion:[12,41,123,165,167,170,203,213,216,230,266,287,300,328,333,358,360,380,389,393,433,467,476,477],criterioni:476,critic:[6,48,49,252,317,322,358],cross:[3,12,22,71,89,146,175,190,192,204,209,215,219,251,253,272,295,303,307,309,318,325,337,353,360,376,385,386,387,394,395,396,401,403,405,423,428,430,432,446,448,455,462,466,472,490],crossov:1,crossterm:462,crozier:[0,7,13],crucial:285,crystal:[4,6,13,73,108,276,277,320,353,361,466,480,483],crystallin:[6,104,277,353,447,483],crystallis:317,crystallogr:[120,166],crystallograph:[353,480],crystallographi:[120,166,353],cs1:166,cs_chunk:6,cs_im:[40,462],cs_re:[40,462],csanyi:[142,424,434],cscl:412,csequ:6,csh:[11,12,378],cshrc:[11,12],csic:[388,444,446,448,451],csinfo:6,csisi:[388,444,446,448,451],csld:[],cst:387,cstherm:6,cstyle:459,csvr:[],ctcm:[366,387],ctemp_cor:223,cterm:299,ctr:9,ctype:11,cu1:166,cu2:166,cu3au:412,cube:[6,41,165,170,213,223,331,353,483],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:371,cummul:[3,6,211,214,215,216,218,227,232,238,240,310,313,314,315,316,318,325,395,480],cumul:[6,203,205,208,209,210,224,230,238,252,254,258,266,295,296,360],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,103,104,110,118,119,132,143,147,155,157,163,165,168,171,189,190,191,192,193,194,197,198,202,205,209,210,211,213,214,215,216,217,218,219,220,224,225,228,230,232,235,236,238,244,251,254,255,259,260,266,271,272,274,280,286,287,289,292,293,294,295,298,299,300,301,302,303,304,306,308,309,310,313,314,315,321,322,325,326,327,328,329,330,332,333,335,348,349,350,351,354,355,357,358,359,360,365,371,378,380,384,387,389,390,393,396,397,400,410,411,412,413,414,417,423,425,426,429,430,431,432,435,446,448,449,452,457,458,459,460,462,463,464,465,466,468,469,470,472,474,476,477,479,480,488,489,490,491,492],curv:[6,167,230,277],curvatur:[392,427,455],custom:[],cut0:460,cut1:471,cut2:471,cut:[],cuthi:[276,288],cutinn:[373,410,411],cutlo:[276,288],cutmax:423,cutoff1:[377,384,401,405,409,420,428],cutoff2:[372,374,375,377,383,384,401,405,409,420,428],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,92,108,110,117,118,142,165,168,170,215,216,221,276,285,286,288,290,292,295,310,323,327,331,333,348,350,351,358,361,362,363,365,366,367,368,369,370,371,372,373,374,375,376,377,379,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,426,427,428,433,434,435,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,460,464,467,471,483,488],cutoffa:388,cutoffc:388,cuu3:387,cval:166,cvd:317,cvel:299,cvff:[],cwiggl:[3,251,327,330,332,488],cyan:[2,192,193],cycl:[3,230,252,254,255,258],cyclic:[3,187],cygwin:12,cylind:[3,4,192,236,281,328,331,465],cylindr:[6,236,307,328],cypress:365,cyrot:371,cyrstal:277,d3q15:241,d3q19:241,d_double_doubl:15,d_e:322,d_flag2:284,d_flag:284,d_name:[115,190,284,312,472],d_single_doubl:15,d_single_singl:15,d_sx:284,d_sy:284,d_sz:284,daan:320,dai:12,daili:12,daivi:272,damag:[],dammak:290,damp:[3,6,196,201,238,239,240,245,254,255,258,282,285,290,295,313,314,326,328,329,357,358,360,372,374,376,381,384,389,393,401,409,420,428,443,449,476,483],damp_com:239,damp_drud:239,dampen:[295,483],dampflag:[328,393],dan:17,danger:[3,12,230,333,385,480],dangl:170,daniel:9,darden:[351,384],darkblu:193,darkcyan:193,darken:192,darkgoldenrod:193,darkgrai:193,darkgreen:193,darkkhaki:193,darkmagenta:193,darkolivegreen:193,darkorang:193,darkorchid:193,darkr:193,darksalmon:193,darkseagreen:193,darkslateblu:193,darkslategrai:193,darkturquois:193,darkviolet:193,dasgupta:286,dash:[393,479],dat:[6,91,187,202,458],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,296],dataset:296,datatyp:3,date:[0,6,12,13,189,425,426,488],datom1:117,datom2:117,datom3:117,datom4:117,datum:[3,6,42,65,68,69,79,93,110,117,190,206],davi:327,david:[9,19,350,351,446,448],daw:[387,423],dbg:14,dcd:[3,6,7,190,191,192,193,194,278,463,467],ddim:189,deactiv:409,dealt:237,debug:[6,7,11,12,13,14,17,120,124,166,167,278,283,348,350,365,397,417,452,460,461,469,472,479,488],deby:[],decai:[92,381,455],decid:[3,6,12,16,71,251,284,295,323,477],decipher:353,declar:191,declin:310,decod:192,decompos:[87,434],decomposit:[3,5,7,18,62,202,278],decoupl:[6,483],decreas:[3,190,199,200,207,216,219,225,228,230,238,321,350],decrement:299,deepli:347,deeppink:193,deepskyblu:193,def:[12,13,460],defaul:61,defect:[6,70,165,415],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,173,174,175,176,177,178,179,181,182,184,185,186,187,188,189,190,191,192,193,196,197,198,199,200,201,202,203,204,205,206,208,209,210,211,212,213,214,215,216,217,219,220,223,224,225,228,229,230,233,236,237,238,239,240,241,249,251,253,254,255,256,257,258,259,260,262,263,264,267,269,270,271,272,273,274,276,277,278,280,281,282,284,286,288,293,295,296,297,298,300,304,308,310,312,313,314,315,316,318,319,320,322,324,325,327,328,329,330,331,332,333,335,336,337,338,339,340,341,344,345,346,348,350,351,353,355,357,358,359,360,361,362,363,364,365,367,368,369,370,372,373,374,375,376,377,378,379,381,382,384,385,386,388,389,391,392,393,394,395,396,397,399,401,402,403,404,405,406,407,408,409,410,411,415,416,417,418,419,420,422,423,425,426,427,428,429,430,431,432,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,459,460,462,463,465,466,467,468,471,472,473,474,476,477,479,480,483,484,485,486,487,488,489],definit:[2,3,6,8,12,13,78,80,118,142,193,205,206,207,208,209,210,211,219,236,258,296,312,324,327,330,332,334,345,348,359,368,371,379,389,399,423,430,432,434,450,460,462,464,471,473,487,488],defint:480,deform:[],deg2theta:166,deg:483,degener:[3,280],degrad:[8,18,277,351,471],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,93,95,97,98,100,102,103,108,114,145,146,147,148,149,150,151,152,153,154,155,156,157,159,160,166,167,173,174,177,178,185,187,189,192,205,216,223,230,232,233,238,239,244,254,255,258,259,260,271,272,274,278,280,294,295,298,313,314,315,320,336,338,341,344,346,358,384,387,395,472,480,483,489],degress:[147,205],del:476,delai:[3,6,12,361,386,480],deleg:396,delet:[2,3,7,8,12,54,57,60,63,165,170,171,196,205,206,208,209,210,211,214,216,227,230,254,296,313,314,333,335,349,359,361,364,417,442,462,463,464,465,473,474,479,484,486,488,489],delete_atom:[],delete_bond:[],delete_el:202,deli:189,delimit:[460,488],deloc:[255,389,433],delr:412,delt_lo:476,delta:[],delta_1:371,delta_3:371,delta_7:371,delta_conf:3,delta_ij:[412,423],delta_mu:3,delta_pi:371,delta_r:423,delta_sigma:371,delx:189,delz:189,demand:290,demo:11,demon:275,demonstr:[285,412],den:281,dendrim:395,denniston:[9,241,243,244,245,277],denomin:[7,172],denot:[120,223,239,277,288,290,381,394,396,426,430,432],dens:[71,216,389],densiti:[3,6,7,9,18,40,41,59,101,118,128,142,153,165,167,197,198,202,205,209,210,213,219,228,241,244,247,248,277,281,282,286,322,327,353,355,359,366,371,387,412,413,414,423,427,433,437,439,440,441,462,471,472,480,487],density_continu:432,density_summ:432,depart:[0,7],departur:[252,285],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,93,104,110,111,114,115,116,117,121,142,145,150,154,155,161,167,168,173,174,175,176,177,178,179,181,182,184,185,186,187,189,190,192,193,196,197,198,199,200,203,205,207,208,209,211,212,213,215,217,219,225,226,229,232,233,234,236,238,239,241,243,244,251,254,256,257,258,259,260,261,269,271,272,274,276,287,290,292,295,297,298,304,310,313,314,315,317,319,321,322,324,326,327,330,331,332,333,335,336,337,338,339,340,341,344,346,351,353,358,359,361,362,363,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,387,388,389,390,391,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,412,413,415,416,418,419,420,422,423,425,426,427,428,433,434,435,443,444,445,446,447,448,449,450,451,453,454,455,457,459,462,464,465,468,472,474,476,479,480,482,488,489],dependend:6,depflag:12,dephas:[457,476],depos:220,deposit:[],deprec:[286,425],depth:[51,146,192,322,392,427],dequidt:9,der:[87,109,379,380,409,425,426,454,483],deriv:[6,7,8,9,38,56,63,87,142,161,187,206,217,219,230,238,251,254,256,257,258,259,260,276,282,286,290,319,320,322,327,328,331,357,359,367,371,379,384,389,390,394,403,407,408,412,415,425,426,443,445,454,483],derjagin:454,derlet:276,descend:193,descent:[7,357],descib:[40,286],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,112,115,118,120,132,142,143,146,147,151,152,155,158,160,161,165,166,167,169,170,179,184,187,190,191,196,197,198,205,206,207,208,209,210,211,213,216,217,218,219,220,222,223,231,232,235,236,237,238,239,240,241,243,244,245,249,253,254,255,258,265,273,276,278,283,284,285,286,287,288,295,299,307,310,311,312,313,314,315,316,317,318,319,320,325,327,328,330,335,350,351,353,356,357,358,359,360,364,367,368,370,372,373,374,376,377,378,379,380,381,384,387,389,390,392,393,394,396,401,402,403,404,405,406,407,408,409,410,411,412,415,416,422,423,424,425,426,427,428,433,434,435,442,443,444,445,446,447,448,449,451,453,454,455,457,459,460,462,463,464,465,466,472,475,476,479,488,489,490],descript:[],descriptor:[142,190,397],deserno:351,design:[0,3,6,7,8,9,11,13,14,15,17,120,149,152,166,202,216,222,223,254,255,276,277,296,317,322,368,369,370,373,376,381,383,389,409,410,411,413,414,423,426,445,471],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,114,119,143,149,167,180,189,205,211,217,219,228,230,231,238,239,240,244,254,272,280,281,282,283,286,290,295,298,310,313,314,315,316,321,328,342,347,350,351,353,356,358,359,360,385,387,395,410,411,444,446,448,458,459,460,462,466,471,476,477,479,480,488,489,490],desk:7,desktop:[4,6,7,10,12,192],despit:483,destabil:371,destre:344,destroi:[11,39,214,215],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,94,103,105,107,109,111,113,114,116,119,121,142,143,145,146,147,150,160,161,162,164,167,168,171,172,175,186,189,190,192,193,196,197,198,202,205,206,207,208,209,211,213,215,216,217,218,219,220,228,230,231,232,233,235,236,238,240,241,245,251,252,253,254,255,256,257,258,259,260,264,266,271,272,273,274,277,280,281,282,284,285,287,288,289,295,298,310,313,314,315,316,317,318,320,321,322,323,324,325,326,333,335,337,345,350,351,354,358,359,361,362,365,366,367,368,370,371,373,375,376,377,378,379,380,381,384,385,389,390,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,411,412,416,417,422,425,426,427,433,434,435,443,450,453,454,460,462,463,464,465,467,468,471,472,474,477,480,481,488,489,492],detect:[2,3,12,61,63,86,92,229,281,321,360,380,395,400,457,459,462,473,476,488],determ:365,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,103,109,111,114,120,121,129,143,155,156,165,166,167,189,190,192,193,194,195,199,200,201,204,205,206,207,208,209,210,211,212,213,217,219,220,223,225,230,233,234,236,238,239,244,249,251,252,254,259,260,271,272,274,276,278,282,285,292,293,294,295,296,297,300,302,304,310,313,314,315,317,323,324,327,328,329,330,331,332,333,345,350,351,353,359,361,362,365,367,368,375,380,384,386,387,391,393,396,397,405,412,415,417,426,427,433,442,445,449,454,459,462,463,465,467,469,472,476,478,479,481,487,488,489],detil:110,devan:[9,428],devanathan:448,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,235,258,280,285,286,289,367,371,389,414,415,433,451,464],devemi:9,deviat:[252,258,276,391],deviator:9,devic:[1,3,12,15,17,235,365],device_typ:365,devin:[287,380],devis:414,dfactor:192,dff:483,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,351],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,289,415],dhi:[59,189,219,281],dhug:[252,285],dhugoniot:[252,285],dia:412,diagnost:[],diagon:[3,6,83,142,143,144,217,254,282,295,325,430,432],diagonalstyl:434,diagram:[41,120,166,186,213,278],diallo:395,diam:[192,193,281,359],diamet:[3,6,40,115,167,190,192,193,197,198,238,281,295,310,326,328,359,379,392,393,399,403,427,450,454,462,463,472],diamond:[353,389,412],diamter:[40,281],dick:6,dicsuss:251,dictat:[203,252],did:[3,12,358,385,386,387,393,417,446,448,470],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,163,324,350],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,92,95,97,98,122,142,145,146,147,148,150,153,154,155,156,157,159,160,161,167,168,170,175,186,187,189,190,192,193,196,198,201,203,205,208,213,214,215,216,217,218,219,223,229,230,231,232,233,234,235,238,239,241,251,254,255,256,257,259,260,262,264,267,269,270,271,274,276,278,280,282,285,286,287,290,293,295,298,299,307,308,310,313,314,315,318,319,320,322,325,326,327,328,331,335,336,345,347,349,350,351,353,354,356,357,359,360,362,363,364,365,366,367,371,375,376,378,379,380,385,387,389,392,393,394,396,399,401,402,404,405,412,413,414,416,417,419,423,425,426,427,428,429,430,432,433,434,435,443,444,445,446,448,450,451,454,456,457,459,460,462,464,465,466,467,470,471,472,474,476,477,479,480,481,483,487,488,489,490],differenti:[1,3,6,29,187,350,381,423,447],difficult:[217,278,365,395,471],difficulti:[92,108,298,425],diffract:[],diffus:[],digit:[2,3,193,335,415],dih_table1:187,dih_table2:187,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:215,dihydrid:389,dij:298,dilat:[],dim1:3,dim2:3,dim:[3,59,71,145,148,149,150,153,154,155,156,157,159,167,189,209,219,236,328,353,412,465,487,488,489],dimdim:488,dimems:277,dimens:[],dimension:[3,39,92,114,120,142,145,147,148,149,150,153,154,155,156,157,159,166,188,205,209,253,277,322,353,356,360,423,462,472],dimensionless:[106,123,124,126,129,131,133,138,142,322,351,434,454],dimentionless:137,dimer:[6,295,412],dimgrai:193,dimstr:[41,213],dinola:[282,313],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,190,312,483],dir1:473,dir2:473,dir:[1,3,4,8,9,11,12,252,276,285,309,423,425,426,460,473,488],dirac:142,direc:423,direct:[],directli:[3,6,8,9,11,12,87,115,142,144,190,191,192,199,225,232,236,241,277,296,314,326,328,329,330,331,353,357,365,366,367,372,374,375,381,384,387,389,401,405,417,420,428,442,460,472,473,474,480,488],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,194,218,237,280,286,289,306,310,319,320,360,364,366,367,371,378,380,381,387,388,390,397,398,409,412,413,414,415,419,423,424,425,426,433,434,444,446,447,448,451,460,462,463,464,473,488],disabl:[3,12,16,322,400,460,475,488],disadvantag:[6,213],disallow:[190,219,254],disappear:464,discard:[2,3,41,71,207,209,213,323,331,459,464,465],discontinu:[9,187,358,407],discourag:412,discov:[13,323],discret:[6,8,40,42,192,193,238,241],discuss:[],disk:[6,84,85,92,160,188,220,230,281,460],disloc:[70,415],disord:[39,70,415],disp:[],dispar:427,disperion:[384,405],dispers:[3,6,7,9,165,277,350,351,375,384,405,410,417,426,445,451],displac:[],displace_atom:[],displace_box:59,displacemet:465,displai:[11,13,22,37,44,55,175,186,190,192,337,345,378,443],dispters:3,disregard:415,dissip:[6,231,238,277,319,320,373,385,393,410,411,443],dissolut:214,dist:[6,69,91,110,119,190,278,294,386,442,457,489],distanc:[3,6,7,9,12,20,21,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,92,94,104,105,106,107,108,110,116,117,118,119,120,122,136,142,156,162,165,167,168,169,170,174,189,190,192,193,201,205,209,210,214,215,216,217,219,220,221,224,230,236,241,251,252,253,254,258,266,276,277,281,285,286,293,294,295,298,299,303,307,308,309,310,317,318,320,321,322,325,327,328,329,330,331,332,336,350,351,353,356,358,360,361,362,365,368,369,370,371,372,373,374,375,376,377,379,381,382,383,384,385,386,387,388,389,391,392,393,394,395,399,400,401,402,403,404,405,406,407,408,409,410,411,412,415,416,417,418,419,420,421,422,423,425,426,427,428,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,460,462,465,471,472,476,480,483,487,489],distinct:[6,223,292,350,427],distinguish:[6,86,142,244,389,461],distort:366,distrbut:366,distribut:[],distro:[113,378,422,423],ditto:[8,11,12,14,15,16,17,18,117,215,455,460],div:8,divd:119,diverg:[3,12,39,295,320,464,483,490],divid:[3,6,16,41,91,114,119,128,130,143,164,165,175,186,193,205,206,208,213,219,276,318,325,330,350,358,360,390,426,433,451,471,479,488],divis:[6,241,371,399,409,459,462,480,488],dl_poli:[6,7],dlambda:161,dlammps_async_imd:235,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,192],dlammps_gzip:[3,12,190,192,321,462,463,467],dlammps_jpeg:[3,12,192],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,192],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,190],dlen:472,dlmp_intel_offload:[12,16],dlo:[59,189,219,281],dlopen:6,dlvo:[7,379,454],dm_lb:241,dmax:[310,356],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,94,103,105,106,107,109,111,113,114,116,119,121,143,146,147,160,162,164,167,168,169,175,186,189,190,191,192,193,194,196,197,198,203,204,205,206,207,208,209,210,211,220,230,238,239,249,254,255,259,260,264,271,272,273,274,281,284,295,307,310,313,314,315,324,328,331,333,335,337,345,349,358,359,360,365,366,367,370,378,380,381,387,388,390,395,396,398,399,412,413,414,417,419,422,423,424,434,443,444,446,448,450,451,460,462,463,464,465,467,470,471,472,479,480,488,489,490,491],docuement:427,dodgerblu:193,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,50,54,56,59,62,63,67,70,71,72,87,88,91,105,112,118,119,120,144,146,147,149,150,155,157,161,166,167,168,169,171,173,175,180,186,187,189,190,191,192,193,196,202,203,205,209,212,213,215,216,217,219,223,225,227,230,231,234,236,238,239,241,244,250,254,255,256,257,259,260,271,272,273,274,282,283,284,288,290,293,295,310,313,315,317,318,322,325,326,327,330,331,332,333,338,339,341,342,344,349,350,351,352,353,359,360,361,366,367,368,369,370,371,373,375,376,377,379,380,381,382,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,403,404,406,407,408,410,411,412,413,414,415,417,423,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,453,454,455,457,458,459,460,462,463,464,465,466,469,470,472,473,474,475,476,479,480,483,488,492],doegenomestolif:7,doesn:[3,7,8,12,167,190,203,209,210,307,359,361,365,367,380,388,398,425,426,444,446,447,448,451,462,464],dof:[3,8,114,146,147,160,205,295,489],dof_per_atom:[147,205],dof_per_chunk:[147,205],doff:[359,462],doi:[6,218],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,120,156,166,169,189,191,192,193,196,203,213,217,219,220,234,237,241,254,255,278,290,295,322,327,328,350,351,360,365,386,417,457,459,462,466,479],domin:[1,389,476],don:[0,8,11,12,13,118,170,199,225,239,284,331,412,433,460,462],donadio:314,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,161,164,167,170,187,190,192,193,202,203,205,207,208,209,210,211,213,214,215,216,217,219,220,228,230,235,236,238,239,246,254,259,260,271,272,274,275,277,278,279,284,292,295,296,298,310,313,314,315,317,319,320,333,335,349,350,351,358,360,361,364,365,367,375,387,396,397,398,405,411,412,417,425,442,445,450,457,458,459,460,463,466,467,470,480,481,483,488,489],donor:395,dot:[143,163,199,225,233,253],doti:[371,423],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,219,228,283,331,335,349,351,364,365,371,390,394,415,425,426,458,462,466,470,475,488,489],dover:202,down:[3,6,7,8,11,39,71,217,230,238,310,326,365,389,417,433,461,481],downhil:[356,357],download:[5,7,8,9,11,12,13,17,235,397,424],downsid:6,downward:292,dozen:[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06,216,217,230,252,254,255,272,273,285,286,287,288,318,319,320,325,380,381,425,426,458,472],equilibria:325,equilibribum:[214,215],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,150,151,174,176,217,219,230,231,232,239,241,254,258,272,285,290,294,298,299,307,310,317,318,320,325,336,338,341,344,380,412,419,433,483],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:202,equival:[6,12,13,29,59,61,126,127,135,140,165,169,193,208,211,217,219,230,238,254,272,282,294,295,330,385,389,433,446,448,462,465,470,471,480,483],equlibrium:6,equliibr:[286,288],er3:166,eradiu:[40,115,389,462],eras:[297,319],erat:[219,411],erc:381,erfc:[381,401,417],erforc:115,erg:487,erhart:[203,387,446,448],ermscal:368,ernst:9,eror:3,eros:412,erose_form:412,erot:[],errata:[446,448],erratum:327,erron:3,error:[],erta:393,ervel:[115,462],escap:[220,483],especi:[8,11,16,155,167,196,203,213,230,285,290,293,294,365,459],espresso:[9,289],essenti:[8,11,12,27,88,130,148,149,150,153,154,155,156,157,159,176,206,258,277,326,351,367,381,401,448,467,480],essex:29,establish:[87,234],estim:[1,3,6,10,12,38,41,56,91,143,202,213,224,252,310,317,350,351,356,417,426,445,476,480],esu:487,esub:412,eta:[6,241,254,285,286,288,326,388,390,392,423,447,451,487],eta_dot:254,eta_ij:423,eta_ji:390,etag:[40,462],etail:480,etap:254,etap_dot:254,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,95,111,112,115,117,143,145,147,148,149,150,151,153,154,155,156,157,159,161,167,169,170,171,180,190,192,193,196,197,202,203,204,205,208,209,210,211,214,215,219,220,228,230,231,238,254,281,292,296,322,323,331,335,349,350,358,359,360,361,363,387,388,396,409,411,415,421,425,426,444,446,448,451,457,460,462,463,464,469,471,472,476,478,479,480,481,483,487,488,490,492],ethernet:18,etol:[358,360,457,476],etot0:285,etot:[6,95,97,98,112,143,153,193,223,239,252,285,479,480],eu2:166,eu3:166,euler:[358,360],eulerian:202,euqat:436,europhi:241,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,109,119,142,144,147,157,165,167,189,190,192,193,197,198,199,200,202,204,205,206,207,208,209,210,211,212,219,225,231,233,234,236,237,238,239,277,283,286,297,300,304,313,314,315,324,327,330,332,333,335,350,351,356,358,365,415,417,423,429,431,433,445,457,458,460,464,465,467,469,470,471,472,476,478,480,488,489],evalut:[335,460],evan:[155,272],evanseck:[6,20,173,376,474],evapor:[],evaul:[8,358],evdwl:[109,425,426,480],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,121,168,169,183,187,190,193,196,197,198,203,204,205,208,209,210,211,213,214,215,217,219,220,223,236,239,252,254,255,277,290,292,295,296,306,310,318,322,325,327,331,333,343,350,356,358,360,365,370,389,390,393,396,417,427,451,452,462,463,465,467,468,469,471,472,474,477,479,480,481,483,492],evenli:[3,41,143,187,213,241,399,452,462],event:[],eventu:[3,6,12,15,169,286,476],ever:[54,56,237,310],evera:[379,392,427,443],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,115,121,130,155,170,190,191,192,193,194,196,197,198,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,224,227,228,230,232,234,235,236,241,242,250,254,255,258,275,276,277,281,282,283,284,285,286,287,288,290,292,293,295,296,298,299,310,312,313,314,315,316,317,318,321,322,323,324,325,333,335,349,351,360,361,362,365,385,386,396,409,425,426,433,439,456,457,458,462,464,466,467,469,470,471,476,477,478,480,488,492],everyth:[8,109],everywher:[118,403],eviri:389,evolut:[232,241,278,457],evolv:[241,278,323],ewald:[2,3,5,6,7,8,12,88,112,120,143,323,350,351,358,372,374,375,381,384,389,401,405,420,428,443,445],ewald_disp:384,ewalddisp:3,exact:[22,41,44,71,124,161,170,175,213,216,231,232,238,239,240,281,290,291,310,322,337,350,378,464,469,476,488,490,492],exactli:[3,6,12,14,17,38,41,56,59,71,72,91,118,146,151,158,167,187,197,198,208,213,219,224,231,238,239,240,255,265,266,273,277,285,310,315,316,329,365,378,385,387,393,396,399,410,417,445,464,465,472,476,488],exager:483,examin:[6,8,9,17,216,277],examp:[460,488],exampl:[],exce:[3,6,16,17,18,41,58,71,169,204,205,208,209,210,211,213,217,219,224,227,254,277,292,296,301,302,310,358,365,462,488],exceed:[3,41,59,213,219,254,310,470],excel:389,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,110,111,114,119,143,145,146,147,148,149,150,151,153,154,155,156,157,158,159,160,167,171,173,174,175,176,177,178,179,181,182,184,185,186,187,189,190,193,196,199,205,206,208,212,213,217,219,226,229,230,233,236,238,240,254,255,256,257,258,259,260,261,265,266,269,271,272,273,274,278,287,288,295,297,298,307,310,313,315,316,322,326,330,333,335,336,337,338,339,340,341,344,345,346,350,351,353,355,359,360,361,363,364,365,366,367,369,372,373,374,375,376,377,378,379,380,381,383,384,385,387,388,389,390,391,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,411,413,418,419,420,422,425,426,427,428,435,443,444,445,446,447,448,450,451,453,454,455,457,459,460,462,464,465,467,470,471,472,473,474,476,480,483,487,488,489,491],excess:[207,389],exchang:[2,3,6,8,9,61,62,196,202,203,230,238,287,295,318,322,325,350,365,389,477],exchange:350,excit:[9,389],exclud:[3,6,9,12,16,17,63,71,114,142,147,154,155,171,190,205,209,214,215,242,250,280,293,295,317,328,333,358,359,361,373,393,396,410,411,417,442,474],exclus:[1,3,9,12,16,87,365,380,415,417,471,481],excurs:457,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,168,192,235,289,335,349,352,364,458,460,470,473,476,488],exempl:433,exemplari:231,exemplifi:389,exert:[6,236,239,290,329,330,331,351],exhaust:[202,364,488],exhibit:[92,254,357,389,471],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,124,167,168,186,191,192,193,196,201,212,215,217,220,230,280,281,283,333,336,338,339,341,345,354,359,365,396,425,442,452,458,460,462,463,464,473,474,475,488,489,490],exit:[2,3,11,12,41,57,190,213,349,364,460,461,470,479,488],exlanatori:3,exp:[],expand:[],expans:[12,142,190,473,488],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,103,148,159,165,187,213,225,230,232,251,276,282,284,285,290,295,333,351,361,378,412,415,417,457,460,462,464,467,471,476,488],expens:[6,10,71,193,276,280,295,322,333,350,351,361,365,460],experi:[6,13,15,17,212,220,235,244,253,282,294,295,356,360,385,417,471,476],experienc:[6,12,243,244],experiment:[230,350,365,476],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,93,147,155,187,190,192,193,196,205,206,211,213,215,217,219,254,276,284,295,307,333,335,349,350,353,359,360,364,370,387,399,433,435,450,460,463,464,467,469,472,483,488,492],explan:[3,6,59,115,142,190,205,253,276,396,456,459,460,462,471],explanatori:[3,8,119,190,204,205,208,209,210,295,359,459,488],explantori:[3,291],explic:416,explicit:[6,9,11,22,44,77,87,115,118,161,175,197,198,219,301,302,337,355,367,368,371,376,378,387,389,400,410,449,456,459,463,466],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,111,114,145,154,157,165,167,173,174,176,177,178,179,181,182,184,185,187,190,193,199,209,212,219,226,229,231,233,238,254,256,257,258,259,260,261,269,271,272,274,284,285,287,295,297,298,313,315,316,322,326,330,336,338,339,340,341,344,346,359,365,366,367,369,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,413,415,417,418,419,420,422,427,428,435,436,437,438,439,440,441,443,444,445,446,447,448,449,450,451,453,454,455,462,464,471,472,474,475,481,483],explictli:[16,475],exploit:[9,15,17,278],explor:[120,166],expon:[3,286,288,387,392,395,409,416,428],exponenti:[87,423,444,451,455,476,488],expos:11,exposit:[202,385,386],express:[6,142,153,167,197,198,217,251,276,286,322,328,335,371,387,389,403,412,433,434,443,488],expressiont:371,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,95,98,99,109,111,119,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,196,199,200,203,211,212,218,221,225,228,229,230,232,233,234,236,238,240,252,254,258,266,276,277,293,294,295,297,299,304,307,309,313,314,315,316,317,319,320,322,324,327,331,332,392,412,415,426,427,434,479,480],extent:[1,3,41,45,57,71,165,169,190,201,209,213,236,329,332,350,353,367,429,431,445,459,462,465],exterior:[3,6,331],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,103,111,112,114,120,143,145,146,148,150,153,154,155,156,157,159,160,166,167,168,169,173,193,208,213,215,254,283,284,285,295,310,358,359,362,363,384,393,396,399,412,417,459,460,462,465,474,483,488],extract:[3,6,11,13,36,63,87,109,117,119,121,197,198,288,360,381,390,412,434,460,467,479],extract_atom:11,extract_comput:[11,460],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,192,207,217,219,254,320,389,447,483],extrema:409,extrins:202,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[163,324],f_a:[446,447,448],f_ave:119,f_c:447,f_f:448,f_fix_id:285,f_harm:320,f_i:[29,423],f_id:[6,71,119,121,190,196,204,205,206,207,208,209,210,211,249,312,324,480,488],f_ij:423,f_indent:211,f_int:319,f_j:29,f_jj:91,f_k:423,f_langevin:322,f_max:[285,290],f_msst:252,f_r:[239,446,447,448],f_sigma:371,f_solid:320,f_ss:6,f_temp:239,face:[3,6,57,59,71,155,165,169,201,209,210,327,329,330,331,332,353,392,412,427,462,465],face_threshold:165,facet:165,facil:[0,12],facilit:[6,13],fact:[6,8,16,232,310,320,393,433,474],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,87,91,103,110,117,118,120,142,161,166,169,173,184,189,190,192,193,197,198,206,213,217,219,220,230,235,238,240,241,252,254,255,258,278,282,294,298,300,302,310,314,318,325,326,327,331,341,351,353,359,365,367,368,371,372,374,376,381,382,383,385,389,393,396,400,401,412,415,417,419,420,426,428,435,444,449,459,462,465,466,471,474,476,477,480,483,487,488],factori:[3,460],factoriz:350,fail:[3,11,12,59,171,217,220,350,358,360,383,426,460],failur:[123,430,461,488],fairli:[11,417,471,476],faken:73,falcon:235,fall:[3,6,193,208,281,460,488],fals:[86,333,335,433,488],fame:8,famili:[451,459],familiar:[0,11],fan:423,far:[3,6,12,17,57,59,61,86,190,193,194,213,214,215,217,220,254,276,294,295,310,327,338,341,356,360,361,450,460,462,467,480],farago:238,farrel:[446,448],farther:190,fashion:[6,8,41,71,167,193,196,197,198,203,209,213,215,220,230,232,236,251,252,254,256,257,258,259,260,268,271,272,273,274,284,285,287,295,299,303,309,312,320,322,326,327,328,330,332,360,396,410,465,474,488,491],fasolino:398,fast:[6,7,9,12,13,17,39,190,263,285,323,350,351,373,410,411,415,443,445,464,469,471,480,489,492],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,106,111,114,145,154,173,174,176,177,178,179,181,182,184,185,187,190,193,199,212,213,219,226,229,233,237,238,254,256,257,258,259,260,261,269,271,272,274,282,286,287,295,297,298,310,313,315,317,319,322,326,330,336,338,339,340,341,344,346,350,351,362,363,365,366,367,369,371,372,373,374,375,376,377,378,379,380,381,384,385,387,388,390,391,392,393,394,395,396,399,401,402,403,404,405,406,407,408,409,410,413,418,419,420,422,427,428,435,443,444,445,446,447,448,450,451,453,454,455,457,471,475,483],fastest:[1,6,14,17,155,209,322,323,365,459],fatal:[3,479],fault:[70,426],faulti:12,fava:392,favor:216,favorit:7,fbmc:317,fcc:[],fcm:[268,488],fdirect:223,fdotr:397,fdti:87,fe2:166,fe3:166,fe_md_boundari:202,featu:8,featur:[],fecr:387,feedback:[7,235],feel:[7,235,236,244,276,331,333,360,417],felling:414,felt:331,femtosecond:487,fene:[],fennel:[381,401],fep:[],ferguson:[6,173,474],fermi:[1,12,15,153,365,448],fermion:[9,389],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,194,204,205,206,208,209,210,211,239,254,281,284,286,298,324,350,358,359,360,367,433,459,462,467,471,473,481,488,490],fewer:[1,3,11,15,16,61,244,471],fewest:3,fextern:228,feynman:278,fff:460,ffield:[380,390,425,426,433],ffmpeg:[3,12,192],ffplai:192,fft:[1,3,7,12,14,15,88,111,112,143,277,350,351,471],fft_inc:[12,351],fft_lib:12,fft_path:12,fftbench:[350,481],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:442,fictiti:[6,199,200,225,228,232,278,294,381,401,405,442],field1:[463,467],field2:463,field:[],fifth:[307,419],figur:[1,3,8,11,12,285,459,460],fij:384,file0:276,file1:[11,13,276,321,335,359,467,469,473],file2:[11,13,321,335,359,467,469,473],file:[],file_from:191,filen:359,filenam:[3,12,13,38,41,56,187,190,192,193,194,202,205,206,207,208,209,210,211,213,218,276,280,283,286,287,288,291,292,295,296,321,322,347,348,349,359,360,366,367,371,381,387,388,390,398,412,413,414,419,423,424,425,426,433,434,444,445,446,447,448,451,458,459,460,463,464,469,473,480,488,490,491,492],filennam:469,filep:[3,190,193,464,469,492],filepo:292,fill:[7,9,167,192,281,322,353,361,371,415,426,465],filter:[193,202],final_integr:8,final_integrate_respa:8,finchham:[6,149,383],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,119,170,187,194,203,216,217,227,230,253,276,282,290,294,356,358,360,361,381,396,401,405,412,433,443,445,483,488],find_custom:8,fine:[16,17,171,199,225,320,361,365,488],finer:[142,167,488],finest:350,finger:[167,189,251,465],finish:[6,11,41,213,335,347,349,350,362,364,365,450,467,488,489],finit:[],finni:[7,387,443],finvers:223,fiorin:[9,218],fire:[356,357,358,360,476],firebrick:193,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,104,105,106,108,114,118,119,129,132,135,136,140,143,152,155,161,163,165,166,168,169,170,174,187,190,191,192,193,194,196,197,205,206,208,209,210,211,213,216,219,230,231,236,241,251,252,253,254,276,278,283,284,285,287,292,295,298,299,307,308,310,311,312,319,320,321,322,324,328,333,335,336,342,353,358,359,360,361,364,365,366,367,370,371,372,374,376,378,380,381,387,389,390,393,394,396,397,398,400,401,405,410,411,412,414,415,417,419,423,425,426,433,434,442,444,445,446,447,448,451,455,457,458,459,460,462,463,464,467,469,471,474,475,476,479,480,483,488,489,490,492],fischer:[6,9,19,20,173,376,474],fit:[3,6,9,12,38,56,187,294,310,367,371,398,412,417,438,445,447,470,488],five:[73,153,285,359,371,413,462,476],fix:[],fix_adapt:[161,198,409],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,203,281],fix_evapor:203,fix_flux:202,fix_gcmc:[203,359],fix_gl:232,fix_gld:232,fix_grav:281,fix_id:[3,217,252,254,256,257,258,259,260,282,285],fix_modifi:[],fix_mov:[189,328],fix_nh:8,fix_npt:232,fix_nvt:[203,230],fix_poem:[3,6],fix_pour:[3,220],fix_qbmsst:9,fix_qeq:[3,380],fix_rattl:298,fix_reax_bond:425,fix_rigid:[244,370],fix_saed_vtk:296,fix_setforc:8,fix_shak:298,fix_srd:3,fix_styl:258,fix_temp_rescal:316,fixedpoint:[217,254],fixextern:228,fixid:202,fji:384,flag1:[222,363],flag2:[222,363],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,94,104,105,107,120,162,166,170,190,192,193,194,211,216,218,222,235,238,242,244,250,251,277,284,295,307,309,310,317,321,330,333,348,351,359,363,364,365,367,395,400,412,415,442,457,459,460,462,463,464,466,467,468,472,488],flag_buck:375,flag_coul:[375,384,405],flag_lj:[384,405],flagfld:[373,410,411],flaghi:[3,373,410,411],flaglog:[373,410,411],flagn:222,flagvf:[373,410,411],flat:[6,322,327,328,332],flavor:[2,7,12],fld:[9,327,373,410,411],flen:368,flex_press:368,flexibl:[3,6,8,168,192,205,209,218,232,255,318,325,389,447,480],flip:[3,6,219,254,329,330],floor:488,flop:12,floralwhit:193,flow:[],fluctuat:[6,64,87,217,230,231,238,241,254,258,276,277,320,322,344],fluid:[],fluid_veloc:245,flush:[3,193,479],flux:[],flv:192,fly:[7,9,12,41,192,196,202,207,220,223,295,298,323,371,415,480,483],fmackai:9,fmag:221,fmass:278,fmax:[358,480],fmomentum:223,fmsec:[2,193,238,239,251,254,282,295,313,314,471,482,487,489],fname:349,fno:[12,16],fnorm:[358,480],fnpt:223,fnvt:223,foce:396,fock:368,focu:298,fogarti:[9,288,426],foil:[142,276,434],fold:[308,471],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,92,97,98,108,115,118,119,121,142,143,146,147,153,155,160,163,165,167,168,173,176,177,178,179,181,182,184,185,187,190,191,192,193,196,202,203,204,205,206,207,208,209,210,211,213,218,219,220,223,224,228,230,231,232,235,237,238,239,241,244,252,254,258,259,260,271,272,274,277,278,280,283,284,285,286,288,290,292,294,295,296,298,312,313,314,315,318,319,320,321,322,324,325,333,334,338,339,340,341,344,346,348,353,355,358,359,360,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,422,423,424,425,426,427,428,430,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,453,454,455,457,459,460,462,463,465,467,469,470,471,474,476,477,478,483,488,489,491],foo:[4,8,11,12,190,192,228,460,473,488],foot:6,footprint:[12,365],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:244,forcefield:[294,395],forcegroup:241,forcezero:356,ford:384,forestgreen:193,forev:71,forget:[239,483],forgiv:254,fork:[12,190],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,92,94,104,105,107,118,142,143,161,162,171,175,193,196,197,198,215,231,232,238,240,244,251,272,277,288,290,294,295,322,327,331,336,337,344,355,357,359,360,367,368,371,378,387,389,391,395,396,400,412,414,415,419,420,423,425,426,427,433,434,435,443,445,446,447,448,454,456,459,460,462,467,472,479,483,488],formal:[6,78,80,91,231,232,238,254,278,310,318,433],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,175,187,190,191,192,193,194,205,208,209,210,211,213,215,277,280,284,286,288,291,295,296,306,321,322,333,334,337,355,359,360,366,367,371,378,387,390,400,412,414,424,425,426,428,434,445,451,452,459,460,462,463,464,467,478,479,480,488,490],former:[6,12,16,39,41,193,213,322,326,371,373,468,474,488],formerli:[7,13],formul:[1,40,64,143,199,225,238,254,272,286,288,294,298,321,350,367,371,387,389,392,412,422],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,95,97,98,107,114,120,143,145,146,147,148,149,150,151,153,154,155,156,157,158,159,160,166,167,172,174,175,186,189,190,197,198,199,200,205,206,207,208,211,212,219,225,233,234,236,238,239,251,276,277,283,292,297,304,308,310,313,314,315,324,327,330,332,333,335,336,337,339,345,353,359,367,368,370,371,376,377,378,379,384,385,387,388,392,393,394,395,397,400,401,403,404,405,407,408,410,411,412,416,417,418,427,428,435,443,444,446,447,448,451,453,454,458,462,465,472,479,480,487,488,489],forth:[1,6,11,12,13,14,15,364,460,465,469],fortran:[3,6,9,11,12,13,228,387,396,412,425,426],fortun:8,forward:[3,8,87,349,360,365],foster:[371,422,423],foul:170,found:[3,6,9,12,73,161,190,216,218,230,235,241,277,317,323,335,349,361,378,381,384,457,463,464,479],four:[6,11,54,81,104,105,142,163,252,322,344,359,360,415,457],fourier:[],fourth:[6,106,294,307,317,376,419,433],fox:[6,120,173,441,474],fphi:[38,56,445],fpic:12,fplo:[38,56,445],fprime:445,fqdn:237,fqq:384,frac:[223,239,449,483],fraction:[1,3,6,8,12,16,39,41,80,111,143,170,189,192,193,203,214,215,216,217,252,281,285,292,293,310,315,316,353,360,365,371,373,393,410,411,467,472],fragment:[42,235,292],frame:[83,142,193,202,252,285,329,392],framer:[192,193],framework:[5,232,366,434],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,161,198,276,310,319,320,321,322,357,360,368,389,409,415,423,454,459],freedom:[3,6,8,95,97,98,100,102,103,114,145,146,147,148,149,150,151,152,153,154,155,156,157,159,160,205,216,223,230,232,238,239,244,254,255,258,259,260,271,272,274,278,280,295,298,313,314,315,320,358,384,480,483,489],freeli:[0,6,7,12,146,160,165,192],freez:[],frenkel:[230,320],freq:201,frequenc:[3,6,16,39,104,193,207,266,277,278,285,290,348,385,389,426,433,457,471,476,488,491],frequent:[3,64,67,70,72,73,77,88,92,108,142,193,214,215,227,318,325,417,469],fri:[252,285],friction:[4,5,6,10,42,196,232,238,285,290,295,322,326,328,393,472],friedrich:300,from:[],front:[252,285,329],frontend:[192,289],frozen:[6,114,171,229,231,239,361,391],fs2:[6,91],fscale:235,fstr:488,fstring:460,ftol:[358,360,457,476],fuchsia:193,fuction:381,fudg:298,fugac:230,fugacity_coeff:230,fulfil:6,full:[1,2,6,9,12,17,38,39,40,91,192,206,207,218,241,276,350,351,365,371,387,389,390,392,449,462,464,469,470,474,476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325,326,327,330,331,332,358,360,362,456,470],imposs:1,improp:[],improper_coeff:[],improper_styl:[],impropercoeff:3,impropertyp:215,imprort:98,improt:[197,198],improv:[0,1,9,16,39,41,193,213,254,277,365,395,401,415,417,426,444,447],in3:166,inaccur:[1,3,6,170,252,350],inaccuraci:331,inact:395,inappropri:167,incid:[120,166,220],includ:[],includig:[335,349],inclus:[],incom:235,incompat:[3,11,397],incomplet:[3,11,462],incompress:[255,389],inconsist:[3,171,216,463],inconveni:353,incorpor:[285,371,382],incorrect:[3,150,238,412],incorrectli:[3,353,393,488],increas:[1,3,6,10,18,38,56,57,59,111,120,143,187,190,192,193,207,214,215,216,219,230,238,282,293,294,295,318,321,325,350,351,360,365,389,392,426,445,447,460,471,476,488],increasingli:389,increment:[3,11,130,199,200,212,213,220,225,227,254,299,300,333,349,364,399,433,457,460,474,476,488],incur:[14,17,205,209,210,227,322,459],inde:150,indefatig:7,indefinit:319,indent:[],independ:[4,6,9,11,12,16,17,41,59,63,91,119,121,153,167,189,196,204,205,206,208,209,210,211,213,216,217,218,219,220,231,233,238,239,241,244,254,277,282,286,290,295,296,299,309,320,322,353,393,415,457,460,479,489],indetermin:[190,193],index:[0,3,6,8,11,12,38,39,40,56,68,69,119,121,187,190,193,204,206,235,237,278,296,322,333,334,335,355,364,417,425,426,445,452,462,477,488],indianr:193,indigo:193,indirectli:[6,488],indistinguish:238,indium:434,individu:[],induc:[],industri:7,ineffici:[3,6,40,64,67,70,72,73,77,92,108,142,155,192,219,254,277,350,362],inelig:203,inerti:411,inertia:[],inexpens:[232,471],inf:[2,3,12,325,465],infer:[3,95,97,98,161,199,200,213,214,215,225,235,280,310,318,325,353,378,390,462,474,480],infil:[3,13,295,459],infin:[3,358,467,480],infininti:192,infinit:[3,220,229,236,238,241,277,310,322,328,329,351,353,389,466,487],infinitesim:6,inflect:[382,403],influenc:[3,9,41,80,149,251,281,350,351,417,446,447,448],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,39,41,42,59,61,62,63,68,88,117,119,120,166,167,173,190,191,192,193,194,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,225,226,227,228,229,230,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,253,261,262,263,264,265,266,267,268,269,270,275,276,277,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,300,307,308,310,311,313,314,315,316,317,318,319,321,324,325,326,327,329,330,331,332,334,348,350,351,354,357,358,359,360,361,363,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,420,422,423,424,425,426,427,428,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,451,453,454,455,459,460,462,463,464,466,467,469,474,476,477,479,481,488,490,491,492],infrequ:[6,385,457,476],infti:[382,410,411],ingtegr:371,inher:[350,358,417],inherit:[6,449],inhomogen:[18,322,417],inidividu:358,init:[3,8,293,433],init_fil:322,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,39,40,41,56,57,59,62,71,80,81,86,87,104,105,132,163,168,169,187,189,190,192,193,194,197,198,201,202,206,213,215,216,217,219,226,230,231,235,236,237,238,239,241,246,250,251,252,253,254,258,266,277,278,279,284,285,290,293,294,295,297,309,310,312,317,319,320,321,322,323,324,327,328,329,330,332,333,335,350,354,357,358,360,367,368,384,385,386,415,424,425,426,433,445,457,459,460,462,464,465,467,469,470,472,476,477,480,483,488,489,490,492],initial_integr:8,initial_integrate_respa:8,initialis:424,initialt:322,inlclud:11,inlcud:488,inlin:460,inner2:[376,394],inner:[3,8,16,190,236,335,349,356,357,358,360,364,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,384,385,386,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,422,424,425,426,427,428,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,450,451,452,453,454,455,471,476,488],inner_distance_cutoff:395,innergroup:244,innermost:[38,56,363,445,471],innernod:244,innner:407,inordin:323,inorgan:[6,451],inp:[218,335,434,451],input1:[65,68,69,79,93,110,115,116,117,119,121,312],input2:[65,68,69,79,93,110,115,116,117,119,121,312],input:[],input_doubl:3,inquir:300,insensit:12,insert:[3,5,7,8,12,59,167,196,220,230,236,281,350,434,442,460,466,483],insid:[2,3,6,8,11,71,131,137,167,190,193,204,209,210,220,221,227,230,236,241,244,281,295,310,327,329,330,331,332,333,348,353,403,460,461,462,464,465,472,476,488],insight:[6,13],instabl:[241,384,432],instal:[],instanc:[6,11,197,218,232,329,391,396,417,423,460,483],instantan:[6,63,216,217,231,232,254,258,277,282,285,290,292,295,317,468,480],instanti:[6,11,12,202,396,459],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,90,104,119,146,149,171,187,190,198,205,208,209,210,211,213,217,218,230,238,241,244,245,277,283,293,295,312,330,348,350,351,354,361,365,374,375,387,400,402,409,412,415,457,465,469,476,478,483,488],institut:[9,235,280],instruct:[3,8,11,13,20,21,23,24,25,26,27,28,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,111,114,145,154,165,173,174,176,177,178,179,181,182,184,185,187,188,192,199,212,219,226,229,233,238,256,257,258,259,260,269,271,272,274,287,295,297,298,313,315,326,330,336,338,339,340,341,344,346,351,366,367,369,372,373,374,375,376,377,379,380,381,384,385,387,388,390,391,392,393,394,395,399,401,402,403,404,405,406,407,408,409,410,413,418,419,420,422,427,428,435,444,445,446,447,448,450,453,454,455,471,483],insuffici:[3,6,12],insult:254,insur:[3,6,11,12,17,39,40,61,73,103,105,167,168,187,190,192,193,199,214,215,220,225,226,227,228,230,233,238,250,283,284,293,295,310,322,327,331,332,333,335,349,359,361,365,379,392,396,421,427,445,459,460,462,463,467,470,471,479,480,488,489],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,108,115,117,119,121,142,165,167,170,171,173,177,178,182,187,189,190,192,193,203,205,209,210,214,215,216,220,222,228,230,231,232,235,238,239,240,241,277,280,281,284,285,290,295,310,312,314,317,321,322,340,350,353,373,385,386,399,412,425,426,430,432,434,457,459,460,461,462,470,471,472,476,479,488,489],integr:[],integrate_ulsph:301,intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,207,231,424,462],intens:[1,3,6,9,63,66,74,75,86,89,90,91,94,104,105,106,107,114,116,118,119,120,121,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,164,166,196,205,206,208,209,210,211,213,214,215,216,224,227,234,244,252,254,258,292,295,296,310,318,322,324,325,479,480],intepol:488,inter:[14,18,42,61,62,147,170,171,190,216,238,240,253,287,295,350,360,371,472,483,488,490,492],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,72,77,79,87,88,92,93,108,109,110,112,114,117,118,124,125,126,127,129,130,131,132,133,134,135,137,138,139,140,142,143,144,146,160,161,165,168,169,170,171,172,173,175,179,180,186,190,196,197,198,214,215,216,229,230,235,236,238,240,244,266,276,278,280,286,288,294,295,301,302,310,311,317,322,326,327,328,331,332,337,338,339,341,345,350,351,358,359,360,361,362,363,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,422,423,426,427,428,430,432,433,434,435,442,443,444,446,447,448,449,450,451,452,453,454,455,457,460,462,464,466,467,471,472,474,479,480,483,490],interatom:[3,4,7,167,190,253,319,320,366,371,387,389,397,412,415,433,447,488],intercept:120,interchang:6,interconnect:18,interconvert:389,intereract:39,interesect:331,interest:[1,5,7,8,9,11,13,71,166,278,317,320,351,388,411,425,426,460,488],interf:365,interfac:[],interfer:[12,254,367],interg:[6,483],intergr:[471,475],interi:411,interior:[3,6,41,331,465],interlac:412,interleav:[6,167,470],intermedi:[6,12,59,192,253,276,344,360,460,461,470,474],intermix:457,intermolecular:367,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,100,102,120,143,147,149,166,174,187,192,193,196,197,198,202,215,219,223,235,247,248,252,254,258,277,295,299,336,338,341,344,348,358,359,436,437,445,460,462,464,467,476,479,480,487,488,489,490],internal_element_set:202,internal_quadratur:202,internet:237,interpenetr:412,interpentr:[437,438,440],interpol:[6,15,38,56,101,187,192,193,202,241,276,350,351,360,371,417,426,439,445,446],interpret:[2,6,11,192,208,393,435,457,460,476,488],interrupt:285,intersect:[3,6,120,193,331,333,465],intersert:331,interspers:358,interstiti:[165,415],intertia:[3,94],interv:[3,6,91,191,206,238,285,290,291,302,433,439,457,476,488],intestieti:120,intial:[6,365,367],intiial:[41,467],intiti:[3,309],intra:295,intra_energi:230,intramolecular:[29,230],introduc:[6,9,92,108,192,254,285,290,295,344,350,366,381,389,401,405,409,444,476,488],introduct:[],intsal:[],intuit:353,inv:[120,166,296],invalid:[3,12,71,89,170,266,360,410,411,464],invari:[108,135,140,142],invent:298,invers:[],invert:[1,6,171,277],invis:331,invoc:[165,216,365,430,432,460],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,94,104,105,107,111,112,113,114,119,145,154,161,162,165,167,168,170,171,173,174,176,177,178,179,181,182,184,185,187,190,192,193,194,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,238,239,240,241,242,243,244,245,246,247,248,250,251,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,279,280,281,282,283,284,286,287,288,289,290,291,292,293,295,296,297,298,299,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,336,338,339,340,341,344,346,349,350,351,352,353,358,360,365,366,367,369,372,373,374,375,376,377,379,380,381,384,385,387,388,390,391,392,393,394,395,396,397,399,401,402,403,404,405,406,407,408,409,410,411,413,417,418,419,420,422,427,428,430,432,434,435,444,4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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 hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix 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 mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":214,"default":[37,39,40,55,57,58,59,61,62,71,87,88,92,103,104,106,108,109,120,124,125,142,147,155,156,160,166,167,170,172,186,188,189,190,192,193,194,195,197,198,199,201,202,203,205,209,210,211,214,215,217,218,219,220,224,227,230,231,236,238,239,240,241,242,244,249,252,254,255,258,272,273,277,278,281,282,283,284,285,287,290,292,293,295,296,310,312,317,318,319,320,323,325,327,329,333,345,348,350,351,353,354,356,357,359,361,362,363,365,368,371,373,389,410,411,415,417,425,426,442,443,457,458,459,462,463,465,467,469,470,471,474,476,478,479,480,481,482,487,489,490,491],"function":488,"long":[207,372,374,375,376,377,381,383,384,401,405,409,420,428],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[197,198],addforc:199,addit:[12,13],addtorqu:200,adiabat:6,adjust_dt:300,adp:366,airebo:367,alloi:387,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:201,arrai:6,aspher:[6,82,146,256,259,262,263,271],atc:[9,202],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,92,96,97,100,101,102,108,112,113,115,142,143,165,201,203,204,284,488],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:212,awpmd:[9,368],balanc:[41,213],barostat:6,basal:67,beck:369,berendsen:[282,313],between:6,binary2txt:13,bodi:[6,8,42,68,264,370],bond:[8,13,69,214,215,216,291],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:371,born:[372,383],boundari:[7,57],box:[6,58,217],brownian:373,buck:[374,375,383],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,173,376,409],chunk:[6,66,71,75,90,94,105,107,116,147,162,164,205],citat:7,class2:[21,43,174,336,377],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[327,379,454],colvar:[9,13,218],com:[74,75,148],comb3:380,comb:[287,380],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,488],compute_modifi:103,condit:7,conduct:[6,318],constant:6,constraint:7,contact:76,contact_radiu:122,coord:77,core:6,correl:[206,207],cosin:[23,24,25,26,27,28,176],cossq:338,coul:[372,374,375,376,377,381,382,383,394,401,405,409,420,428],coupl:6,creat:215,create_atom:167,create_bond:168,create_box:169,createatom:13,creation:7,csld:314,csvr:314,cubic:403,cuda:[9,14,111,114,145,154,199,212,226,229,233,254,261,297,298,313,315,326,372,374,376,377,387,393,394,401,402,404,407,418,444,446],custom:8,cut:[49,368,374,377,381,384,389,391,401,402,409,416,420],cvff:339,damag:[78,123],data2xmovi:13,data:6,databas:13,deby:[381,401],dec:0,deform:[150,151,219],delete_atom:170,delete_bond:171,delta:24,deposit:220,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],diagnost:7,diel:382,dielectr:172,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:175,dihedral_styl:[2,173,174,176,177,178,179,180,181,182,183,184,185,186,187],dilat:80,dimens:188,dipol:[6,29,384],direct:223,discuss:6,disp:6,displac:[81,86],displace_atom:189,distribut:[7,12],document:0,dpd:385,drag:221,dreid:[6,395],drude:[6,9,152,222,223,239],dsf:[381,401],dsmc:386,dump:[6,8,190,191,192,194],dump_modifi:193,dynam:286,eam:[13,387],echo:195,edip:388,eff:[9,13,97,98,151,153,158,240,255,265,273,316,389],efield:225,eim:390,elast:6,emac:13,enforce2d:226,ensembl:7,erot:[82,83,84,85],error:3,evapor:227,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],exp:[27,176],expand:[46,404],extend:[8,11],extern:228,fcc:276,featur:[7,8,488],fene:[45,46],fep:[9,13,87,198],field:[6,7],file:6,finit:6,fix:[2,6,8,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,488],fix_modifi:[197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,25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442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],rho:128,rhosum:439,rigid:[6,83,99,244,295],ring:344,rotat:159,rule:2,run:[6,11,12,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,470],run_styl:471,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,428],self:309,serial:11,set:[6,472],setforc:297,setvel:304,shake:298,share:[11,12],shell:[6,473],shield:286,shift:[26,27,48,49,176],simpl:31,simul:6,size:6,slater:286,slice:121,sllod:[272,273],small:295,smd:[9,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,299,300,301,302,303,304,306,429,430,431,432],smooth:[407,408],smtbq:[9,433],sna:142,snad:142,snap:434,snapshot:6,snav:142,soft:[409,435],solver:2,sourc:7,spatial:[209,210],spc:6,speci:292,special:[7,417,488],special_bond:474,sph:[9,436,437,438,439,440,441],sphere:[84,85,160,210,244,257,260,269,274],spheric:6,spline:[413,414],spring:[307,308,309,320],squar:28,srd:[310,332],srp:442,standard:9,start:[12,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332],state:312,stationari:248,stop:[197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332],store:[311,312],strategi:1,streitz:381,stress:[143,144],structur:2,style:[1,2,6,8],submit:8,suffix:475,summari:6,swap:[203,216],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492],system:6,tabl:[0,6,38,56,187,445,446],tad:476,taitwat:[440,441],talli:144,temp:[145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,313,314,315,316],temper:477,temperatur:6,tersoff:[446,447,448],test:11,tfmc:317,thermal:[6,318],thermo:[6,478],thermo_modifi:479,thermo_styl:480,thermodynam:[6,8],thermostat:6,thole:449,time:[6,211],timer:481,timestep:482,tip3p:6,tip4p:[6,381,401,405,409],tip:12,tlsph:430,tlsph_defgrad:129,tlsph_dt:130,tlsph_num_neigh:131,tlsph_shape:132,tlsph_strain:133,tlsph_strain_rat:134,tlsph_stress:135,tmd:321,tool:[12,13],torqu:162,transform:223,tri:[270,450],tri_surfac:431,triangle_mesh_vertic:136,triclin:6,tstat:385,ttm:322,tune:323,type:7,ulsph:432,ulsph_num_neigh:137,ulsph_strain:138,ulsph_strain_r:139,ulsph_stress:140,umbrella:346,uncomput:484,undump:485,unfix:486,unit:487,user:[9,12,14,16,18],vacf:163,valu:[6,488],variabl:[6,8,488],variou:1,vashishta:451,vcm:164,vector:[6,324,488],veloc:489,version:[0,5,12],via:12,vim:13,viscos:[6,325],viscou:[245,326],visual:6,vol:141,voronoi:[9,165],vtk:296,wall:[6,327,328,329,330,331,332],wall_surfac:306,warn:3,water:6,weight:208,what:[7,12],wolf:[372,381],wrapper:11,write:6,write_data:490,write_dump:491,write_restart:492,xmgrace:13,xmovi:13,xrd:166,xtc:9,yukawa:[453,454],zbl:[448,455]}}) 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