diff --git a/doc/Section_errors.html b/doc/Section_errors.html
index 7d82a3aded..5fe3bc734e 100644
--- a/doc/Section_errors.html
+++ b/doc/Section_errors.html
@@ -296,6 +296,10 @@ setting.
All angle coeffs are not set
All angle coefficients must be set in the data file or by the
angle_coeff command before running a simulation.
+All atom IDs = 0 but atom_modify id = yes
+Self-explanatory.
+All atoms of a swapped type must have same charge.
+Self-explanatory.
All atoms of a swapped type must have the same charge.
Self-explanatory.
All bond coeffs are not set
@@ -398,16 +402,12 @@ must be of type m (shrink/minimum).
Self-explanatory.
Assigning line parameters to non-line atom
Self-explanatory.
+Assigning quat to non-body atom
+Self-explanatory.
Assigning tri parameters to non-tri atom
Self-explanatory.
-Atom ID is negative
+At least one atom of each swapped type must be present to define charges.
Self-explanatory.
-Atom ID is too big
-The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
-setting in your Makefile. See Section_start 2.2 of the manual for
-more details.
-Atom ID is zero
-Either all atoms IDs must be zero or none of them.
Atom IDs must be consecutive for velocity create loop all
Self-explanatory.
Atom IDs must be used for molecular systems
@@ -439,6 +439,8 @@ command or turn off sorting.
The defined molecule(s) does not specify atom types.
Atom style was redefined after using fix property/atom
This is not allowed.
+Atom type must be zero in fix gcmc mol command
+Self-explanatory.
Atom vector in equal-style variable formula
Atom vectors generate one value per atom which is not allowed
in an equal-style variable.
@@ -644,12 +646,16 @@ See the region prism command for details.
Self-explanatory. See doc page discussion of command-line switches.
Can only use -pscreen with multiple partitions
Self-explanatory. See doc page discussion of command-line switches.
+Can only use Kokkos supported regions with Kokkos package
+Self-explanatory.
Can only use NEB with 1-processor replicas
This is current restriction for NEB as implemented in LAMMPS.
Can only use TAD with 1-processor replicas for NEB
This is current restriction for NEB as implemented in LAMMPS.
Cannot (yet) do analytic differentiation with pppm/gpu
This is a current restriction of this command.
+Cannot (yet) request ghost atoms with Kokkos half neighbor list
+This feature is not yet supported.
Cannot (yet) use ‘electron’ units with dipoles
This feature is not yet supported.
Cannot (yet) use Ewald with triclinic box and slab correction
@@ -672,6 +678,12 @@ See the region prism command for details.
This feature is not yet supported.
Cannot (yet) use molecular templates with Kokkos
Self-explanatory.
+Cannot (yet) use respa with Kokkos
+Self-explanatory.
+Cannot (yet) use rigid bodies with fix deform and Kokkos
+Self-explanatory.
+Cannot (yet) use rigid bodies with fix nh and Kokkos
+Self-explanatory.
Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)
Single precision cannot be used with MSM.
Cannot add atoms to fix move variable
@@ -755,8 +767,6 @@ will not be a correct amount of per-atom info.
Self-explanatory.
Cannot delete_atoms bond yes for non-molecular systems
Self-explanatory.
-Cannot delete_atoms mol yes for non-molecular systems
-Self-explanatory.
Cannot displace_atoms after reading restart file with per-atom info
This is because the restart file info cannot be migrated with the
atoms. You can get around this by performing a 0-timestep run which
@@ -836,6 +846,9 @@ and name are correct.
Cannot open Tersoff potential file %s
The specified potential file cannot be opened. Check that the path
and name are correct.
+Cannot open Vashishta potential file %s
+The specified Vashishta potential file cannot be opened. Check that the path
+and name are correct.
Cannot open balance output file
Self-explanatory.
Cannot open coul/streitz potential file %s
@@ -850,8 +863,7 @@ correct.
Using a “*” in the name of the restart file will open the current
directory to search for matching file names.
Cannot open dump file
-The output file for the dump command cannot be opened. Check that the
-path and name are correct.
+Self-explanatory.
Cannot open dump file %s
The output file for the dump command cannot be opened. Check that the
path and name are correct.
@@ -936,6 +948,9 @@ and name are correct.
Cannot open pair_write file
The specified output file for pair energies and forces cannot be
opened. Check that the path and name are correct.
+Cannot open polymorphic potential file %s
+The specified polymorphic potential file cannot be opened. Check that
+the path and name are correct.
Cannot open print file %s
Self-explanatory.
Cannot open processors output file
@@ -952,6 +967,8 @@ file.
The screen file specified as a command-line argument cannot be
opened. Check that the directory you are running in allows for files
to be created.
+Cannot open temporary file for world counter.
+Self-explanatory.
Cannot open universe log file
For a multi-partition run, the master log file cannot be opened.
Check that the directory you are running in allows for files to be
@@ -963,11 +980,8 @@ created.
Cannot read from restart file - MPI error: %s
This error was generated by MPI when reading/writing an MPI-IO restart
file.
-Cannot read_data add and merge
-These options are not yet supported.
-Cannot read_data after simulation box is defined
-The read_data command cannot be used after a read_data,
-read_restart, or create_box command.
+Cannot read_data without add keyword after simulation box is defined
+Self-explanatory.
Cannot read_restart after simulation box is defined
The read_restart command cannot be used after a read_data,
read_restart, or create_box command.
@@ -1000,12 +1014,20 @@ they are static settings in the molecule template files.
In the rRESPA integrator, you must compute pairwise potentials either
all together (pair), or in pieces (inner/middle/outer). You can’t do
both.
+Cannot set cutoff/multi before simulation box is defined
+Self-explanatory.
+Cannot set dpd/theta for this atom style
+Self-explanatory.
Cannot set dump_modify flush for dump xtc
Self-explanatory.
Cannot set mass for this atom style
This atom style does not support mass settings for each atom type.
Instead they are defined on a per-atom basis in the data file.
-Cannot set meso_rho for this atom style
+Cannot set meso/cv for this atom style
+Self-explanatory.
+Cannot set meso/e for this atom style
+Self-explanatory.
+Cannot set meso/rho for this atom style
Self-explanatory.
Cannot set non-zero image flag for non-periodic dimension
Self-explanatory.
@@ -1013,12 +1035,22 @@ Instead they are defined on a per-atom basis in the data file.
Self-explanatory.
Cannot set quaternion for atom that has none
Self-explanatory.
+Cannot set quaternion with xy components for 2d system
+Self-explanatory.
+Cannot set respa hybrid and any of pair/inner/middle/outer
+In the rRESPA integrator, you must compute pairwise potentials either
+all together (pair), with different cutoff regions (inner/middle/outer),
+or per hybrid sub-style (hybrid). You cannot mix those.
Cannot set respa middle without inner/outer
In the rRESPA integrator, you must define both a inner and outer
setting in order to use a middle setting.
Cannot set restart file size - MPI error: %s
This error was generated by MPI when reading/writing an MPI-IO restart
file.
+Cannot set smd/contact/radius for this atom style
+Self-explanatory.
+Cannot set smd/mass/density for this atom style
+Self-explanatory.
Cannot set temperature for fix rigid/nph
The temp keyword cannot be specified.
Cannot set theta for atom that is not a line
@@ -1055,7 +1087,7 @@ solver/pair style.
You cannot use both the GPU and USER-CUDA packages
together. Use one or the other.
Cannot use Kokkos pair style with rRESPA inner/middle
-rRESPA inner/middle options are not yet supported by Kokkos.
+Self-explanatory.
Cannot use NEB unless atom map exists
Use the atom_modify command to create an atom map.
Cannot use NEB with a single replica
@@ -1098,22 +1130,60 @@ type p (periodic).
Self-explanatory. See the atom_modify command to create a map.
Cannot use both com and bias with compute temp/chunk
Self-explanatory.
+Cannot use chosen neighbor list style with buck/coul/cut/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with buck/coul/long/kk
+Self-explanatory.
Cannot use chosen neighbor list style with buck/kk
That style is not supported by Kokkos.
Cannot use chosen neighbor list style with coul/cut/kk
That style is not supported by Kokkos.
+Cannot use chosen neighbor list style with coul/debye/kk
+Self-explanatory.
Cannot use chosen neighbor list style with coul/dsf/kk
That style is not supported by Kokkos.
Cannot use chosen neighbor list style with coul/wolf/kk
That style is not supported by Kokkos.
+Cannot use chosen neighbor list style with lj/charmm/coul/charmm/implicit/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with lj/charmm/coul/charmm/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with lj/charmm/coul/long/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with lj/class2/coul/cut/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with lj/class2/coul/long/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with lj/class2/kk
+Self-explanatory.
Cannot use chosen neighbor list style with lj/cut/coul/cut/kk
That style is not supported by Kokkos.
+Cannot use chosen neighbor list style with lj/cut/coul/debye/kk
+Self-explanatory.
Cannot use chosen neighbor list style with lj/cut/coul/long/kk
That style is not supported by Kokkos.
Cannot use chosen neighbor list style with lj/cut/kk
That style is not supported by Kokkos.
+Cannot use chosen neighbor list style with lj/expand/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with lj/gromacs/coul/gromacs/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with lj/gromacs/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with lj/sdk/kk
+That style is not supported by Kokkos.
Cannot use chosen neighbor list style with pair eam/kk
That style is not supported by Kokkos.
+Cannot use chosen neighbor list style with pair eam/kk/alloy
+Self-explanatory.
+Cannot use chosen neighbor list style with pair eam/kk/fs
+Self-explanatory.
+Cannot use chosen neighbor list style with pair sw/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with tersoff/kk
+Self-explanatory.
+Cannot use chosen neighbor list style with tersoff/zbl/kk
+Self-explanatory.
Cannot use compute chunk/atom bin z for 2d model
Self-explanatory.
Cannot use compute cluster/atom unless atoms have IDs
@@ -1317,10 +1387,16 @@ neighbor cutoff. Use the “nsq” style instead of “bin” s
Self-explanatory.
Cannot use newton pair with dipole/cut/gpu pair style
Self-explanatory.
+Cannot use newton pair with dipole/sf/gpu pair style
+Self-explanatory.
Cannot use newton pair with dpd/gpu pair style
Self-explanatory.
Cannot use newton pair with dpd/tstat/gpu pair style
Self-explanatory.
+Cannot use newton pair with eam/alloy/gpu pair style
+Self-explanatory.
+Cannot use newton pair with eam/fs/gpu pair style
+Self-explanatory.
Cannot use newton pair with eam/gpu pair style
Self-explanatory.
Cannot use newton pair with gauss/gpu pair style
@@ -1333,6 +1409,8 @@ neighbor cutoff. Use the “nsq” style instead of “bin” s
Self-explanatory.
Cannot use newton pair with lj/class2/gpu pair style
Self-explanatory.
+Cannot use newton pair with lj/cubic/gpu pair style
+Self-explanatory.
Cannot use newton pair with lj/cut/coul/cut/gpu pair style
Self-explanatory.
Cannot use newton pair with lj/cut/coul/debye/gpu pair style
@@ -1349,6 +1427,10 @@ neighbor cutoff. Use the “nsq” style instead of “bin” s
Self-explanatory.
Cannot use newton pair with lj/gromacs/gpu pair style
Self-explanatory.
+Cannot use newton pair with lj/sdk/coul/long/gpu pair style
+Self-explanatory.
+Cannot use newton pair with lj/sdk/gpu pair style
+Self-explanatory.
Cannot use newton pair with lj96/cut/gpu pair style
Self-explanatory.
Cannot use newton pair with mie/cut/gpu pair style
@@ -1365,11 +1447,11 @@ neighbor cutoff. Use the “nsq” style instead of “bin” s
Self-explanatory.
Cannot use newton pair with yukawa/gpu pair style
Self-explanatory.
+Cannot use newton pair with zbl/gpu pair style
+Self-explantory.
Cannot use non-zero forces in an energy minimization
Fix setforce cannot be used in this manner. Use fix addforce
instead.
-Cannot use non-zero z offset in read_data for 2d simulation
-The offset option is not yet supported.
Cannot use nonperiodic boundares with fix ttm
This fix requires a fully periodic simulation box.
Cannot use nonperiodic boundaries with Ewald
@@ -1400,6 +1482,14 @@ slab with a non-periodic z dimension.
See the command-line -partition switch.
Cannot use ramp in variable formula between runs
This is because the ramp() function is time dependent.
+Cannot use read_data add before simulation box is defined
+Self-explanatory.
+Cannot use read_data extra with add flag
+Self-explanatory.
+Cannot use read_data offset without add flag
+Self-explanatory.
+Cannot use read_data shift without add flag
+Self-explanatory.
Cannot use region INF or EDGE when box does not exist
Regions that extend to the box boundaries can only be used after the
create_box command has been used.
@@ -1445,10 +1535,16 @@ file.
Self-explanatory.
Cannot yet use comm_style tiled with triclinic box
Self-explanatory.
+Cannot yet use compute tally with Kokkos
+This feature is not yet supported.
Cannot yet use fix bond/break with this improper style
This is a current restriction in LAMMPS.
Cannot yet use fix bond/create with this improper style
This is a current restriction in LAMMPS.
+Cannot yet use minimize with Kokkos
+This feature is not yet supported.
+Cannot yet use pair hybrid with Kokkos
+This feature is not yet supported.
Cannot zero Langevin force of 0 atoms
The group has zero atoms, so you cannot request its force
be zeroed.
@@ -1500,6 +1596,8 @@ command or if your box dimensions grow during a run. You can set the
cutoff explicitly via the comm_modify cutoff command.
Compute %s does not allow use of dynamic group
Dynamic groups have not yet been enabled for this compute.
+Compute ID for compute chunk /atom does not exist
+Self-explanatory.
Compute ID for compute chunk/atom does not exist
Self-explanatory.
Compute ID for compute reduce does not exist
@@ -1535,6 +1633,10 @@ cutoff explicitly via the comm_modify cutoff command.
Compute centro/atom requires a pair style be defined
This is because the computation of the centro-symmetry values
uses a pairwise neighbor list.
+Compute chunk/atom bin/cylinder radius is too large for periodic box
+Radius cannot be bigger than 1/2 of a non-axis periodic dimention.
+Compute chunk/atom bin/sphere radius is too large for periodic box
+Radius cannot be bigger than 1/2 of any periodic dimention.
Compute chunk/atom compute array is accessed out-of-range
The index for the array is out of bounds.
Compute chunk/atom compute does not calculate a per-atom array
@@ -1543,6 +1645,8 @@ uses a pairwise neighbor list.
Self-explanatory.
Compute chunk/atom compute does not calculate per-atom values
Self-explanatory.
+Compute chunk/atom cylinder axis must be z for 2d
+Self-explanatory.
Compute chunk/atom fix array is accessed out-of-range
the index for the array is out of bounds.
Compute chunk/atom fix does not calculate a per-atom array
@@ -1558,6 +1662,8 @@ uses a pairwise neighbor list.
chunks may change.
Compute chunk/atom molecule for non-molecular system
Self-explanatory.
+Compute chunk/atom sphere z origin must be 0.0 for 2d
+Self-explanatory.
Compute chunk/atom stores no IDs for compute property/chunk
It will only store IDs if its compress option is enabled.
Compute chunk/atom stores no coord1 for compute property/chunk
@@ -1625,6 +1731,10 @@ developers.
Self-explanatory.
Compute heat/flux compute ID does not compute stress/atom
Self-explanatory.
+Compute hexorder/atom cutoff is longer than pairwise cutoff
+Cannot compute order parameter beyond cutoff.
+Compute hexorder/atom requires a pair style be defined
+Self-explantory.
Compute improper/local used when impropers are not allowed
The atom style does not support impropers.
Compute inertia/chunk does not use chunk/atom compute
@@ -1641,8 +1751,14 @@ nchunk to be static.
Self-explanatory.
Compute nvt/nph/npt asphere requires atom style ellipsoid
Self-explanatory.
+Compute nvt/nph/npt body requires atom style body
+Self-explanatory.
Compute omega/chunk does not use chunk/atom compute
The style of the specified compute is not chunk/atom.
+Compute orientorder/atom cutoff is longer than pairwise cutoff
+Cannot compute order parameter beyond cutoff.
+Compute orientorder/atom requires a pair style be defined
+Self-explantory.
Compute pair must use group all
Pair styles accumlate energy on all atoms.
Compute pe must use group all
@@ -1745,6 +1861,10 @@ togther. E.g. bond and angle quantities cannot be mixed.
Self-explanatory.
Compute temp/asphere requires extended particles
This compute cannot be used with point paritlces.
+Compute temp/body requires atom style body
+Self-explanatory.
+Compute temp/body requires bodies
+This compute can only be applied to body particles.
Compute temp/chunk does not use chunk/atom compute
The style of the specified compute is not chunk/atom.
Compute temp/cs requires ghost atoms store velocity
@@ -1859,6 +1979,8 @@ define a callable function with the required name.
Self-explanatory.
Could not find compute msd fix ID
Self-explanatory.
+Could not find compute msd/chunk fix ID
+The compute creates an internal fix, which has been deleted.
Could not find compute pressure temperature ID
The compute ID for calculating temperature does not exist.
Could not find compute stress/atom temperature ID
@@ -1930,8 +2052,13 @@ a secondary fix that fix adapt created internally.
Self-explanatory.
Could not find group delete group ID
Self-explanatory.
+Could not find pair fix ID
+A fix is created internally by the pair style to store shear
+history information. You cannot delete it.
Could not find set group ID
Group ID specified in set command does not exist.
+Could not find specified fix gcmc group ID
+Self-explanatory.
Could not find thermo compute ID
Compute ID specified in thermo_style command does not exist.
Could not find thermo custom compute ID
@@ -2051,6 +2178,8 @@ the bodies in a ring (or cycle).
read_restart, or create_box command.
Delete_atoms cutoff > max neighbor cutoff
Can only delete atoms in atom pairs that will be in neighbor list.
+Delete_atoms mol yes requires atom attribute molecule
+Cannot use this option with a non-molecular system.
Delete_atoms requires a pair style be defined
This is because atom deletion within a cutoff uses a pairwise
neighbor list.
@@ -2059,8 +2188,6 @@ neighbor list.
read_restart, or create_box command.
Delete_bonds command with no atoms existing
No atoms are yet defined so the delete_bonds command cannot be used.
-Delta_mu not allowed when not using semi-grand in fix atom/swap command
-Self-explanatory.
Deposition region extends outside simulation box
Self-explanatory.
Did not assign all atoms correctly
@@ -2171,6 +2298,8 @@ used. Most likely, one or more atoms have been blown out of the
simulation box to a great distance.
Double precision is not supported on this accelerator
Self-explanatory
+Dump atom/gz only writes compressed files
+The dump atom/gz output file name must have a .gz suffix.
Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu
Self-explanatory.
Dump cfg arguments must start with ‘mass type xs ys zs’ or ‘mass type xsu ysu zsu’
@@ -2178,6 +2307,8 @@ simulation box to a great distance.
page for more details.
Dump cfg requires one snapshot per file
Use the wildcard “*” character in the filename.
+Dump cfg/gz only writes compressed files
+The dump cfg/gz output file name must have a .gz suffix.
Dump custom and fix not computed at compatible times
The fix must produce per-atom quantities on timesteps that dump custom
needs them.
@@ -2200,6 +2331,8 @@ needs them.
Dump custom variable is not atom-style variable
Only atom-style variables generate per-atom quantities, needed for
dump output.
+Dump custom/gz only writes compressed files
+The dump custom/gz output file name must have a .gz suffix.
Dump dcd of non-matching # of atoms
Every snapshot written by dump dcd must contain the same # of atoms.
Dump dcd requires sorting by atom ID
@@ -2213,14 +2346,20 @@ creates one large file for all processors.
Self-explanatory.
Dump file is incorrectly formatted
Self-explanatory.
+Dump image body yes requires atom style body
+Self-explanatory.
Dump image bond not allowed with no bond types
Self-explanatory.
Dump image cannot perform sorting
Self-explanatory.
+Dump image line requires atom style line
+Self-explanatory.
Dump image persp option is not yet supported
Self-explanatory.
Dump image requires one snapshot per file
Use a “*” in the filename.
+Dump image tri requires atom style tri
+Self-explanatory.
Dump local and fix not computed at compatible times
The fix must produce per-atom quantities on timesteps that dump local
needs them.
@@ -2274,6 +2413,8 @@ needs them.
Self-explanatory.
Dump xtc requires sorting by atom ID
Use the dump_modify sort command to enable this.
+Dump xyz/gz only writes compressed files
+The dump xyz/gz output file name must have a .gz suffix.
Dump_modify buffer yes not allowed for this style
Self-explanatory.
Dump_modify format string is too short
@@ -2284,6 +2425,8 @@ format string specifies.
Dumping an atom property that isn’t allocated
The chosen atom style does not define the per-atom quantity being
dumped.
+Duplicate atom IDs exist
+Self-explanatory.
Duplicate fields in read_dump command
Self-explanatory.
Duplicate particle in PeriDynamic bond - simulation box is too small
@@ -2291,6 +2434,8 @@ dumped.
the bond length.
Electronic temperature dropped below zero
Something has gone wrong with the fix ttm electron temperature model.
+Element not defined in potential file
+The specified element is not in the potential file.
Empty brackets in variable
There is no variable syntax that uses empty brackets. Check
the variable doc page.
@@ -2305,6 +2450,16 @@ variable doc page for ideas on how to make this work.
Error in vdw spline: inner radius > outer radius
A pre-tabulated spline is invalid. Likely a problem with the
potential parameters.
+Error writing averaged chunk data
+Something in the output to the file triggered an error.
+Error writing file header
+Something in the output to the file triggered an error.
+Error writing out correlation data
+Something in the output to the file triggered an error.
+Error writing out histogram data
+Something in the output to the file triggered an error.
+Error writing out time averaged data
+Something in the output to the file triggered an error.
Failed to allocate %ld bytes for array %s
Your LAMMPS simulation has run out of memory. You need to run a
smaller simulation or on more processors.
@@ -2493,6 +2648,8 @@ to a larger value, and re-compile the code.
Fix ave/histo inputs are not all global, peratom, or local
All inputs in a single fix ave/histo command must be of the
same style.
+Fix ave/histo/weight value and weight vector lengths do not match
+Self-explanatory.
Fix ave/spatial compute does not calculate a per-atom array
Self-explanatory.
Fix ave/spatial compute does not calculate a per-atom vector
@@ -2654,6 +2811,8 @@ requesting a value on a non-allowed timestep.
The atom style defined does not have this attribute.
Fix gcmc and fix shake not using same molecule template ID
Self-explanatory.
+Fix gcmc atom has charge, but atom style does not
+Self-explanatory.
Fix gcmc cannot exchange individual atoms belonging to a molecule
This is an error since you should not delete only one atom of a
molecule. The user has specified atomic (non-molecular) gas
@@ -2664,6 +2823,8 @@ exchanges, but an atom belonging to a molecule could be deleted.
Should not choose the gcmc molecule feature if no molecules are being
simulated. The general molecule flag is off, but gcmc’s molecule flag
is on.
+Fix gcmc molecule has charges, but atom style does not
+Self-explanatory.
Fix gcmc molecule must have atom types
The defined molecule does not specify atom types.
Fix gcmc molecule must have coordinates
@@ -2671,6 +2832,8 @@ is on.
Fix gcmc molecule template ID must be same as atom_style template ID
When using atom_style template, you cannot insert molecules that are
not in that template.
+Fix gcmc put atom outside box
+This should not normally happen. Contact the developers.
Fix gcmc ran out of available atom IDs
See the setting for tagint in the src/lmptype.h file.
Fix gcmc ran out of available molecule IDs
@@ -2764,7 +2927,7 @@ on a short timescale.
Self-explanatory.
Fix nve/line requires line particles
Self-explanatory.
-Fix nve/sphere requires atom attribute mu
+Fix nve/sphere dipole requires atom attribute mu
An atom style with this attribute is needed.
Fix nve/sphere requires atom style sphere
Self-explanatory.
@@ -2779,6 +2942,8 @@ on a short timescale.
Fix nvt/nph/npt asphere requires extended particles
The shape setting for a particle in the fix group has shape = 0.0,
which means it is a point particle.
+Fix nvt/nph/npt body requires bodies
+Self-explanatory.
Fix nvt/nph/npt sphere requires atom style sphere
Self-explanatory.
Fix nvt/npt/nph damping parameters must be > 0.0
@@ -2848,6 +3013,10 @@ such a region with the fix pour command.
Self-explanatory.
Fix qeq/dynamic requires atom attribute q
Self-explanatory.
+Fix qeq/fire group has no atoms
+Self-explanatory.
+Fix qeq/fire requires atom attribute q
+Self-explanatory.
Fix qeq/point group has no atoms
Self-explanatory.
Fix qeq/point has insufficient QEq matrix size
@@ -2990,8 +3159,10 @@ fix store/state.
Self-explanatory.
Fix temp/berendsen variable returned negative temperature
Self-explanatory.
-Fix temp/csvr is not compatible with fix shake
-These two commands cannot currently be used toghether.
+Fix temp/csld is not compatible with fix rattle or fix shake
+These two commands cannot currently be used together with fix temp/csld.
+Fix temp/csld variable returned negative temperature
+Self-explanatory.
Fix temp/csvr variable returned negative temperature
Self-explanatory.
Fix temp/rescale variable returned negative temperature
@@ -3091,6 +3262,8 @@ non-hydrostatic pressure control can not be used in this case.
the host. See the package command.
GPU split param must be positive for hybrid pair styles
See the package gpu command.
+GPUs are requested but Kokkos has not been compiled for CUDA
+Recompile Kokkos with CUDA support to use GPUs.
Ghost velocity forward comm not yet implemented with Kokkos
This is a current restriction.
Gmask function in equal-style variable formula
@@ -3139,6 +3312,9 @@ invalid.
Illegal Tersoff parameter
One or more of the coefficients defined in the potential file is
invalid.
+Illegal Vashishta parameter
+One or more of the coefficients defined in the potential file is
+invalid.
Illegal compute voronoi/atom command (occupation and (surface or edges))
Self-explanatory.
Illegal coul/streitz parameter
@@ -3166,8 +3342,18 @@ invalid.
There must be at least 2 table entries.
Illegal number of pair table entries
There must be at least 2 table entries.
+Illegal or unset periodicity in restart
+This error should not normally occur unless the restart file is invalid.
+Illegal range increment value
+The increment must be >= 1.
Illegal simulation box
The lower bound of the simulation box is greater than the upper bound.
+Illegal size double vector read requested
+This error should not normally occur unless the restart file is invalid.
+Illegal size integer vector read requested
+This error should not normally occur unless the restart file is invalid.
+Illegal size string or corrupt restart
+This error should not normally occur unless the restart file is invalid.
Imageint setting in lmptype.h is invalid
Imageint must be as large or larger than smallint.
Imageint setting in lmptype.h is not compatible
@@ -3295,6 +3481,8 @@ bonus data must be formatted for certain atom styles.
Format of file read by fix tmd command is incorrect.
Incorrect format in Tersoff potential file
Incorrect number of words per line in the potential file.
+Incorrect format in Vashishta potential file
+Incorrect number of words per line in the potential file.
Incorrect format in coul/streitz potential file
Incorrect number of words per line in the potential file.
Incorrect format in nb3b/harmonic potential file
@@ -3303,12 +3491,16 @@ bonus data must be formatted for certain atom styles.
See doc page for body style.
Incorrect multiplicity arg for dihedral coefficients
Self-explanatory. Check the input script or data file.
+Incorrect number of elements in potential file
+Self-explanatory.
Incorrect rigid body format in fix rigid file
The number of fields per line is not what expected.
Incorrect rigid body format in fix rigid/small file
The number of fields per line is not what expected.
Incorrect sign arg for dihedral coefficients
Self-explanatory. Check the input script or data file.
+Incorrect table format check for element types
+Self-explanatory.
Incorrect velocity format in data file
Each atom style defines a format for the Velocity section
of the data file. The read-in lines do not match.
@@ -3345,16 +3537,38 @@ package
This error should not occur. Contact the developers.
Invalid -reorder N value
Self-explanatory.
+Invalid Angles section in molecule file
+Self-explanatory.
+Invalid Bonds section in molecule file
+Self-explanatory.
Invalid Boolean syntax in if command
Self-explanatory.
+Invalid Charges section in molecule file
+Self-explanatory.
+Invalid Coords section in molecule file
+Self-explanatory.
+Invalid Diameters section in molecule file
+Self-explanatory.
+Invalid Dihedrals section in molecule file
+Self-explanatory.
+Invalid Impropers section in molecule file
+Self-explanatory.
Invalid Kokkos command-line args
Self-explanatory. See Section 2.7 of the manual for details.
Invalid LAMMPS restart file
The file does not appear to be a LAMMPS restart file since
it doesn’t contain the correct magic string at the beginning.
+Invalid Masses section in molecule file
+Self-explanatory.
Invalid REAX atom type
There is a mis-match between LAMMPS atom types and the elements
listed in the ReaxFF force field file.
+Invalid Special Bond Counts section in molecule file
+Self-explanatory.
+Invalid Types section in molecule file
+Self-explanatory.
+Invalid angle count in molecule file
+Self-explanatory.
Invalid angle table length
Length must be 2 or greater.
Invalid angle type in Angles section of data file
@@ -3436,8 +3650,6 @@ for each atom must be between 1 to N, where N is the number of atom
types.
Invalid atom type in fix gcmc command
The atom type specified in the gcmc command does not exist.
-Invalid atom type in fix gcmc mol command
-Self-explanatory.
Invalid atom type in fix pour command
Self-explanatory.
Invalid atom type in fix pour mol command
@@ -3479,6 +3691,8 @@ is the number of atom types.
The lo/hi values are inconsistent.
Invalid body nparticle command
Arguments in atom-style command are not correct.
+Invalid bond count in molecule file
+Self-explanatory.
Invalid bond table length
Length must be 2 or greater.
Invalid bond type in Bonds section of data file
@@ -3566,6 +3780,8 @@ GPU.
Density must be > 0.0.
Invalid diameter in set command
Self-explanatory.
+Invalid dihedral count in molecule file
+Self-explanatory.
Invalid dihedral type in Dihedrals section of data file
Dihedral type must be positive integer and within range of specified
dihedral types.
@@ -3647,9 +3863,6 @@ specified.
The format of this section of the file is not correct.
Invalid flag in type arrays section of restart file
Unrecognized entry in restart file.
-Invalid format in Bodies section of data file
-The specified number of integer or floating point values does not
-appear.
Invalid frequency in temper command
Nevery must be > 0.
Invalid group ID in neigh_modify command
@@ -3662,6 +3875,8 @@ appear.
Up vector cannot be (0,0,0).
Invalid immediate variable
Syntax of immediate value is incorrect.
+Invalid improper count in molecule file
+Self-explanatory.
Invalid improper type in Impropers section of data file
Improper type must be positive integer and within range of specified
improper types.
@@ -3671,6 +3886,12 @@ improper types.
Only indices 1,2,3 can be used for non-body particles.
Invalid index in compute body/local command
Self-explanatory.
+Invalid is_active() function in variable formula
+Self-explanatory.
+Invalid is_available() function in variable formula
+Self-explanatory.
+Invalid is_defined() function in variable formula
+Self-explanatory.
Invalid keyword in angle table parameters
Self-explanatory.
Invalid keyword in bond table parameters
@@ -3885,6 +4106,8 @@ simulation boxes.
long-range Coulombic or dispersion components be used.
Keyword %s in MEAM parameter file not recognized
Self-explanatory.
+Kokkos has been compiled for CUDA but no GPUs are requested
+One or more GPUs must be used when Kokkos is compiled for CUDA.
Kspace style does not support compute group/group
Self-explanatory.
Kspace style pppm/disp/tip4p requires newton on
@@ -3977,20 +4200,28 @@ formula.
Molecule IDs too large for compute chunk/atom
The IDs must not be larger than can be stored in a 32-bit integer
since chunk IDs are 32-bit integers.
+Molecule auto special bond generation overflow
+Counts exceed maxspecial setting for other atoms in system.
Molecule file has angles but no nangles setting
Self-explanatory.
-Molecule file has bonds but no nbonds setting
+Molecule file has body params but no setting for them
Self-explanatory.
-Molecule file has bonds but no special flags
+Molecule file has bonds but no nbonds setting
Self-explanatory.
Molecule file has dihedrals but no ndihedrals setting
Self-explanatory.
Molecule file has impropers but no nimpropers setting
Self-explanatory.
+Molecule file has no Body Doubles section
+Self-explanatory.
+Molecule file has no Body Integers section
+Self-explanatory.
Molecule file has special flags but no bonds
Self-explanatory.
Molecule file needs both Special Bond sections
Self-explanatory.
+Molecule file requires atom style body
+Self-explanatory.
Molecule file shake flags not before shake atoms
The order of the two sections is important.
Molecule file shake flags not before shake bonds
@@ -4003,6 +4234,10 @@ since chunk IDs are 32-bit integers.
Self-explanatory.
Molecule file z coord must be 0.0 for 2d
Self-explanatory.
+Molecule natoms must be 1 for body particle
+Self-explanatory.
+Molecule sizescale must be 1.0 for body particle
+Self-explanatory.
Molecule template ID for atom_style template does not exist
Self-explanatory.
Molecule template ID for create_atoms does not exist
@@ -4034,6 +4269,8 @@ values.
potentials access it.
More than one fix shake
Only one fix shake can be defined.
+Mu not allowed when not using semi-grand in fix atom/swap command
+Self-explanatory.
Must define angle_style before Angle Coeffs
Must use an angle_style command before reading a data file that
defines Angle Coeffs.
@@ -4129,6 +4366,8 @@ command for details on this setting.
Must use -in switch with multiple partitions
A multi-partition simulation cannot read the input script from stdin.
The -in command-line option must be used to specify a file.
+Must use Kokkos half/thread or full neighbor list with threads or GPUs
+Using Kokkos half-neighbor lists with threading is not allowed.
Must use a block or cylinder region with fix pour
Self-explanatory.
Must use a block region with fix pour for 2d simulations
@@ -4163,7 +4402,7 @@ variable E-field.
Self-explanatory.
NL ramp in wall/piston only implemented in zlo for now
The ramp keyword can only be used for piston applied to face zlo.
-Need ntypes-1 delta_mu values in fix atom/swap command
+Need nswaptypes mu values in fix atom/swap command
Self-explanatory.
Needed bonus data not in data file
Some atom styles require bonus data. See the read_data doc page for
@@ -4218,8 +4457,6 @@ OpenMP support.
Self-explanatory.
No angles allowed with this atom style
Self-explanatory.
-No atom count in molecule file
-Self-explanatory.
No atoms in data file
The header of the data file indicated that atoms would be included,
but they are not present.
@@ -4233,6 +4470,8 @@ but they are not present.
Self-explanatory.
No box information in dump. You have to use ‘box no’
Self-explanatory.
+No count or invalid atom count in molecule file
+The number of atoms must be specified.
No dihedral style is defined for compute dihedral/local
Self-explanatory.
No dihedrals allowed with this atom style
@@ -4279,6 +4518,10 @@ because this info if inferred from the molecule templates.
The fix specification did not end up defining any rigid bodies.
No triangles allowed with this atom style
Self-explanatory. Check data file.
+No values in fix ave/chunk command
+Self-explanatory.
+No values in fix ave/time command
+Self-explanatory.
Non digit character between brackets in variable
Self-explantory.
Non integer # of swaps in temper command
@@ -4286,8 +4529,10 @@ because this info if inferred from the molecule templates.
timesteps.
Non-numeric box dimensions - simulation unstable
The box size has apparently blown up.
-Not all atom IDs are 0
-Either all atoms IDs must be zero or none of them.
+Non-zero atom IDs with atom_modify id = no
+Self-explanatory.
+Non-zero read_data shift z value for 2d simulation
+Self-explanatory.
Nprocs not a multiple of N for -reorder
Self-explanatory.
Number of core atoms != number of shell atoms
@@ -4296,9 +4541,19 @@ timesteps.
A command with an argument that specifies an integer or range of
integers is using a value that is less than 1 or greater than the
maximum allowed limit.
+One or more Atom IDs is negative
+Atom IDs must be positive integers.
+One or more atom IDs is too big
+The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
+setting in your Makefile. See Section_start 2.2 of the manual for
+more details.
+One or more atom IDs is zero
+Either all atoms IDs must be zero or none of them.
One or more atoms belong to multiple rigid bodies
Two or more rigid bodies defined by the fix rigid command cannot
contain the same atom.
+One or more rigid bodies are a single particle
+Self-explanatory.
One or zero atoms in rigid body
Any rigid body defined by the fix rigid command must contain 2 or more
atoms.
@@ -4444,6 +4699,8 @@ rRESPA cutoffs.
The atom style defined does not have this attribute.
Pair dipole/long requires atom attributes q, mu, torque
The atom style defined does not have these attributes.
+Pair dipole/sf/gpu requires atom attributes q, mu, torque
+The atom style defined does not one or more of these attributes.
Pair distance < table inner cutoff
Two atoms are closer together than the pairwise table allows.
Pair distance > table outer cutoff
@@ -4461,13 +4718,15 @@ have these 3 coefficients set at least once.
Self-explanatory.
Pair gayberne/gpu requires atoms with same type have same shape
Self-explanatory.
-Pair granular requires atom style sphere
-Self-explanatory.
+Pair granular requires atom attributes radius, rmass
+The atom style defined does not have these attributes.
Pair granular requires ghost atoms store velocity
Use the comm_modify vel yes command to enable this.
Pair granular with shear history requires newton pair off
This is a current restriction of the implementation of pair
granular styles with history.
+Pair hybrid single calls do not support per sub-style special bond values
+Self-explanatory.
Pair hybrid sub-style does not support single call
You are attempting to invoke a single() call on a pair style
that doesn’t support it.
@@ -4571,6 +4830,11 @@ potential.
Pair style Tersoff requires newton pair on
See the newton command. This is a restriction to use the Tersoff
potential.
+Pair style Vashishta requires atom IDs
+This is a requirement to use the Vashishta potential.
+Pair style Vashishta requires newton pair on
+See the newton command. This is a restriction to use the Vashishta
+potential.
Pair style bop requires comm ghost cutoff at least 3x larger than %g
Use the communicate ghost command to set this. See the pair bop
doc page for more details.
@@ -4641,6 +4905,9 @@ cannot be tracked by the granular pair potential.
Self-explanatory.
Pair style hybrid cannot have none as an argument
Self-explanatory.
+Pair style is incompatible with KSpace style
+If a pair style with a long-range Coulombic component is selected,
+then a kspace style must also be used.
Pair style is incompatible with TIP4P KSpace style
The pair style does not have the requires TIP4P settings.
Pair style lj/charmm/coul/charmm requires atom attribute q
@@ -4696,6 +4963,8 @@ requires them to find O,H atoms with a water molecule.
Pair style lj/long/tip4p/long requires newton pair on
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors.
+Pair style lj/sdk/coul/long/gpu requires atom attribute q
+The atom style defined does not have this attribute.
Pair style nb3b/harmonic requires atom IDs
This is a requirement to use this potential.
Pair style nb3b/harmonic requires newton pair on
@@ -4706,6 +4975,11 @@ molecule adds forces to atoms owned by other processors.
The atom style defined does not have this attribute.
Pair style peri requires atom style peri
Self-explanatory.
+Pair style polymorphic requires atom IDs
+This is a requirement to use the polymorphic potential.
+Pair style polymorphic requires newton pair on
+See the newton command. This is a restriction to use the polymorphic
+potential.
Pair style reax requires atom IDs
This is a requirement to use the ReaxFF potential.
Pair style reax requires atom attribute q
@@ -4720,6 +4994,10 @@ molecule adds forces to atoms owned by other processors.
This is a requirement to use this potential.
Pair style sw/gpu requires newton pair off
See the newton command. This is a restriction to use this potential.
+Pair style tersoff/gpu requires atom IDs
+This is a requirement to use the tersoff/gpu potential.
+Pair style tersoff/gpu requires newton pair off
+See the newton command. This is a restriction to use this pair style.
Pair style tip4p/cut requires atom IDs
This is a requirement to use this potential.
Pair style tip4p/cut requires atom attribute q
@@ -4742,6 +5020,8 @@ long-range solver starts at that cutoff.
List of pair table parameters must include N setting.
Pair tersoff/zbl requires metal or real units
This is a current restriction of this pair potential.
+Pair tersoff/zbl/kk requires metal or real units
+This is a current restriction of this pair potential.
Pair tri/lj requires atom style tri
Self-explanatory.
Pair yukawa/colloid requires atom style sphere
@@ -4759,14 +5039,17 @@ long-range solver starts at that cutoff.
read_restart, or create_box command.
Pair_modify command before pair_style is defined
Self-explanatory.
+Pair_modify special setting for pair hybrid incompatible with global special_bonds setting
+Cannot override a setting of 0.0 or 1.0 or change a setting between
+0.0 and 1.0.
Pair_write command before pair_style is defined
Self-explanatory.
Particle on or inside fix wall surface
Particles must be “exterior” to the wall in order for energy/force to
be calculated.
-Particle on or inside surface of region used in fix wall/region
-Particles must be “exterior” to the region surface in order for
-energy/force to be calculated.
+Particle outside surface of region used in fix wall/region
+Particles must be inside the region for energy/force to be calculated.
+A particle outside the region generates an error.
Per-atom compute in equal-style variable formula
Equal-style variables cannot use per-atom quantities.
Per-atom energy was not tallied on needed timestep
@@ -4811,6 +5094,8 @@ exist.
Self-explanatory.
Pressure control can not be used with fix nvt/asphere
Self-explanatory.
+Pressure control can not be used with fix nvt/body
+Self-explanatory.
Pressure control can not be used with fix nvt/sllod
Self-explanatory.
Pressure control can not be used with fix nvt/sphere
@@ -4819,6 +5104,8 @@ exist.
Self-explanatory.
Pressure control must be used with fix nph/asphere
Self-explanatory.
+Pressure control must be used with fix nph/body
+Self-explanatory.
Pressure control must be used with fix nph/small
Self-explanatory.
Pressure control must be used with fix nph/sphere
@@ -4830,6 +5117,8 @@ provided.
Self-explanatory.
Pressure control must be used with fix npt/asphere
Self-explanatory.
+Pressure control must be used with fix npt/body
+Self-explanatory.
Pressure control must be used with fix npt/sphere
Self-explanatory.
Processor count in z must be 1 for 2d simulation
@@ -4881,6 +5170,9 @@ specified by the fix rattle command is numerically invalid.
Certain constraints were not satisfied.
RATTLE velocity constraints are not satisfied up to desired tolerance
Self-explanatory.
+Read data add offset is too big
+It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit
+integer.
Read dump of atom property that isn’t allocated
Self-explanatory.
Read rerun dump file timestep > specified stop
@@ -5141,6 +5433,18 @@ match the number of processors LAMMPS is being run on.
Self-explanatory.
Sqrt of negative value in variable formula
Self-explanatory.
+Subsequent read data induced too many angles per atom
+See the create_box extra/angle/per/atom or read_data “extra angle per
+atom” header value to set this limit larger.
+Subsequent read data induced too many bonds per atom
+See the create_box extra/bond/per/atom or read_data “extra bond per
+atom” header value to set this limit larger.
+Subsequent read data induced too many dihedrals per atom
+See the create_box extra/dihedral/per/atom or read_data “extra
+dihedral per atom” header value to set this limit larger.
+Subsequent read data induced too many impropers per atom
+See the create_box extra/improper/per/atom or read_data “extra
+improper per atom” header value to set this limit larger.
Substitution for illegal variable
Input script line contained a variable that could not be substituted
for.
@@ -5153,8 +5457,8 @@ for.
System in data file is too big
See the setting for bigint in the src/lmptype.h file.
System is not charge neutral, net charge = %g
-The total charge on all atoms on the system is not 0.0, which
-is not valid for the long-range Coulombic solvers.
+The total charge on all atoms on the system is not 0.0.
+For some KSpace solvers this is an error.
TAD nsteps must be multiple of t_event
Self-explanatory.
TIP4P hydrogen has incorrect atom type
@@ -5202,14 +5506,21 @@ create_box command.
Self-explanatory.
Temperature ID for fix temp/berendsen does not exist
Self-explanatory.
+Temperature ID for fix temp/csld does not exist
+Self-explanatory.
Temperature ID for fix temp/csvr does not exist
Self-explanatory.
Temperature ID for fix temp/rescale does not exist
Self-explanatory.
+Temperature compute degrees of freedom < 0
+This should not happen if you are calculating the temperature
+on a valid set of atoms.
Temperature control can not be used with fix nph
Self-explanatory.
Temperature control can not be used with fix nph/asphere
Self-explanatory.
+Temperature control can not be used with fix nph/body
+Self-explanatory.
Temperature control can not be used with fix nph/sphere
Self-explanatory.
Temperature control must be used with fix nphug
@@ -5218,12 +5529,16 @@ create_box command.
Self-explanatory.
Temperature control must be used with fix npt/asphere
Self-explanatory.
+Temperature control must be used with fix npt/body
+Self-explanatory.
Temperature control must be used with fix npt/sphere
Self-explanatory.
Temperature control must be used with fix nvt
Self-explanatory.
Temperature control must be used with fix nvt/asphere
Self-explanatory.
+Temperature control must be used with fix nvt/body
+Self-explanatory.
Temperature control must be used with fix nvt/sllod
Self-explanatory.
Temperature control must be used with fix nvt/sphere
@@ -5313,8 +5628,6 @@ not defined by the atom style used in this simulation.
Specified timestep is invalid.
Too big a problem to use velocity create loop all
The system size must fit in a 32-bit integer to use this option.
-Too big a timestep
-Specified timestep is too large.
Too big a timestep for dump dcd
The timestep must fit in a 32-bit integer to use this dump style.
Too big a timestep for dump xtc
@@ -5322,6 +5635,12 @@ not defined by the atom style used in this simulation.
Too few bits for lookup table
Table size specified via pair_modify command does not work with your
machine’s floating point representation.
+Too few lines in %s section of data file
+Self-explanatory.
+Too few values in body lines in data file
+Self-explanatory.
+Too few values in body section of molecule file
+Self-explanatory.
Too many -pk arguments in command line
The string formed by concatenating the arguments is too long. Use a
package command in the input script instead.
@@ -5386,6 +5705,10 @@ for NEB.
Too many total bits for bitmapped lookup table
Table size specified via pair_modify command is too large. Note that
a value of N generates a 2^N size table.
+Too many values in body lines in data file
+Self-explanatory.
+Too many values in body section of molecule file
+Self-explanatory.
Too much buffered per-proc info for dump
The size of the buffered string must fit in a 32-bit integer for a
dump.
@@ -5464,6 +5787,12 @@ number of processor partitions.
The choice of body style is unknown.
Unknown bond style
The choice of bond style is unknown.
+Unknown category for info is_active()
+Self-explanatory.
+Unknown category for info is_available()
+Self-explanatory.
+Unknown category for info is_defined()
+Self-explanatory.
Unknown command: %s
The command is not known to LAMMPS. Check the input script.
Unknown compute style
@@ -5486,6 +5815,12 @@ number of processor partitions.
One or more specified keywords are not recognized.
Unknown kspace style
The choice of kspace style is unknown.
+Unknown name for info newton category
+Self-explanatory.
+Unknown name for info package category
+Self-explanatory.
+Unknown name for info pair category
+Self-explanatory.
Unknown pair style
The choice of pair style is unknown.
Unknown pair_modify hybrid sub-style
@@ -5518,6 +5853,10 @@ valid.
Only 1/r^6 dispersion or dipole terms are supported.
Unsupported order in kspace_style pppm/disp, pair_style %s
Only pair styles with 1/r and 1/r^6 dependence are currently supported.
+Use cutoff keyword to set cutoff in single mode
+Mode is single so cutoff/multi keyword cannot be used.
+Use cutoff/multi keyword to set cutoff in multi mode
+Mode is multi so cutoff keyword cannot be used.
Using fix nvt/sllod with inconsistent fix deform remap option
Fix nvt/sllod requires that deforming atoms have a velocity profile
provided by “remap v” as a fix deform option.
@@ -5540,6 +5879,10 @@ deform needs to be used.
Self-explanatory.
Using suffix omp without USER-OMP package installed
Self-explanatory.
+Using update dipole flag requires atom attribute mu
+Self-explanatory.
+Using update dipole flag requires atom style sphere
+Self-explanatory.
Variable ID in variable formula does not exist
Self-explanatory.
Variable atom ID is too large
@@ -5555,6 +5898,8 @@ before the simulation has been setup.
Self-explanatory.
Variable for create_atoms is invalid style
The variables must be equal-style variables.
+Variable for displace_atoms is invalid style
+It must be an equal-style or atom-style variable.
Variable for dump every is invalid style
Only equal-style variables can be used.
Variable for dump image center is invalid style
@@ -5593,6 +5938,8 @@ before the simulation has been setup.
Only equal-style variables can be used.
Variable for fix temp/berendsen is invalid style
Only equal-style variables can be used.
+Variable for fix temp/csld is invalid style
+Only equal-style variables can be used.
Variable for fix temp/csvr is invalid style
Only equal-style variables can be used.
Variable for fix temp/rescale is invalid style
@@ -5647,6 +5994,8 @@ longer chains of dependence are also not allowed.
Self-explanatory.
Variable name for create_atoms does not exist
Self-explanatory.
+Variable name for displace_atoms does not exist
+Self-explanatory.
Variable name for dump every does not exist
Self-explanatory.
Variable name for dump image center does not exist
@@ -5697,6 +6046,8 @@ longer chains of dependence are also not allowed.
Self-explanatory.
Variable name for fix temp/berendsen does not exist
Self-explanatory.
+Variable name for fix temp/csld does not exist
+Self-explanatory.
Variable name for fix temp/csvr does not exist
Self-explanatory.
Variable name for fix temp/rescale does not exist
@@ -5835,6 +6186,12 @@ length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch.
Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero
Self-explantory.
+Calling write_dump before a full system init.
+The write_dump command is used before the system has been fully
+initialized as part of a ‘run’ or ‘minimize’ command. Not all dump
+styles and features are fully supported at this point and thus the
+command may fail or produce incomplete or incorrect output. Insert
+a “run 0” command, if a full system init is required.
Cannot count rigid body degrees-of-freedom before bodies are fully initialized
This means the temperature associated with the rigid bodies may be
incorrect on this timestep.
@@ -5881,6 +6238,10 @@ to check your simulation geometry.
Dump dcd/xtc timestamp may be wrong with fix dt/reset
If the fix changes the timestep, the dump dcd file will not
reflect the change.
+Energy tally does not account for ‘zero yes’
+The energy removed by using the ‘zero yes’ flag is not accounted
+for in the energy tally and thus energy conservation cannot be
+monitored in this case.
Estimated error in splitting of dispersion coeffs is %g
Error is greater than 0.0001 percent.
Ewald/disp Newton solver failed, using old method to estimate g_ewald
@@ -5899,6 +6260,10 @@ will be truncated to attempt to prevent the bond from blowing up.
Fix bond/swap will ignore defined angles
See the doc page for fix bond/swap for more info on this
restriction.
+Fix deposit near setting < possible overlap separation %g
+This test is performed for finite size particles with a diameter, not
+for point particles. The near setting is smaller than the particle
+diameter which can lead to overlaps.
Fix evaporate may delete atom with non-zero molecule ID
This is probably an error, since you should not delete only one atom
of a molecule.
@@ -5908,10 +6273,8 @@ is required for systems like the one specified by the user. User input
included one or more of the following: kspace, triclinic, a hybrid
pair style, an eam pair style, or no “single” function for the pair
style.
-Fix move does not update angular momentum
-Atoms store this quantity, but fix move does not (yet) update it.
-Fix move does not update quaternions
-Atoms store this quantity, but fix move does not (yet) update it.
+Fix property/atom mol or charge w/out ghost communication
+A model typically needs these properties defined for ghost atoms.
Fix qeq CG convergence failed (%g) after %d iterations at %ld step
Self-explanatory.
Fix qeq has non-zero lower Taper radius cutoff
@@ -5920,6 +6283,8 @@ style.
Value should typically be >= 5.0.
Fix qeq/dynamic tolerance may be too small for damped dynamics
Self-explanatory.
+Fix qeq/fire tolerance may be too small for damped fires
+Self-explanatory.
Fix rattle should come after all other integration fixes
This fix is designed to work after all other integration fixes change
atom positions. Thus it should be the last integration fix specified.
@@ -5963,8 +6328,11 @@ feature is disabled by using ‘pair_modify table 0’.
The fix_modify command is specifying a temperature computation that
computes a temperature on a different group of atoms than the fix
itself operates on. This is probably not what you want to do.
-H matrix size has been exceeded: m_fill=%d H.m=%d\n
+H matrix size has been exceeded: m_fill=%d H.m=%dn
This is the size of the matrix.
+Ignoring unknown or incorrect info command flag
+Self-explanatory. An unknown argument was given to the info command.
+Compare your input with the documentation.
Improper atoms missing at step %ld
One or more of 4 atoms needed to compute a particular improper are
missing on this processor. Typically this is because the pairwise
@@ -6056,8 +6424,12 @@ type, i.e. the first molecule in the template.
Self-explanatory.
More than one compute erotate/sphere/atom
It is not efficient to use compute erorate/sphere/atom more than once.
+More than one compute hexorder/atom
+It is not efficient to use compute hexorder/atom more than once.
More than one compute ke/atom
It is not efficient to use compute ke/atom more than once.
+More than one compute orientorder/atom
+It is not efficient to use compute orientorder/atom more than once.
More than one compute plasticity/atom
Self-explanatory.
More than one compute sna/atom
@@ -6215,17 +6587,22 @@ warning.
The determinant of the quadratic equation being solved for a single
cluster specified by the fix shake command is numerically suspect. LAMMPS
will set it to 0.0 and continue.
+Shell command ‘%s’ failed with error ‘%s’
+Self-explanatory.
+Shell command returned with non-zero status
+This may indicate the shell command did not operate as expected.
Should not allow rigid bodies to bounce off relecting walls
LAMMPS allows this, but their dynamics are not computed correctly.
-Should not use fix nve/limit with fix shake
-This will lead to invalid constraint forces in the SHAKE computation.
+Should not use fix nve/limit with fix shake or fix rattle
+This will lead to invalid constraint forces in the SHAKE/RATTLE
+computation.
Simulations might be very slow because of large number of structure factors
Self-explanatory.
Slab correction not needed for MSM
Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM.
System is not charge neutral, net charge = %g
-The total charge on all atoms on the system is not 0.0, which
-is not valid for the long-range Coulombic solvers.
+The total charge on all atoms on the system is not 0.0.
+For some KSpace solvers this is only a warning.
Table inner cutoff >= outer cutoff
You specified an inner cutoff for a Coulombic table that is longer
than the global cutoff. Probably not what you wanted.
@@ -6296,10 +6673,16 @@ be dangerous.
Self-explanatory.
Using package gpu without any pair style defined
Self-explanatory.
+Using pair potential shift with pair_modify compute no
+The shift effects will thus not be computed.
Using pair tail corrections with nonperiodic system
This is probably a bogus thing to do, since tail corrections are
computed by integrating the density of a periodic system out to
infinity.
+Using pair tail corrections with pair_modify compute no
+The tail corrections will thus not be computed.
+pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c
+Self-explanatory.
diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt
index 94330073e4..c4fd0883c1 100644
--- a/doc/Section_errors.txt
+++ b/doc/Section_errors.txt
@@ -200,6 +200,14 @@ setting. :dd
All angle coefficients must be set in the data file or by the
angle_coeff command before running a simulation. :dd
+{All atom IDs = 0 but atom_modify id = yes} :dt
+
+Self-explanatory. :dd
+
+{All atoms of a swapped type must have same charge.} :dt
+
+Self-explanatory. :dd
+
{All atoms of a swapped type must have the same charge.} :dt
Self-explanatory. :dd
@@ -372,24 +380,18 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Assigning quat to non-body atom} :dt
+
+Self-explanatory. :dd
+
{Assigning tri parameters to non-tri atom} :dt
Self-explanatory. :dd
-{Atom ID is negative} :dt
+{At least one atom of each swapped type must be present to define charges.} :dt
Self-explanatory. :dd
-{Atom ID is too big} :dt
-
-The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
-setting in your Makefile. See Section_start 2.2 of the manual for
-more details. :dd
-
-{Atom ID is zero} :dt
-
-Either all atoms IDs must be zero or none of them. :dd
-
{Atom IDs must be consecutive for velocity create loop all} :dt
Self-explanatory. :dd
@@ -445,6 +447,10 @@ The defined molecule(s) does not specify atom types. :dd
This is not allowed. :dd
+{Atom type must be zero in fix gcmc mol command} :dt
+
+Self-explanatory. :dd
+
{Atom vector in equal-style variable formula} :dt
Atom vectors generate one value per atom which is not allowed
@@ -808,6 +814,10 @@ Self-explanatory. See doc page discussion of command-line switches. :dd
Self-explanatory. See doc page discussion of command-line switches. :dd
+{Can only use Kokkos supported regions with Kokkos package} :dt
+
+Self-explanatory. :dd
+
{Can only use NEB with 1-processor replicas} :dt
This is current restriction for NEB as implemented in LAMMPS. :dd
@@ -820,6 +830,10 @@ This is current restriction for NEB as implemented in LAMMPS. :dd
This is a current restriction of this command. :dd
+{Cannot (yet) request ghost atoms with Kokkos half neighbor list} :dt
+
+This feature is not yet supported. :dd
+
{Cannot (yet) use 'electron' units with dipoles} :dt
This feature is not yet supported. :dd
@@ -864,6 +878,18 @@ This feature is not yet supported. :dd
Self-explanatory. :dd
+{Cannot (yet) use respa with Kokkos} :dt
+
+Self-explanatory. :dd
+
+{Cannot (yet) use rigid bodies with fix deform and Kokkos} :dt
+
+Self-explanatory. :dd
+
+{Cannot (yet) use rigid bodies with fix nh and Kokkos} :dt
+
+Self-explanatory. :dd
+
{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)} :dt
Single precision cannot be used with MSM. :dd
@@ -1013,10 +1039,6 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{Cannot delete_atoms mol yes for non-molecular systems} :dt
-
-Self-explanatory. :dd
-
{Cannot displace_atoms after reading restart file with per-atom info} :dt
This is because the restart file info cannot be migrated with the
@@ -1154,6 +1176,11 @@ and name are correct. :dd
The specified potential file cannot be opened. Check that the path
and name are correct. :dd
+{Cannot open Vashishta potential file %s} :dt
+
+The specified Vashishta potential file cannot be opened. Check that the path
+and name are correct. :dd
+
{Cannot open balance output file} :dt
Self-explanatory. :dd
@@ -1179,8 +1206,7 @@ directory to search for matching file names. :dd
{Cannot open dump file} :dt
-The output file for the dump command cannot be opened. Check that the
-path and name are correct. :dd
+Self-explanatory. :dd
{Cannot open dump file %s} :dt
@@ -1322,6 +1348,11 @@ and name are correct. :dd
The specified output file for pair energies and forces cannot be
opened. Check that the path and name are correct. :dd
+{Cannot open polymorphic potential file %s} :dt
+
+The specified polymorphic potential file cannot be opened. Check that
+the path and name are correct. :dd
+
{Cannot open print file %s} :dt
Self-explanatory. :dd
@@ -1350,6 +1381,10 @@ The screen file specified as a command-line argument cannot be
opened. Check that the directory you are running in allows for files
to be created. :dd
+{Cannot open temporary file for world counter.} :dt
+
+Self-explanatory. :dd
+
{Cannot open universe log file} :dt
For a multi-partition run, the master log file cannot be opened.
@@ -1367,14 +1402,9 @@ created. :dd
This error was generated by MPI when reading/writing an MPI-IO restart
file. :dd
-{Cannot read_data add and merge} :dt
+{Cannot read_data without add keyword after simulation box is defined} :dt
-These options are not yet supported. :dd
-
-{Cannot read_data after simulation box is defined} :dt
-
-The read_data command cannot be used after a read_data,
-read_restart, or create_box command. :dd
+Self-explanatory. :dd
{Cannot read_restart after simulation box is defined} :dt
@@ -1426,6 +1456,14 @@ In the rRESPA integrator, you must compute pairwise potentials either
all together (pair), or in pieces (inner/middle/outer). You can't do
both. :dd
+{Cannot set cutoff/multi before simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Cannot set dpd/theta for this atom style} :dt
+
+Self-explanatory. :dd
+
{Cannot set dump_modify flush for dump xtc} :dt
Self-explanatory. :dd
@@ -1435,7 +1473,15 @@ Self-explanatory. :dd
This atom style does not support mass settings for each atom type.
Instead they are defined on a per-atom basis in the data file. :dd
-{Cannot set meso_rho for this atom style} :dt
+{Cannot set meso/cv for this atom style} :dt
+
+Self-explanatory. :dd
+
+{Cannot set meso/e for this atom style} :dt
+
+Self-explanatory. :dd
+
+{Cannot set meso/rho for this atom style} :dt
Self-explanatory. :dd
@@ -1451,6 +1497,16 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Cannot set quaternion with xy components for 2d system} :dt
+
+Self-explanatory. :dd
+
+{Cannot set respa hybrid and any of pair/inner/middle/outer} :dt
+
+In the rRESPA integrator, you must compute pairwise potentials either
+all together (pair), with different cutoff regions (inner/middle/outer),
+or per hybrid sub-style (hybrid). You cannot mix those. :dd
+
{Cannot set respa middle without inner/outer} :dt
In the rRESPA integrator, you must define both a inner and outer
@@ -1461,6 +1517,14 @@ setting in order to use a middle setting. :dd
This error was generated by MPI when reading/writing an MPI-IO restart
file. :dd
+{Cannot set smd/contact/radius for this atom style} :dt
+
+Self-explanatory. :dd
+
+{Cannot set smd/mass/density for this atom style} :dt
+
+Self-explanatory. :dd
+
{Cannot set temperature for fix rigid/nph} :dt
The temp keyword cannot be specified. :dd
@@ -1528,7 +1592,7 @@ together. Use one or the other. :dd
{Cannot use Kokkos pair style with rRESPA inner/middle} :dt
-rRESPA inner/middle options are not yet supported by Kokkos. :dd
+Self-explanatory. :dd
{Cannot use NEB unless atom map exists} :dt
@@ -1608,6 +1672,14 @@ Self-explanatory. See the atom_modify command to create a map. :dd
Self-explanatory. :dd
+{Cannot use chosen neighbor list style with buck/coul/cut/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with buck/coul/long/kk} :dt
+
+Self-explanatory. :dd
+
{Cannot use chosen neighbor list style with buck/kk} :dt
That style is not supported by Kokkos. :dd
@@ -1616,6 +1688,10 @@ That style is not supported by Kokkos. :dd
That style is not supported by Kokkos. :dd
+{Cannot use chosen neighbor list style with coul/debye/kk} :dt
+
+Self-explanatory. :dd
+
{Cannot use chosen neighbor list style with coul/dsf/kk} :dt
That style is not supported by Kokkos. :dd
@@ -1624,10 +1700,38 @@ That style is not supported by Kokkos. :dd
That style is not supported by Kokkos. :dd
+{Cannot use chosen neighbor list style with lj/charmm/coul/charmm/implicit/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with lj/charmm/coul/charmm/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with lj/charmm/coul/long/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with lj/class2/coul/cut/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with lj/class2/coul/long/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with lj/class2/kk} :dt
+
+Self-explanatory. :dd
+
{Cannot use chosen neighbor list style with lj/cut/coul/cut/kk} :dt
That style is not supported by Kokkos. :dd
+{Cannot use chosen neighbor list style with lj/cut/coul/debye/kk} :dt
+
+Self-explanatory. :dd
+
{Cannot use chosen neighbor list style with lj/cut/coul/long/kk} :dt
That style is not supported by Kokkos. :dd
@@ -1636,10 +1740,46 @@ That style is not supported by Kokkos. :dd
That style is not supported by Kokkos. :dd
+{Cannot use chosen neighbor list style with lj/expand/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with lj/gromacs/coul/gromacs/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with lj/gromacs/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with lj/sdk/kk} :dt
+
+That style is not supported by Kokkos. :dd
+
{Cannot use chosen neighbor list style with pair eam/kk} :dt
That style is not supported by Kokkos. :dd
+{Cannot use chosen neighbor list style with pair eam/kk/alloy} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with pair eam/kk/fs} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with pair sw/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with tersoff/kk} :dt
+
+Self-explanatory. :dd
+
+{Cannot use chosen neighbor list style with tersoff/zbl/kk} :dt
+
+Self-explanatory. :dd
+
{Cannot use compute chunk/atom bin z for 2d model} :dt
Self-explanatory. :dd
@@ -2017,6 +2157,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Cannot use newton pair with dipole/sf/gpu pair style} :dt
+
+Self-explanatory. :dd
+
{Cannot use newton pair with dpd/gpu pair style} :dt
Self-explanatory. :dd
@@ -2025,6 +2169,14 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Cannot use newton pair with eam/alloy/gpu pair style} :dt
+
+Self-explanatory. :dd
+
+{Cannot use newton pair with eam/fs/gpu pair style} :dt
+
+Self-explanatory. :dd
+
{Cannot use newton pair with eam/gpu pair style} :dt
Self-explanatory. :dd
@@ -2049,6 +2201,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Cannot use newton pair with lj/cubic/gpu pair style} :dt
+
+Self-explanatory. :dd
+
{Cannot use newton pair with lj/cut/coul/cut/gpu pair style} :dt
Self-explanatory. :dd
@@ -2081,6 +2237,14 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Cannot use newton pair with lj/sdk/coul/long/gpu pair style} :dt
+
+Self-explanatory. :dd
+
+{Cannot use newton pair with lj/sdk/gpu pair style} :dt
+
+Self-explanatory. :dd
+
{Cannot use newton pair with lj96/cut/gpu pair style} :dt
Self-explanatory. :dd
@@ -2113,15 +2277,15 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Cannot use newton pair with zbl/gpu pair style} :dt
+
+Self-explantory. :dd
+
{Cannot use non-zero forces in an energy minimization} :dt
Fix setforce cannot be used in this manner. Use fix addforce
instead. :dd
-{Cannot use non-zero z offset in read_data for 2d simulation} :dt
-
-The offset option is not yet supported. :dd
-
{Cannot use nonperiodic boundares with fix ttm} :dt
This fix requires a fully periodic simulation box. :dd
@@ -2174,6 +2338,22 @@ See the command-line -partition switch. :dd
This is because the ramp() function is time dependent. :dd
+{Cannot use read_data add before simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Cannot use read_data extra with add flag} :dt
+
+Self-explanatory. :dd
+
+{Cannot use read_data offset without add flag} :dt
+
+Self-explanatory. :dd
+
+{Cannot use read_data shift without add flag} :dt
+
+Self-explanatory. :dd
+
{Cannot use region INF or EDGE when box does not exist} :dt
Regions that extend to the box boundaries can only be used after the
@@ -2259,6 +2439,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Cannot yet use compute tally with Kokkos} :dt
+
+This feature is not yet supported. :dd
+
{Cannot yet use fix bond/break with this improper style} :dt
This is a current restriction in LAMMPS. :dd
@@ -2267,6 +2451,14 @@ This is a current restriction in LAMMPS. :dd
This is a current restriction in LAMMPS. :dd
+{Cannot yet use minimize with Kokkos} :dt
+
+This feature is not yet supported. :dd
+
+{Cannot yet use pair hybrid with Kokkos} :dt
+
+This feature is not yet supported. :dd
+
{Cannot zero Langevin force of 0 atoms} :dt
The group has zero atoms, so you cannot request its force
@@ -2362,6 +2554,10 @@ cutoff explicitly via the comm_modify cutoff command. :dd
Dynamic groups have not yet been enabled for this compute. :dd
+{Compute ID for compute chunk /atom does not exist} :dt
+
+Self-explanatory. :dd
+
{Compute ID for compute chunk/atom does not exist} :dt
Self-explanatory. :dd
@@ -2431,6 +2627,14 @@ The atom style does not support bonds. :dd
This is because the computation of the centro-symmetry values
uses a pairwise neighbor list. :dd
+{Compute chunk/atom bin/cylinder radius is too large for periodic box} :dt
+
+Radius cannot be bigger than 1/2 of a non-axis periodic dimention. :dd
+
+{Compute chunk/atom bin/sphere radius is too large for periodic box} :dt
+
+Radius cannot be bigger than 1/2 of any periodic dimention. :dd
+
{Compute chunk/atom compute array is accessed out-of-range} :dt
The index for the array is out of bounds. :dd
@@ -2447,6 +2651,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Compute chunk/atom cylinder axis must be z for 2d} :dt
+
+Self-explanatory. :dd
+
{Compute chunk/atom fix array is accessed out-of-range} :dt
the index for the array is out of bounds. :dd
@@ -2476,6 +2684,10 @@ chunks may change. :dd
Self-explanatory. :dd
+{Compute chunk/atom sphere z origin must be 0.0 for 2d} :dt
+
+Self-explanatory. :dd
+
{Compute chunk/atom stores no IDs for compute property/chunk} :dt
It will only store IDs if its compress option is enabled. :dd
@@ -2605,6 +2817,14 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Compute hexorder/atom cutoff is longer than pairwise cutoff} :dt
+
+Cannot compute order parameter beyond cutoff. :dd
+
+{Compute hexorder/atom requires a pair style be defined} :dt
+
+Self-explantory. :dd
+
{Compute improper/local used when impropers are not allowed} :dt
The atom style does not support impropers. :dd
@@ -2635,10 +2855,22 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Compute nvt/nph/npt body requires atom style body} :dt
+
+Self-explanatory. :dd
+
{Compute omega/chunk does not use chunk/atom compute} :dt
The style of the specified compute is not chunk/atom. :dd
+{Compute orientorder/atom cutoff is longer than pairwise cutoff} :dt
+
+Cannot compute order parameter beyond cutoff. :dd
+
+{Compute orientorder/atom requires a pair style be defined} :dt
+
+Self-explantory. :dd
+
{Compute pair must use group all} :dt
Pair styles accumlate energy on all atoms. :dd
@@ -2837,6 +3069,14 @@ Self-explanatory. :dd
This compute cannot be used with point paritlces. :dd
+{Compute temp/body requires atom style body} :dt
+
+Self-explanatory. :dd
+
+{Compute temp/body requires bodies} :dt
+
+This compute can only be applied to body particles. :dd
+
{Compute temp/chunk does not use chunk/atom compute} :dt
The style of the specified compute is not chunk/atom. :dd
@@ -3037,6 +3277,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Could not find compute msd/chunk fix ID} :dt
+
+The compute creates an internal fix, which has been deleted. :dd
+
{Could not find compute pressure temperature ID} :dt
The compute ID for calculating temperature does not exist. :dd
@@ -3178,10 +3422,19 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Could not find pair fix ID} :dt
+
+A fix is created internally by the pair style to store shear
+history information. You cannot delete it. :dd
+
{Could not find set group ID} :dt
Group ID specified in set command does not exist. :dd
+{Could not find specified fix gcmc group ID} :dt
+
+Self-explanatory. :dd
+
{Could not find thermo compute ID} :dt
Compute ID specified in thermo_style command does not exist. :dd
@@ -3401,6 +3654,10 @@ read_restart, or create_box command. :dd
Can only delete atoms in atom pairs that will be in neighbor list. :dd
+{Delete_atoms mol yes requires atom attribute molecule} :dt
+
+Cannot use this option with a non-molecular system. :dd
+
{Delete_atoms requires a pair style be defined} :dt
This is because atom deletion within a cutoff uses a pairwise
@@ -3415,10 +3672,6 @@ read_restart, or create_box command. :dd
No atoms are yet defined so the delete_bonds command cannot be used. :dd
-{Delta_mu not allowed when not using semi-grand in fix atom/swap command} :dt
-
-Self-explanatory. :dd
-
{Deposition region extends outside simulation box} :dt
Self-explanatory. :dd
@@ -3603,6 +3856,10 @@ simulation box to a great distance. :dd
Self-explanatory :dd
+{Dump atom/gz only writes compressed files} :dt
+
+The dump atom/gz output file name must have a .gz suffix. :dd
+
{Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu} :dt
Self-explanatory. :dd
@@ -3616,6 +3873,10 @@ page for more details. :dd
Use the wildcard "*" character in the filename. :dd
+{Dump cfg/gz only writes compressed files} :dt
+
+The dump cfg/gz output file name must have a .gz suffix. :dd
+
{Dump custom and fix not computed at compatible times} :dt
The fix must produce per-atom quantities on timesteps that dump custom
@@ -3658,6 +3919,10 @@ Self-explanatory. :dd
Only atom-style variables generate per-atom quantities, needed for
dump output. :dd
+{Dump custom/gz only writes compressed files} :dt
+
+The dump custom/gz output file name must have a .gz suffix. :dd
+
{Dump dcd of non-matching # of atoms} :dt
Every snapshot written by dump dcd must contain the same # of atoms. :dd
@@ -3683,6 +3948,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Dump image body yes requires atom style body} :dt
+
+Self-explanatory. :dd
+
{Dump image bond not allowed with no bond types} :dt
Self-explanatory. :dd
@@ -3691,6 +3960,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Dump image line requires atom style line} :dt
+
+Self-explanatory. :dd
+
{Dump image persp option is not yet supported} :dt
Self-explanatory. :dd
@@ -3699,6 +3972,10 @@ Self-explanatory. :dd
Use a "*" in the filename. :dd
+{Dump image tri requires atom style tri} :dt
+
+Self-explanatory. :dd
+
{Dump local and fix not computed at compatible times} :dt
The fix must produce per-atom quantities on timesteps that dump local
@@ -3804,6 +4081,10 @@ Self-explanatory. :dd
Use the dump_modify sort command to enable this. :dd
+{Dump xyz/gz only writes compressed files} :dt
+
+The dump xyz/gz output file name must have a .gz suffix. :dd
+
{Dump_modify buffer yes not allowed for this style} :dt
Self-explanatory. :dd
@@ -3822,6 +4103,10 @@ Self-explanatory. :dd
The chosen atom style does not define the per-atom quantity being
dumped. :dd
+{Duplicate atom IDs exist} :dt
+
+Self-explanatory. :dd
+
{Duplicate fields in read_dump command} :dt
Self-explanatory. :dd
@@ -3835,6 +4120,10 @@ the bond length. :dd
Something has gone wrong with the fix ttm electron temperature model. :dd
+{Element not defined in potential file} :dt
+
+The specified element is not in the potential file. :dd
+
{Empty brackets in variable} :dt
There is no variable syntax that uses empty brackets. Check
@@ -3859,6 +4148,26 @@ The pair style is not providing the needed epsilon or sigma values. :dd
A pre-tabulated spline is invalid. Likely a problem with the
potential parameters. :dd
+{Error writing averaged chunk data} :dt
+
+Something in the output to the file triggered an error. :dd
+
+{Error writing file header} :dt
+
+Something in the output to the file triggered an error. :dd
+
+{Error writing out correlation data} :dt
+
+Something in the output to the file triggered an error. :dd
+
+{Error writing out histogram data} :dt
+
+Something in the output to the file triggered an error. :dd
+
+{Error writing out time averaged data} :dt
+
+Something in the output to the file triggered an error. :dd
+
{Failed to allocate %ld bytes for array %s} :dt
Your LAMMPS simulation has run out of memory. You need to run a
@@ -4227,6 +4536,10 @@ Self-explanatory. :dd
All inputs in a single fix ave/histo command must be of the
same style. :dd
+{Fix ave/histo/weight value and weight vector lengths do not match} :dt
+
+Self-explanatory. :dd
+
{Fix ave/spatial compute does not calculate a per-atom array} :dt
Self-explanatory. :dd
@@ -4522,6 +4835,10 @@ The atom style defined does not have this attribute. :dd
Self-explanatory. :dd
+{Fix gcmc atom has charge, but atom style does not} :dt
+
+Self-explanatory. :dd
+
{Fix gcmc cannot exchange individual atoms belonging to a molecule} :dt
This is an error since you should not delete only one atom of a
@@ -4538,6 +4855,10 @@ Should not choose the gcmc molecule feature if no molecules are being
simulated. The general molecule flag is off, but gcmc's molecule flag
is on. :dd
+{Fix gcmc molecule has charges, but atom style does not} :dt
+
+Self-explanatory. :dd
+
{Fix gcmc molecule must have atom types} :dt
The defined molecule does not specify atom types. :dd
@@ -4551,6 +4872,10 @@ The defined molecule does not specify coordinates. :dd
When using atom_style template, you cannot insert molecules that are
not in that template. :dd
+{Fix gcmc put atom outside box} :dt
+
+This should not normally happen. Contact the developers. :dd
+
{Fix gcmc ran out of available atom IDs} :dt
See the setting for tagint in the src/lmptype.h file. :dd
@@ -4732,7 +5057,7 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{Fix nve/sphere requires atom attribute mu} :dt
+{Fix nve/sphere dipole requires atom attribute mu} :dt
An atom style with this attribute is needed. :dd
@@ -4761,6 +5086,10 @@ Self-explanatory. :dd
The shape setting for a particle in the fix group has shape = 0.0,
which means it is a point particle. :dd
+{Fix nvt/nph/npt body requires bodies} :dt
+
+Self-explanatory. :dd
+
{Fix nvt/nph/npt sphere requires atom style sphere} :dt
Self-explanatory. :dd
@@ -4894,6 +5223,14 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Fix qeq/fire group has no atoms} :dt
+
+Self-explanatory. :dd
+
+{Fix qeq/fire requires atom attribute q} :dt
+
+Self-explanatory. :dd
+
{Fix qeq/point group has no atoms} :dt
Self-explanatory. :dd
@@ -5166,9 +5503,13 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{Fix temp/csvr is not compatible with fix shake} :dt
+{Fix temp/csld is not compatible with fix rattle or fix shake} :dt
-These two commands cannot currently be used toghether. :dd
+These two commands cannot currently be used together with fix temp/csld. :dd
+
+{Fix temp/csld variable returned negative temperature} :dt
+
+Self-explanatory. :dd
{Fix temp/csvr variable returned negative temperature} :dt
@@ -5359,6 +5700,10 @@ the host. See the package command. :dd
See the package gpu command. :dd
+{GPUs are requested but Kokkos has not been compiled for CUDA} :dt
+
+Recompile Kokkos with CUDA support to use GPUs. :dd
+
{Ghost velocity forward comm not yet implemented with Kokkos} :dt
This is a current restriction. :dd
@@ -5447,6 +5792,11 @@ invalid. :dd
One or more of the coefficients defined in the potential file is
invalid. :dd
+{Illegal Vashishta parameter} :dt
+
+One or more of the coefficients defined in the potential file is
+invalid. :dd
+
{Illegal compute voronoi/atom command (occupation and (surface or edges))} :dt
Self-explanatory. :dd
@@ -5466,7 +5816,7 @@ Self-explanatory. :dd
{Illegal fix gcmc gas mass <= 0} :dt
-The computed mass of the designated gas molecule or atom type was less
+The computed mass of the designated gas molecule or atom type was less
than or equal to zero. :dd
{Illegal fix tfmc random seed} :dt
@@ -5498,10 +5848,30 @@ There must be at least 2 table entries. :dd
There must be at least 2 table entries. :dd
+{Illegal or unset periodicity in restart} :dt
+
+This error should not normally occur unless the restart file is invalid. :dd
+
+{Illegal range increment value} :dt
+
+The increment must be >= 1. :dd
+
{Illegal simulation box} :dt
The lower bound of the simulation box is greater than the upper bound. :dd
+{Illegal size double vector read requested} :dt
+
+This error should not normally occur unless the restart file is invalid. :dd
+
+{Illegal size integer vector read requested} :dt
+
+This error should not normally occur unless the restart file is invalid. :dd
+
+{Illegal size string or corrupt restart} :dt
+
+This error should not normally occur unless the restart file is invalid. :dd
+
{Imageint setting in lmptype.h is invalid} :dt
Imageint must be as large or larger than smallint. :dd
@@ -5727,6 +6097,10 @@ Format of file read by fix tmd command is incorrect. :dd
Incorrect number of words per line in the potential file. :dd
+{Incorrect format in Vashishta potential file} :dt
+
+Incorrect number of words per line in the potential file. :dd
+
{Incorrect format in coul/streitz potential file} :dt
Incorrect number of words per line in the potential file. :dd
@@ -5743,6 +6117,10 @@ See doc page for body style. :dd
Self-explanatory. Check the input script or data file. :dd
+{Incorrect number of elements in potential file} :dt
+
+Self-explanatory. :dd
+
{Incorrect rigid body format in fix rigid file} :dt
The number of fields per line is not what expected. :dd
@@ -5755,6 +6133,10 @@ The number of fields per line is not what expected. :dd
Self-explanatory. Check the input script or data file. :dd
+{Incorrect table format check for element types} :dt
+
+Self-explanatory. :dd
+
{Incorrect velocity format in data file} :dt
Each atom style defines a format for the Velocity section
@@ -5821,10 +6203,38 @@ This error should not occur. Contact the developers. :dd
Self-explanatory. :dd
+{Invalid Angles section in molecule file} :dt
+
+Self-explanatory. :dd
+
+{Invalid Bonds section in molecule file} :dt
+
+Self-explanatory. :dd
+
{Invalid Boolean syntax in if command} :dt
Self-explanatory. :dd
+{Invalid Charges section in molecule file} :dt
+
+Self-explanatory. :dd
+
+{Invalid Coords section in molecule file} :dt
+
+Self-explanatory. :dd
+
+{Invalid Diameters section in molecule file} :dt
+
+Self-explanatory. :dd
+
+{Invalid Dihedrals section in molecule file} :dt
+
+Self-explanatory. :dd
+
+{Invalid Impropers section in molecule file} :dt
+
+Self-explanatory. :dd
+
{Invalid Kokkos command-line args} :dt
Self-explanatory. See Section 2.7 of the manual for details. :dd
@@ -5834,11 +6244,27 @@ Self-explanatory. See Section 2.7 of the manual for details. :dd
The file does not appear to be a LAMMPS restart file since
it doesn't contain the correct magic string at the beginning. :dd
+{Invalid Masses section in molecule file} :dt
+
+Self-explanatory. :dd
+
{Invalid REAX atom type} :dt
There is a mis-match between LAMMPS atom types and the elements
listed in the ReaxFF force field file. :dd
+{Invalid Special Bond Counts section in molecule file} :dt
+
+Self-explanatory. :dd
+
+{Invalid Types section in molecule file} :dt
+
+Self-explanatory. :dd
+
+{Invalid angle count in molecule file} :dt
+
+Self-explanatory. :dd
+
{Invalid angle table length} :dt
Length must be 2 or greater. :dd
@@ -5984,10 +6410,6 @@ types. :dd
The atom type specified in the gcmc command does not exist. :dd
-{Invalid atom type in fix gcmc mol command} :dt
-
-Self-explanatory. :dd
-
{Invalid atom type in fix pour command} :dt
Self-explanatory. :dd
@@ -6063,6 +6485,10 @@ The lo/hi values are inconsistent. :dd
Arguments in atom-style command are not correct. :dd
+{Invalid bond count in molecule file} :dt
+
+Self-explanatory. :dd
+
{Invalid bond table length} :dt
Length must be 2 or greater. :dd
@@ -6232,6 +6658,10 @@ Density must be > 0.0. :dd
Self-explanatory. :dd
+{Invalid dihedral count in molecule file} :dt
+
+Self-explanatory. :dd
+
{Invalid dihedral type in Dihedrals section of data file} :dt
Dihedral type must be positive integer and within range of specified
@@ -6383,11 +6813,6 @@ The format of this section of the file is not correct. :dd
Unrecognized entry in restart file. :dd
-{Invalid format in Bodies section of data file} :dt
-
-The specified number of integer or floating point values does not
-appear. :dd
-
{Invalid frequency in temper command} :dt
Nevery must be > 0. :dd
@@ -6412,6 +6837,10 @@ Up vector cannot be (0,0,0). :dd
Syntax of immediate value is incorrect. :dd
+{Invalid improper count in molecule file} :dt
+
+Self-explanatory. :dd
+
{Invalid improper type in Impropers section of data file} :dt
Improper type must be positive integer and within range of specified
@@ -6429,6 +6858,18 @@ Only indices 1,2,3 can be used for non-body particles. :dd
Self-explanatory. :dd
+{Invalid is_active() function in variable formula} :dt
+
+Self-explanatory. :dd
+
+{Invalid is_available() function in variable formula} :dt
+
+Self-explanatory. :dd
+
+{Invalid is_defined() function in variable formula} :dt
+
+Self-explanatory. :dd
+
{Invalid keyword in angle table parameters} :dt
Self-explanatory. :dd
@@ -6825,6 +7266,10 @@ long-range Coulombic or dispersion components be used. :dd
Self-explanatory. :dd
+{Kokkos has been compiled for CUDA but no GPUs are requested} :dt
+
+One or more GPUs must be used when Kokkos is compiled for CUDA. :dd
+
{Kspace style does not support compute group/group} :dt
Self-explanatory. :dd
@@ -6987,15 +7432,19 @@ Self-explanatory. :dd
The IDs must not be larger than can be stored in a 32-bit integer
since chunk IDs are 32-bit integers. :dd
+{Molecule auto special bond generation overflow} :dt
+
+Counts exceed maxspecial setting for other atoms in system. :dd
+
{Molecule file has angles but no nangles setting} :dt
Self-explanatory. :dd
-{Molecule file has bonds but no nbonds setting} :dt
+{Molecule file has body params but no setting for them} :dt
Self-explanatory. :dd
-{Molecule file has bonds but no special flags} :dt
+{Molecule file has bonds but no nbonds setting} :dt
Self-explanatory. :dd
@@ -7007,6 +7456,14 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Molecule file has no Body Doubles section} :dt
+
+Self-explanatory. :dd
+
+{Molecule file has no Body Integers section} :dt
+
+Self-explanatory. :dd
+
{Molecule file has special flags but no bonds} :dt
Self-explanatory. :dd
@@ -7015,6 +7472,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Molecule file requires atom style body} :dt
+
+Self-explanatory. :dd
+
{Molecule file shake flags not before shake atoms} :dt
The order of the two sections is important. :dd
@@ -7039,6 +7500,14 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Molecule natoms must be 1 for body particle} :dt
+
+Self-explanatory. :dd
+
+{Molecule sizescale must be 1.0 for body particle} :dt
+
+Self-explanatory. :dd
+
{Molecule template ID for atom_style template does not exist} :dt
Self-explanatory. :dd
@@ -7096,6 +7565,10 @@ potentials access it. :dd
Only one fix shake can be defined. :dd
+{Mu not allowed when not using semi-grand in fix atom/swap command} :dt
+
+Self-explanatory. :dd
+
{Must define angle_style before Angle Coeffs} :dt
Must use an angle_style command before reading a data file that
@@ -7263,6 +7736,10 @@ The kspace scalar pressure option is not compatible with kspace_style msm/cg. :d
A multi-partition simulation cannot read the input script from stdin.
The -in command-line option must be used to specify a file. :dd
+{Must use Kokkos half/thread or full neighbor list with threads or GPUs} :dt
+
+Using Kokkos half-neighbor lists with threading is not allowed. :dd
+
{Must use a block or cylinder region with fix pour} :dt
Self-explanatory. :dd
@@ -7327,7 +7804,7 @@ Self-explanatory. :dd
The ramp keyword can only be used for piston applied to face zlo. :dd
-{Need ntypes-1 delta_mu values in fix atom/swap command} :dt
+{Need nswaptypes mu values in fix atom/swap command} :dt
Self-explanatory. :dd
@@ -7426,10 +7903,6 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{No atom count in molecule file} :dt
-
-Self-explanatory. :dd
-
{No atoms in data file} :dt
The header of the data file indicated that atoms would be included,
@@ -7455,6 +7928,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{No count or invalid atom count in molecule file} :dt
+
+The number of atoms must be specified. :dd
+
{No dihedral style is defined for compute dihedral/local} :dt
Self-explanatory. :dd
@@ -7543,6 +8020,14 @@ The fix specification did not end up defining any rigid bodies. :dd
Self-explanatory. Check data file. :dd
+{No values in fix ave/chunk command} :dt
+
+Self-explanatory. :dd
+
+{No values in fix ave/time command} :dt
+
+Self-explanatory. :dd
+
{Non digit character between brackets in variable} :dt
Self-explantory. :dd
@@ -7556,9 +8041,13 @@ timesteps. :dd
The box size has apparently blown up. :dd
-{Not all atom IDs are 0} :dt
+{Non-zero atom IDs with atom_modify id = no} :dt
-Either all atoms IDs must be zero or none of them. :dd
+Self-explanatory. :dd
+
+{Non-zero read_data shift z value for 2d simulation} :dt
+
+Self-explanatory. :dd
{Nprocs not a multiple of N for -reorder} :dt
@@ -7574,11 +8063,29 @@ A command with an argument that specifies an integer or range of
integers is using a value that is less than 1 or greater than the
maximum allowed limit. :dd
+{One or more Atom IDs is negative} :dt
+
+Atom IDs must be positive integers. :dd
+
+{One or more atom IDs is too big} :dt
+
+The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
+setting in your Makefile. See Section_start 2.2 of the manual for
+more details. :dd
+
+{One or more atom IDs is zero} :dt
+
+Either all atoms IDs must be zero or none of them. :dd
+
{One or more atoms belong to multiple rigid bodies} :dt
Two or more rigid bodies defined by the fix rigid command cannot
contain the same atom. :dd
+{One or more rigid bodies are a single particle} :dt
+
+Self-explanatory. :dd
+
{One or zero atoms in rigid body} :dt
Any rigid body defined by the fix rigid command must contain 2 or more
@@ -7602,7 +8109,7 @@ Self-explanatory. :dd
{Out of range atoms - cannot compute MSM} :dt
-One or more atoms are attempting to map their charge to a MSM grid point
+One or more atoms are attempting to map their charge to a MSM grid point
that is not owned by a processor. This is likely for one of two
reasons, both of them bad. First, it may mean that an atom near the
boundary of a processor's sub-domain has moved more than 1/2 the
@@ -7814,6 +8321,10 @@ The atom style defined does not have this attribute. :dd
The atom style defined does not have these attributes. :dd
+{Pair dipole/sf/gpu requires atom attributes q, mu, torque} :dt
+
+The atom style defined does not one or more of these attributes. :dd
+
{Pair distance < table inner cutoff} :dt
Two atoms are closer together than the pairwise table allows. :dd
@@ -7847,9 +8358,9 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{Pair granular requires atom style sphere} :dt
+{Pair granular requires atom attributes radius, rmass} :dt
-Self-explanatory. :dd
+The atom style defined does not have these attributes. :dd
{Pair granular requires ghost atoms store velocity} :dt
@@ -7860,6 +8371,10 @@ Use the comm_modify vel yes command to enable this. :dd
This is a current restriction of the implementation of pair
granular styles with history. :dd
+{Pair hybrid single calls do not support per sub-style special bond values} :dt
+
+Self-explanatory. :dd
+
{Pair hybrid sub-style does not support single call} :dt
You are attempting to invoke a single() call on a pair style
@@ -8053,6 +8568,15 @@ This is a requirement to use the Tersoff potential. :dd
See the newton command. This is a restriction to use the Tersoff
potential. :dd
+{Pair style Vashishta requires atom IDs} :dt
+
+This is a requirement to use the Vashishta potential. :dd
+
+{Pair style Vashishta requires newton pair on} :dt
+
+See the newton command. This is a restriction to use the Vashishta
+potential. :dd
+
{Pair style bop requires comm ghost cutoff at least 3x larger than %g} :dt
Use the communicate ghost command to set this. See the pair bop
@@ -8183,6 +8707,11 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Pair style is incompatible with KSpace style} :dt
+
+If a pair style with a long-range Coulombic component is selected,
+then a kspace style must also be used. :dd
+
{Pair style is incompatible with TIP4P KSpace style} :dt
The pair style does not have the requires TIP4P settings. :dd
@@ -8288,6 +8817,10 @@ The atom style defined does not have these attributes. :dd
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors. :dd
+{Pair style lj/sdk/coul/long/gpu requires atom attribute q} :dt
+
+The atom style defined does not have this attribute. :dd
+
{Pair style nb3b/harmonic requires atom IDs} :dt
This is a requirement to use this potential. :dd
@@ -8308,6 +8841,15 @@ The atom style defined does not have this attribute. :dd
Self-explanatory. :dd
+{Pair style polymorphic requires atom IDs} :dt
+
+This is a requirement to use the polymorphic potential. :dd
+
+{Pair style polymorphic requires newton pair on} :dt
+
+See the newton command. This is a restriction to use the polymorphic
+potential. :dd
+
{Pair style reax requires atom IDs} :dt
This is a requirement to use the ReaxFF potential. :dd
@@ -8336,6 +8878,14 @@ This is a requirement to use this potential. :dd
See the newton command. This is a restriction to use this potential. :dd
+{Pair style tersoff/gpu requires atom IDs} :dt
+
+This is a requirement to use the tersoff/gpu potential. :dd
+
+{Pair style tersoff/gpu requires newton pair off} :dt
+
+See the newton command. This is a restriction to use this pair style. :dd
+
{Pair style tip4p/cut requires atom IDs} :dt
This is a requirement to use this potential. :dd
@@ -8376,6 +8926,10 @@ List of pair table parameters must include N setting. :dd
This is a current restriction of this pair potential. :dd
+{Pair tersoff/zbl/kk requires metal or real units} :dt
+
+This is a current restriction of this pair potential. :dd
+
{Pair tri/lj requires atom style tri} :dt
Self-explanatory. :dd
@@ -8409,6 +8963,11 @@ read_restart, or create_box command. :dd
Self-explanatory. :dd
+{Pair_modify special setting for pair hybrid incompatible with global special_bonds setting} :dt
+
+Cannot override a setting of 0.0 or 1.0 or change a setting between
+0.0 and 1.0. :dd
+
{Pair_write command before pair_style is defined} :dt
Self-explanatory. :dd
@@ -8418,10 +8977,10 @@ Self-explanatory. :dd
Particles must be "exterior" to the wall in order for energy/force to
be calculated. :dd
-{Particle on or inside surface of region used in fix wall/region} :dt
+{Particle outside surface of region used in fix wall/region} :dt
-Particles must be "exterior" to the region surface in order for
-energy/force to be calculated. :dd
+Particles must be inside the region for energy/force to be calculated.
+A particle outside the region generates an error. :dd
{Per-atom compute in equal-style variable formula} :dt
@@ -8503,6 +9062,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Pressure control can not be used with fix nvt/body} :dt
+
+Self-explanatory. :dd
+
{Pressure control can not be used with fix nvt/sllod} :dt
Self-explanatory. :dd
@@ -8519,6 +9082,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Pressure control must be used with fix nph/body} :dt
+
+Self-explanatory. :dd
+
{Pressure control must be used with fix nph/small} :dt
Self-explanatory. :dd
@@ -8540,6 +9107,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Pressure control must be used with fix npt/body} :dt
+
+Self-explanatory. :dd
+
{Pressure control must be used with fix npt/sphere} :dt
Self-explanatory. :dd
@@ -8631,6 +9202,11 @@ Certain constraints were not satisfied. :dd
Self-explanatory. :dd
+{Read data add offset is too big} :dt
+
+It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit
+integer. :dd
+
{Read dump of atom property that isn't allocated} :dt
Self-explanatory. :dd
@@ -9085,6 +9661,26 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Subsequent read data induced too many angles per atom} :dt
+
+See the create_box extra/angle/per/atom or read_data "extra angle per
+atom" header value to set this limit larger. :dd
+
+{Subsequent read data induced too many bonds per atom} :dt
+
+See the create_box extra/bond/per/atom or read_data "extra bond per
+atom" header value to set this limit larger. :dd
+
+{Subsequent read data induced too many dihedrals per atom} :dt
+
+See the create_box extra/dihedral/per/atom or read_data "extra
+dihedral per atom" header value to set this limit larger. :dd
+
+{Subsequent read data induced too many impropers per atom} :dt
+
+See the create_box extra/improper/per/atom or read_data "extra
+improper per atom" header value to set this limit larger. :dd
+
{Substitution for illegal variable} :dt
Input script line contained a variable that could not be substituted
@@ -9108,8 +9704,8 @@ See the setting for bigint in the src/lmptype.h file. :dd
{System is not charge neutral, net charge = %g} :dt
-The total charge on all atoms on the system is not 0.0, which
-is not valid for the long-range Coulombic solvers. :dd
+The total charge on all atoms on the system is not 0.0.
+For some KSpace solvers this is an error. :dd
{TAD nsteps must be multiple of t_event} :dt
@@ -9200,6 +9796,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Temperature ID for fix temp/csld does not exist} :dt
+
+Self-explanatory. :dd
+
{Temperature ID for fix temp/csvr does not exist} :dt
Self-explanatory. :dd
@@ -9208,6 +9808,11 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Temperature compute degrees of freedom < 0} :dt
+
+This should not happen if you are calculating the temperature
+on a valid set of atoms. :dd
+
{Temperature control can not be used with fix nph} :dt
Self-explanatory. :dd
@@ -9216,6 +9821,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Temperature control can not be used with fix nph/body} :dt
+
+Self-explanatory. :dd
+
{Temperature control can not be used with fix nph/sphere} :dt
Self-explanatory. :dd
@@ -9232,6 +9841,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Temperature control must be used with fix npt/body} :dt
+
+Self-explanatory. :dd
+
{Temperature control must be used with fix npt/sphere} :dt
Self-explanatory. :dd
@@ -9244,6 +9857,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Temperature control must be used with fix nvt/body} :dt
+
+Self-explanatory. :dd
+
{Temperature control must be used with fix nvt/sllod} :dt
Self-explanatory. :dd
@@ -9407,10 +10024,6 @@ Specified timestep is invalid. :dd
The system size must fit in a 32-bit integer to use this option. :dd
-{Too big a timestep} :dt
-
-Specified timestep is too large. :dd
-
{Too big a timestep for dump dcd} :dt
The timestep must fit in a 32-bit integer to use this dump style. :dd
@@ -9424,6 +10037,18 @@ The timestep must fit in a 32-bit integer to use this dump style. :dd
Table size specified via pair_modify command does not work with your
machine's floating point representation. :dd
+{Too few lines in %s section of data file} :dt
+
+Self-explanatory. :dd
+
+{Too few values in body lines in data file} :dt
+
+Self-explanatory. :dd
+
+{Too few values in body section of molecule file} :dt
+
+Self-explanatory. :dd
+
{Too many -pk arguments in command line} :dt
The string formed by concatenating the arguments is too long. Use a
@@ -9534,6 +10159,14 @@ See the setting for bigint in the src/lmptype.h file. :dd
Table size specified via pair_modify command is too large. Note that
a value of N generates a 2^N size table. :dd
+{Too many values in body lines in data file} :dt
+
+Self-explanatory. :dd
+
+{Too many values in body section of molecule file} :dt
+
+Self-explanatory. :dd
+
{Too much buffered per-proc info for dump} :dt
The size of the buffered string must fit in a 32-bit integer for a
@@ -9678,6 +10311,18 @@ The choice of body style is unknown. :dd
The choice of bond style is unknown. :dd
+{Unknown category for info is_active()} :dt
+
+Self-explanatory. :dd
+
+{Unknown category for info is_available()} :dt
+
+Self-explanatory. :dd
+
+{Unknown category for info is_defined()} :dt
+
+Self-explanatory. :dd
+
{Unknown command: %s} :dt
The command is not known to LAMMPS. Check the input script. :dd
@@ -9722,6 +10367,18 @@ One or more specified keywords are not recognized. :dd
The choice of kspace style is unknown. :dd
+{Unknown name for info newton category} :dt
+
+Self-explanatory. :dd
+
+{Unknown name for info package category} :dt
+
+Self-explanatory. :dd
+
+{Unknown name for info pair category} :dt
+
+Self-explanatory. :dd
+
{Unknown pair style} :dt
The choice of pair style is unknown. :dd
@@ -9784,6 +10441,14 @@ Only 1/r^6 dispersion or dipole terms are supported. :dd
Only pair styles with 1/r and 1/r^6 dependence are currently supported. :dd
+{Use cutoff keyword to set cutoff in single mode} :dt
+
+Mode is single so cutoff/multi keyword cannot be used. :dd
+
+{Use cutoff/multi keyword to set cutoff in multi mode} :dt
+
+Mode is multi so cutoff keyword cannot be used. :dd
+
{Using fix nvt/sllod with inconsistent fix deform remap option} :dt
Fix nvt/sllod requires that deforming atoms have a velocity profile
@@ -9826,6 +10491,14 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Using update dipole flag requires atom attribute mu} :dt
+
+Self-explanatory. :dd
+
+{Using update dipole flag requires atom style sphere} :dt
+
+Self-explanatory. :dd
+
{Variable ID in variable formula does not exist} :dt
Self-explanatory. :dd
@@ -9855,6 +10528,10 @@ Self-explanatory. :dd
The variables must be equal-style variables. :dd
+{Variable for displace_atoms is invalid style} :dt
+
+It must be an equal-style or atom-style variable. :dd
+
{Variable for dump every is invalid style} :dt
Only equal-style variables can be used. :dd
@@ -9931,6 +10608,10 @@ Only equal-style variables can be used. :dd
Only equal-style variables can be used. :dd
+{Variable for fix temp/csld is invalid style} :dt
+
+Only equal-style variables can be used. :dd
+
{Variable for fix temp/csvr is invalid style} :dt
Only equal-style variables can be used. :dd
@@ -10037,6 +10718,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Variable name for displace_atoms does not exist} :dt
+
+Self-explanatory. :dd
+
{Variable name for dump every does not exist} :dt
Self-explanatory. :dd
@@ -10137,6 +10822,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Variable name for fix temp/csld does not exist} :dt
+
+Self-explanatory. :dd
+
{Variable name for fix temp/csvr does not exist} :dt
Self-explanatory. :dd
@@ -10384,6 +11073,14 @@ for a dihedral) and adding a small amount of stretch. :dd
Self-explantory. :dd
+{Calling write_dump before a full system init.} :dt
+
+The write_dump command is used before the system has been fully
+initialized as part of a 'run' or 'minimize' command. Not all dump
+styles and features are fully supported at this point and thus the
+command may fail or produce incomplete or incorrect output. Insert
+a "run 0" command, if a full system init is required. :dd
+
{Cannot count rigid body degrees-of-freedom before bodies are fully initialized} :dt
This means the temperature associated with the rigid bodies may be
@@ -10462,6 +11159,12 @@ Self-explanatory. :dd
If the fix changes the timestep, the dump dcd file will not
reflect the change. :dd
+{Energy tally does not account for 'zero yes'} :dt
+
+The energy removed by using the 'zero yes' flag is not accounted
+for in the energy tally and thus energy conservation cannot be
+monitored in this case. :dd
+
{Estimated error in splitting of dispersion coeffs is %g} :dt
Error is greater than 0.0001 percent. :dd
@@ -10494,6 +11197,12 @@ You likely want to set this in your input script. :dd
See the doc page for fix bond/swap for more info on this
restriction. :dd
+{Fix deposit near setting < possible overlap separation %g} :dt
+
+This test is performed for finite size particles with a diameter, not
+for point particles. The near setting is smaller than the particle
+diameter which can lead to overlaps. :dd
+
{Fix evaporate may delete atom with non-zero molecule ID} :dt
This is probably an error, since you should not delete only one atom
@@ -10507,13 +11216,9 @@ included one or more of the following: kspace, triclinic, a hybrid
pair style, an eam pair style, or no "single" function for the pair
style. :dd
-{Fix move does not update angular momentum} :dt
+{Fix property/atom mol or charge w/out ghost communication} :dt
-Atoms store this quantity, but fix move does not (yet) update it. :dd
-
-{Fix move does not update quaternions} :dt
-
-Atoms store this quantity, but fix move does not (yet) update it. :dd
+A model typically needs these properties defined for ghost atoms. :dd
{Fix qeq CG convergence failed (%g) after %d iterations at %ld step} :dt
@@ -10531,6 +11236,10 @@ Value should typically be >= 5.0. :dd
Self-explanatory. :dd
+{Fix qeq/fire tolerance may be too small for damped fires} :dt
+
+Self-explanatory. :dd
+
{Fix rattle should come after all other integration fixes} :dt
This fix is designed to work after all other integration fixes change
@@ -10600,10 +11309,15 @@ The fix_modify command is specifying a temperature computation that
computes a temperature on a different group of atoms than the fix
itself operates on. This is probably not what you want to do. :dd
-{H matrix size has been exceeded: m_fill=%d H.m=%d\\n} :dt
+{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt
This is the size of the matrix. :dd
+{Ignoring unknown or incorrect info command flag} :dt
+
+Self-explanatory. An unknown argument was given to the info command.
+Compare your input with the documentation. :dd
+
{Improper atoms missing at step %ld} :dt
One or more of 4 atoms needed to compute a particular improper are
@@ -10757,10 +11471,18 @@ Self-explanatory. :dd
It is not efficient to use compute erorate/sphere/atom more than once. :dd
+{More than one compute hexorder/atom} :dt
+
+It is not efficient to use compute hexorder/atom more than once. :dd
+
{More than one compute ke/atom} :dt
It is not efficient to use compute ke/atom more than once. :dd
+{More than one compute orientorder/atom} :dt
+
+It is not efficient to use compute orientorder/atom more than once. :dd
+
{More than one compute plasticity/atom} :dt
Self-explanatory. :dd
@@ -11016,13 +11738,22 @@ The determinant of the quadratic equation being solved for a single
cluster specified by the fix shake command is numerically suspect. LAMMPS
will set it to 0.0 and continue. :dd
+{Shell command '%s' failed with error '%s'} :dt
+
+Self-explanatory. :dd
+
+{Shell command returned with non-zero status} :dt
+
+This may indicate the shell command did not operate as expected. :dd
+
{Should not allow rigid bodies to bounce off relecting walls} :dt
LAMMPS allows this, but their dynamics are not computed correctly. :dd
-{Should not use fix nve/limit with fix shake} :dt
+{Should not use fix nve/limit with fix shake or fix rattle} :dt
-This will lead to invalid constraint forces in the SHAKE computation. :dd
+This will lead to invalid constraint forces in the SHAKE/RATTLE
+computation. :dd
{Simulations might be very slow because of large number of structure factors} :dt
@@ -11034,8 +11765,8 @@ Slab correction is intended to be used with Ewald or PPPM and is not needed by M
{System is not charge neutral, net charge = %g} :dt
-The total charge on all atoms on the system is not 0.0, which
-is not valid for the long-range Coulombic solvers. :dd
+The total charge on all atoms on the system is not 0.0.
+For some KSpace solvers this is only a warning. :dd
{Table inner cutoff >= outer cutoff} :dt
@@ -11153,11 +11884,23 @@ Self-explanatory. :dd
Self-explanatory. :dd
+{Using pair potential shift with pair_modify compute no} :dt
+
+The shift effects will thus not be computed. :dd
+
{Using pair tail corrections with nonperiodic system} :dt
This is probably a bogus thing to do, since tail corrections are
computed by integrating the density of a periodic system out to
infinity. :dd
+{Using pair tail corrections with pair_modify compute no} :dt
+
+The tail corrections will thus not be computed. :dd
+
+{pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c} :dt
+
+Self-explanatory. :dd
+
:dle
diff --git a/doc/_sources/Section_errors.txt b/doc/_sources/Section_errors.txt
index 4e74cec06e..aac6dd2de1 100644
--- a/doc/_sources/Section_errors.txt
+++ b/doc/_sources/Section_errors.txt
@@ -199,6 +199,12 @@ Errors:
All angle coefficients must be set in the data file or by the
angle_coeff command before running a simulation.
+*All atom IDs = 0 but atom_modify id = yes*
+ Self-explanatory.
+
+*All atoms of a swapped type must have same charge.*
+ Self-explanatory.
+
*All atoms of a swapped type must have the same charge.*
Self-explanatory.
@@ -336,20 +342,15 @@ Errors:
*Assigning line parameters to non-line atom*
Self-explanatory.
+*Assigning quat to non-body atom*
+ Self-explanatory.
+
*Assigning tri parameters to non-tri atom*
Self-explanatory.
-*Atom ID is negative*
+*At least one atom of each swapped type must be present to define charges.*
Self-explanatory.
-*Atom ID is too big*
- The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
- setting in your Makefile. See Section_start 2.2 of the manual for
- more details.
-
-*Atom ID is zero*
- Either all atoms IDs must be zero or none of them.
-
*Atom IDs must be consecutive for velocity create loop all*
Self-explanatory.
@@ -393,6 +394,9 @@ Errors:
*Atom style was redefined after using fix property/atom*
This is not allowed.
+*Atom type must be zero in fix gcmc mol command*
+ Self-explanatory.
+
*Atom vector in equal-style variable formula*
Atom vectors generate one value per atom which is not allowed
in an equal-style variable.
@@ -677,6 +681,9 @@ Errors:
*Can only use -pscreen with multiple partitions*
Self-explanatory. See doc page discussion of command-line switches.
+*Can only use Kokkos supported regions with Kokkos package*
+ Self-explanatory.
+
*Can only use NEB with 1-processor replicas*
This is current restriction for NEB as implemented in LAMMPS.
@@ -686,6 +693,9 @@ Errors:
*Cannot (yet) do analytic differentiation with pppm/gpu*
This is a current restriction of this command.
+*Cannot (yet) request ghost atoms with Kokkos half neighbor list*
+ This feature is not yet supported.
+
*Cannot (yet) use 'electron' units with dipoles*
This feature is not yet supported.
@@ -719,6 +729,15 @@ Errors:
*Cannot (yet) use molecular templates with Kokkos*
Self-explanatory.
+*Cannot (yet) use respa with Kokkos*
+ Self-explanatory.
+
+*Cannot (yet) use rigid bodies with fix deform and Kokkos*
+ Self-explanatory.
+
+*Cannot (yet) use rigid bodies with fix nh and Kokkos*
+ Self-explanatory.
+
*Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)*
Single precision cannot be used with MSM.
@@ -835,9 +854,6 @@ Errors:
*Cannot delete_atoms bond yes for non-molecular systems*
Self-explanatory.
-*Cannot delete_atoms mol yes for non-molecular systems*
- Self-explanatory.
-
*Cannot displace_atoms after reading restart file with per-atom info*
This is because the restart file info cannot be migrated with the
atoms. You can get around this by performing a 0-timestep run which
@@ -946,6 +962,10 @@ Errors:
The specified potential file cannot be opened. Check that the path
and name are correct.
+*Cannot open Vashishta potential file %s*
+ The specified Vashishta potential file cannot be opened. Check that the path
+ and name are correct.
+
*Cannot open balance output file*
Self-explanatory.
@@ -965,8 +985,7 @@ Errors:
directory to search for matching file names.
*Cannot open dump file*
- The output file for the dump command cannot be opened. Check that the
- path and name are correct.
+ Self-explanatory.
*Cannot open dump file %s*
The output file for the dump command cannot be opened. Check that the
@@ -1080,6 +1099,10 @@ Errors:
The specified output file for pair energies and forces cannot be
opened. Check that the path and name are correct.
+*Cannot open polymorphic potential file %s*
+ The specified polymorphic potential file cannot be opened. Check that
+ the path and name are correct.
+
*Cannot open print file %s*
Self-explanatory.
@@ -1102,6 +1125,9 @@ Errors:
opened. Check that the directory you are running in allows for files
to be created.
+*Cannot open temporary file for world counter.*
+ Self-explanatory.
+
*Cannot open universe log file*
For a multi-partition run, the master log file cannot be opened.
Check that the directory you are running in allows for files to be
@@ -1116,12 +1142,8 @@ Errors:
This error was generated by MPI when reading/writing an MPI-IO restart
file.
-*Cannot read_data add and merge*
- These options are not yet supported.
-
-*Cannot read_data after simulation box is defined*
- The read_data command cannot be used after a read_data,
- read_restart, or create_box command.
+*Cannot read_data without add keyword after simulation box is defined*
+ Self-explanatory.
*Cannot read_restart after simulation box is defined*
The read_restart command cannot be used after a read_data,
@@ -1164,6 +1186,12 @@ Errors:
all together (pair), or in pieces (inner/middle/outer). You can't do
both.
+*Cannot set cutoff/multi before simulation box is defined*
+ Self-explanatory.
+
+*Cannot set dpd/theta for this atom style*
+ Self-explanatory.
+
*Cannot set dump_modify flush for dump xtc*
Self-explanatory.
@@ -1171,7 +1199,13 @@ Errors:
This atom style does not support mass settings for each atom type.
Instead they are defined on a per-atom basis in the data file.
-*Cannot set meso_rho for this atom style*
+*Cannot set meso/cv for this atom style*
+ Self-explanatory.
+
+*Cannot set meso/e for this atom style*
+ Self-explanatory.
+
+*Cannot set meso/rho for this atom style*
Self-explanatory.
*Cannot set non-zero image flag for non-periodic dimension*
@@ -1183,6 +1217,14 @@ Errors:
*Cannot set quaternion for atom that has none*
Self-explanatory.
+*Cannot set quaternion with xy components for 2d system*
+ Self-explanatory.
+
+*Cannot set respa hybrid and any of pair/inner/middle/outer*
+ In the rRESPA integrator, you must compute pairwise potentials either
+ all together (pair), with different cutoff regions (inner/middle/outer),
+ or per hybrid sub-style (hybrid). You cannot mix those.
+
*Cannot set respa middle without inner/outer*
In the rRESPA integrator, you must define both a inner and outer
setting in order to use a middle setting.
@@ -1191,6 +1233,12 @@ Errors:
This error was generated by MPI when reading/writing an MPI-IO restart
file.
+*Cannot set smd/contact/radius for this atom style*
+ Self-explanatory.
+
+*Cannot set smd/mass/density for this atom style*
+ Self-explanatory.
+
*Cannot set temperature for fix rigid/nph*
The temp keyword cannot be specified.
@@ -1242,7 +1290,7 @@ Errors:
together. Use one or the other.
*Cannot use Kokkos pair style with rRESPA inner/middle*
- rRESPA inner/middle options are not yet supported by Kokkos.
+ Self-explanatory.
*Cannot use NEB unless atom map exists*
Use the atom_modify command to create an atom map.
@@ -1304,30 +1352,87 @@ Errors:
*Cannot use both com and bias with compute temp/chunk*
Self-explanatory.
+*Cannot use chosen neighbor list style with buck/coul/cut/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with buck/coul/long/kk*
+ Self-explanatory.
+
*Cannot use chosen neighbor list style with buck/kk*
That style is not supported by Kokkos.
*Cannot use chosen neighbor list style with coul/cut/kk*
That style is not supported by Kokkos.
+*Cannot use chosen neighbor list style with coul/debye/kk*
+ Self-explanatory.
+
*Cannot use chosen neighbor list style with coul/dsf/kk*
That style is not supported by Kokkos.
*Cannot use chosen neighbor list style with coul/wolf/kk*
That style is not supported by Kokkos.
+*Cannot use chosen neighbor list style with lj/charmm/coul/charmm/implicit/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/charmm/coul/charmm/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/charmm/coul/long/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/class2/coul/cut/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/class2/coul/long/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/class2/kk*
+ Self-explanatory.
+
*Cannot use chosen neighbor list style with lj/cut/coul/cut/kk*
That style is not supported by Kokkos.
+*Cannot use chosen neighbor list style with lj/cut/coul/debye/kk*
+ Self-explanatory.
+
*Cannot use chosen neighbor list style with lj/cut/coul/long/kk*
That style is not supported by Kokkos.
*Cannot use chosen neighbor list style with lj/cut/kk*
That style is not supported by Kokkos.
+*Cannot use chosen neighbor list style with lj/expand/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/gromacs/coul/gromacs/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/gromacs/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with lj/sdk/kk*
+ That style is not supported by Kokkos.
+
*Cannot use chosen neighbor list style with pair eam/kk*
That style is not supported by Kokkos.
+*Cannot use chosen neighbor list style with pair eam/kk/alloy*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with pair eam/kk/fs*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with pair sw/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with tersoff/kk*
+ Self-explanatory.
+
+*Cannot use chosen neighbor list style with tersoff/zbl/kk*
+ Self-explanatory.
+
*Cannot use compute chunk/atom bin z for 2d model*
Self-explanatory.
@@ -1618,12 +1723,21 @@ Errors:
*Cannot use newton pair with dipole/cut/gpu pair style*
Self-explanatory.
+*Cannot use newton pair with dipole/sf/gpu pair style*
+ Self-explanatory.
+
*Cannot use newton pair with dpd/gpu pair style*
Self-explanatory.
*Cannot use newton pair with dpd/tstat/gpu pair style*
Self-explanatory.
+*Cannot use newton pair with eam/alloy/gpu pair style*
+ Self-explanatory.
+
+*Cannot use newton pair with eam/fs/gpu pair style*
+ Self-explanatory.
+
*Cannot use newton pair with eam/gpu pair style*
Self-explanatory.
@@ -1642,6 +1756,9 @@ Errors:
*Cannot use newton pair with lj/class2/gpu pair style*
Self-explanatory.
+*Cannot use newton pair with lj/cubic/gpu pair style*
+ Self-explanatory.
+
*Cannot use newton pair with lj/cut/coul/cut/gpu pair style*
Self-explanatory.
@@ -1666,6 +1783,12 @@ Errors:
*Cannot use newton pair with lj/gromacs/gpu pair style*
Self-explanatory.
+*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
+ Self-explanatory.
+
+*Cannot use newton pair with lj/sdk/gpu pair style*
+ Self-explanatory.
+
*Cannot use newton pair with lj96/cut/gpu pair style*
Self-explanatory.
@@ -1690,13 +1813,13 @@ Errors:
*Cannot use newton pair with yukawa/gpu pair style*
Self-explanatory.
+*Cannot use newton pair with zbl/gpu pair style*
+ Self-explantory.
+
*Cannot use non-zero forces in an energy minimization*
Fix setforce cannot be used in this manner. Use fix addforce
instead.
-*Cannot use non-zero z offset in read_data for 2d simulation*
- The offset option is not yet supported.
-
*Cannot use nonperiodic boundares with fix ttm*
This fix requires a fully periodic simulation box.
@@ -1738,6 +1861,18 @@ Errors:
*Cannot use ramp in variable formula between runs*
This is because the ramp() function is time dependent.
+*Cannot use read_data add before simulation box is defined*
+ Self-explanatory.
+
+*Cannot use read_data extra with add flag*
+ Self-explanatory.
+
+*Cannot use read_data offset without add flag*
+ Self-explanatory.
+
+*Cannot use read_data shift without add flag*
+ Self-explanatory.
+
*Cannot use region INF or EDGE when box does not exist*
Regions that extend to the box boundaries can only be used after the
create_box command has been used.
@@ -1803,12 +1938,21 @@ Errors:
*Cannot yet use comm_style tiled with triclinic box*
Self-explanatory.
+*Cannot yet use compute tally with Kokkos*
+ This feature is not yet supported.
+
*Cannot yet use fix bond/break with this improper style*
This is a current restriction in LAMMPS.
*Cannot yet use fix bond/create with this improper style*
This is a current restriction in LAMMPS.
+*Cannot yet use minimize with Kokkos*
+ This feature is not yet supported.
+
+*Cannot yet use pair hybrid with Kokkos*
+ This feature is not yet supported.
+
*Cannot zero Langevin force of 0 atoms*
The group has zero atoms, so you cannot request its force
be zeroed.
@@ -1882,6 +2026,9 @@ Errors:
*Compute %s does not allow use of dynamic group*
Dynamic groups have not yet been enabled for this compute.
+*Compute ID for compute chunk /atom does not exist*
+ Self-explanatory.
+
*Compute ID for compute chunk/atom does not exist*
Self-explanatory.
@@ -1934,6 +2081,12 @@ Errors:
This is because the computation of the centro-symmetry values
uses a pairwise neighbor list.
+*Compute chunk/atom bin/cylinder radius is too large for periodic box*
+ Radius cannot be bigger than 1/2 of a non-axis periodic dimention.
+
+*Compute chunk/atom bin/sphere radius is too large for periodic box*
+ Radius cannot be bigger than 1/2 of any periodic dimention.
+
*Compute chunk/atom compute array is accessed out-of-range*
The index for the array is out of bounds.
@@ -1946,6 +2099,9 @@ Errors:
*Compute chunk/atom compute does not calculate per-atom values*
Self-explanatory.
+*Compute chunk/atom cylinder axis must be z for 2d*
+ Self-explanatory.
+
*Compute chunk/atom fix array is accessed out-of-range*
the index for the array is out of bounds.
@@ -1968,6 +2124,9 @@ Errors:
*Compute chunk/atom molecule for non-molecular system*
Self-explanatory.
+*Compute chunk/atom sphere z origin must be 0.0 for 2d*
+ Self-explanatory.
+
*Compute chunk/atom stores no IDs for compute property/chunk*
It will only store IDs if its compress option is enabled.
@@ -2066,6 +2225,12 @@ Errors:
*Compute heat/flux compute ID does not compute stress/atom*
Self-explanatory.
+*Compute hexorder/atom cutoff is longer than pairwise cutoff*
+ Cannot compute order parameter beyond cutoff.
+
+*Compute hexorder/atom requires a pair style be defined*
+ Self-explantory.
+
*Compute improper/local used when impropers are not allowed*
The atom style does not support impropers.
@@ -2089,9 +2254,18 @@ Errors:
*Compute nvt/nph/npt asphere requires atom style ellipsoid*
Self-explanatory.
+*Compute nvt/nph/npt body requires atom style body*
+ Self-explanatory.
+
*Compute omega/chunk does not use chunk/atom compute*
The style of the specified compute is not chunk/atom.
+*Compute orientorder/atom cutoff is longer than pairwise cutoff*
+ Cannot compute order parameter beyond cutoff.
+
+*Compute orientorder/atom requires a pair style be defined*
+ Self-explantory.
+
*Compute pair must use group all*
Pair styles accumlate energy on all atoms.
@@ -2242,6 +2416,12 @@ Errors:
*Compute temp/asphere requires extended particles*
This compute cannot be used with point paritlces.
+*Compute temp/body requires atom style body*
+ Self-explanatory.
+
+*Compute temp/body requires bodies*
+ This compute can only be applied to body particles.
+
*Compute temp/chunk does not use chunk/atom compute*
The style of the specified compute is not chunk/atom.
@@ -2399,6 +2579,9 @@ Errors:
*Could not find compute msd fix ID*
Self-explanatory.
+*Could not find compute msd/chunk fix ID*
+ The compute creates an internal fix, which has been deleted.
+
*Could not find compute pressure temperature ID*
The compute ID for calculating temperature does not exist.
@@ -2505,9 +2688,16 @@ Errors:
*Could not find group delete group ID*
Self-explanatory.
+*Could not find pair fix ID*
+ A fix is created internally by the pair style to store shear
+ history information. You cannot delete it.
+
*Could not find set group ID*
Group ID specified in set command does not exist.
+*Could not find specified fix gcmc group ID*
+ Self-explanatory.
+
*Could not find thermo compute ID*
Compute ID specified in thermo_style command does not exist.
@@ -2677,6 +2867,9 @@ Errors:
*Delete_atoms cutoff > max neighbor cutoff*
Can only delete atoms in atom pairs that will be in neighbor list.
+*Delete_atoms mol yes requires atom attribute molecule*
+ Cannot use this option with a non-molecular system.
+
*Delete_atoms requires a pair style be defined*
This is because atom deletion within a cutoff uses a pairwise
neighbor list.
@@ -2688,9 +2881,6 @@ Errors:
*Delete_bonds command with no atoms existing*
No atoms are yet defined so the delete_bonds command cannot be used.
-*Delta_mu not allowed when not using semi-grand in fix atom/swap command*
- Self-explanatory.
-
*Deposition region extends outside simulation box*
Self-explanatory.
@@ -2838,6 +3028,9 @@ Errors:
*Double precision is not supported on this accelerator*
Self-explanatory
+*Dump atom/gz only writes compressed files*
+ The dump atom/gz output file name must have a .gz suffix.
+
*Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu*
Self-explanatory.
@@ -2848,6 +3041,9 @@ Errors:
*Dump cfg requires one snapshot per file*
Use the wildcard "*" character in the filename.
+*Dump cfg/gz only writes compressed files*
+ The dump cfg/gz output file name must have a .gz suffix.
+
*Dump custom and fix not computed at compatible times*
The fix must produce per-atom quantities on timesteps that dump custom
needs them.
@@ -2880,6 +3076,9 @@ Errors:
Only atom-style variables generate per-atom quantities, needed for
dump output.
+*Dump custom/gz only writes compressed files*
+ The dump custom/gz output file name must have a .gz suffix.
+
*Dump dcd of non-matching # of atoms*
Every snapshot written by dump dcd must contain the same # of atoms.
@@ -2899,18 +3098,27 @@ Errors:
*Dump file is incorrectly formatted*
Self-explanatory.
+*Dump image body yes requires atom style body*
+ Self-explanatory.
+
*Dump image bond not allowed with no bond types*
Self-explanatory.
*Dump image cannot perform sorting*
Self-explanatory.
+*Dump image line requires atom style line*
+ Self-explanatory.
+
*Dump image persp option is not yet supported*
Self-explanatory.
*Dump image requires one snapshot per file*
Use a "*" in the filename.
+*Dump image tri requires atom style tri*
+ Self-explanatory.
+
*Dump local and fix not computed at compatible times*
The fix must produce per-atom quantities on timesteps that dump local
needs them.
@@ -2990,6 +3198,9 @@ Errors:
*Dump xtc requires sorting by atom ID*
Use the dump_modify sort command to enable this.
+*Dump xyz/gz only writes compressed files*
+ The dump xyz/gz output file name must have a .gz suffix.
+
*Dump_modify buffer yes not allowed for this style*
Self-explanatory.
@@ -3004,6 +3215,9 @@ Errors:
The chosen atom style does not define the per-atom quantity being
dumped.
+*Duplicate atom IDs exist*
+ Self-explanatory.
+
*Duplicate fields in read_dump command*
Self-explanatory.
@@ -3014,6 +3228,9 @@ Errors:
*Electronic temperature dropped below zero*
Something has gone wrong with the fix ttm electron temperature model.
+*Element not defined in potential file*
+ The specified element is not in the potential file.
+
*Empty brackets in variable*
There is no variable syntax that uses empty brackets. Check
the variable doc page.
@@ -3033,6 +3250,21 @@ Errors:
A pre-tabulated spline is invalid. Likely a problem with the
potential parameters.
+*Error writing averaged chunk data*
+ Something in the output to the file triggered an error.
+
+*Error writing file header*
+ Something in the output to the file triggered an error.
+
+*Error writing out correlation data*
+ Something in the output to the file triggered an error.
+
+*Error writing out histogram data*
+ Something in the output to the file triggered an error.
+
+*Error writing out time averaged data*
+ Something in the output to the file triggered an error.
+
*Failed to allocate %ld bytes for array %s*
Your LAMMPS simulation has run out of memory. You need to run a
smaller simulation or on more processors.
@@ -3311,6 +3543,9 @@ Errors:
All inputs in a single fix ave/histo command must be of the
same style.
+*Fix ave/histo/weight value and weight vector lengths do not match*
+ Self-explanatory.
+
*Fix ave/spatial compute does not calculate a per-atom array*
Self-explanatory.
@@ -3539,6 +3774,9 @@ Errors:
*Fix gcmc and fix shake not using same molecule template ID*
Self-explanatory.
+*Fix gcmc atom has charge, but atom style does not*
+ Self-explanatory.
+
*Fix gcmc cannot exchange individual atoms belonging to a molecule*
This is an error since you should not delete only one atom of a
molecule. The user has specified atomic (non-molecular) gas
@@ -3552,6 +3790,9 @@ Errors:
simulated. The general molecule flag is off, but gcmc's molecule flag
is on.
+*Fix gcmc molecule has charges, but atom style does not*
+ Self-explanatory.
+
*Fix gcmc molecule must have atom types*
The defined molecule does not specify atom types.
@@ -3562,6 +3803,9 @@ Errors:
When using atom_style template, you cannot insert molecules that are
not in that template.
+*Fix gcmc put atom outside box*
+ This should not normally happen. Contact the developers.
+
*Fix gcmc ran out of available atom IDs*
See the setting for tagint in the src/lmptype.h file.
@@ -3699,7 +3943,7 @@ Errors:
*Fix nve/line requires line particles*
Self-explanatory.
-*Fix nve/sphere requires atom attribute mu*
+*Fix nve/sphere dipole requires atom attribute mu*
An atom style with this attribute is needed.
*Fix nve/sphere requires atom style sphere*
@@ -3721,6 +3965,9 @@ Errors:
The shape setting for a particle in the fix group has shape = 0.0,
which means it is a point particle.
+*Fix nvt/nph/npt body requires bodies*
+ Self-explanatory.
+
*Fix nvt/nph/npt sphere requires atom style sphere*
Self-explanatory.
@@ -3822,6 +4069,12 @@ Errors:
*Fix qeq/dynamic requires atom attribute q*
Self-explanatory.
+*Fix qeq/fire group has no atoms*
+ Self-explanatory.
+
+*Fix qeq/fire requires atom attribute q*
+ Self-explanatory.
+
*Fix qeq/point group has no atoms*
Self-explanatory.
@@ -4029,8 +4282,11 @@ Errors:
*Fix temp/berendsen variable returned negative temperature*
Self-explanatory.
-*Fix temp/csvr is not compatible with fix shake*
- These two commands cannot currently be used toghether.
+*Fix temp/csld is not compatible with fix rattle or fix shake*
+ These two commands cannot currently be used together with fix temp/csld.
+
+*Fix temp/csld variable returned negative temperature*
+ Self-explanatory.
*Fix temp/csvr variable returned negative temperature*
Self-explanatory.
@@ -4176,6 +4432,9 @@ Errors:
*GPU split param must be positive for hybrid pair styles*
See the package gpu command.
+*GPUs are requested but Kokkos has not been compiled for CUDA*
+ Recompile Kokkos with CUDA support to use GPUs.
+
*Ghost velocity forward comm not yet implemented with Kokkos*
This is a current restriction.
@@ -4244,6 +4503,10 @@ Errors:
One or more of the coefficients defined in the potential file is
invalid.
+*Illegal Vashishta parameter*
+ One or more of the coefficients defined in the potential file is
+ invalid.
+
*Illegal compute voronoi/atom command (occupation and (surface or edges))*
Self-explanatory.
@@ -4258,7 +4521,7 @@ Errors:
Self-explanatory.
*Illegal fix gcmc gas mass <= 0*
- The computed mass of the designated gas molecule or atom type was less
+ The computed mass of the designated gas molecule or atom type was less
than or equal to zero.
*Illegal fix tfmc random seed*
@@ -4283,9 +4546,24 @@ Errors:
*Illegal number of pair table entries*
There must be at least 2 table entries.
+*Illegal or unset periodicity in restart*
+ This error should not normally occur unless the restart file is invalid.
+
+*Illegal range increment value*
+ The increment must be >= 1.
+
*Illegal simulation box*
The lower bound of the simulation box is greater than the upper bound.
+*Illegal size double vector read requested*
+ This error should not normally occur unless the restart file is invalid.
+
+*Illegal size integer vector read requested*
+ This error should not normally occur unless the restart file is invalid.
+
+*Illegal size string or corrupt restart*
+ This error should not normally occur unless the restart file is invalid.
+
*Imageint setting in lmptype.h is invalid*
Imageint must be as large or larger than smallint.
@@ -4462,6 +4740,9 @@ Errors:
*Incorrect format in Tersoff potential file*
Incorrect number of words per line in the potential file.
+*Incorrect format in Vashishta potential file*
+ Incorrect number of words per line in the potential file.
+
*Incorrect format in coul/streitz potential file*
Incorrect number of words per line in the potential file.
@@ -4474,6 +4755,9 @@ Errors:
*Incorrect multiplicity arg for dihedral coefficients*
Self-explanatory. Check the input script or data file.
+*Incorrect number of elements in potential file*
+ Self-explanatory.
+
*Incorrect rigid body format in fix rigid file*
The number of fields per line is not what expected.
@@ -4483,6 +4767,9 @@ Errors:
*Incorrect sign arg for dihedral coefficients*
Self-explanatory. Check the input script or data file.
+*Incorrect table format check for element types*
+ Self-explanatory.
+
*Incorrect velocity format in data file*
Each atom style defines a format for the Velocity section
of the data file. The read-in lines do not match.
@@ -4534,9 +4821,30 @@ Errors:
*Invalid -reorder N value*
Self-explanatory.
+*Invalid Angles section in molecule file*
+ Self-explanatory.
+
+*Invalid Bonds section in molecule file*
+ Self-explanatory.
+
*Invalid Boolean syntax in if command*
Self-explanatory.
+*Invalid Charges section in molecule file*
+ Self-explanatory.
+
+*Invalid Coords section in molecule file*
+ Self-explanatory.
+
+*Invalid Diameters section in molecule file*
+ Self-explanatory.
+
+*Invalid Dihedrals section in molecule file*
+ Self-explanatory.
+
+*Invalid Impropers section in molecule file*
+ Self-explanatory.
+
*Invalid Kokkos command-line args*
Self-explanatory. See Section 2.7 of the manual for details.
@@ -4544,10 +4852,22 @@ Errors:
The file does not appear to be a LAMMPS restart file since
it doesn't contain the correct magic string at the beginning.
+*Invalid Masses section in molecule file*
+ Self-explanatory.
+
*Invalid REAX atom type*
There is a mis-match between LAMMPS atom types and the elements
listed in the ReaxFF force field file.
+*Invalid Special Bond Counts section in molecule file*
+ Self-explanatory.
+
+*Invalid Types section in molecule file*
+ Self-explanatory.
+
+*Invalid angle count in molecule file*
+ Self-explanatory.
+
*Invalid angle table length*
Length must be 2 or greater.
@@ -4661,9 +4981,6 @@ Errors:
*Invalid atom type in fix gcmc command*
The atom type specified in the gcmc command does not exist.
-*Invalid atom type in fix gcmc mol command*
- Self-explanatory.
-
*Invalid atom type in fix pour command*
Self-explanatory.
@@ -4722,6 +5039,9 @@ Errors:
*Invalid body nparticle command*
Arguments in atom-style command are not correct.
+*Invalid bond count in molecule file*
+ Self-explanatory.
+
*Invalid bond table length*
Length must be 2 or greater.
@@ -4850,6 +5170,9 @@ Errors:
*Invalid diameter in set command*
Self-explanatory.
+*Invalid dihedral count in molecule file*
+ Self-explanatory.
+
*Invalid dihedral type in Dihedrals section of data file*
Dihedral type must be positive integer and within range of specified
dihedral types.
@@ -4966,10 +5289,6 @@ Errors:
*Invalid flag in type arrays section of restart file*
Unrecognized entry in restart file.
-*Invalid format in Bodies section of data file*
- The specified number of integer or floating point values does not
- appear.
-
*Invalid frequency in temper command*
Nevery must be > 0.
@@ -4988,6 +5307,9 @@ Errors:
*Invalid immediate variable*
Syntax of immediate value is incorrect.
+*Invalid improper count in molecule file*
+ Self-explanatory.
+
*Invalid improper type in Impropers section of data file*
Improper type must be positive integer and within range of specified
improper types.
@@ -5001,6 +5323,15 @@ Errors:
*Invalid index in compute body/local command*
Self-explanatory.
+*Invalid is_active() function in variable formula*
+ Self-explanatory.
+
+*Invalid is_available() function in variable formula*
+ Self-explanatory.
+
+*Invalid is_defined() function in variable formula*
+ Self-explanatory.
+
*Invalid keyword in angle table parameters*
Self-explanatory.
@@ -5306,6 +5637,9 @@ Errors:
*Keyword %s in MEAM parameter file not recognized*
Self-explanatory.
+*Kokkos has been compiled for CUDA but no GPUs are requested*
+ One or more GPUs must be used when Kokkos is compiled for CUDA.
+
*Kspace style does not support compute group/group*
Self-explanatory.
@@ -5433,13 +5767,16 @@ Errors:
The IDs must not be larger than can be stored in a 32-bit integer
since chunk IDs are 32-bit integers.
+*Molecule auto special bond generation overflow*
+ Counts exceed maxspecial setting for other atoms in system.
+
*Molecule file has angles but no nangles setting*
Self-explanatory.
-*Molecule file has bonds but no nbonds setting*
+*Molecule file has body params but no setting for them*
Self-explanatory.
-*Molecule file has bonds but no special flags*
+*Molecule file has bonds but no nbonds setting*
Self-explanatory.
*Molecule file has dihedrals but no ndihedrals setting*
@@ -5448,12 +5785,21 @@ Errors:
*Molecule file has impropers but no nimpropers setting*
Self-explanatory.
+*Molecule file has no Body Doubles section*
+ Self-explanatory.
+
+*Molecule file has no Body Integers section*
+ Self-explanatory.
+
*Molecule file has special flags but no bonds*
Self-explanatory.
*Molecule file needs both Special Bond sections*
Self-explanatory.
+*Molecule file requires atom style body*
+ Self-explanatory.
+
*Molecule file shake flags not before shake atoms*
The order of the two sections is important.
@@ -5472,6 +5818,12 @@ Errors:
*Molecule file z coord must be 0.0 for 2d*
Self-explanatory.
+*Molecule natoms must be 1 for body particle*
+ Self-explanatory.
+
+*Molecule sizescale must be 1.0 for body particle*
+ Self-explanatory.
+
*Molecule template ID for atom_style template does not exist*
Self-explanatory.
@@ -5516,6 +5868,9 @@ Errors:
*More than one fix shake*
Only one fix shake can be defined.
+*Mu not allowed when not using semi-grand in fix atom/swap command*
+ Self-explanatory.
+
*Must define angle_style before Angle Coeffs*
Must use an angle_style command before reading a data file that
defines Angle Coeffs.
@@ -5647,6 +6002,9 @@ Errors:
A multi-partition simulation cannot read the input script from stdin.
The -in command-line option must be used to specify a file.
+*Must use Kokkos half/thread or full neighbor list with threads or GPUs*
+ Using Kokkos half-neighbor lists with threading is not allowed.
+
*Must use a block or cylinder region with fix pour*
Self-explanatory.
@@ -5696,7 +6054,7 @@ Errors:
*NL ramp in wall/piston only implemented in zlo for now*
The ramp keyword can only be used for piston applied to face zlo.
-*Need ntypes-1 delta_mu values in fix atom/swap command*
+*Need nswaptypes mu values in fix atom/swap command*
Self-explanatory.
*Needed bonus data not in data file*
@@ -5773,9 +6131,6 @@ Errors:
*No angles allowed with this atom style*
Self-explanatory.
-*No atom count in molecule file*
- Self-explanatory.
-
*No atoms in data file*
The header of the data file indicated that atoms would be included,
but they are not present.
@@ -5795,6 +6150,9 @@ Errors:
*No box information in dump. You have to use 'box no'*
Self-explanatory.
+*No count or invalid atom count in molecule file*
+ The number of atoms must be specified.
+
*No dihedral style is defined for compute dihedral/local*
Self-explanatory.
@@ -5862,6 +6220,12 @@ Errors:
*No triangles allowed with this atom style*
Self-explanatory. Check data file.
+*No values in fix ave/chunk command*
+ Self-explanatory.
+
+*No values in fix ave/time command*
+ Self-explanatory.
+
*Non digit character between brackets in variable*
Self-explantory.
@@ -5872,8 +6236,11 @@ Errors:
*Non-numeric box dimensions - simulation unstable*
The box size has apparently blown up.
-*Not all atom IDs are 0*
- Either all atoms IDs must be zero or none of them.
+*Non-zero atom IDs with atom_modify id = no*
+ Self-explanatory.
+
+*Non-zero read_data shift z value for 2d simulation*
+ Self-explanatory.
*Nprocs not a multiple of N for -reorder*
Self-explanatory.
@@ -5886,10 +6253,24 @@ Errors:
integers is using a value that is less than 1 or greater than the
maximum allowed limit.
+*One or more Atom IDs is negative*
+ Atom IDs must be positive integers.
+
+*One or more atom IDs is too big*
+ The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
+ setting in your Makefile. See Section_start 2.2 of the manual for
+ more details.
+
+*One or more atom IDs is zero*
+ Either all atoms IDs must be zero or none of them.
+
*One or more atoms belong to multiple rigid bodies*
Two or more rigid bodies defined by the fix rigid command cannot
contain the same atom.
+*One or more rigid bodies are a single particle*
+ Self-explanatory.
+
*One or zero atoms in rigid body*
Any rigid body defined by the fix rigid command must contain 2 or more
atoms.
@@ -5907,7 +6288,7 @@ Errors:
Self-explanatory.
*Out of range atoms - cannot compute MSM*
- One or more atoms are attempting to map their charge to a MSM grid point
+ One or more atoms are attempting to map their charge to a MSM grid point
that is not owned by a processor. This is likely for one of two
reasons, both of them bad. First, it may mean that an atom near the
boundary of a processor's sub-domain has moved more than 1/2 the
@@ -6080,6 +6461,9 @@ Errors:
*Pair dipole/long requires atom attributes q, mu, torque*
The atom style defined does not have these attributes.
+*Pair dipole/sf/gpu requires atom attributes q, mu, torque*
+ The atom style defined does not one or more of these attributes.
+
*Pair distance < table inner cutoff*
Two atoms are closer together than the pairwise table allows.
@@ -6105,8 +6489,8 @@ Errors:
*Pair gayberne/gpu requires atoms with same type have same shape*
Self-explanatory.
-*Pair granular requires atom style sphere*
- Self-explanatory.
+*Pair granular requires atom attributes radius, rmass*
+ The atom style defined does not have these attributes.
*Pair granular requires ghost atoms store velocity*
Use the comm_modify vel yes command to enable this.
@@ -6115,6 +6499,9 @@ Errors:
This is a current restriction of the implementation of pair
granular styles with history.
+*Pair hybrid single calls do not support per sub-style special bond values*
+ Self-explanatory.
+
*Pair hybrid sub-style does not support single call*
You are attempting to invoke a single() call on a pair style
that doesn't support it.
@@ -6263,6 +6650,13 @@ Errors:
See the newton command. This is a restriction to use the Tersoff
potential.
+*Pair style Vashishta requires atom IDs*
+ This is a requirement to use the Vashishta potential.
+
+*Pair style Vashishta requires newton pair on*
+ See the newton command. This is a restriction to use the Vashishta
+ potential.
+
*Pair style bop requires comm ghost cutoff at least 3x larger than %g*
Use the communicate ghost command to set this. See the pair bop
doc page for more details.
@@ -6363,6 +6757,10 @@ Errors:
*Pair style hybrid cannot have none as an argument*
Self-explanatory.
+*Pair style is incompatible with KSpace style*
+ If a pair style with a long-range Coulombic component is selected,
+ then a kspace style must also be used.
+
*Pair style is incompatible with TIP4P KSpace style*
The pair style does not have the requires TIP4P settings.
@@ -6443,6 +6841,9 @@ Errors:
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors.
+*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
+ The atom style defined does not have this attribute.
+
*Pair style nb3b/harmonic requires atom IDs*
This is a requirement to use this potential.
@@ -6458,6 +6859,13 @@ Errors:
*Pair style peri requires atom style peri*
Self-explanatory.
+*Pair style polymorphic requires atom IDs*
+ This is a requirement to use the polymorphic potential.
+
+*Pair style polymorphic requires newton pair on*
+ See the newton command. This is a restriction to use the polymorphic
+ potential.
+
*Pair style reax requires atom IDs*
This is a requirement to use the ReaxFF potential.
@@ -6479,6 +6887,12 @@ Errors:
*Pair style sw/gpu requires newton pair off*
See the newton command. This is a restriction to use this potential.
+*Pair style tersoff/gpu requires atom IDs*
+ This is a requirement to use the tersoff/gpu potential.
+
+*Pair style tersoff/gpu requires newton pair off*
+ See the newton command. This is a restriction to use this pair style.
+
*Pair style tip4p/cut requires atom IDs*
This is a requirement to use this potential.
@@ -6510,6 +6924,9 @@ Errors:
*Pair tersoff/zbl requires metal or real units*
This is a current restriction of this pair potential.
+*Pair tersoff/zbl/kk requires metal or real units*
+ This is a current restriction of this pair potential.
+
*Pair tri/lj requires atom style tri*
Self-explanatory.
@@ -6535,6 +6952,10 @@ Errors:
*Pair_modify command before pair_style is defined*
Self-explanatory.
+*Pair_modify special setting for pair hybrid incompatible with global special_bonds setting*
+ Cannot override a setting of 0.0 or 1.0 or change a setting between
+ 0.0 and 1.0.
+
*Pair_write command before pair_style is defined*
Self-explanatory.
@@ -6542,9 +6963,9 @@ Errors:
Particles must be "exterior" to the wall in order for energy/force to
be calculated.
-*Particle on or inside surface of region used in fix wall/region*
- Particles must be "exterior" to the region surface in order for
- energy/force to be calculated.
+*Particle outside surface of region used in fix wall/region*
+ Particles must be inside the region for energy/force to be calculated.
+ A particle outside the region generates an error.
*Per-atom compute in equal-style variable formula*
Equal-style variables cannot use per-atom quantities.
@@ -6608,6 +7029,9 @@ Errors:
*Pressure control can not be used with fix nvt/asphere*
Self-explanatory.
+*Pressure control can not be used with fix nvt/body*
+ Self-explanatory.
+
*Pressure control can not be used with fix nvt/sllod*
Self-explanatory.
@@ -6620,6 +7044,9 @@ Errors:
*Pressure control must be used with fix nph/asphere*
Self-explanatory.
+*Pressure control must be used with fix nph/body*
+ Self-explanatory.
+
*Pressure control must be used with fix nph/small*
Self-explanatory.
@@ -6636,6 +7063,9 @@ Errors:
*Pressure control must be used with fix npt/asphere*
Self-explanatory.
+*Pressure control must be used with fix npt/body*
+ Self-explanatory.
+
*Pressure control must be used with fix npt/sphere*
Self-explanatory.
@@ -6707,6 +7137,10 @@ Errors:
*RATTLE velocity constraints are not satisfied up to desired tolerance*
Self-explanatory.
+*Read data add offset is too big*
+ It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit
+ integer.
+
*Read dump of atom property that isn't allocated*
Self-explanatory.
@@ -7064,6 +7498,22 @@ Errors:
*Sqrt of negative value in variable formula*
Self-explanatory.
+*Subsequent read data induced too many angles per atom*
+ See the create_box extra/angle/per/atom or read_data "extra angle per
+ atom" header value to set this limit larger.
+
+*Subsequent read data induced too many bonds per atom*
+ See the create_box extra/bond/per/atom or read_data "extra bond per
+ atom" header value to set this limit larger.
+
+*Subsequent read data induced too many dihedrals per atom*
+ See the create_box extra/dihedral/per/atom or read_data "extra
+ dihedral per atom" header value to set this limit larger.
+
+*Subsequent read data induced too many impropers per atom*
+ See the create_box extra/improper/per/atom or read_data "extra
+ improper per atom" header value to set this limit larger.
+
*Substitution for illegal variable*
Input script line contained a variable that could not be substituted
for.
@@ -7081,8 +7531,8 @@ Errors:
See the setting for bigint in the src/lmptype.h file.
*System is not charge neutral, net charge = %g*
- The total charge on all atoms on the system is not 0.0, which
- is not valid for the long-range Coulombic solvers.
+ The total charge on all atoms on the system is not 0.0.
+ For some KSpace solvers this is an error.
*TAD nsteps must be multiple of t_event*
Self-explanatory.
@@ -7152,18 +7602,28 @@ Errors:
*Temperature ID for fix temp/berendsen does not exist*
Self-explanatory.
+*Temperature ID for fix temp/csld does not exist*
+ Self-explanatory.
+
*Temperature ID for fix temp/csvr does not exist*
Self-explanatory.
*Temperature ID for fix temp/rescale does not exist*
Self-explanatory.
+*Temperature compute degrees of freedom < 0*
+ This should not happen if you are calculating the temperature
+ on a valid set of atoms.
+
*Temperature control can not be used with fix nph*
Self-explanatory.
*Temperature control can not be used with fix nph/asphere*
Self-explanatory.
+*Temperature control can not be used with fix nph/body*
+ Self-explanatory.
+
*Temperature control can not be used with fix nph/sphere*
Self-explanatory.
@@ -7176,6 +7636,9 @@ Errors:
*Temperature control must be used with fix npt/asphere*
Self-explanatory.
+*Temperature control must be used with fix npt/body*
+ Self-explanatory.
+
*Temperature control must be used with fix npt/sphere*
Self-explanatory.
@@ -7185,6 +7648,9 @@ Errors:
*Temperature control must be used with fix nvt/asphere*
Self-explanatory.
+*Temperature control must be used with fix nvt/body*
+ Self-explanatory.
+
*Temperature control must be used with fix nvt/sllod*
Self-explanatory.
@@ -7311,9 +7777,6 @@ Errors:
*Too big a problem to use velocity create loop all*
The system size must fit in a 32-bit integer to use this option.
-*Too big a timestep*
- Specified timestep is too large.
-
*Too big a timestep for dump dcd*
The timestep must fit in a 32-bit integer to use this dump style.
@@ -7324,6 +7787,15 @@ Errors:
Table size specified via pair_modify command does not work with your
machine's floating point representation.
+*Too few lines in %s section of data file*
+ Self-explanatory.
+
+*Too few values in body lines in data file*
+ Self-explanatory.
+
+*Too few values in body section of molecule file*
+ Self-explanatory.
+
*Too many -pk arguments in command line*
The string formed by concatenating the arguments is too long. Use a
package command in the input script instead.
@@ -7411,6 +7883,12 @@ Errors:
Table size specified via pair_modify command is too large. Note that
a value of N generates a 2^N size table.
+*Too many values in body lines in data file*
+ Self-explanatory.
+
+*Too many values in body section of molecule file*
+ Self-explanatory.
+
*Too much buffered per-proc info for dump*
The size of the buffered string must fit in a 32-bit integer for a
dump.
@@ -7522,6 +8000,15 @@ Errors:
*Unknown bond style*
The choice of bond style is unknown.
+*Unknown category for info is_active()*
+ Self-explanatory.
+
+*Unknown category for info is_available()*
+ Self-explanatory.
+
+*Unknown category for info is_defined()*
+ Self-explanatory.
+
*Unknown command: %s*
The command is not known to LAMMPS. Check the input script.
@@ -7555,6 +8042,15 @@ Errors:
*Unknown kspace style*
The choice of kspace style is unknown.
+*Unknown name for info newton category*
+ Self-explanatory.
+
+*Unknown name for info package category*
+ Self-explanatory.
+
+*Unknown name for info pair category*
+ Self-explanatory.
+
*Unknown pair style*
The choice of pair style is unknown.
@@ -7602,6 +8098,12 @@ Errors:
*Unsupported order in kspace_style pppm/disp, pair_style %s*
Only pair styles with 1/r and 1/r^6 dependence are currently supported.
+*Use cutoff keyword to set cutoff in single mode*
+ Mode is single so cutoff/multi keyword cannot be used.
+
+*Use cutoff/multi keyword to set cutoff in multi mode*
+ Mode is multi so cutoff keyword cannot be used.
+
*Using fix nvt/sllod with inconsistent fix deform remap option*
Fix nvt/sllod requires that deforming atoms have a velocity profile
provided by "remap v" as a fix deform option.
@@ -7634,6 +8136,12 @@ Errors:
*Using suffix omp without USER-OMP package installed*
Self-explanatory.
+*Using update dipole flag requires atom attribute mu*
+ Self-explanatory.
+
+*Using update dipole flag requires atom style sphere*
+ Self-explanatory.
+
*Variable ID in variable formula does not exist*
Self-explanatory.
@@ -7656,6 +8164,9 @@ Errors:
*Variable for create_atoms is invalid style*
The variables must be equal-style variables.
+*Variable for displace_atoms is invalid style*
+ It must be an equal-style or atom-style variable.
+
*Variable for dump every is invalid style*
Only equal-style variables can be used.
@@ -7713,6 +8224,9 @@ Errors:
*Variable for fix temp/berendsen is invalid style*
Only equal-style variables can be used.
+*Variable for fix temp/csld is invalid style*
+ Only equal-style variables can be used.
+
*Variable for fix temp/csvr is invalid style*
Only equal-style variables can be used.
@@ -7793,6 +8307,9 @@ Errors:
*Variable name for create_atoms does not exist*
Self-explanatory.
+*Variable name for displace_atoms does not exist*
+ Self-explanatory.
+
*Variable name for dump every does not exist*
Self-explanatory.
@@ -7868,6 +8385,9 @@ Errors:
*Variable name for fix temp/berendsen does not exist*
Self-explanatory.
+*Variable name for fix temp/csld does not exist*
+ Self-explanatory.
+
*Variable name for fix temp/csvr does not exist*
Self-explanatory.
@@ -8064,6 +8584,13 @@ Warnings:
*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
Self-explantory.
+*Calling write_dump before a full system init.*
+ The write_dump command is used before the system has been fully
+ initialized as part of a 'run' or 'minimize' command. Not all dump
+ styles and features are fully supported at this point and thus the
+ command may fail or produce incomplete or incorrect output. Insert
+ a "run 0" command, if a full system init is required.
+
*Cannot count rigid body degrees-of-freedom before bodies are fully initialized*
This means the temperature associated with the rigid bodies may be
incorrect on this timestep.
@@ -8126,6 +8653,11 @@ Warnings:
If the fix changes the timestep, the dump dcd file will not
reflect the change.
+*Energy tally does not account for 'zero yes'*
+ The energy removed by using the 'zero yes' flag is not accounted
+ for in the energy tally and thus energy conservation cannot be
+ monitored in this case.
+
*Estimated error in splitting of dispersion coeffs is %g*
Error is greater than 0.0001 percent.
@@ -8151,6 +8683,11 @@ Warnings:
See the doc page for fix bond/swap for more info on this
restriction.
+*Fix deposit near setting < possible overlap separation %g*
+ This test is performed for finite size particles with a diameter, not
+ for point particles. The near setting is smaller than the particle
+ diameter which can lead to overlaps.
+
*Fix evaporate may delete atom with non-zero molecule ID*
This is probably an error, since you should not delete only one atom
of a molecule.
@@ -8162,11 +8699,8 @@ Warnings:
pair style, an eam pair style, or no "single" function for the pair
style.
-*Fix move does not update angular momentum*
- Atoms store this quantity, but fix move does not (yet) update it.
-
-*Fix move does not update quaternions*
- Atoms store this quantity, but fix move does not (yet) update it.
+*Fix property/atom mol or charge w/out ghost communication*
+ A model typically needs these properties defined for ghost atoms.
*Fix qeq CG convergence failed (%g) after %d iterations at %ld step*
Self-explanatory.
@@ -8180,6 +8714,9 @@ Warnings:
*Fix qeq/dynamic tolerance may be too small for damped dynamics*
Self-explanatory.
+*Fix qeq/fire tolerance may be too small for damped fires*
+ Self-explanatory.
+
*Fix rattle should come after all other integration fixes*
This fix is designed to work after all other integration fixes change
atom positions. Thus it should be the last integration fix specified.
@@ -8236,9 +8773,13 @@ Warnings:
computes a temperature on a different group of atoms than the fix
itself operates on. This is probably not what you want to do.
-*H matrix size has been exceeded: m_fill=%d H.m=%d\\n*
+*H matrix size has been exceeded: m_fill=%d H.m=%d\n*
This is the size of the matrix.
+*Ignoring unknown or incorrect info command flag*
+ Self-explanatory. An unknown argument was given to the info command.
+ Compare your input with the documentation.
+
*Improper atoms missing at step %ld*
One or more of 4 atoms needed to compute a particular improper are
missing on this processor. Typically this is because the pairwise
@@ -8361,9 +8902,15 @@ Warnings:
*More than one compute erotate/sphere/atom*
It is not efficient to use compute erorate/sphere/atom more than once.
+*More than one compute hexorder/atom*
+ It is not efficient to use compute hexorder/atom more than once.
+
*More than one compute ke/atom*
It is not efficient to use compute ke/atom more than once.
+*More than one compute orientorder/atom*
+ It is not efficient to use compute orientorder/atom more than once.
+
*More than one compute plasticity/atom*
Self-explanatory.
@@ -8570,11 +9117,18 @@ Warnings:
cluster specified by the fix shake command is numerically suspect. LAMMPS
will set it to 0.0 and continue.
+*Shell command '%s' failed with error '%s'*
+ Self-explanatory.
+
+*Shell command returned with non-zero status*
+ This may indicate the shell command did not operate as expected.
+
*Should not allow rigid bodies to bounce off relecting walls*
LAMMPS allows this, but their dynamics are not computed correctly.
-*Should not use fix nve/limit with fix shake*
- This will lead to invalid constraint forces in the SHAKE computation.
+*Should not use fix nve/limit with fix shake or fix rattle*
+ This will lead to invalid constraint forces in the SHAKE/RATTLE
+ computation.
*Simulations might be very slow because of large number of structure factors*
Self-explanatory.
@@ -8583,8 +9137,8 @@ Warnings:
Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM.
*System is not charge neutral, net charge = %g*
- The total charge on all atoms on the system is not 0.0, which
- is not valid for the long-range Coulombic solvers.
+ The total charge on all atoms on the system is not 0.0.
+ For some KSpace solvers this is only a warning.
*Table inner cutoff >= outer cutoff*
You specified an inner cutoff for a Coulombic table that is longer
@@ -8679,11 +9233,20 @@ Warnings:
*Using package gpu without any pair style defined*
Self-explanatory.
+*Using pair potential shift with pair_modify compute no*
+ The shift effects will thus not be computed.
+
*Using pair tail corrections with nonperiodic system*
This is probably a bogus thing to do, since tail corrections are
computed by integrating the density of a periodic system out to
infinity.
+*Using pair tail corrections with pair_modify compute no*
+ The tail corrections will thus not be computed.
+
+*pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c*
+ Self-explanatory.
+
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 7c9ab29db2..804be08ae2 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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er:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,195,196,201,208,209,211,212,213,214,217,218,219,220,222,223,233,239,241,243,249,256,260,261,262,263,265,266,267,273,278,279,280,282,303,304,317,331,341,354,360,366,367,368,370,371,372,375,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,222,375,391],afil:237,aforement:18,afresh:[291,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,199,200,201,205,206,208,209,216,217,218,219,220,222,226,235,246,247,248,249,250,255,256,257,259,265,266,267,273,278,279,280,282,285,289,293,301,303,306,315,320,322,323,324,326,327,328,329,330,334,336,338,342,345,346,352,359,365,366,368,369,371,373,374,375,376,377,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,196,222,239,289,345,359,370,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,223,370,439,440],aggreg:[6,12,65,68,69,79,95,112,119,239,255,301,303,317,471,503],aggress:[239,490],agilio:[9,13],agre:[3,8,190,368,377,411,440],agreement:[5,7],ahd:408,ahead:338,aidan:[0,5,7,9,13,363],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:195,akohlmei:[7,9,13,197,240],aktulga:[7,9,296,440],al2o3:447,al2o3_001:[122,304],al3:169,ala:[246,447],alain:9,alat:[284,426],alb:[437,460,462],albeit:302,albert:9,alchem:[89,164],alcohol:334,alcu:[376,382],alcu_eam:437,alderton:395,alejandr:[259,260],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,196,205,216,219,222,246,248,249,273,286,294,303,306,307,326,327,331,334,339,366,367,368,372,375,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,361],aliceblu:196,align:[6,12,29,41,71,172,190,212,216,241,363,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,252,254,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,311,315,316,318,319,320,321,322,323,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,350,355,358,359,360,361,362,363,365,368,369,370,371,372,374,375,376,377,378,380,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:343,alloc:[3,5,6,8,9,11,12,60,233,333,369,371,375,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,195,196,197,199,200,202,204,205,206,208,209,210,211,212,213,214,216,218,219,220,221,222,223,227,228,233,235,236,237,238,240,243,246,249,250,254,256,259,260,284,288,289,290,291,292,293,297,303,304,306,308,310,311,315,319,326,327,328,329,331,332,333,334,335,336,342,344,346,355,360,361,363,368,369,370,371,374,375,378,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,241,293,331,361,372,375,456],alo:392,alon:[6,7,219,299,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,195,208,219,241,246,247,251,256,258,293,303,306,308,312,316,317,326,330,331,337,340,342,363,366,367,368,370,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,200,246,285,293,294,298,368,376,379,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,199,346,355,369,389,457,476],alphanumer:[3,63,199,292,300,344,369,502],alreadi:[3,7,8,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_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,345,346,355,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,410,429,431,459,473,474,502],compens:[6,217,218,301,371,402],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,429,476,477,481,502],compl:17,complain:[11,12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,402,429,459,474,476,479,502],compli:[326,330],complic:[6,7,9,12,13,206,235,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,381,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,206,246,400],compound:[391,402,403,465],compres:[71,118,208],compress:[],compris:[40,340,441,464],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,382],computational:497,compute_arrai:8,compute_fep:[201,422],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:340,concentr:[71,400],concept:[6,150,160,208,485],conceptu:[3,6,71,158,220,222,370,392,409,426,481],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,502],conden:[331,460,462],condens:[6,152,331,377,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,431,474],conform:[3,6,13,59,219,220,258,302,308,330,354,370,402,488],confus:[3,465],conjuct:396,conjug:[7,8,243,367,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,219,240,288,303,306,316,370,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,392,414,418,471,477,479],consequ:[1,6,206,331,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,243,244,322,323,324,375,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,298,435,502],consumpt:358,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,205,331,444,446],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,444,446,468,505],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:205,controlfil:440,convect:93,conveni:[6,12,29,193,197,214,304,363,448,502],convent:[3,8,9,29,181,188,189,196,302,316,343,400,402,502],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,391,392,414,447,471,483,490],convers:[3,8,144,195,196,206,209,290,360,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,340,381],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:447,coordbb:447,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,195,340,341,363,464,476],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,394,424,429,473,474,476,486,501,503],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,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196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[406,493],dat:[6,93,190,205,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:425,davi:336,david:[9,19,360,361,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,477,481],ddim:192,deactiv:422,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,256,292,303,332,491],decipher:363,declar:194,declin:319,decod:195,decompos:[89,448],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,497],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,288],degrad:[8,18,285,361,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,395,400,408,486,494,497,503],degress:[150,208],del:490,delai:[3,6,12,371,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[474,502],deloc:[260,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:3,delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:381,delx:192,delz:192,dem:381,demand:298,demo:11,demon:283,demonstr:[293,426],den:289,dendrim:408,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,392,407,409,440,444,446],dens:[71,219,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:223,deposit:[],deprec:[294,439],depth:[51,148,195,331,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,195],despit:497,destabil:382,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,234,289,330,370,391,408,413,471,473,476,487,490,502],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:307,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,382,402,428,429,447,465,478],devemi:9,deviat:[257,264,284,404],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,391],devis:428,dfactor:195,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,429],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,444,446],diagonalstyl:448,diagram:[41,122,169,189,216,286],diallo:408,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,381,390,405,406,416,441,464,468,476,477,486],diamond:[363,402,426],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,262,263,265,266,267,269,271,274,276,277,278,279,282,284,286,288,290,293,294,295,298,301,303,306,308,316,317,319,322,323,324,327,328,329,331,334,335,336,337,340,344,345,355,357,359,360,361,363,364,366,367,369,370,372,373,374,375,376,377,382,386,387,389,390,391,396,397,398,400,402,405,406,407,409,412,414,415,417,418,425,426,427,428,430,431,433,437,439,440,441,442,443,444,446,447,448,449,457,458,459,460,462,464,465,468,470,471,473,474,476,478,479,480,481,484,485,486,488,490,491,493,494,495,497,501,502,503,504],differenti:[1,3,6,29,190,360,392,437,461],difficult:[220,286,375,408,485],difficulti:[94,110,306,439],diffract:[],diffus:[],digit:[2,3,196,344,429],dih_table1:190,dih_table2:190,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:218,dihydrid:402,dij:306,dilat:[],dim1:3,dim2:3,dim:[3,59,71,147,151,152,153,156,157,158,159,160,162,170,192,212,222,241,337,363,426,479,501,502,503],dimdim:502,dimems:285,dimens:[],dimensinon:71,dimension:[3,39,94,116,122,144,147,150,151,152,153,156,157,158,159,160,162,169,191,208,212,258,285,331,363,366,370,437,476,486],dimensionless:[108,125,126,128,131,133,135,140,144,331,361,448,468],dimentionless:139,dimer:[6,303,426],dimgrai:196,dimstr:[41,216],dinola:[290,322],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,193,321,497],dir1:487,dir2:487,dir:[1,3,4,8,9,11,12,257,284,293,318,437,439,440,474,487,502],dirac:144,direc:437,direct:[],directli:[3,6,8,9,11,12,89,117,144,146,193,194,195,202,228,237,241,246,285,304,323,335,337,338,339,340,363,367,375,376,377,383,385,386,392,395,400,402,414,418,431,434,442,456,474,486,487,488,494,502],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,197,221,242,288,294,297,307,315,319,328,329,370,374,376,377,382,389,391,392,400,401,403,410,411,422,426,427,428,429,433,437,438,439,440,447,448,458,460,461,462,465,474,476,477,478,487,502],disabl:[3,12,16,331,413,474,489,502],disadvantag:[6,216],disallow:[193,222,259],disappear:478,discard:[2,3,41,71,210,212,216,332,340,473,478,479],discontinu:[9,190,368,420],discourag:426,discov:[13,332],discret:[6,8,40,42,195,196,243,246,381],discuss:[],disk:[6,86,87,94,163,191,223,235,289,474],disloc:[70,429],disord:[39,70,429],disp:[],dispar:441,disperion:[395,418],dispers:[3,6,7,9,168,285,360,361,386,395,418,423,431,440,459,465],displac:[],displace_atom:[],displace_box:59,displacemet:479,displai:[11,13,22,37,44,55,178,189,193,195,346,355,389,457],dispters:3,disregard:429,dissip:[6,9,40,82,83,230,236,243,285,307,328,329,384,396,397,398,406,423,424,457],dissolut:217,dist:[6,69,93,112,121,193,286,302,399,456,471,503],distanc:[],distinct:[6,226,300,360,441],distinguish:[6,88,144,249,381,402,475],distort:[168,376],distrbut:376,distribut:[],distro:[115,389,436,437],ditto:[8,12,14,15,16,17,18,42,119,218,469,474],div:8,divd:121,diverg:[3,12,39,303,329,478,497,504],divid:[3,6,16,41,93,116,121,130,132,145,167,168,178,189,196,208,209,211,216,222,284,327,334,339,360,368,370,403,440,447,465,485,493,502],divis:[6,246,382,412,422,473,494,502],dl_poli:[6,7],dlambda:164,dlammps_async_imd:240,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,195],dlammps_gzip:[3,12,193,195,330,476,477,481],dlammps_jpeg:[3,12,195],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,195],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,193],dlen:486,dlmp_intel_offload:[12,16],dlo:[59,192,222,289],dlopen:6,dlvo:[7,390,468],dm_lb:246,dmax:[319,366],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,89,92,96,105,107,108,109,111,113,115,116,118,121,123,145,148,149,150,163,165,167,170,171,172,178,189,192,193,194,195,196,197,199,200,201,206,207,208,209,210,211,212,213,214,223,235,243,244,254,259,260,265,266,267,271,278,279,280,281,282,289,292,303,316,319,322,323,324,333,337,340,342,344,346,355,359,368,369,370,375,376,377,380,381,389,391,392,400,401,403,408,409,411,412,426,427,428,431,433,436,437,438,448,457,458,460,462,464,465,474,476,477,478,479,481,484,485,486,493,494,502,503,504,505],docuement:441,dodd:[42,381],dodgerblu:196,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,89,90,93,107,114,120,121,122,146,148,150,152,153,158,160,164,169,170,171,172,174,176,178,183,189,190,192,193,194,195,196,199,205,206,208,212,215,216,218,219,220,222,226,228,231,232,235,236,239,241,243,244,246,249,255,259,260,261,262,263,265,266,267,278,279,280,281,282,290,291,292,296,298,301,303,319,322,324,326,327,331,334,335,336,339,340,341,342,347,348,349,351,352,354,359,360,361,362,363,369,370,371,376,377,378,379,380,381,382,384,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,409,410,411,412,413,416,417,419,420,421,423,424,426,427,428,429,431,437,438,439,440,441,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,467,468,469,471,472,473,474,476,477,478,479,480,483,484,486,487,488,489,490,493,494,497,502,506],doegenomestolif:7,doesn:[3,7,8,12,170,193,206,212,213,316,369,371,375,377,391,401,411,439,440,458,460,461,462,465,476,478],dof:[3,8,116,148,149,150,163,208,303,503],dof_per_atom:[150,208],dof_per_chunk:[150,208],doff:[369,476],doi:[6,221],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,122,159,169,172,192,194,195,196,199,206,216,220,222,223,239,242,246,259,260,286,298,303,307,331,336,337,360,361,370,375,399,431,471,473,476,480,493],domin:[1,402,490],don:[0,8,12,13,120,173,202,228,244,292,340,426,447,474,476],donadio:323,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,164,167,170,173,190,193,195,196,205,206,208,210,211,212,213,214,216,217,218,219,220,222,223,231,233,235,240,241,243,244,251,259,265,266,267,278,279,280,282,283,285,286,287,289,292,300,303,304,306,319,322,323,324,326,328,329,342,344,359,360,361,368,370,371,374,375,377,386,400,409,410,411,418,424,425,426,431,439,456,459,464,471,472,473,474,477,480,481,484,494,495,497,502,503],donor:408,dot:[145,166,202,228,238,258],doti:[382,437],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,89,222,233,291,340,344,359,361,374,375,382,403,407,429,439,440,472,476,480,484,489,502,503],dover:205,down:[3,6,7,8,11,39,71,220,235,243,319,335,375,402,431,447,475,495],downhil:[366,367],download:[5,7,8,9,11,12,13,17,240,410,438],downsid:6,downward:300,dozen:[8,12,111,199,439,440],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:252,dpdtheta:[40,82,83,398],dpdtheta_i:[230,231],dproduct:378,dr_ewald:[122,304],drag:[],dragforc:246,drai:[257,293],drain:[239,335,368],dramat:[59,192,217,218,219,220,222,259,319,322,323,361,375,431,447,473],drautz:382,draw:195,drawback:292,drawn:[42,193,195,196,236,471],drayleigh:[257,293],dreid:[],drfourth:108,drho:[117,376,400],drift:[6,106,108,236,237,243,244,255,301,319,485,493,497],drive:[11,12,203,220,222,238,259,284,290,303,338,370],driven:[6,182],driver:[6,12,14,15,199,233,240],drop:[3,196,396],droplet:409,drsquar:108,drude:[],dry:232,dsecriptor:410,dsf:[],dsmc:[],dstyle:289,dt_collis:246,dt_lb:246,dt_md:246,dt_srd:319,dtilt:[59,222],dtneb:490,dtqm:293,dtype:[119,218],dual:[16,17,319,375],dudarev:169,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,88,90,91,92,96,105,106,107,108,109,114,120,122,130,144,145,147,148,149,151,153,156,157,158,159,160,162,163,165,169,170,173,174,193,195,199,202,203,211,215,217,218,219,220,221,222,223,228,229,232,233,236,237,240,241,243,244,245,246,249,250,251,255,256,257,258,259,264,273,284,287,289,301,302,303,305,316,318,319,320,322,323,324,325,326,328,329,331,335,336,338,339,340,342,361,366,368,370,371,372,393,396,397,398,400,404,405,409,423,424,431,437,439,441,442,456,459,460,462,466,468,469,471,473,476,477,478,485,490,493,494,495,497,502,503],duffi:331,duin:[9,294,299,439,440],duke:361,dummi:[12,29,461],dump1:481,dump2:481,dump2vtk_tri:138,dump:[],dump_atom:8,dump_custom:8,dump_h5md:194,dump_modifi:[],dumpcustom:8,dumptimestep:481,dunbrack:[6,20,176,387,488],dunweg:[243,245],duplic:[2,3,14,15,17,41,42,171,216,237,284,476,501],dupont:[5,7,13],durat:[37,55,147,148,149,151,152,153,155,156,157,158,159,162,163,189,196,208,235,298,331,355,406,457],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,89,130,132,146,152,171,174,190,193,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,227,228,229,231,232,233,234,235,236,237,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,255,256,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,308,312,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,361,368,370,374,375,396,422,429,431,440,459,471,472,474,476,479,481,483,484,486,488,490,491,494,495,502,505,506],dvector:8,dvlo:468,dvx:6,dx_lb:246,dy3:169,dyamic:12,dyanam:6,dyanmic:490,dynam:[],dynamo:[5,376,400,426],dyne:501,dyre:419,dysam:479,e28637:29,e_1:382,e_2:382,e_b:403,e_e:402,e_hbond:408,e_i:[6,382,403],e_j:[6,382],e_k:[382,402],e_kl:6,e_lj:[377,395],e_n:[382,402],e_nn:402,e_pr:402,e_rebo:377,e_tors:377,e_tot:429,e_vol:429,eaa:345,eaat:177,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,91,92,94,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,113,114,115,116,117,118,119,120,121,122,123,124,138,144,145,146,148,149,150,151,152,153,154,157,158,159,160,162,163,164,165,166,167,168,169,170,173,174,176,177,178,179,180,181,182,183,184,185,187,188,189,190,192,193,194,195,196,197,198,199,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,249,250,251,252,253,255,256,257,258,259,261,262,263,264,265,266,267,268,269,270,271,273,274,275,276,277,278,279,280,281,282,284,285,286,287,288,289,290,291,292,294,295,296,298,300,303,304,305,306,307,308,312,313,315,316,317,318,319,320,321,322,323,324,326,329,330,331,332,333,3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88,494,502],elt:426,emac:[],email:[0,3,5,7,8,9,11,403],emb:[3,9,340],emb_lin_neg:426,embed:[3,5,7,11,12,13,29,90,146,168,331,376,400,403,422,426,427,428,437,457,466,474],embt:177,emi:[7,9],emil:9,emol:[439,440,494],emphas:406,empir:[205,323,377,402],emploi:[9,285,294,298,461],empti:[3,57,71,168,172,303,360,371,413,476,487,488,502],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,85,89,99,100,101,102,103,104,108,113,115,116,122,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,147,148,149,152,154,156,157,161,162,164,168,169,176,177,179,180,181,182,183,184,185,187,188,189,190,193,194,196,197,199,200,201,202,203,204,206,210,213,215,217,218,219,221,222,223,228,229,232,233,234,235,236,237,238,240,241,242,243,244,245,246,247,248,249,250,252,253,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,276,277,278,279,280,281,282,284,285,286,288,289,293,294,295,296,297,298,299,300,302,303,305,306,308,309,310,311,312,313,315,316,318,319,322,324,325,326,327,328,329,331,332,334,335,336,337,338,339,340,343,345,347,348,350,351,352,354,355,356,361,368,370,374,375,376,377,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,467,468,469,474,477,478,479,483,485,495,502,506],enclos:[2,6,12,172,193,291,344,426,447,472,474,484,502],encod:[13,39,42,193,195,196,292,409],encompass:[3,6,40,42,57,59,120,171,315,333,457,479],encount:[3,8,12,59,110,211,374,481,502],encourag:[7,8,297,317],end12i:117,end12x:117,end12z:117,end1i:117,end1x:117,end1z:117,end2i:117,end2x:117,end2z:117,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,42,57,59,71,117,173,174,177,192,193,195,196,197,200,201,209,211,213,214,219,222,236,241,243,245,258,259,260,273,290,302,303,308,319,322,323,324,325,327,330,331,334,338,341,342,359,360,369,370,374,375,396,400,405,412,425,429,441,444,446,448,449,466,471,474,476,477,478,479,481,483,484,488,492,494,497,502,506],end_of_step:8,endbondtors:[3,177,183,476],endif:8,energet:[219,377,440],energi:[],energy_compon:447,energy_update_freq:440,enforc:[6,57,58,107,192,193,194,195,197,199,206,219,222,259,283,285,295,303,306,344,360,414,473,502,503],enforce2d:[],eng:[11,65,69,112,193,233,342,344,391,428],eng_previ:344,engil:9,engilitycorp:9,engin:[205,222,288,308,328,400,427],engr:[439,440],enhanc:[201,205,471],enlarg:[59,195],enough:[3,40,61,88,170,171,173,174,216,244,289,293,298,303,332,336,337,340,371,375,392,435,476,480,481],enpub:400,enrti:[],ensembl:[],ensight:6,ensur:[3,6,144,193,206,210,220,235,236,259,309,330,361,382,399,422,458,465],enter:[57,160,403,429,465,490],enthalpi:[127,261,262,263,400,493,494,502],entir:[0,2,3,6,11,14,15,41,42,63,82,83,90,113,114,116,120,122,145,150,169,170,196,199,200,201,208,212,213,216,219,221,232,235,236,239,243,244,255,259,261,262,263,264,265,266,267,284,286,288,301,303,317,331,333,344,375,395,418,431,459,476,484,485],entireti:464,entiti:[6,8,40,42,193,303],entri:[3,8,12,38,42,56,65,69,79,95,112,119,122,131,134,135,136,137,138,140,141,142,168,190,196,211,212,213,221,231,293,342,369,382,401,426,433,440,448,458,459,460,461,462,465,502],entropi:490,entry1:[38,56,196,389,459],entry2:196,entryn:196,enumer:[171,193],enumuer:6,env:375,environ:[1,3,6,11,12,16,17,18,195,237,242,284,375,376,382,389,391,401,402,437,460,473,487,502],epair:[111,196,404,408,439,440,494],epen:[439,440],epfl:[237,242],epp:395,epq:395,eps0:468,eps14:422,epsilon0:462,epsilon:[3,6,36,45,46,50,53,54,89,176,200,201,235,303,319,336,340,366,368,380,381,387,388,390,392,393,394,395,405,407,408,409,412,413,414,415,416,417,418,419,420,421,422,425,430,434,441,442,452,458,464,467,468,485,497,501],epsilon_0:469,epsilon_14:387,epsilon_:441,epsilon_d:393,epsilon_i:[405,431,441],epsilon_i_:441,epsilon_i_a:[405,441],epsilon_i_b:[405,441],epsilon_i_c:[405,441],epsilon_ij:431,epsilon_j:[405,431,441],epsilon_j_:441,epsilon_j_a:[405,441],epsilon_j_b:[405,441],epsilon_j_c:[405,441],epsilon_lj:441,epton:436,eqch:165,eqeq:[439,440],eqp:395,eqq:395,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,71,76,79,88,89,93,95,112,114,119,121,123,145,148,164,166,168,170,192,195,196,199,200,201,202,203,206,209,210,211,214,215,216,220,222,223,228,235,236,238,239,241,243,244,246,249,250,256,257,264,275,284,286,289,291,293,294,295,298,300,302,303,305,308,313,315,322,323,324,327,328,329,331,333,334,336,339,341,342,344,359,363,368,370,371,372,374,375,391,396,398,404,405,408,412,423,429,430,437,439,440,441,443,444,445,447,448,449,459,464,465,469,472,473,474,476,478,479,483,484,487,490,492,494,502,503],equat:[3,6,7,8,9,93,110,116,122,169,178,189,199,220,226,227,230,231,237,243,244,246,249,257,258,259,260,264,280,284,286,293,294,298,306,307,319,327,331,334,336,337,339,341,354,360,361,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:260,equidist:258,equil:[3,294,364,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,391,392,439,440,472,486],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,402,476],eras:[305,328],erat:[222,424],erc:392,erfc:[392,414,431],erforc:117,erg:501,erhart:[206,400,460,462],ermscal:378,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:336,erron:3,error:[],erta:406,ervel:[117,476],escap:[223,497],especi:[8,16,158,170,199,206,216,235,293,298,301,302,375,473],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,392,414,462,481,494],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,431,440,459,490,494],esu:501,esub:426,eta:[6,246,259,293,294,296,335,401,403,405,437,461,465,501],eta_dot:259,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[368,370,471,490],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,493,494],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:450,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[344,474],evan:[158,280],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,368],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,216,246,412,466],event:[],eventu:[3,6,12,15,172,294,490],ever:[54,56,242,319],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[237,246,286,471],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,219,285],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,476,502],exceed:[3,41,59,216,222,259,319,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[210,402],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,402,491],exchange:360,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,375,391,429,431,485,495],excurs:[259,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,472,474,484,487,490,502],exempl:447,exemplari:236,exemplifi:402,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,502],exhibit:[94,259,367,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,216,231,359,374,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,474],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,396,431,485,490],experienc:[6,12,248,249],experiment:[235,360,375,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,208,258,284,409,470,473,474,476,485],explanatori:[3,8,121,193,207,208,211,212,213,303,369,473,502],explantori:[3,299],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[205,396,399],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,443,445,459,473,476,479],exterior:[3,6,168,340],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,402,461,497],extrema:422,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:293,f_harm:329,f_i:[29,437],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,494,502],f_ij:437,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:437,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,460,461,462],f_sigma:382,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:240,fall:[3,6,196,211,289,474,502],fals:[88,342,344,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,464,474,476,481,494],farago:243,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,212,331,332,375,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,502],fdirect:226,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:400,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,431],felling:428,felt:340,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,375,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,249,485],fewest:3,fextern:233,feynman:286,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,11,12,14,15,90,113,114,145,285,360,361,485],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,495],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:456,fictiti:[6,202,203,228,233,237,286,302,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[316,433],figur:[1,3,8,12,293,473,474],fij:395,file0:284,file1:[11,13,284,330,344,369,481,483,487],file2:[11,13,330,344,369,481,483,487],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,196,478,483,506],filepo:300,fill:[7,9,170,195,289,331,363,371,382,429,440,479],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,202,228,329,371,375,502],finer:[144,170,502],finest:360,finger:[170,192,256,479],finish:[6,11,41,216,344,357,359,360,372,374,375,464,481,502,503],finit:[],finni:[7,400,457],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,231,302,319,377,382,411,426,431,452,459,461,484,502],five:[73,156,293,369,382,427,476,490],fix:[],fix_adapt:[164,201,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:306,fix_reax_bond:439,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:395,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,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,95,112,117,118,119,121,123,321],input:[],input_doubl:3,inquir:309,insensit:12,insert:[3,5,7,8,12,59,170,199,223,235,241,289,360,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,196,207,212,213,223,224,232,235,241,246,249,289,303,319,336,338,339,340,341,342,358,363,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[246,395,446],instal:[],instanc:[6,11,200,221,237,338,404,409,431,437,474,497],instantan:[6,63,219,220,236,237,259,264,285,290,293,298,300,303,326,482,494],instanti:[6,11,12,205,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,201,208,211,212,213,214,216,220,221,235,243,246,249,250,285,291,301,303,321,339,358,360,361,364,371,375,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,240,288],instruct:[],insuffici:[3,6,12],insult:259,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,195,196,202,217,218,223,228,229,232,233,235,238,243,255,291,292,301,303,319,331,336,340,341,342,344,359,369,371,375,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,195,196,206,208,212,213,217,218,219,223,225,233,235,236,237,240,243,244,245,246,285,288,289,292,293,298,303,319,321,323,326,330,331,350,360,363,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,210,236,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,199,208,209,211,212,213,214,216,217,218,219,227,232,239,249,257,259,264,300,303,304,319,327,331,333,334,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,219,243,245,258,295,303,360,370,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,199,200,201,217,218,219,234,235,240,241,243,245,249,273,284,286,288,289,294,296,302,303,310,311,319,320,326,331,335,336,337,340,341,346,347,348,349,351,355,360,361,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,258,328,329,376,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:340,interest:[1,5,7,8,9,11,13,71,169,286,326,329,361,401,424,439,440,474,502],interf:375,interfac:[],interfer:[12,259,377],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,340,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,195,258,284,354,370,474,475,484,488],intermix:471,intermolecular:377,intern:[],internal_element_set:205,internal_quadratur:205,internet:242,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,195,196,205,231,246,284,360,361,370,382,431,440,453,459,460],interpret:[2,6,11,195,211,406,449,471,474,490,502],interrupt:293,intersect:[3,6,122,196,340,342,479],intersert:340,interspers:368,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,194,209,243,259,293,298,299,311,447,453,471,490,502],intestieti:122,intial:[6,375,377],intiial:[41,481],intiti:[3,318],intra:303,intra_energi:235,intramolecular:[29,235],introduc:[6,9,94,110,195,259,293,298,303,354,360,376,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:363,inv:[122,169,304],invalid:[3,12,71,91,173,273,370,423,424,478],invari:[110,137,142,144],invent:306,invers:[],invert:[1,6,174,285],invis:340,invoc:[168,219,375,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,227,228,229,232,233,234,235,236,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,255,256,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,294,295,296,297,298,299,300,301,303,304,305,306,308,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,345,347,348,350,351,354,356,359,360,361,362,363,368,370,375,376,377,379,383,384,385,386,387,388,390,391,392,395,396,400,401,4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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 dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[210,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,alloi:400,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380,381],bond:[8,13,69,217,218,219,299],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,220],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,390,468],colvar:[9,13,221],com:[74,75,151],comb3:391,comb:[295,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,327],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:416,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:8,cut:[49,378,385,388,392,395,402,404,414,415,422,430,434],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,29,395],direct:226,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:349,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:224,dreid:[6,408],drude:[6,9,155,225,226,244],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,197],dump_modifi:196,dynam:294,eam:[13,400],echo:198,edip:401,eff:[9,13,99,100,154,156,161,245,260,272,281,325,402],efield:228,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:229,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:232,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:233,fcc:284,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,201],field:[6,7],file:6,finit:6,fire:294,fix:[2,6,8,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,3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er:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,195,196,201,208,209,211,212,213,214,217,218,219,220,222,223,233,239,241,243,249,256,260,261,262,263,265,266,267,273,278,279,280,282,303,304,317,331,341,354,360,366,367,368,370,371,372,375,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,222,375,391],afil:237,aforement:18,afresh:[291,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,199,200,201,205,206,208,209,216,217,218,219,220,222,226,235,246,247,248,249,250,255,256,257,259,265,266,267,273,278,279,280,282,285,289,293,301,303,306,315,320,322,323,324,326,327,328,329,330,334,336,338,342,345,346,352,359,365,366,368,369,371,373,374,375,376,377,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,196,222,239,289,345,359,370,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,223,370,439,440],aggreg:[6,12,65,68,69,79,95,112,119,239,255,301,303,317,471,503],aggress:[239,490],agilio:[9,13],agre:[3,8,190,368,377,411,440],agreement:[5,7],ahd:408,ahead:338,aidan:[0,5,7,9,13,363],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:195,akohlmei:[7,9,13,197,240],aktulga:[7,9,296,440],al2o3:447,al2o3_001:[122,304],al3:169,ala:[246,447],alain:9,alat:[284,426],alb:[437,460,462],albeit:302,albert:9,alchem:[89,164],alcohol:334,alcu:[376,382],alcu_eam:437,alderton:395,alejandr:[259,260],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,196,205,216,219,222,246,248,249,273,286,294,303,306,307,326,327,331,334,339,366,367,368,372,375,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,361],aliceblu:196,align:[6,12,29,41,71,172,190,212,216,241,363,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,252,254,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,311,315,316,318,319,320,321,322,323,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,350,355,358,359,360,361,362,363,365,368,369,370,371,372,374,375,376,377,378,380,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:343,alloc:[3,5,6,8,9,11,12,60,233,333,369,371,375,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,195,196,197,199,200,202,204,205,206,208,209,210,211,212,213,214,216,218,219,220,221,222,223,227,228,233,235,236,237,238,240,243,246,249,250,254,256,259,260,284,288,289,290,291,292,293,297,303,304,306,308,310,311,315,319,326,327,328,329,331,332,333,334,335,336,342,344,346,355,360,361,363,368,369,370,371,374,375,378,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,241,293,331,361,372,375,456],alo:392,alon:[6,7,219,299,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,195,208,219,241,246,247,251,256,258,293,303,306,308,312,316,317,326,330,331,337,340,342,363,366,367,368,370,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,200,246,285,293,294,298,368,376,379,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,199,346,355,369,389,457,476],alphanumer:[3,63,199,292,300,344,369,502],alreadi:[3,7,8,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449,456,460,461,462,470,471,474,477,483,485,491,497,502,506],ansi:[12,16],answer:[3,4,8,12,303,372,373],anthoni:329,antiquewhit:196,antisymmetr:[9,40,378],antisymmetri:402,antonelli:[328,329],antonio:436,anymor:329,anyon:7,anyparticl:88,anyth:[8,11,170,222,242,458,460,462,487],anywai:[173,375,497,504],anywher:[12,170,389,426,448,502],aoff:[369,476],aparam:[89,200,201],apart:[3,171,249,316,371,380,449,476,485],aperiod:285,api:[11,12,197,410,474],appar:3,appear:[2,3,6,11,12,13,39,40,41,72,77,89,94,110,112,119,120,144,153,170,171,173,193,195,196,208,212,213,216,220,223,226,235,240,289,300,301,330,342,344,345,360,368,369,370,390,400,426,431,447,459,465,472,473,474,476,477,478,481,483,497,502,506],append:[],appendix:[29,395,447],appl:[220,259,260,465],appli:[2,3,4,5,6,8,9,12,17,18,29,33,41,50,57,59,61,63,71,72,89,90,108,120,144,145,150,156,158,160,164,169,170,172,176,178,183,189,192,193,195,196,199,200,201,202,203,205,208,215,216,220,221,222,224,227,228,230,231,233,234,235,236,237,238,240,241,243,244,245,246,250,259,260,264,265,266,267,273,278,279,282,283,284,286,290,293,301,302,303,305,306,308,309,312,316,317,318,320,322,323,324,325,327,329,330,331,334,342,360,363,368,369,370,380,383,385,387,392,395,402,406,407,408,409,411,412,414,420,424,429,431,434,439,442,443,444,445,446,456,463,468,476,477,479,480,481,485,486,488,493,497,502,503,504,505],applic:[1,6,9,12,17,197,205,219,223,224,233,235,237,240,284,289,302,308,316,327,334,360,375,462,486,497],applyt:3,appopri:17,approach:[6,7,9,14,193,205,236,285,286,298,303,326,327,329,331,334,360,382,392,394,398,399,405,409,429,441,443,445,456,466],appropri:[1,2,3,6,8,11,12,13,15,17,33,38,42,50,56,61,73,90,93,120,121,148,149,150,178,183,189,190,192,193,196,208,209,212,213,214,219,220,222,233,234,237,246,254,256,257,259,261,262,263,264,265,266,267,278,279,280,282,286,289,290,293,298,303,307,319,322,323,324,327,334,336,337,339,340,341,352,361,370,377,382,386,390,391,392,401,406,409,411,418,422,429,438,439,440,458,459,460,461,462,465,466,476,477,478,480,481,489,490,493,502,503],approri:238,approxim:[6,9,122,126,169,235,237,246,286,304,306,326,360,366,367,368,384,394,402,405,423,424,429,431,438,441,447,468,490,497],april:11,aprpopri:471,apu:[423,424],aqua:[195,196],aquamarin:196,ar_therm:205,ar_ttm:205,ara:13,arbitrari:[6,40,58,120,193,195,197,221,222,238,259,286,294,458,474,487,502],arbitrarili:[11,59,120,144,192,220,259,392,502],arcco:3,arch:[1,12,14,15,17],architect:358,architectur:[16,375,429],archiv:[6,7,11,12,321,389,483],arcsin:3,area:[6,41,93,116,120,168,216,222,246,327,334,399,406,436,464,473,486],aren:[120,292,344],arflag:12,arg:[3,11,12,22,40,41,44,55,59,63,71,89,121,158,164,168,170,173,174,178,192,193,194,196,199,200,201,202,204,206,208,209,210,211,212,213,214,215,216,217,218,221,222,223,228,233,235,238,239,240,241,249,256,261,262,263,289,302,303,304,305,309,312,313,315,326,329,336,337,338,339,341,342,346,358,370,375,383,384,385,387,388,389,394,395,398,402,407,409,414,418,422,423,424,425,434,442,444,446,457,473,474,476,479,481,483,485,487,489,494,495,502,503,505,506],argon:235,argonn:12,argument:[2,3,6,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,63,73,89,93,110,113,116,120,144,145,147,152,157,158,159,164,168,170,171,172,174,176,177,178,179,180,181,182,184,185,187,188,190,193,196,199,200,201,202,204,207,208,209,210,211,212,213,214,215,216,220,221,222,229,231,233,234,235,237,238,242,243,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,288,289,291,295,300,303,304,305,306,319,322,324,331,333,335,337,339,342,344,345,346,347,348,350,351,352,354,356,358,359,361,362,363,365,370,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,398,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,425,426,427,428,431,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,470,471,472,473,474,475,476,477,479,481,484,485,486,487,491,493,494,502,503,505],aris:[12,468],arithmet:[3,6,106,360,387,390,417,431,463,464],arkansa:9,arl:[9,82,83,230,307],armi:[9,82,83,230,307],armv8:17,arnold:360,around:[1,3,4,6,12,42,57,58,59,66,70,71,72,73,77,120,144,148,165,168,170,172,192,195,196,203,204,220,222,223,241,256,259,292,294,298,303,312,316,319,336,337,340,359,369,447,476,479,486,487,497,502],aroung:3,arrai:[],arrang:144,arrheniu:490,art:[9,471,490],artefact:237,articl:[6,447],articul:[7,288],artifact:[90,168,497],artifici:[257,293,451,452,454],arun:13,arxiv:[144,194,448],ascend:[41,196,240,249,303,481],asci:7,ascii:[13,304,330,370,400,403,426,476],ash:[423,424],asid:[8,170,426],asin:502,ask:[3,11],askari:436,askoos:13,asoci:195,aspect:[6,7,59,222,235,405,441,464,476,486,490],aspect_ratio:304,asper:4,aspher:[],asq:[423,424],assembl:4,assign:[1,2,3,6,7,11,12,14,15,17,18,33,39,40,41,50,57,59,61,63,66,71,72,75,92,96,107,109,114,117,118,122,144,145,150,165,167,169,170,173,183,192,193,194,195,196,197,199,200,201,204,208,211,216,2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90,checkqeq:440,checku:190,chem:[6,13,20,21,25,39,40,43,45,46,89,90,110,116,145,176,177,187,210,221,226,236,237,244,246,258,259,260,280,281,286,290,293,295,303,307,308,319,322,323,326,327,328,329,336,345,354,356,360,361,367,370,377,383,387,388,391,392,393,395,396,398,402,404,405,407,408,414,418,419,422,426,430,431,434,447,456,463,485,488,490,497],chemic:[9,122,164,169,193,205,206,235,294,299,300,326,361,439,440,452],chemistri:[9,293,294,296,382,402,439,440],chen:331,cheng:391,chenoweth:[439,440],chenoweth_2008:[439,440],chi:[95,159,192,284,294,296,403,405,503],chiefli:438,child:8,chip:[7,12,17,18,375,489],chipot:221,chiral:354,chmod:[11,12],cho:426,chocol:[7,196],choic:[3,6,12,15,16,18,40,41,54,89,145,148,149,163,174,190,208,212,213,216,219,222,223,237,243,246,257,259,286,294,303,326,355,361,366,367,370,372,375,409,422,431,435,476,485,486,489,490,496,497,501],choos:[1,3,6,7,8,12,16,17,18,29,39,54,89,121,160,161,195,217,218,219,220,223,232,243,246,257,259,261,262,263,264,265,266,267,289,290,307,319,323,337,360,361,367,466,471,473,485,491],chose:[460,462],chosen:[2,3,6,12,17,144,170,173,182,190,195,201,206,220,223,232,235,236,244,246,257,259,264,286,289,300,319,323,326,327,332,334,335,341,361,362,367,375,397,398,402,406,413,416,442,460,471,485,490,497],chri:168,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,92,96,107,109,118,150,165,167,208],chute:[4,10,238],ciccotti:306,cieplak:[6,176,488],cii:209,cij:209,ciko:2,circl:[42,71,315],circular:[3,6,148,191],circumst:18,circumv:[94,110,298],citat:[],cite:[3,7,8,12,243,447],civ:9,ckio:2,cko:2,cl1:169,clarendon:[29,395],clarifi:[7,460,462],clariti:344,clark:434,class2:[],classic:[0,3,5,6,7,8,9,233,286,293,298,331,356,402],classifi:[9,457,465],claus:474,clean:[6,12,14,15,17,484],cleanli:[475,505],clear:[],clearli:7,clebsch:144,clermont:[9,13],clever:480,click:[2,11,22,37,44,55,170,178,189,195,240,346,355,370,389,457],client:[240,242],climb:[258,370,490],clinic:[7,13],clo:[159,192,503],clock:[12,471,490],clockwis:337,close:[3,6,11,12,13,39,41,67,71,145,173,193,218,219,220,237,244,246,259,280,303,306,337,340,359,361,364,366,367,370,375,377,382,392,393,412,426,431,443,445,462,480,486,497,499],closer:[3,41,120,168,192,193,216,220,224,328,370],closest:[218,284,303,334,405,441,456,466],cloud:[447,497],clovertown:18,clsuter:72,clump1:[288,303],clump2:[288,303],clump3:[288,303],clump:303,cluster:[],clutter:[3,9],cmap:476,cmatrix:237,cmax:426,cmd:[11,12,286,487],cmdarg:11,cmin:426,cmm:[],cmoput:137,cn1:209,cn2:209,cna:[],cnn:209,cnr:[9,13],cnt:[409,480],co2:[40,169,306,369],coars:[7,9,29,36,40,54,182,288,303,319,407,442,485,488],coarser:[361,502],coarsest:144,code:[],coeff:[3,7,8,12,21,22,33,44,50,176,177,178,183,345,346,352,389,409,413,431,444,446,449,476],coeffcient:476,coeffici:[],coefficienct:396,coefficient0:400,coefficient1:400,coeffieci:[6,379,412],coeffincientn:400,coexist:[9,235,402],cohes:[6,403,426],coincid:[126,340,387,423,424,471],colberg:194,cold:[6,155,235,239,371,497],coldest:327,coleman8:9,coleman:[9,122,169,304],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,85,92,96,101,107,109,118,150,158,165,167,170,193,196,208,221,249,255,288,298,301,303,342,360,369,371,390,476,483,489,495,506],collid:[227,319,341],colliex:169,collinear:[3,288],collis:[3,246,319,337,341,399,406,469],colllis:319,colloid:[],colombo:39,colon:[197,342,477],color1:196,color2:196,color:[3,9,41,193,195,196,216,236,293,298],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,83,92,94,95,96,107,109,110,112,114,117,118,119,120,121,123,144,145,150,158,165,167,168,169,190,193,196,199,207,208,209,211,212,213,214,249,256,257,293,303,320,321,331,341,404,408,439,440,477,491,493,502],columnar:168,colvar:[],colvarmodul:12,com:[],comamnd:222,comand:219,comannd:375,comb3:[],comb:[],comb_1:295,comb_2:295,combiant:393,combin:[3,6,7,9,11,13,36,40,63,65,69,79,89,95,106,112,119,148,149,163,193,195,205,211,240,249,259,286,292,307,323,332,340,343,345,360,361,363,367,375,390,392,393,398,402,403,409,421,422,448,458,460,462,465,468,479,484,489,497,502],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,194,240,242,243,361,370,375,396,431,436,459,478],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,176,190,193,231,244,303,331,369,370,376,400,401,403,413,426,433,440,447,448,458,459,460,461,462,465,473,474,476,497,502],commerci:7,commmand:[3,6,12,59,111,281,412,470,471,473,490,505],common:[],commonli:[3,6,12,17,25,57,59,108,110,172,193,195,197,356,407,416,448,460,462,476,479,488],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,173,174,195,196,216,217,218,220,221,222,240,242,246,248,249,250,259,285,292,294,295,296,303,307,319,331,342,358,360,371,372,373,375,398,399,435,473,474,485,486,502,504,506],communc:360,comp:[7,194,242,243,306,361,370,402,431,436,441,455,459,461],compact:[63,199,389,457],compani:[5,7],compar:[1,3,4,6,8,12,17,39,88,114,122,153,169,178,189,196,226,294,342,344,360,361,368,370,426,447,471,490,491,497,501],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,345,346,355,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,410,429,431,459,473,474,502],compens:[6,217,218,301,371,402],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,429,476,477,481,502],compl:17,complain:[11,12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,402,429,459,474,476,479,502],compli:[326,330],complic:[6,7,9,12,13,206,235,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,381,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,206,246,400],compound:[391,402,403,465],compres:[71,118,208],compress:[],compris:[40,340,441,464],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,382],computational:497,compute_arrai:8,compute_fep:[201,422],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:340,concentr:[71,400],concept:[6,150,160,208,485],conceptu:[3,6,71,158,220,222,370,392,409,426,481],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,502],conden:[331,460,462],condens:[6,152,331,377,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,431,474],conform:[3,6,13,59,219,220,258,302,308,330,354,370,402,488],confus:[3,465],conjuct:396,conjug:[7,8,243,367,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,219,240,288,303,306,316,370,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,392,414,418,471,477,479],consequ:[1,6,206,331,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,243,244,322,323,324,375,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,298,435,502],consumpt:358,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,205,331,444,446],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,444,446,468,505],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:205,controlfil:440,convect:93,conveni:[6,12,29,193,197,214,304,363,448,502],convent:[3,8,9,29,181,188,189,196,302,316,343,400,402,502],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,391,392,414,447,471,483,490],convers:[3,8,144,195,196,206,209,290,360,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,340,381],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:447,coordbb:447,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,195,340,341,363,464,476],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,394,424,429,473,474,476,486,501,503],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],corrupt:3,cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,404,408,431,494,502],counter:[3,337,471,482,484,490],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,471],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,423,449,473,476,489,497,502,504],courtesi:363,cov:447,coval:[6,29,402,426,447,497],covari:237,cover:[6,71,190,196,205,246,402,464],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,497],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,436,464,478,481,502],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,480,494,497],crystallin:[6,106,285,363,461,497],crystallis:326,crystallogr:[122,169],crystallograph:[363,494],crystallographi:[122,169,363],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[376,400],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,216,226,340,363,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,408,494],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,235,285],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[284,296],cutinn:[384,423,424],cutlo:[284,296],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:381,cutoff_inn:381,cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,502],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,479],cylindr:[6,241,316,337],cypress:375,cyrot:382,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,486],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:244,damp_drud:244,dampen:[303,497],dampflag:[337,406],dan:17,danger:[3,12,235,342,396,494],dangl:173,daniel:9,darden:[361,395],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[406,493],dat:[6,93,190,205,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:425,davi:336,david:[9,19,360,361,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,477,481],ddim:192,deactiv:422,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,256,292,303,332,491],decipher:363,declar:194,declin:319,decod:195,decompos:[89,448],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,497],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,288],degrad:[8,18,285,361,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,395,400,408,486,494,497,503],degress:[150,208],del:490,delai:[3,6,12,371,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[474,502],deloc:[260,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:[],delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:381,delx:192,delz:192,dem:381,demand:298,demo:11,demon:283,demonstr:[293,426],den:289,dendrim:408,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,392,407,409,440,444,446],dens:[71,219,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:223,deposit:[],deprec:[3,294,439],depth:[51,148,195,331,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,195],despit:497,destabil:382,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,234,289,330,370,391,408,413,471,473,476,487,490,502],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:307,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,382,402,428,429,447,465,478],devemi:9,deviat:[257,264,284,404],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,391],devis:428,dfactor:195,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,429],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,444,446],diagonalstyl:448,diagram:[41,122,169,189,216,286],diallo:408,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,381,390,405,406,416,441,464,468,476,477,486],diamond:[363,402,426],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,262,263,265,266,267,269,271,274,276,277,278,279,282,284,286,288,290,293,294,295,298,301,303,306,308,316,317,319,322,323,324,327,328,329,331,334,335,336,337,340,344,345,355,357,359,360,361,363,364,366,367,369,370,372,373,374,375,376,377,382,386,387,389,390,391,396,397,398,400,402,405,406,407,409,412,414,415,417,418,425,426,427,428,430,431,433,437,439,440,441,442,443,444,446,447,448,449,457,458,459,460,462,464,465,468,470,471,473,474,476,478,479,480,481,484,485,486,488,490,491,493,494,495,497,501,502,503,504],differenti:[1,3,6,29,190,360,392,437,461],difficult:[220,286,375,408,485],difficulti:[94,110,306,439],diffract:[],diffus:[],digit:[2,3,196,344,429],dih_table1:190,dih_table2:190,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:218,dihydrid:402,dij:306,dilat:[],dim1:3,dim2:3,dim:[3,59,71,147,151,152,153,156,157,158,159,160,162,170,192,212,222,241,337,363,426,479,501,502,503],dimdim:502,dimems:285,dimens:[],dimensinon:71,dimension:[3,39,94,116,122,144,147,150,151,152,153,156,157,158,159,160,162,169,191,208,212,258,285,331,363,366,370,437,476,486],dimensionless:[108,125,126,128,131,133,135,140,144,331,361,448,468],diment:3,dimentionless:139,dimer:[6,303,426],dimgrai:196,dimstr:[41,216],dinola:[290,322],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,193,321,497],dir1:487,dir2:487,dir:[1,3,4,8,9,11,12,257,284,293,318,437,439,440,474,487,502],dirac:144,direc:437,direct:[],directli:[3,6,8,9,11,12,89,117,144,146,193,194,195,202,228,237,241,246,285,304,323,335,337,338,339,340,363,367,375,376,377,383,385,386,392,395,400,402,414,418,431,434,442,456,474,486,487,488,494,502],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,197,221,242,288,294,297,307,315,319,328,329,370,374,376,377,382,389,391,392,400,401,403,410,411,422,426,427,428,429,433,437,438,439,440,447,448,458,460,461,462,465,474,476,477,478,487,502],disabl:[3,12,16,331,413,474,489,502],disadvantag:[6,216],disallow:[193,222,259],disappear:478,discard:[2,3,41,71,210,212,216,332,340,473,478,479],discontinu:[9,190,368,420],discourag:426,discov:[13,332],discret:[6,8,40,42,195,196,243,246,381],discuss:[],disk:[6,86,87,94,163,191,223,235,289,474],disloc:[70,429],disord:[39,70,429],disp:[],dispar:441,disperion:[395,418],dispers:[3,6,7,9,168,285,360,361,386,395,418,423,431,440,459,465],displac:[],displace_atom:[],displace_box:59,displacemet:479,displai:[11,13,22,37,44,55,178,189,193,195,346,355,389,457],dispters:3,disregard:429,dissip:[6,9,40,82,83,230,236,243,285,307,328,329,384,396,397,398,406,423,424,457],dissolut:217,dist:[6,69,93,112,121,193,286,302,399,456,471,503],distanc:[],distinct:[6,226,300,360,441],distinguish:[6,88,144,249,381,402,475],distort:[168,376],distrbut:376,distribut:[],distro:[115,389,436,437],ditto:[8,12,14,15,16,17,18,42,119,218,469,474],div:8,divd:121,diverg:[3,12,39,303,329,478,497,504],divid:[3,6,16,41,93,116,121,130,132,145,167,168,178,189,196,208,209,211,216,222,284,327,334,339,360,368,370,403,440,447,465,485,493,502],divis:[6,246,382,412,422,473,494,502],dl_poli:[6,7],dlambda:164,dlammps_async_imd:240,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,195],dlammps_gzip:[3,12,193,195,330,476,477,481],dlammps_jpeg:[3,12,195],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,195],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,193],dlen:486,dlmp_intel_offload:[12,16],dlo:[59,192,222,289],dlopen:6,dlvo:[7,390,468],dm_lb:246,dmax:[319,366],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,89,92,96,105,107,108,109,111,113,115,116,118,121,123,145,148,149,150,163,165,167,170,171,172,178,189,192,193,194,195,196,197,199,200,201,206,207,208,209,210,211,212,213,214,223,235,243,244,254,259,260,265,266,267,271,278,279,280,281,282,289,292,303,316,319,322,323,324,333,337,340,342,344,346,355,359,368,369,370,375,376,377,380,381,389,391,392,400,401,403,408,409,411,412,426,427,428,431,433,436,437,438,448,457,458,460,462,464,465,474,476,477,478,479,481,484,485,486,493,494,502,503,504,505],docuement:441,dodd:[42,381],dodgerblu:196,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,89,90,93,107,114,120,121,122,146,148,150,152,153,158,160,164,169,170,171,172,174,176,178,183,189,190,192,193,194,195,196,199,205,206,208,212,215,216,218,219,220,222,226,228,231,232,235,236,239,241,243,244,246,249,255,259,260,261,262,263,265,266,267,278,279,280,281,282,290,291,292,296,298,301,303,319,322,324,326,327,331,334,335,336,339,340,341,342,347,348,349,351,352,354,359,360,361,362,363,369,370,371,376,377,378,379,380,381,382,384,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,409,410,411,412,413,416,417,419,420,421,423,424,426,427,428,429,431,437,438,439,440,441,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,467,468,469,471,472,473,474,476,477,478,479,480,483,484,486,487,488,489,490,493,494,497,502,506],doegenomestolif:7,doesn:[3,7,8,12,170,193,206,212,213,316,369,371,375,377,391,401,411,439,440,458,460,461,462,46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4,298,306,307,319,327,331,334,336,337,339,341,354,360,361,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:260,equidist:258,equil:[3,294,364,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,391,392,439,440,472,486],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,402,476],eras:[305,328],erat:[222,424],erc:392,erfc:[392,414,431],erforc:117,erg:501,erhart:[206,400,460,462],ermscal:378,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:336,erron:3,error:[],erta:406,ervel:[117,476],escap:[223,497],especi:[8,16,158,170,199,206,216,235,293,298,301,302,375,473],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,392,414,462,481,494],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,431,440,459,490,494],esu:501,esub:426,eta:[6,246,259,293,294,296,335,401,403,405,437,461,465,501],eta_dot:259,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[368,370,471,490],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,493,494],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:450,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[344,474],evan:[158,280],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,368],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,216,246,412,466],event:[],eventu:[3,6,12,15,172,294,490],ever:[54,56,242,319],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[237,246,286,471],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,219,285],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,476,502],exceed:[3,41,59,216,222,259,319,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[210,402],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,402,491],exchange:360,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,375,391,429,431,485,495],excurs:[259,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,472,474,484,487,490,502],exempl:447,exemplari:236,exemplifi:402,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,502],exhibit:[94,259,367,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,216,231,359,374,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,474],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,396,431,485,490],experienc:[6,12,248,249],experiment:[235,360,375,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,208,258,284,409,470,473,474,476,485],explanatori:[3,8,121,193,207,208,211,212,213,303,369,473,502],explantori:[3,299],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[205,396,399],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,443,445,459,473,476,479],exterior:[3,6,168,340],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,402,461,497],extrema:422,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:293,f_harm:329,f_i:[29,437],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,494,502],f_ij:437,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:437,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,460,461,462],f_sigma:382,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:240,fall:[3,6,196,211,289,474,502],fals:[88,342,344,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,464,474,476,481,494],farago:243,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,212,331,332,375,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,502],fdirect:226,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:400,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,431],felling:428,felt:340,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,375,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,249,485],fewest:3,fextern:233,feynman:286,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,11,12,14,15,90,113,114,145,285,360,361,485],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,495],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:456,fictiti:[6,202,203,228,233,237,286,302,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[316,433],figur:[1,3,8,12,293,473,474],fij:395,file0:284,file1:[11,13,284,330,344,369,481,483,487],file2:[11,13,330,344,369,481,483,487],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,196,478,483,506],filepo:300,fill:[7,9,170,195,289,331,363,371,382,429,440,479],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,202,228,329,371,375,502],finer:[144,170,502],finest:360,finger:[170,192,256,479],finish:[6,11,41,216,344,357,359,360,372,374,375,464,481,502,503],finit:[],finni:[7,400,457],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,231,302,319,377,382,411,426,431,452,459,461,484,502],five:[73,156,293,369,382,427,476,490],fix:[],fix_adapt:[164,201,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:306,fix_reax_bond:439,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:395,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[210,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,alloi:400,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380,381],bond:[8,13,69,217,218,219,299],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,220],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,390,468],colvar:[9,13,221],com:[74,75,151],comb3:391,comb:[295,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,327],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:416,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:8,cut:[49,378,385,388,392,395,402,404,414,415,422,430,434],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,29,395],direct:226,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:349,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:224,dreid:[6,408],drude:[6,9,155,225,226,244],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,197],dump_modifi:196,dynam:294,eam:[13,400],echo:198,edip:401,eff:[9,13,99,100,154,156,161,245,260,272,281,325,402],efield:228,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:229,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:232,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:233,fcc:284,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,201],field:[6,7],file:6,finit:6,fire:294,fix:[2,6,8,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,3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