lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

1 Oct 06 release 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@18 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp 2006-09-27 19:12:31 +00:00
parent d66323cfcc
commit 5b1f5c520a
101 changed files with 994 additions and 819 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
doc/Manual.html
View File

@ -13,7 +13,7 @@
<CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER>(17 July 2006 version of LAMMPS)
<CENTER>(1 Oct 2006 version of LAMMPS)
</CENTER>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
@ -25,7 +25,7 @@ funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</P>
<P>The developers of LAMMPS are <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and
Aidan Thompson who can be contacted at "sjplimp, pscrozi, athomps at
Aidan Thompson who can be contacted at sjplimp,pscrozi,athomps at
sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at http://lammps.sandia.gov has
more information about the code and its uses.
</P>

BIN
doc/Manual.pdf
View File

Binary file not shown.

4
doc/Manual.txt
View File

@ -10,7 +10,7 @@
LAMMPS Documentation :c,h3
(17 July 2006 version of LAMMPS) :c
(1 Oct 2006 version of LAMMPS) :c
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
@ -22,7 +22,7 @@ funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
The developers of LAMMPS are "Steve Plimpton"_sjp, Paul Crozier, and
Aidan Thompson who can be contacted at "sjplimp, pscrozi, athomps at
Aidan Thompson who can be contacted at sjplimp,pscrozi,athomps at
sandia.gov. The "LAMMPS WWW Site"_lws at http://lammps.sandia.gov has
more information about the code and its uses.

418
doc/Section_errors.html
View File

@ -247,6 +247,11 @@ definitions.
<DD>Self-explanatory.
<DT><I>Another input script is already being processed</I>
<DD>Cannot attempt to open a 2nd input script, when the original file is
still being processed.
<DT><I>Atom count is inconsistent, cannot write restart file</I>
<DD>Sum of atoms across processors does not equal initial total count.
@ -284,11 +289,6 @@ been defined.
<DD>Self-explanatory.
<DT><I>Atom style granular must perform 3d simulations</I>
<DD>Atom style granular cannot be used with 2d simulations, because
the pairwise potentials are inherently 3d.
<DT><I>Atom style hybrid cannot have hybrid as an argument</I>
<DD>Self-explanatory. Check the input script.
@ -456,6 +456,11 @@ factor that partitions the computation between real space and k-space.
<DD>Must use the lattice command before using the create_atoms
command.
<DT><I>Cannot create an atom map unless atoms have IDs</I>
<DD>The simulation requires a mapping from global atom IDs to local atoms,
but the atoms that have been defined have no IDs.
<DT><I>Cannot create_box after simulation box is defined</I>
<DD>The create_box command cannot be used after a read_data, read_restart,
@ -465,10 +470,6 @@ or create_box command.
<DD>Self-explanatory.
<DT><I>Cannot create vels with loop all for non-contiguous atom IDs</I>
<DD>You cannot use the loop all option if you atom IDs do not span 1 to natoms
<DT><I>Cannot evaluate variable equal command</I>
<DD>Syntax or keyword names in mathematical expression are not
@ -499,12 +500,19 @@ recognized.
<DD>Volume can only be rescaled uniaxially if system is periodic in all 3
dimensions.
<DT><I>Cannot invoke single() with pairwise TIP4P potential</I>
<DT><I>Cannot have both pair_modify shift and tail set to yes</I>
<DD>Commands that invoke the single() function within pairwise potentials
cannot be used with a TIP4P potential, due to the way it computes
forces on other atoms besides the i,j pair. This includes the eng and
stress tensor components for the dump custom command.
<DD>These 2 options are contradictory.
<DT><I>Cannot open dir to search for restart file</I>
<DD>Using a "*" in the name of the restart file will open the current
directory to search for matching file names.
<DT><I>Cannot open dump file</I>
<DD>The output file for the dump command cannot be opened. Check that the
path and name are correct.
<DT><I>Cannot open EAM potential file %s</I>
@ -526,6 +534,10 @@ the path and name are correct.
<DD>The output file for the fix gran/diag command cannot be opened. Check
that the path and name are correct.
<DT><I>Cannot open fix gyration file %s</I>
<DD>Self-explanatory.
<DT><I>Cannot open fix msd file %s</I>
<DD>The output file for the fix msd command cannot be opened. Check that
@ -551,6 +563,29 @@ the path and name are correct.
<DD>LAMMPS is attempting to open a gzipped version of the specified file
but was unsuccessful. Check that the path and name are correct.
<DT><I>Cannot open input script %s</I>
<DD>Self-explanatory.
<DT><I>Cannot open input script %s</I>
<DD>Self-explanatory.
<DT><I>Cannot open logfile</I>
<DD>The LAMMPS log file named in a command-line argument cannot be opened.
Check that the path and name are correct.
<DT><I>Cannot open logfile %s</I>
<DD>The LAMMPS log file specified in the input script cannot be opened.
Check that the path and name are correct.
<DT><I>Cannot open log.lammps</I>
<DD>The default LAMMPS log file cannot be opened. Check that the
directory you are running in allows for files to be created.
<DT><I>Cannot open pair_write file</I>
<DD>The specified output file for pair energies and forces cannot be
@ -558,8 +593,25 @@ opened. Check that the path and name are correct.
<DT><I>Cannot open restart file %s</I>
<DD>The output restart file cannot be opened. Check that the path and
name are correct and that disk space is available.
<DD>Self-explanatory.
<DT><I>Cannot open screen file</I>
<DD>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.
<DT><I>Cannot open universe log file</I>
<DD>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
created.
<DT><I>Cannot open universe screen file</I>
<DD>For a multi-partition run, the master screen file cannot be opened.
Check that the directory you are running in allows for files to be
created.
<DT><I>Cannot read_data after simulation box is defined</I>
@ -621,14 +673,19 @@ Instead they are defined on a per-atom basis in the data file.
<DD>In the rRESPA integrator, you must define both a inner and outer
setting in order to use a middle setting.
<DT><I>Cannot set these values with this atom style</I>
<DT><I>Cannot set this attribute for this atom style</I>
<DD>Choice of set style does not match attribute of atom style.
<DD>The attribute being set does not exist for the defined atom style.
<DT><I>Cannot use atom style granular with chosen thermo settings</I>
<DD>Cannot output temperature or pressure with atom style granular.
<DT><I>Cannot use delete_atoms unless atoms have IDs</I>
<DD>Your atoms do not have IDs, so the delete_atoms command cannot be
used.
<DT><I>Cannot use delete_bonds with non-molecular system</I>
<DD>Your choice of atom style does not have bonds.
@ -646,6 +703,23 @@ setting in order to use a middle setting.
<DD>Self-explanatory.
<DT><I>Cannot use fix nph with no per-type mass defined</I>
<DD>The defined atom style uses per-atom mass, not per-type mass.
<DT><I>Cannot use fix npt with no per-type mass defined</I>
<DD>The defined atom style uses per-atom mass, not per-type mass.
<DT><I>Cannot zero momentum of 0 atoms</I>
<DD>The collection of atoms for which momentum is being computed has no
atoms.
<DT><I>Cannot use fix nvt with no per-type mass defined</I>
<DD>The defined atom style uses per-atom mass, not per-type mass.
<DT><I>Cannot use fix poems with atom style granular</I>
<DD>This fix is not yet enabled for this atom style.
@ -658,11 +732,6 @@ setting in order to use a middle setting.
<DD>Your choice of atom style does not have bonds.
<DT><I>Cannot use multiple long-range potentials with pair hybrid</I>
<DD>Only one sub-style potential with a long-range component can be
used with pair_style hybrid.
<DT><I>Cannot use nonperiodic boundaries with Ewald</I>
<DD>For kspace style ewald, all 3 dimensions must have periodic boundaries
@ -675,6 +744,10 @@ non-periodic z dimension.
unless you use the kspace_modify command to define a 2d slab with a
non-periodic z dimension.
<DT><I>Cannot use pair tail corrections with 2d simulations</I>
<DD>The correction factors are only currently defined for 3d systems.
<DT><I>Cannot use PPPM with 2d simulation</I>
<DD>The kspace style pppm cannot be used in 2d simulations. You can use
@ -685,15 +758,26 @@ non-periodic z dimension.
<DD>Regions that extend to the box boundaries can only be used after the
create_box command has been used.
<DT><I>Cannot use rRESPA with full neighbor lists</I>
<DD>Defined pair style uses full neighbor lists (as opposed to
half neighbor lists), which are incompatible with the current
implementation of rRESPA.
<DT><I>Cannot use vectors in variables unless atom map exists</I>
<DD>Vectors require an atom map to be able to lookup the vector index.
Only atom styles with molecular information creat a global map.
<DT><I>Cannot zero momentum for less than 2 atoms</I>
<DT><I>Cannot use velocity create loop all unless atoms have IDs</I>
<DD>Velocity command is being used with momentum-zeroing options on a
group with 0 or 1 atoms.
<DD>Atoms in the simulation to do not have IDs, so this style
of velocity creation cannot be performed.
<DT><I>Cannot use velocity create loop all with non-contiguous atom IDs</I>
<DD>Atoms in the simulation to do not have consecutive IDs, so this style
of velocity creation cannot be performed.
<DT><I>Command-line variable already exists</I>
@ -732,14 +816,6 @@ more than once.
<DD>A group ID used in the fix command does not exist.
<DT><I>Could not find fix poems group ID</I>
<DD>A group ID used in the fix poems command does not exist.
<DT><I>Could not find fix rigid group ID</I>
<DD>A group ID used in the fix rigid command does not exist.
<DT><I>Could not find fix_modify ID</I>
<DD>A fix ID used in the fix_modify command does not exist.
@ -748,9 +824,21 @@ more than once.
<DD>A temperature ID used in the fix_modify command does not exist.
<DT><I>Could not find fix spring vector group ID</I>
<DT><I>Could not find fix poems group ID</I>
<DD>Group ID used with fix spring command does not exist.
<DD>A group ID used in the fix poems command does not exist.
<DT><I>Could not find fix recenter group ID</I>
<DD>A group ID used in the fix recenter command does not exist.
<DT><I>Could not find fix rigid group ID</I>
<DD>A group ID used in the fix rigid command does not exist.
<DT><I>Could not find fix spring couple group ID</I>
<DD>Self-explanatory.
<DT><I>Could not find temp_modify ID</I>
@ -784,54 +872,6 @@ more than once.
<DD>A temperature ID used in the velocity command does not exist.
<DT><I>Could not open dump file</I>
<DD>The output file for the dump command cannot be opened. Check that the
path and name are correct.
<DT><I>Could not open input script</I>
<DD>The input script file named in a command-line argument could not be
opened.
<DT><I>Could not open log.lammps</I>
<DD>The default LAMMPS log file cannot be opened. Check that the
directory you are running in allows for files to be created.
<DT><I>Could not open logfile</I>
<DD>The LAMMPS log file named in a command-line argument cannot be opened.
Check that the path and name are correct.
<DT><I>Could not open logfile %s</I>
<DD>The LAMMPS log file specified in the input script cannot be opened.
Check that the path and name are correct.
<DT><I>Could not open new input file %s</I>
<DD>The input script file named in an include or jump command could not be
opened. Check that the path and name are correct.
<DT><I>Could not open screen file</I>
<DD>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.
<DT><I>Could not open universe log file</I>
<DD>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
created.
<DT><I>Could not open universe screen file</I>
<DD>For a multi-partition run, the master screen file cannot be opened.
Check that the directory you are running in allows for files to be
created.
<DT><I>Create_atoms command before simulation box is defined</I>
<DD>The create_atoms command cannot be used before a read_data,
@ -1015,6 +1055,14 @@ create_box command.
<DD>Self-explanatory.
<DT><I>Fix msd group has no atoms</I>
<DD>Cannot compute diffusion for no atoms.
<DT><I>Fix momentum group has no atoms</I>
<DD>Self-explanatory.
<DT><I>Fix nph periods must be > 0.0</I>
<DD>The time window for pressure relaxation must be > 0
@ -1047,6 +1095,10 @@ error occurs, it is likely a bug, so send an email to the
<DD>Cannot use the rdf fix unless a pair style with a cutoff has been
defined.
<DT><I>Fix recenter group has no atoms</I>
<DD>Self-explanatory.
<DT><I>Fix temp/rescale region ID does not exist</I>
<DD>Self-explanatory.
@ -1061,13 +1113,21 @@ details.
<DD>Self-explanatory.
<DT><I>Found no restart file matching pattern</I>
<DD>When using a "*" in the restart file name, no matching file was found.
<DT><I>Granular pair styles do not use pair_coeff settings</I>
<DD>The pair_coeff command cannot be used with granular force fields.
<DT><I>Gravity must point in -z to use with fix insert</I>
<DT><I>Gravity must point in -y to use with fix insert in 2d</I>
<DD>The fix insert command assumes the theta angle for gravity is 180.0.
<DD>Gravity must be pointing "down" in a 2d box.
<DT><I>Gravity must point in -z to use with fix insert in 3d</I>
<DD>Gravity must be pointing "down" in a 3d box, i.e. theta = 180.0.
<DT><I>Group command before simulation box is defined</I>
@ -1085,7 +1145,9 @@ create_box command.
<DT><I>Illegal ... command</I>
<DD>Self-explanatory. Check the input script syntax and compare to the
documentation for the command.
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see what is the offending
line.
<DT><I>Improper atoms %d %d %d %d missing on proc %d at step %d</I>
@ -1218,11 +1280,6 @@ simulation box.
<DD>Eigensolve for rigid body was not sufficiently accurate.
<DT><I>Invalid $ variable</I>
<DD>The character following a $ in the input script is not between "a" and
"z".
<DT><I>Invalid angle style</I>
<DD>The choice of angle style is unknown.
@ -1531,17 +1588,13 @@ types.
<DD>Type used in set command must be from 1-N where N is the number
of atom types (bond types, angle types, etc).
<DT><I>Invalid variable in command-line argument</I>
<DD>Command-line arg -var must set a variable from "a" to "z".
<DT><I>Invalid variable in next command</I>
<DD>Next command in input script must set variables from "a" to "z".
<DT><I>Invalid variable in variable command</I>
<DT><I>Invalid variable name</I>
<DD>Variable command in input script must set a variable from "a" to "z".
<DD>Variable name used in an input script line is invalid.
<DT><I>Invalid variable style with next command</I>
@ -1552,6 +1605,12 @@ command.
<DD>One or more vector names are not recognized.
<DT><I>Invoked pair single on pair style none</I>
<DD>A command (e.g. a dump) attempted to invoke the single() function on a
pair style none, which is illegal. You are probably attempting to
compute per-atom quantities with an undefined pair style.
<DT><I>KSpace style has not yet been set</I>
<DD>Cannot use kspace_modify command until a kspace style is set.
@ -1707,15 +1766,14 @@ other.
<DD>Self-explanatory.
<DT><I>Must use -in switch with multiple partitions</I>
<DD>A multi-partition simulation cannot read the input script from stdin.
The -in command-line option must be used to specify a file.
<DT><I>Must use a block or cylinder region with fix insert</I>
<DD>Self-explanatory.
<DT><I>Must use a block region with fix insert for 2d simulations</I>
<DD>Self-explanatory.
<DT><I>Must use a molecular atom style with fix poems molecule</I>
<DD>Self-explanatory.
@ -1724,9 +1782,10 @@ The -in command-line option must be used to specify a file.
<DD>Self-explanatory.
<DT><I>Must use molecular atom style with neigh_modify exclude molecule</I>
<DT><I>Must use atom style dipole with chosen thermo settings</I>
<DD>Self-explanatory.
<DD>A thermo quantity being printed can only be computed if the atom
style includes dipole quantities.
<DT><I>Must use a z-axis cylinder with fix insert</I>
@ -1737,10 +1796,6 @@ be oriented along the z dimension.
<DD>Self-explanatory.
<DT><I>Must use atom style granular with lj units</I>
<DD>Self-explanatory.
<DT><I>Must use atom style granular with pair style granular</I>
<DD>Self-explanatory.
@ -1806,11 +1861,18 @@ gravity.
<DD>Self-explanatory.
<DT><I>Must use newton pairwise on with TIP4P potential</I>
<DT><I>Must use -in switch with multiple partitions</I>
<DD>Use of a TIP4P pair potential requires the newton command setting for
pairwise interactions be "on", because of the way forces are computed
on other atoms due to TIP4P interactions.
<DD>A multi-partition simulation cannot read the input script from stdin.
The -in command-line option must be used to specify a file.
<DT><I>Must use lj units with atom style granular</I>
<DD>Self-explanatory.
<DT><I>Must use molecular atom style with neigh_modify exclude molecule</I>
<DD>Self-explanatory.
<DT><I>Must use region with side = in with fix insert</I>
@ -1852,10 +1914,6 @@ after a read_data, read_restart, or create_box command.
<DD>The header of the data file indicated that atoms would be included,
but they were not present.
<DT><I>No atoms to compute diffusion for</I>
<DD>The fix msd command has no atoms to compute on.
<DT><I>No bonds allowed with this atom style</I>
<DD>Self-explanatory. Check data file.
@ -1915,10 +1973,6 @@ an atom has moved to far in a single timestep.
<DD>Two atoms are further apart than the pairwise table allows.
<DT><I>Pair style must be defined to use bond style quartic</I>
<DD>Bond style quartic requires a pair style be defined.
<DT><I>Pair table parameters did not set N</I>
<DD>List of pair table parameters must include N setting.
@ -1948,15 +2002,6 @@ kspace_modify command will reduce the stencil distance.
<DD>One or more pairwise cutoffs are too short to use with the specified
rRESPA cutoffs.
<DT><I>Pair style hybrid cannot have hybrid as an argument</I>
<DD>Self-explanatory. Check the input script.
<DT><I>Pair style hybrid cannot use same pair style twice</I>
<DD>The sub-style arguments of pair_style hybrid cannot be duplicated.
Check the input script.
<DT><I>Pair inner cutoff < Respa interior cutoff</I>
<DD>One or more pairwise cutoffs are too short to use with the specified
@ -1966,6 +2011,45 @@ rRESPA cutoffs.
<DD>The specified cutoffs for the pair style are inconsistent.
<DT><I>Pair style does not support bond_style quartic</I>
<DD>The pair style does not have a single() function, so it can
not be invoked by bond_style quartic.
<DT><I>Pair style does not support dumping per-atom energy</I>
<DD>The pair style does not have a single() function, so it can not be
invoked by the dump command.
<DT><I>Pair style does not support dumping per-atom stress</I>
<DD>The pair style does not have a single() function, so it can not be
invoked by the dump command.
<DT><I>Pair style does not support pair_write</I>
<DD>The pair style does not have a single() function, so it can
not be invoked by the pair_write command.
<DT><I>Pair style does not support rRESPA inner/middle/outer</I>
<DD>You are attempting to use rRESPA options with a pair style that
does not support them.
<DT><I>Pair style granular with history requires atoms have IDs</I>
<DD>Atoms in the simulation do not have IDs, so history effects
cannot be tracked by the granular pair potential.
<DT><I>Pair style hybrid cannot have hybrid as an argument</I>
<DD>Self-explanatory. Check the input script.
<DT><I>Pair style hybrid cannot use same pair style twice</I>
<DD>The sub-style arguments of pair_style hybrid cannot be duplicated.
Check the input script.
<DT><I>Pair style is incompatible with DihedralCharmm</I>
<DD>When using a dihedral style charmm, a pair style with a CHARMM
@ -1977,6 +2061,16 @@ specified.
<DD>If a pair style with a long-range Coulombic component is selected,
then a kspace style must also be used.
<DT><I>Pair style lj/cut/coul/long/tip4p requires atom IDs</I>
<DD>There are no atom IDs defined in the system and the TIP4P potential
requires them to find O,H atoms with a water molecule.
<DT><I>Pair style lj/cut/coul/long/tip4p requires newton pair on</I>
<DD>This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors.
<DT><I>Pair table cutoffs must all be equal to use with KSpace</I>
<DD>When using pair style table with a long-range KSpace solver, the
@ -1996,6 +2090,10 @@ read_restart, or create_box command.
<DD>Self-explanatory.
<DT><I>Pair_style granular command before simulation box is defined</I>
<DD>This pair style cannot be used before a simulation box is defined.
<DT><I>Pair_write command before pair_style is defined</I>
<DD>Self-explanatory.
@ -2071,11 +2169,6 @@ types in setfl potential file.
<DD>The first cutoff must be <= the second cutoff.
<DT><I>Respa inner/middle/outer used with invalid pair style</I>
<DD>Only a few pair potentials support the use of respa inner, middle,
outer options.
<DT><I>Respa levels must be >= 1</I>
<DD>Self-explanatory.
@ -2117,6 +2210,18 @@ incorrect.
<DD>The run command cannot be used before a read_data, read_restart, or
create_box command.
<DT><I>Run command upto value is before current timestep</I>
<DD>Self-explanatory.
<DT><I>Run command start value is after start of run</I>
<DD>Self-explanatory.
<DT><I>Run command stop value is before end of run</I>
<DD>Self-explanatory.
<DT><I>Run_style command before simulation box is defined</I>
<DD>The run_style command cannot be used before a read_data,
@ -2180,6 +2285,14 @@ SHAKE fix contribution to the pressure virial is incorrect.
<DD>The variable specified with a $ symbol in an input script command has
not been previously defined with a variable command.
<DT><I>Target T for fix nvt cannot be 0.0</I>
<DD>Self-explanatory.
<DT><I>Target T for fix npt cannot be 0.0</I>
<DD>Self-explanatory.
<DT><I>Temperature region ID does not exist</I>
<DD>The region ID specified in the temperature command does not exist.
@ -2232,9 +2345,11 @@ within a water molecule.
<DD>The target file for the fix tmd command did not list all atoms in the
fix group.
<DT><I>Too big a problem to run with a molecular atom style</I>
<DT><I>Too big a problem to replicate with molecular atom style</I>
<DD>Cannot run a problem with > 2^31 atoms with molecular attributes.
<DD>Molecular problems cannot become bigger than 2^31 atoms (or bonds,
etc) when replicated, else the atom IDs and other quantities cannot be
stored in 32 bit quantities.
<DT><I>Too few bits for lookup table</I>
@ -2246,20 +2361,6 @@ machine's floating point representation.
<DD>The atoms to be created by the create_atoms command must have a valid
type.
<DT><I>Too many atoms in data file</I>
<DD>A data file cannot contain more than 2^31 atoms.
<DT><I>Too many atoms to use delete atoms command</I>
<DD>Cannot use delete_atoms command if number of atoms is greater than
2^31.
<DT><I>Too many atoms to use velocity create with loop all</I>
<DD>Cannot use velocity create command with loop all setting if number of
atoms is greater than 2^31. Switch to local or geom setting.
<DT><I>Too many exponent bits for lookup table</I>
<DD>Table size specified via pair_modify command does not work with your
@ -2372,6 +2473,10 @@ definition until the simulation box has been defined.
<DD>Cannot use thermodynamic keywords in a equal style variable definition
until a simulation run has been performed.
<DT><I>Variable equal group ID does not exist</I>
<DD>Self-explanatory.
<DT><I>Velocity command before simulation box is defined</I>
<DD>The velocity command cannot be used before a read_data, read_restart,
@ -2411,6 +2516,11 @@ will be truncated to attempt to prevent the bond from blowing up.
<DD>A FENE bond has stretched dangerously far. It's interaction strength
will be truncated to attempt to prevent the bond from blowing up.
<DT><I>Fix recenter should come after all other integration fixes</I>
<DD>Other fixes may change the position of the center-of-mass, so
fix recenter should come last.
<DT><I>Group for fix_modify temp != fix group</I>
<DD>The fix_modify command is specifying a temperature computation that
@ -2647,6 +2757,12 @@ style region. Since thermo computes a global pressure, the kinetic
energy contribution from the temperature is assumed to also be for all
atoms. Thus the pressure printed by thermo could be inaccurate.
<DT><I>Using pair tail corrections with nonperiodic system</I>
<DD>This is probably a bogus thing to do, since tail corrections are
computed by integrating the density of a periodic system out to
infinity.
<DT><I>Using variable equal keyword with non-current thermo</I>
<DD>The variable expression is being evaluated with a thermodynamic

420
doc/Section_errors.txt
View File

@ -244,6 +244,11 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Another input script is already being processed} :dt
Cannot attempt to open a 2nd input script, when the original file is
still being processed. :dd
{Atom count is inconsistent, cannot write restart file} :dt
Sum of atoms across processors does not equal initial total count.
@ -281,11 +286,6 @@ been defined. :dd
Self-explanatory. :dd
{Atom style granular must perform 3d simulations} :dt
Atom style granular cannot be used with 2d simulations, because
the pairwise potentials are inherently 3d. :dd
{Atom style hybrid cannot have hybrid as an argument} :dt
Self-explanatory. Check the input script. :dd
@ -453,6 +453,11 @@ LAMMPS failed to compute a valid PPPM grid spacing in the z dimension. :dd
Must use the lattice command before using the create_atoms
command. :dd
{Cannot create an atom map unless atoms have IDs} :dt
The simulation requires a mapping from global atom IDs to local atoms,
but the atoms that have been defined have no IDs. :dd
{Cannot create_box after simulation box is defined} :dt
The create_box command cannot be used after a read_data, read_restart,
@ -462,10 +467,6 @@ or create_box command. :dd
Self-explanatory. :dd
{Cannot create vels with loop all for non-contiguous atom IDs} :dt
You cannot use the loop all option if you atom IDs do not span 1 to natoms :dd
{Cannot evaluate variable equal command} :dt
Syntax or keyword names in mathematical expression are not
@ -496,12 +497,19 @@ Volume can only be rescaled on a dimension that is periodic. :dd
Volume can only be rescaled uniaxially if system is periodic in all 3
dimensions. :dd
{Cannot invoke single() with pairwise TIP4P potential} :dt
{Cannot have both pair_modify shift and tail set to yes} :dt
Commands that invoke the single() function within pairwise potentials
cannot be used with a TIP4P potential, due to the way it computes
forces on other atoms besides the i,j pair. This includes the eng and
stress tensor components for the dump custom command. :dd
These 2 options are contradictory. :dd
{Cannot open dir to search for restart file} :dt
Using a "*" in the name of the restart file will open the current
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
{Cannot open EAM potential file %s} :dt
@ -523,6 +531,10 @@ the path and name are correct. :dd
The output file for the fix gran/diag command cannot be opened. Check
that the path and name are correct. :dd
{Cannot open fix gyration file %s} :dt
Self-explanatory. :dd
{Cannot open fix msd file %s} :dt
The output file for the fix msd command cannot be opened. Check that
@ -548,6 +560,29 @@ the path and name are correct. :dd
LAMMPS is attempting to open a gzipped version of the specified file
but was unsuccessful. Check that the path and name are correct. :dd
{Cannot open input script %s} :dt
Self-explanatory. :dd
{Cannot open input script %s} :dt
Self-explanatory. :dd
{Cannot open logfile} :dt
The LAMMPS log file named in a command-line argument cannot be opened.
Check that the path and name are correct. :dd
{Cannot open logfile %s} :dt
The LAMMPS log file specified in the input script cannot be opened.
Check that the path and name are correct. :dd
{Cannot open log.lammps} :dt
The default LAMMPS log file cannot be opened. Check that the
directory you are running in allows for files to be created. :dd
{Cannot open pair_write file} :dt
The specified output file for pair energies and forces cannot be
@ -555,8 +590,25 @@ opened. Check that the path and name are correct. :dd
{Cannot open restart file %s} :dt
The output restart file cannot be opened. Check that the path and
name are correct and that disk space is available. :dd
Self-explanatory. :dd
{Cannot open screen file} :dt
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 universe log file} :dt
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
created. :dd
{Cannot open universe screen file} :dt
For a multi-partition run, the master screen file cannot be opened.
Check that the directory you are running in allows for files to be
created. :dd
{Cannot read_data after simulation box is defined} :dt
@ -618,14 +670,19 @@ Instead they are defined on a per-atom basis in the data file. :dd
In the rRESPA integrator, you must define both a inner and outer
setting in order to use a middle setting. :dd
{Cannot set these values with this atom style} :dt
{Cannot set this attribute for this atom style} :dt
Choice of set style does not match attribute of atom style. :dd
The attribute being set does not exist for the defined atom style. :dd
{Cannot use atom style granular with chosen thermo settings} :dt
Cannot output temperature or pressure with atom style granular. :dd
{Cannot use delete_atoms unless atoms have IDs} :dt
Your atoms do not have IDs, so the delete_atoms command cannot be
used. :dd
{Cannot use delete_bonds with non-molecular system} :dt
Your choice of atom style does not have bonds. :dd
@ -643,6 +700,23 @@ The kspace style ewald cannot be used in 2d simulations. You can use
Self-explanatory. :dd
{Cannot use fix nph with no per-type mass defined} :dt
The defined atom style uses per-atom mass, not per-type mass. :dd
{Cannot use fix npt with no per-type mass defined} :dt
The defined atom style uses per-atom mass, not per-type mass. :dd
{Cannot zero momentum of 0 atoms} :dt
The collection of atoms for which momentum is being computed has no
atoms. :dd
{Cannot use fix nvt with no per-type mass defined} :dt
The defined atom style uses per-atom mass, not per-type mass. :dd
{Cannot use fix poems with atom style granular} :dt
This fix is not yet enabled for this atom style. :dd
@ -655,11 +729,6 @@ This fix is not yet enabled for this atom style. :dd
Your choice of atom style does not have bonds. :dd
{Cannot use multiple long-range potentials with pair hybrid} :dt
Only one sub-style potential with a long-range component can be
used with pair_style hybrid. :dd
{Cannot use nonperiodic boundaries with Ewald} :dt
For kspace style ewald, all 3 dimensions must have periodic boundaries
@ -672,6 +741,10 @@ For kspace style pppm, All 3 dimensions must have periodic boundaries
unless you use the kspace_modify command to define a 2d slab with a
non-periodic z dimension. :dd
{Cannot use pair tail corrections with 2d simulations} :dt
The correction factors are only currently defined for 3d systems. :dd
{Cannot use PPPM with 2d simulation} :dt
The kspace style pppm cannot be used in 2d simulations. You can use
@ -682,15 +755,26 @@ The kspace style pppm cannot be used in 2d simulations. You can use
Regions that extend to the box boundaries can only be used after the
create_box command has been used. :dd
{Cannot use rRESPA with full neighbor lists} :dt
Defined pair style uses full neighbor lists (as opposed to
half neighbor lists), which are incompatible with the current
implementation of rRESPA. :dd
{Cannot use vectors in variables unless atom map exists} :dt
Vectors require an atom map to be able to lookup the vector index.
Only atom styles with molecular information creat a global map. :dd
{Cannot zero momentum for less than 2 atoms} :dt
Velocity command is being used with momentum-zeroing options on a
group with 0 or 1 atoms. :dd
{Cannot use velocity create loop all unless atoms have IDs} :dt
Atoms in the simulation to do not have IDs, so this style
of velocity creation cannot be performed. :dd
{Cannot use velocity create loop all with non-contiguous atom IDs} :dt
Atoms in the simulation to do not have consecutive IDs, so this style
of velocity creation cannot be performed. :dd
{Command-line variable already exists} :dt
@ -729,14 +813,6 @@ A group ID used in the dump command does not exist. :dd
A group ID used in the fix command does not exist. :dd
{Could not find fix poems group ID} :dt
A group ID used in the fix poems command does not exist. :dd
{Could not find fix rigid group ID} :dt
A group ID used in the fix rigid command does not exist. :dd
{Could not find fix_modify ID} :dt
A fix ID used in the fix_modify command does not exist. :dd
@ -745,9 +821,21 @@ A fix ID used in the fix_modify command does not exist. :dd
A temperature ID used in the fix_modify command does not exist. :dd
{Could not find fix spring vector group ID} :dt
{Could not find fix poems group ID} :dt
Group ID used with fix spring command does not exist. :dd
A group ID used in the fix poems command does not exist. :dd
{Could not find fix recenter group ID} :dt
A group ID used in the fix recenter command does not exist. :dd
{Could not find fix rigid group ID} :dt
A group ID used in the fix rigid command does not exist. :dd
{Could not find fix spring couple group ID} :dt
Self-explanatory. :dd
{Could not find temp_modify ID} :dt
@ -781,54 +869,6 @@ A group ID used in the velocity command does not exist. :dd
A temperature ID used in the velocity command does not exist. :dd
{Could not open dump file} :dt
The output file for the dump command cannot be opened. Check that the
path and name are correct. :dd
{Could not open input script} :dt
The input script file named in a command-line argument could not be
opened. :dd
{Could not open log.lammps} :dt
The default LAMMPS log file cannot be opened. Check that the
directory you are running in allows for files to be created. :dd
{Could not open logfile} :dt
The LAMMPS log file named in a command-line argument cannot be opened.
Check that the path and name are correct. :dd
{Could not open logfile %s} :dt
The LAMMPS log file specified in the input script cannot be opened.
Check that the path and name are correct. :dd
{Could not open new input file %s} :dt
The input script file named in an include or jump command could not be
opened. Check that the path and name are correct. :dd
{Could not open screen file} :dt
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
{Could not open universe log file} :dt
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
created. :dd
{Could not open universe screen file} :dt
For a multi-partition run, the master screen file cannot be opened.
Check that the directory you are running in allows for files to be
created. :dd
{Create_atoms command before simulation box is defined} :dt
The create_atoms command cannot be used before a read_data,
@ -1012,6 +1052,14 @@ The time window for temperature relaxation must be > 0 :dd
Self-explanatory. :dd
{Fix msd group has no atoms} :dt
Cannot compute diffusion for no atoms. :dd
{Fix momentum group has no atoms} :dt
Self-explanatory. :dd
{Fix nph periods must be > 0.0} :dt
The time window for pressure relaxation must be > 0 :dd
@ -1044,6 +1092,10 @@ error occurs, it is likely a bug, so send an email to the
Cannot use the rdf fix unless a pair style with a cutoff has been
defined. :dd
{Fix recenter group has no atoms} :dt
Self-explanatory. :dd
{Fix temp/rescale region ID does not exist} :dt
Self-explanatory. :dd
@ -1058,13 +1110,21 @@ details. :dd
Self-explanatory. :dd
{Found no restart file matching pattern} :dt
When using a "*" in the restart file name, no matching file was found. :dd
{Granular pair styles do not use pair_coeff settings} :dt
The pair_coeff command cannot be used with granular force fields. :dd
{Gravity must point in -z to use with fix insert} :dt
{Gravity must point in -y to use with fix insert in 2d} :dt
The fix insert command assumes the theta angle for gravity is 180.0. :dd
Gravity must be pointing "down" in a 2d box. :dd
{Gravity must point in -z to use with fix insert in 3d} :dt
Gravity must be pointing "down" in a 3d box, i.e. theta = 180.0. :dd
{Group command before simulation box is defined} :dt
@ -1082,7 +1142,9 @@ A region ID used in the group command does not exist. :dd
{Illegal ... command} :dt
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. :dd
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see what is the offending
line. :dd
{Improper atoms %d %d %d %d missing on proc %d at step %d} :dt
@ -1215,11 +1277,6 @@ Eigensolve for rigid body was not sufficiently accurate. :dd
Eigensolve for rigid body was not sufficiently accurate. :dd
{Invalid $ variable} :dt
The character following a $ in the input script is not between "a" and
"z". :dd
{Invalid angle style} :dt
The choice of angle style is unknown. :dd
@ -1528,17 +1585,13 @@ types. :dd
Type used in set command must be from 1-N where N is the number
of atom types (bond types, angle types, etc). :dd
{Invalid variable in command-line argument} :dt
Command-line arg -var must set a variable from "a" to "z". :dd
{Invalid variable in next command} :dt
Next command in input script must set variables from "a" to "z". :dd
{Invalid variable in variable command} :dt
{Invalid variable name} :dt
Variable command in input script must set a variable from "a" to "z". :dd
Variable name used in an input script line is invalid. :dd
{Invalid variable style with next command} :dt
@ -1549,6 +1602,12 @@ command. :dd
One or more vector names are not recognized. :dd
{Invoked pair single on pair style none} :dt
A command (e.g. a dump) attempted to invoke the single() function on a
pair style none, which is illegal. You are probably attempting to
compute per-atom quantities with an undefined pair style. :dd
{KSpace style has not yet been set} :dt
Cannot use kspace_modify command until a kspace style is set. :dd
@ -1704,15 +1763,14 @@ other. :dd
Self-explanatory. :dd
{Must use -in switch with multiple partitions} :dt
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 a block or cylinder region with fix insert} :dt
Self-explanatory. :dd
{Must use a block region with fix insert for 2d simulations} :dt
Self-explanatory. :dd
{Must use a molecular atom style with fix poems molecule} :dt
Self-explanatory. :dd
@ -1721,9 +1779,10 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Must use molecular atom style with neigh_modify exclude molecule} :dt
{Must use atom style dipole with chosen thermo settings} :dt
Self-explanatory. :dd
A thermo quantity being printed can only be computed if the atom
style includes dipole quantities. :dd
{Must use a z-axis cylinder with fix insert} :dt
@ -1734,10 +1793,6 @@ be oriented along the z dimension. :dd
Self-explanatory. :dd
{Must use atom style granular with lj units} :dt
Self-explanatory. :dd
{Must use atom style granular with pair style granular} :dt
Self-explanatory. :dd
@ -1803,11 +1858,18 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Must use newton pairwise on with TIP4P potential} :dt
{Must use -in switch with multiple partitions} :dt
Use of a TIP4P pair potential requires the newton command setting for
pairwise interactions be "on", because of the way forces are computed
on other atoms due to TIP4P interactions. :dd
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 lj units with atom style granular} :dt
Self-explanatory. :dd
{Must use molecular atom style with neigh_modify exclude molecule} :dt
Self-explanatory. :dd
{Must use region with side = in with fix insert} :dt
@ -1849,10 +1911,6 @@ Self-explanatory. Check data file. :dd
The header of the data file indicated that atoms would be included,
but they were not present. :dd
{No atoms to compute diffusion for} :dt
The fix msd command has no atoms to compute on. :dd
{No bonds allowed with this atom style} :dt
Self-explanatory. Check data file. :dd
@ -1912,10 +1970,6 @@ Two atoms are closer together than the pairwise table allows. :dd
Two atoms are further apart than the pairwise table allows. :dd
{Pair style must be defined to use bond style quartic} :dt
Bond style quartic requires a pair style be defined. :dd
{Pair table parameters did not set N} :dt
List of pair table parameters must include N setting. :dd
@ -1945,15 +1999,6 @@ Style in pair coeff must have been listed in pair_style command. :dd
One or more pairwise cutoffs are too short to use with the specified
rRESPA cutoffs. :dd
{Pair style hybrid cannot have hybrid as an argument} :dt
Self-explanatory. Check the input script. :dd
{Pair style hybrid cannot use same pair style twice} :dt
The sub-style arguments of pair_style hybrid cannot be duplicated.
Check the input script. :dd
{Pair inner cutoff < Respa interior cutoff} :dt
One or more pairwise cutoffs are too short to use with the specified
@ -1963,6 +2008,45 @@ rRESPA cutoffs. :dd
The specified cutoffs for the pair style are inconsistent. :dd
{Pair style does not support bond_style quartic} :dt
The pair style does not have a single() function, so it can
not be invoked by bond_style quartic. :dd
{Pair style does not support dumping per-atom energy} :dt
The pair style does not have a single() function, so it can not be
invoked by the dump command. :dd
{Pair style does not support dumping per-atom stress} :dt
The pair style does not have a single() function, so it can not be
invoked by the dump command. :dd
{Pair style does not support pair_write} :dt
The pair style does not have a single() function, so it can
not be invoked by the pair_write command. :dd
{Pair style does not support rRESPA inner/middle/outer} :dt
You are attempting to use rRESPA options with a pair style that
does not support them. :dd
{Pair style granular with history requires atoms have IDs} :dt
Atoms in the simulation do not have IDs, so history effects
cannot be tracked by the granular pair potential. :dd
{Pair style hybrid cannot have hybrid as an argument} :dt
Self-explanatory. Check the input script. :dd
{Pair style hybrid cannot use same pair style twice} :dt
The sub-style arguments of pair_style hybrid cannot be duplicated.
Check the input script. :dd
{Pair style is incompatible with DihedralCharmm} :dt
When using a dihedral style charmm, a pair style with a CHARMM
@ -1974,6 +2058,16 @@ specified. :dd
If a pair style with a long-range Coulombic component is selected,
then a kspace style must also be used. :dd
{Pair style lj/cut/coul/long/tip4p requires atom IDs} :dt
There are no atom IDs defined in the system and the TIP4P potential
requires them to find O,H atoms with a water molecule. :dd
{Pair style lj/cut/coul/long/tip4p requires newton pair on} :dt
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors. :dd
{Pair table cutoffs must all be equal to use with KSpace} :dt
When using pair style table with a long-range KSpace solver, the
@ -1993,6 +2087,10 @@ read_restart, or create_box command. :dd
Self-explanatory. :dd
{Pair_style granular command before simulation box is defined} :dt
This pair style cannot be used before a simulation box is defined. :dd
{Pair_write command before pair_style is defined} :dt
Self-explanatory. :dd
@ -2068,11 +2166,6 @@ types in setfl potential file. :dd
The first cutoff must be <= the second cutoff. :dd
{Respa inner/middle/outer used with invalid pair style} :dt
Only a few pair potentials support the use of respa inner, middle,
outer options. :dd
{Respa levels must be >= 1} :dt
Self-explanatory. :dd
@ -2114,6 +2207,18 @@ incorrect. :dd
The run command cannot be used before a read_data, read_restart, or
create_box command. :dd
{Run command upto value is before current timestep} :dt
Self-explanatory. :dd
{Run command start value is after start of run} :dt
Self-explanatory. :dd
{Run command stop value is before end of run} :dt
Self-explanatory. :dd
{Run_style command before simulation box is defined} :dt
The run_style command cannot be used before a read_data,
@ -2177,6 +2282,14 @@ SHAKE fix contribution to the pressure virial is incorrect. :dd
The variable specified with a $ symbol in an input script command has
not been previously defined with a variable command. :dd
{Target T for fix nvt cannot be 0.0} :dt
Self-explanatory. :dd
{Target T for fix npt cannot be 0.0} :dt
Self-explanatory. :dd
{Temperature region ID does not exist} :dt
The region ID specified in the temperature command does not exist. :dd
@ -2229,9 +2342,11 @@ within a water molecule. :dd
The target file for the fix tmd command did not list all atoms in the
fix group. :dd
{Too big a problem to run with a molecular atom style} :dt
{Too big a problem to replicate with molecular atom style} :dt
Cannot run a problem with > 2^31 atoms with molecular attributes. :dd
Molecular problems cannot become bigger than 2^31 atoms (or bonds,
etc) when replicated, else the atom IDs and other quantities cannot be
stored in 32 bit quantities. :dd
{Too few bits for lookup table} :dt
@ -2243,20 +2358,6 @@ machine's floating point representation. :dd
The atoms to be created by the create_atoms command must have a valid
type. :dd
{Too many atoms in data file} :dt
A data file cannot contain more than 2^31 atoms. :dd
{Too many atoms to use delete atoms command} :dt
Cannot use delete_atoms command if number of atoms is greater than
2^31. :dd
{Too many atoms to use velocity create with loop all} :dt
Cannot use velocity create command with loop all setting if number of
atoms is greater than 2^31. Switch to local or geom setting. :dd
{Too many exponent bits for lookup table} :dt
Table size specified via pair_modify command does not work with your
@ -2369,6 +2470,10 @@ definition until the simulation box has been defined. :dd
Cannot use thermodynamic keywords in a equal style variable definition
until a simulation run has been performed. :dd
{Variable equal group ID does not exist} :dt
Self-explanatory. :dd
{Velocity command before simulation box is defined} :dt
The velocity command cannot be used before a read_data, read_restart,
@ -2408,6 +2513,11 @@ will be truncated to attempt to prevent the bond from blowing up. :dd
A FENE bond has stretched dangerously far. It's interaction strength
will be truncated to attempt to prevent the bond from blowing up. :dd
{Fix recenter should come after all other integration fixes} :dt
Other fixes may change the position of the center-of-mass, so
fix recenter should come last. :dd
{Group for fix_modify temp != fix group} :dt
The fix_modify command is specifying a temperature computation that
@ -2644,6 +2754,12 @@ style region. Since thermo computes a global pressure, the kinetic
energy contribution from the temperature is assumed to also be for all
atoms. Thus the pressure printed by thermo could be inaccurate. :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 variable equal keyword with non-current thermo} :dt
The variable expression is being evaluated with a thermodynamic

15
doc/Section_history.html
View File

@ -23,22 +23,21 @@ molecular dynamics codes I've distributed.
<H4><A NAME = "10_1"></A>10.1 Coming attractions
</H4>
<P>The current version of LAMMPS incorporates nearly all the features
from previous parallel MD codes I developed. These include earlier
versions of LAMMPS itself, Warp and ParaDyn for metals, and GranFlow
for granular materials.
from previous parallel MD codes developed at Sandia. These include
earlier versions of LAMMPS itself, Warp and ParaDyn for metals, and
GranFlow for granular materials.
</P>
<P>These are new features I'd like to eventually add to LAMMPS. Some are
being worked on; some haven't been implemented because of lack of time
or interest; others are just a lot of work!
<P>These are new features we'd like to eventually add to LAMMPS. Some
are being worked on; some haven't been implemented because of lack of
time or interest; others are just a lot of work!
</P>
<UL><LI>Monte Carlo bond-swapping for polymers (was in Fortran LAMMPS)
<LI>torsional shear boundary conditions and temperature calculation
<LI>bond creation potentials
<LI>point dipole force fields
<LI>3-body force fields for materials like Si or silica
<LI>many-body and bond-order potentials for materials like C, Si, or silica
<LI>modified EAM (MEAM) potentials for metals
<LI>REAXX force field from Bill Goddard's group
<LI>pressure and energy tail corrections for pairwise interactions
<LI>Parinello-Rahman non-rectilinear simulation box
</UL>
<HR>

15
doc/Section_history.txt
View File

@ -20,22 +20,21 @@ molecular dynamics codes I've distributed.
10.1 Coming attractions :h4,link(10_1)
The current version of LAMMPS incorporates nearly all the features
from previous parallel MD codes I developed. These include earlier
versions of LAMMPS itself, Warp and ParaDyn for metals, and GranFlow
for granular materials.
from previous parallel MD codes developed at Sandia. These include
earlier versions of LAMMPS itself, Warp and ParaDyn for metals, and
GranFlow for granular materials.
These are new features I'd like to eventually add to LAMMPS. Some are
being worked on; some haven't been implemented because of lack of time
or interest; others are just a lot of work!
These are new features we'd like to eventually add to LAMMPS. Some
are being worked on; some haven't been implemented because of lack of
time or interest; others are just a lot of work!
Monte Carlo bond-swapping for polymers (was in Fortran LAMMPS)
torsional shear boundary conditions and temperature calculation
bond creation potentials
point dipole force fields
3-body force fields for materials like Si or silica
many-body and bond-order potentials for materials like C, Si, or silica
modified EAM (MEAM) potentials for metals
REAXX force field from Bill Goddard's group
pressure and energy tail corrections for pairwise interactions
Parinello-Rahman non-rectilinear simulation box :ul
:line

9
doc/Section_howto.html
View File

@ -167,6 +167,10 @@ commands like <A HREF = "pair_coeff.html">pair_coeff</A> or
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
</P>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field. See <A HREF = "#Cornell">(Cornell)</A> for a description of the AMBER force
field.
</P>
@ -577,6 +581,11 @@ back into LAMMPS.
</P>
<HR>
<A NAME = "Cornell"></A>
<P><B>(Cornell)</B> Corenll, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
</P>
<A NAME = "Horn"></A>
<P><B>(Horn)</B> Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,

8
doc/Section_howto.txt
View File

@ -164,6 +164,10 @@ commands like "pair_coeff"_pair_coeff.html or
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#Cornell for a description of the AMBER force
field.
:link(charmm,http://www.scripps.edu/brooks)
:link(amber,http://amber.scripps.edu)
@ -573,6 +577,10 @@ back into LAMMPS.
:line
:link(Cornell)
[(Cornell)] Corenll, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(Horn)
[(Horn)] Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
J Chem Phys, 120, 9665 (2004).

9
doc/Section_start.html
View File

@ -224,16 +224,17 @@ list of packages is as follows:
<TR><TD >dpd </TD><TD > dissipative particle dynamics (DPD) force field</TD></TR>
<TR><TD >granular </TD><TD > force fields and boundary conditions for granular systems</TD></TR>
<TR><TD >kspace </TD><TD > long-range Ewald and particle-mesh (PPPM) solvers</TD></TR>
<TR><TD >manybody </TD><TD > metal, 3-body, bond-order potentials</TD></TR>
<TR><TD >molecule </TD><TD > force fields for molecular systems</TD></TR>
<TR><TD >poems </TD><TD > coupled rigid body motion</TD></TR>
<TR><TD >xtc </TD><TD > dump atom snapshots in XTC format
</TD></TR></TABLE></DIV>
<P>Any or all of these packages can be included or excluded when LAMMPS
is built. The default is to include only the kspace and molecule
packages. You may wish to exclude certain packages if you will never
run certain kinds of simulations. This will produce a smaller
executable which in some cases will also run a bit faster.
is built. The default is to include only the kspace, manybody, and
molecule packages. You may wish to exclude certain packages if you
will never run certain kinds of simulations. This will produce a
smaller executable which in some cases will also run a bit faster.
</P>
<P>Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type

9
doc/Section_start.txt
View File

@ -218,15 +218,16 @@ class2 : class 2 force fields
dpd : dissipative particle dynamics (DPD) force field
granular : force fields and boundary conditions for granular systems
kspace : long-range Ewald and particle-mesh (PPPM) solvers
manybody : metal, 3-body, bond-order potentials
molecule : force fields for molecular systems
poems : coupled rigid body motion
xtc : dump atom snapshots in XTC format :tb(s=:)
Any or all of these packages can be included or excluded when LAMMPS
is built. The default is to include only the kspace and molecule
packages. You may wish to exclude certain packages if you will never
run certain kinds of simulations. This will produce a smaller
executable which in some cases will also run a bit faster.
is built. The default is to include only the kspace, manybody, and
molecule packages. You may wish to exclude certain packages if you
will never run certain kinds of simulations. This will produce a
smaller executable which in some cases will also run a bit faster.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type

5
doc/angle_style.html
View File

@ -67,8 +67,9 @@ specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command
<P>Angle styles can only be set for atom_styles that allow angles to be
defined.
</P>
<P>Angle styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
<P>Angle styles are part of the "molecular" package or other packages as
noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>

5
doc/angle_style.txt
View File

@ -65,8 +65,9 @@ specified by the associated "angle_coeff"_angle_coeff.html command:
Angle styles can only be set for atom_styles that allow angles to be
defined.
Angle styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the "Making
Angle styles are part of the "molecular" package or other packages as
noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

19
doc/angle_style_charmm.html
View File

@ -30,6 +30,9 @@ angle_coeff 1 300.0 107.0 50.0 3.0
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.
</P>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
@ -43,14 +46,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<P><B>Restrictions:</B>
</P>
<P>Angle styles can only be set for atom styles that allow angles to be
defined.
</P>
<P>This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
@ -58,4 +54,11 @@ LAMMPS</A> section for more info.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
</HTML>

18
doc/angle_style_charmm.txt
View File

@ -27,6 +27,9 @@ with an additional Urey_Bradley term based on the distance {r} between
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
@ -40,17 +43,16 @@ r_ub (distance) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:]
Angle styles can only be set for atom styles that allow angles to be
defined.
This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
:line
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

11
doc/angle_style_class2.html
View File

@ -30,6 +30,8 @@ angle_coeff * 75.0
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
the equilibrium bond lengths.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>For this style, only coefficients for the Ea formula can be specified
in the input script. These are the 4 coefficients:
</P>
@ -64,9 +66,6 @@ same value from the Ea formula.
</P>
<P><B>Restrictions:</B>
</P>
<P>Angle styles can only be set for atom styles that allow angles to be
defined.
</P>
<P>This angle style is part of the "class2" package. It is only enabled
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
@ -77,4 +76,10 @@ LAMMPS</A> section for more info.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>

10
doc/angle_style_class2.txt
View File

@ -27,6 +27,8 @@ where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
the equilibrium bond lengths.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
For this style, only coefficients for the Ea formula can be specified
in the input script. These are the 4 coefficients:
@ -61,9 +63,6 @@ same value from the Ea formula.
[Restrictions:]
Angle styles can only be set for atom styles that allow angles to be
defined.
This angle style is part of the "class2" package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
@ -73,3 +72,8 @@ LAMMPS"_Section_start.html#2_2 section for more info.
"angle_coeff"_angle_coeff.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

9
doc/angle_style_cosine.html
View File

@ -35,14 +35,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Angle styles can only be set for atom styles that allow angles to be
defined.
</P>
<P>This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/angle_style_cosine.txt
View File

@ -32,14 +32,7 @@ or "read_restart"_read_restart.html commands:
K (energy) :ul
[Restrictions:]
Angle styles can only be set for atom styles that allow angles to be
defined.
This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

9
doc/angle_style_cosine_squared.html
View File

@ -40,14 +40,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
</P>
<P><B>Restrictions:</B>
</P>
<P>Angle styles can only be set for atom styles that allow angles to be
defined.
</P>
<P>This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/angle_style_cosine_squared.txt
View File

@ -37,14 +37,7 @@ theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
[Restrictions:]
Angle styles can only be set for atom styles that allow angles to be
defined.
This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

9
doc/angle_style_harmonic.html
View File

@ -40,14 +40,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<P><B>Restrictions:</B>
</P>
<P>Angle styles can only be set for atom styles that allow angles to be
defined.
</P>
<P>This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/angle_style_harmonic.txt
View File

@ -37,14 +37,7 @@ theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:]
Angle styles can only be set for atom styles that allow angles to be
defined.
This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

11
doc/angle_style_hybrid.html
View File

@ -40,14 +40,11 @@ angle type 1 to be computed with a <I>harmonic</I> potential with
coefficients 80.0, 1.2 for K, r0. All other angle types (2-N) would
be computed with a <I>cosine</I> potential with coefficient 50.0 for K.
</P>
<P><B>Restrictions:</B>
<P>An angle style of <I>none</I> can be specified as an argument to
angle_style hybrid and the corresponding angle_coeff commands, if you
desire to turn off certain angle types.
</P>
<P>Angle styles can only be set for atom styles that allow angles to be
defined.
</P>
<P>This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

11
doc/angle_style_hybrid.txt
View File

@ -37,14 +37,11 @@ angle type 1 to be computed with a {harmonic} potential with
coefficients 80.0, 1.2 for K, r0. All other angle types (2-N) would
be computed with a {cosine} potential with coefficient 50.0 for K.
[Restrictions:]
An angle style of {none} can be specified as an argument to
angle_style hybrid and the corresponding angle_coeff commands, if you
desire to turn off certain angle types.
Angle styles can only be set for atom styles that allow angles to be
defined.
This angle style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

5
doc/angle_style_none.html
View File

@ -25,10 +25,7 @@
if triplets of angle atoms were listed in the data file read by the
<A HREF = "read_data.html">read_data</A> command.
</P>
<P><B>Restrictions:</B>
</P>
<P>Angle styles can only be set for atom styles that allow angles to be
defined.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>

5
doc/angle_style_none.txt
View File

@ -22,10 +22,7 @@ Using an angle style of none means angle forces are not computed, even
if triplets of angle atoms were listed in the data file read by the
"read_data"_read_data.html command.
[Restrictions:]
Angle styles can only be set for atom styles that allow angles to be
defined.
[Restrictions:] none
[Related commands:] none

5
doc/bond_style.html
View File

@ -78,8 +78,9 @@ specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command:
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>Bond styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
<P>Bond styles are part of the "molecular" package or other packages as
noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>

5
doc/bond_style.txt
View File

@ -75,8 +75,9 @@ specified by the associated "bond_coeff"_bond_coeff.html command:
Bond styles can only be set for atom styles that allow bonds to be
defined.
Bond styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the "Making
Bond styles are part of the "molecular" package or other packages as
noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

11
doc/bond_style_class2.html
View File

@ -28,6 +28,8 @@ bond_coeff 1 1.0 100.0 80.0 80.0
</CENTER>
<P>where r0 is the equilibrium bond distance.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
@ -40,9 +42,6 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
</UL>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>This bond style is part of the "class2" package. It is only enabled
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
@ -53,4 +52,10 @@ LAMMPS</A> section for more info.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>

10
doc/bond_style_class2.txt
View File

@ -25,6 +25,8 @@ The {class2} bond style uses the potential
where r0 is the equilibrium bond distance.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
@ -37,9 +39,6 @@ K4 (energy/distance^2) :ul
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
This bond style is part of the "class2" package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
@ -49,3 +48,8 @@ LAMMPS"_Section_start.html#2_2 section for more info.
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

9
doc/bond_style_fene.html
View File

@ -42,14 +42,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>epsilon (energy)
<LI>sigma (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/bond_style_fene.txt
View File

@ -39,14 +39,7 @@ R0 (distance)
epsilon (energy)
sigma (distance) :ul
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

9
doc/bond_style_fene_expand.html
View File

@ -47,14 +47,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>sigma (distance)
<LI>delta (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/bond_style_fene_expand.txt
View File

@ -44,14 +44,7 @@ epsilon (energy)
sigma (distance)
delta (distance) :ul
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

9
doc/bond_style_harmonic.html
View File

@ -37,14 +37,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<UL><LI>K (energy/distance^2)
<LI>r0 (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/bond_style_harmonic.txt
View File

@ -34,14 +34,7 @@ or "read_restart"_read_restart.html commands:
K (energy/distance^2)
r0 (distance) :ul
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

11
doc/bond_style_hybrid.html
View File

@ -41,14 +41,11 @@ coefficients 80.0, 1.2 for K, r0. All other bond types (2-N) would be
computed with a <I>fene</I> potential with coefficients 30.0, 1.5, 1.0, 1.0
for K, R0, epsilon, sigma.
</P>
<P><B>Restrictions:</B>
<P>A bond style of <I>none</I> can be specified as an argument to bond_style
hybrid and the corresponding bond_coeff commands, if you desire to
turn off certain bond types.
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

11
doc/bond_style_hybrid.txt
View File

@ -38,14 +38,11 @@ coefficients 80.0, 1.2 for K, r0. All other bond types (2-N) would be
computed with a {fene} potential with coefficients 30.0, 1.5, 1.0, 1.0
for K, R0, epsilon, sigma.
[Restrictions:]
A bond style of {none} can be specified as an argument to bond_style
hybrid and the corresponding bond_coeff commands, if you desire to
turn off certain bond types.
Bond styles can only be set for atom styles that allow bonds to be
defined.
This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

9
doc/bond_style_morse.html
View File

@ -38,14 +38,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>alpha (inverse distance)
<LI>r0 (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/bond_style_morse.txt
View File

@ -35,14 +35,7 @@ D (energy)
alpha (inverse distance)
r0 (distance) :ul
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

5
doc/bond_style_none.html
View File

@ -25,10 +25,7 @@
pairs of bonded atoms were listed in the data file read by the
<A HREF = "read_data.html">read_data</A> command.
</P>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>

5
doc/bond_style_none.txt
View File

@ -22,10 +22,7 @@ Using a bond style of none means bond forces are not computed, even if
pairs of bonded atoms were listed in the data file read by the
"read_data"_read_data.html command.
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
[Restrictions:] none
[Related commands:] none

9
doc/bond_style_nonlinear.html
View File

@ -38,14 +38,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>r0 (distance)
<LI>lamda (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/bond_style_nonlinear.txt
View File

@ -35,14 +35,7 @@ epsilon (energy)
r0 (distance)
lamda (distance) :ul
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
This bond style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

7
doc/bond_style_quartic.html
View File

@ -75,17 +75,10 @@ delete_bonds all bond 0 remove
</PRE>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
<P>The <I>quartic</I> style requires that <A HREF = "special_bonds.html">special_bonds</A>
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with <I>quartic</I> bonds.
</P>
<P>This bond style is part of the "molecular" package. It is only enabled
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>

7
doc/bond_style_quartic.txt
View File

@ -72,17 +72,10 @@ delete_bonds all bond 0 remove :pre
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
The {quartic} style requires that "special_bonds"_special_bonds.html
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with {quartic} bonds.
This bond style is part of the "molecular" package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html

5
doc/dihedral_style.html
View File

@ -83,8 +83,9 @@ specified by the associated <A HREF = "dihedral_coeff.html">dihedral_coeff</A> c
<P>Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
</P>
<P>Dihedral styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
<P>Dihedral styles are part of the "molecular" package or other packages
as noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>

5
doc/dihedral_style.txt
View File

@ -81,8 +81,9 @@ specified by the associated "dihedral_coeff"_dihedral_coeff.html command:
Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
Dihedral styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the "Making
Dihedral styles are part of the "molecular" package or other packages
as noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

19
doc/dihedral_style_charmm.html
View File

@ -26,6 +26,9 @@ dihedral_coeff 1 120.0 1 60 0.5
</P>
<CENTER><IMG SRC = "Eqs/dihedral_charmm.jpg">
</CENTER>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field.
</P>
<P>The following coefficients must be defined for each dihedral type via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
@ -45,14 +48,7 @@ should typically be set to 0.0, else the 1-4 interactions in a
dihedral will be computed twice (once by the pair potential, and once
by the dihedral/charmm potential).
</P>
<P><B>Restrictions:</B>
</P>
<P>Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
</P>
<P>This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
@ -60,4 +56,11 @@ LAMMPS</A> section for more info.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
</HTML>

18
doc/dihedral_style_charmm.txt
View File

@ -23,6 +23,9 @@ The {charmm} dihedral style uses the potential
:c,image(Eqs/dihedral_charmm.jpg)
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field.
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
@ -42,17 +45,16 @@ should typically be set to 0.0, else the 1-4 interactions in a
dihedral will be computed twice (once by the pair potential, and once
by the dihedral/charmm potential).
[Restrictions:]
Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
:line
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

11
doc/dihedral_style_class2.html
View File

@ -33,6 +33,8 @@ is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
<P>Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
bond lengths.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>For this style, only coefficients for the Ed formula can be specified
in the input script. These are the 6 coefficients:
</P>
@ -101,9 +103,6 @@ Coeffs" heading and each line lists 3 coefficients:
</UL>
<P><B>Restrictions:</B>
</P>
<P>Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
</P>
<P>This dihedral style is part of the "class2" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
@ -114,4 +113,10 @@ LAMMPS</A> section for more info.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>

10
doc/dihedral_style_class2.txt
View File

@ -30,6 +30,8 @@ is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
bond lengths.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
For this style, only coefficients for the Ed formula can be specified
in the input script. These are the 6 coefficients:
@ -98,9 +100,6 @@ r3 (distance) :ul
[Restrictions:]
Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
This dihedral style is part of the "class2" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
@ -110,3 +109,8 @@ LAMMPS"_Section_start.html#2_2 section for more info.
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

9
doc/dihedral_style_harmonic.html
View File

@ -35,14 +35,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>d (+1 or -1)
<LI>n (integer >= 0)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
</P>
<P>This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/dihedral_style_harmonic.txt
View File

@ -32,14 +32,7 @@ K (energy)
d (+1 or -1)
n (integer >= 0) :ul
[Restrictions:]
Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

9
doc/dihedral_style_helix.html
View File

@ -43,14 +43,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>B (energy)
<LI>C (energy)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
</P>
<P>This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/dihedral_style_helix.txt
View File

@ -40,14 +40,7 @@ A (energy)
B (energy)
C (energy) :ul
[Restrictions:]
Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

11
doc/dihedral_style_hybrid.html
View File

@ -41,14 +41,11 @@ potential with coefficients 80.0, 1.2 for K, d, n. Dihedral type 2
would be computed with a <I>helix</I> potential with coefficients 10.0,
10.0, 10.0 for A, B, C.
</P>
<P><B>Restrictions:</B>
<P>A dihedral style of <I>none</I> can be specified as an argument to
dihedral_style hybrid and the corresponding dihedral_coeff commands,
if you desire to turn off certain dihedral types.
</P>
<P>Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
</P>
<P>This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

11
doc/dihedral_style_hybrid.txt
View File

@ -38,14 +38,11 @@ potential with coefficients 80.0, 1.2 for K, d, n. Dihedral type 2
would be computed with a {helix} potential with coefficients 10.0,
10.0, 10.0 for A, B, C.
[Restrictions:]
A dihedral style of {none} can be specified as an argument to
dihedral_style hybrid and the corresponding dihedral_coeff commands,
if you desire to turn off certain dihedral types.
Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

9
doc/dihedral_style_multi_harmonic.html
View File

@ -37,14 +37,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>A4 (energy)
<LI>A5 (energy)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
</P>
<P>This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/dihedral_style_multi_harmonic.txt
View File

@ -34,14 +34,7 @@ A3 (energy)
A4 (energy)
A5 (energy) :ul
[Restrictions:]
Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

5
doc/dihedral_style_none.html
View File

@ -25,10 +25,7 @@
computed, even if quadruplets of dihedral atoms were listed in the
data file read by the <A HREF = "read_data.html">read_data</A> command.
</P>
<P><B>Restrictions:</B>
</P>
<P>Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>

5
doc/dihedral_style_none.txt
View File

@ -22,10 +22,7 @@ Using an dihedral style of none means dihedral forces are not
computed, even if quadruplets of dihedral atoms were listed in the
data file read by the "read_data"_read_data.html command.
[Restrictions:]
Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
[Restrictions:] none
[Related commands:] none

9
doc/dihedral_style_opls.html
View File

@ -41,14 +41,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>K3 (energy)
<LI>K4 (energy)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
</P>
<P>This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/dihedral_style_opls.txt
View File

@ -38,14 +38,7 @@ K2 (energy)
K3 (energy)
K4 (energy) :ul
[Restrictions:]
Dihedral styles can only be set for atom styles that allow dihedrals to be
defined.
This dihedral style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

5
doc/improper_style.html
View File

@ -62,8 +62,9 @@ specified by the associated <A HREF = "improper_coeff.html">improper_coeff</A> c
<P>Improper styles can only be set for atom_style choices that allow
impropers to be defined.
</P>
<P>Improper styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
<P>Improper styles are part of the "molecular" package or other packages
as noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>

5
doc/improper_style.txt
View File

@ -59,8 +59,9 @@ specified by the associated "improper_coeff"_improper_coeff.html command:
Improper styles can only be set for atom_style choices that allow
impropers to be defined.
Improper styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the "Making
Improper styles are part of the "molecular" package or other packages
as noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

11
doc/improper_style_class2.html
View File

@ -32,6 +32,8 @@ subscripts on the various theta's refer to different combinations of
atoms i,j,k,l used to form the angle; theta1, theta2, theta3 are the
equilibrium positions of those angles.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>The following coefficients must be defined for each improper type via the
<A HREF = "improper_coeff.html">improper_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
@ -62,9 +64,6 @@ radians internally; hence the units of M are in energy/radian^2.
</P>
<P><B>Restrictions:</B>
</P>
<P>Improper styles can only be set for atom styles that allow impropers to be
defined.
</P>
<P>This improper style is part of the "class2" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
@ -75,4 +74,10 @@ LAMMPS</A> section for more info.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>

10
doc/improper_style_class2.txt
View File

@ -29,6 +29,8 @@ subscripts on the various theta's refer to different combinations of
atoms i,j,k,l used to form the angle; theta1, theta2, theta3 are the
equilibrium positions of those angles.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each improper type via the
"improper_coeff"_improper_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
@ -59,9 +61,6 @@ radians internally; hence the units of M are in energy/radian^2.
[Restrictions:]
Improper styles can only be set for atom styles that allow impropers to be
defined.
This improper style is part of the "class2" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
@ -71,3 +70,8 @@ LAMMPS"_Section_start.html#2_2 section for more info.
"improper_coeff"_improper_coeff.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

9
doc/improper_style_cvff.html
View File

@ -37,14 +37,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>d (+1 or -1)
<LI>n (0,1,2,3,4,6)
</UL>
<P><B>Restrictions:</B>
</P>
<P>Improper styles can only be set for atom styles that allow impropers to be
defined.
</P>
<P>This improper style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/improper_style_cvff.txt
View File

@ -34,14 +34,7 @@ K (energy)
d (+1 or -1)
n (0,1,2,3,4,6) :ul
[Restrictions:]
Improper styles can only be set for atom styles that allow impropers to be
defined.
This improper style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

9
doc/improper_style_harmonic.html
View File

@ -40,14 +40,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<P>X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<P><B>Restrictions:</B>
</P>
<P>Improper styles can only be set for atom styles that allow impropers to be
defined.
</P>
<P>This improper style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

9
doc/improper_style_harmonic.txt
View File

@ -37,14 +37,7 @@ X0 (degrees) :ul
X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:]
Improper styles can only be set for atom styles that allow impropers to be
defined.
This improper style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

11
doc/improper_style_hybrid.html
View File

@ -41,14 +41,11 @@ potential with coefficients 120.0, 30 for K, X0. Improper type 2
would be computed with a <I>cvff</I> potential with coefficients 20.0, -1,
2 for K, d, n.
</P>
<P><B>Restrictions:</B>
<P>An improper style of <I>none</I> can be specified as an argument to
improper_style hybrid and the corresponding improper_coeff commands,
if you desire to turn off certain improper types.
</P>
<P>Improper styles can only be set for atom styles that allow impropers to be
defined.
</P>
<P>This improper style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

11
doc/improper_style_hybrid.txt
View File

@ -38,14 +38,11 @@ potential with coefficients 120.0, 30 for K, X0. Improper type 2
would be computed with a {cvff} potential with coefficients 20.0, -1,
2 for K, d, n.
[Restrictions:]
An improper style of {none} can be specified as an argument to
improper_style hybrid and the corresponding improper_coeff commands,
if you desire to turn off certain improper types.
Improper styles can only be set for atom styles that allow impropers to be
defined.
This improper style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Restrictions:] none
[Related commands:]

5
doc/improper_style_none.html
View File

@ -25,10 +25,7 @@
computed, even if quadruplets of improper atoms were listed in the
data file read by the <A HREF = "read_data.html">read_data</A> command.
</P>
<P><B>Restrictions:</B>
</P>
<P>Improper styles can only be set for atom styles that allow impropers
to be defined.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>

5
doc/improper_style_none.txt
View File

@ -22,10 +22,7 @@ Using an improper style of none means improper forces are not
computed, even if quadruplets of improper atoms were listed in the
data file read by the "read_data"_read_data.html command.
[Restrictions:]
Improper styles can only be set for atom styles that allow impropers
to be defined.
[Restrictions:] none
[Related commands:] none

12
doc/next.html
View File

@ -15,20 +15,22 @@
</P>
<PRE>next variables
</PRE>
<UL><LI>variables = one or more lower-case single-character variable names
<UL><LI>variables = one or more variable names
</UL>
<P><B>Examples:</B>
</P>
<PRE>next x
next a t x
next a t x myTemp
</PRE>
<P><B>Description:</B>
</P>
<P>This command is used with variables defined by the
<A HREF = "variable.html">variable</A> command. It assigns the next value to the
variable from the variable's list, so that when $X is subsequently
substituted for in an input script command, the new value is used. X
is a single lower-case character from "a" to "z".
variable from the variable's list, so that when a variable is
subsequently substituted for in an input script command, the new value
is used. If a variable name is a single lower-case character from "a"
to "z", it can be used in an input script command as $a or $z. If it
is multiple letters, it can be used as $<I>myTemp</I>.
</P>
<P>All variables in a single next command must be the same style:
<I>index</I>, <I>loop</I>, or <I>universe</I>. <I>Equal</I>- or <I>world</I>-style variables

12
doc/next.txt
View File

@ -12,20 +12,22 @@ next command :h3
next variables :pre
variables = one or more lower-case single-character variable names :ul
variables = one or more variable names :ul
[Examples:]
next x
next a t x :pre
next a t x myTemp :pre
[Description:]
This command is used with variables defined by the
"variable"_variable.html command. It assigns the next value to the
variable from the variable's list, so that when $X is subsequently
substituted for in an input script command, the new value is used. X
is a single lower-case character from "a" to "z".
variable from the variable's list, so that when a variable is
subsequently substituted for in an input script command, the new value
is used. If a variable name is a single lower-case character from "a"
to "z", it can be used in an input script command as $a or $z. If it
is multiple letters, it can be used as ${myTemp}.
All variables in a single next command must be the same style:
{index}, {loop}, or {universe}. {Equal}- or {world}-style variables

3
doc/pair_modify.html
View File

@ -151,6 +151,9 @@ those interactions.
</UL>
<P><B>Restrictions:</B> none
</P>
<P>Not all pair styles support mixing. See the doc page for individual
pair styles for details.
</P>
<P>You cannot use <I>shift</I> yes with <I>tail</I> yes, since those are
conflicting options.
</P>

3
doc/pair_modify.txt
View File

@ -145,6 +145,9 @@ those interactions. :l,ule
[Restrictions:] none
Not all pair styles support mixing. See the doc page for individual
pair styles for details.
You cannot use {shift} yes with {tail} yes, since those are
conflicting options.

4
doc/pair_style_buck.html
View File

@ -86,6 +86,10 @@ pair_style command.
</P>
<P><B>Restrictions:</B>
</P>
<P>The <I>buck</I> potentials do not support the
<A HREF = "pair_modify.hmtl">pair_modify</A> <I>mix</I> option. Coefficients for all i,j
pairs must be specified explicitly.
</P>
<P>The <I>buck/coul/long</I> style is part of the "kspace" package. It is
only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.

4
doc/pair_style_buck.txt
View File

@ -80,6 +80,10 @@ pair_style command.
[Restrictions:]
The {buck} potentials do not support the
"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j
pairs must be specified explicitly.
The {buck/coul/long} style is part of the "kspace" package. It is
only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.

11
doc/pair_style_charmm.html
View File

@ -54,7 +54,9 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5
<P>The <I>lj/charmm</I> styles compute LJ and Coulombic interactions with an
additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cuoff. It is a widely
used option in the CHARMM MD code.
used potential in the <A HREF = "http://www.scripps.edu/brooks">CHARMM</A> MD code.
See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field.
</P>
<CENTER><IMG SRC = "Eqs/pair_charmm.jpg">
</CENTER>
@ -122,4 +124,11 @@ pages for workarounds on this issue.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
</HTML>

10
doc/pair_style_charmm.txt
View File

@ -48,7 +48,9 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
The {lj/charmm} styles compute LJ and Coulombic interactions with an
additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cuoff. It is a widely
used option in the CHARMM MD code.
used potential in the "CHARMM"_http://www.scripps.edu/brooks MD code.
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field.
:c,image(Eqs/pair_charmm.jpg)
@ -115,3 +117,9 @@ pages for workarounds on this issue.
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

8
doc/pair_style_class2.html
View File

@ -60,6 +60,8 @@ pair_coeff 1 1 100.0 3.5 9.0
Coulombic term as described for the <A HREF = "pair_style_lj.html">lj/cut</A> pair
styles.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
@ -101,4 +103,10 @@ pages for workarounds on this issue.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>

7
doc/pair_style_class2.txt
View File

@ -54,6 +54,8 @@ The {lj/class2/coul/cut} and {lj/class2/coul/long} styles add a
Coulombic term as described for the "lj/cut"_pair_style_lj.html pair
styles.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
@ -94,3 +96,8 @@ pages for workarounds on this issue.
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

4
doc/pair_style_dpd.html
View File

@ -62,6 +62,10 @@ command so it does not need to be specified.
was built with those package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
</P>
<P>The <I>dpd</I> potential does not support the
<A HREF = "pair_modify.hmtl">pair_modify</A> <I>mix</I> option. Coefficients for all i,j
pairs must be specified explicitly.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>

4
doc/pair_style_dpd.txt
View File

@ -59,6 +59,10 @@ This style is part of the "dpd" package. It is only enabled if LAMMPS
was built with those package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
The {dpd} potential does not support the
"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j
pairs must be specified explicitly.
[Related commands:]
"pair_coeff"_pair_coeff.html

52
doc/pair_style_eam.html
View File

@ -57,13 +57,13 @@ Several DYNAMO potential files for different metals are included in
the "potentials" directory of the LAMMPS distribution.
</P>
<P>IMPORTANT NOTE: The <I>eam</I> style reads single-element EAM potentials in
the DYNAMO <I>funcfl</I> format. Single element or alloy systems can be
modeled with <I>funcfl</I> files and style <I>eam</I>; for the alloy case LAMMPS
mixes the single-element potentials to produce alloy potentials the
same way that DYNAMO does. Alternatively, DYNAMO <I>setfl</I> files can be
used by LAMMPS to model alloy systems by invoking the <I>eam/alloy</I>
style as described below. <I>Setfl</I> files require no mixing as they
specify alloy interactions explicitly.
the DYNAMO <I>funcfl</I> format. Either single element or alloy systems
can be modeled with <I>funcfl</I> files and style <I>eam</I>. For the alloy
case LAMMPS mixes the single-element potentials to produce alloy
potentials the same way that DYNAMO does. Alternatively, DYNAMO
<I>setfl</I> files can be used by LAMMPS to model alloy systems by invoking
the <I>eam/alloy</I> style as described below. <I>Setfl</I> files require no
mixing since they specify alloy interactions explicitly.
</P>
<P>For style <I>eam</I>, potential values are read from a file that is in the
DYNAMO single-element <I>funcfl</I> format. If the DYNAMO file was created
@ -93,8 +93,8 @@ same way that the serial DYANMO code originally did it; you do not
need to specify coefficients for these type pairs.
</P>
<P>There are several <I>funcl</I> files in the <I>potentials</I> directory of the
LAMMPS distribution. A DYNAMO single-element <I>funcfl</I> file is
formatted as follows:
LAMMPS distribution, with the suffix ".eam". A DYNAMO single-element
<I>funcfl</I> file is formatted as follows:
</P>
<UL><LI>line 1: comment (ignored)
<LI>line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
@ -152,13 +152,15 @@ and the 4th to be Al, you would use the following pair_coeff command:
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three "1" values map LAMMPS atom types 1,2,3 to the 1st
element (Ni) in the <I>setfl</I> file. The final "2" value maps LAMMPS atom
type 4 to the 2nd element = Al. If a mapping value is "0", the
mapping is not performed. This is useful when EAM potentials are part
of the <I>hybrid</I> pair style, to represent non-EAM atom types.
element (Ni) in the <I>setfl</I> file. The final "2" value maps LAMMPS
atom type 4 to the 2nd element = Al. If a mapping value is "0", the
mapping is not performed. This can be used when an <I>eam/alloy</I>
potential is used as part of the <I>hybrid</I> pair style. The 0 values
are used as placeholders for atom types that will be used with other
potentials.
</P>
<P>There is one <I>setfl</I> file (nialhjea) in the <I>potentials</I> directory of
the LAMMPS distribution. A DYNAMO multi-element <I>setfl</I> file is
<P><I>Setfl</I> files in the <I>potentials</I> directory of the LAMMPS distribution
have a ".eam.alloy" suffix. A DYNAMO multi-element <I>setfl</I> file is
formatted as follows:
</P>
<UL><LI>lines 1,2,3 = comments (ignored)
@ -223,16 +225,20 @@ same as for style <I>eam/alloy</I>, e.g.
</PRE>
<P>where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. The N values determine the mapping
of LAMMPS atom types to EAM elements in the file, as described in
style <I>eam/alloy</I>.
of LAMMPS atom types to EAM elements in the file, as described above
for style <I>eam/alloy</I>. As with <I>eam/alloy</I>, if a mapping value is
"0", the mapping is not performed. This can be used when an <I>eam/fs</I>
potential is used as part of the <I>hybrid</I> pair style. The 0 values
are used as placeholders for atom types that will be used with other
potentials.
</P>
<P>The difference is that files read by <I>eam/fs</I> are in a more general
format than the DYNAMO <I>setfl</I> format read by <I>eam/alloy</I>, so that the
i,j density functionals for all pairs of elements are included as
needed by the Finnis/Sinclair formulation of the EAM.
<P>FS EAM files include more information than the DYNAMO <I>setfl</I> format
files read by <I>eam/alloy</I>, so that the i,j density functionals for all
pairs of elements are included as needed by the Finnis/Sinclair
formulation of the EAM.
</P>
<P>There is one FS file (nialhjea_FS) in the <I>potentials</I> directory of
the LAMMPS distribution. It is formatted as follows:
<P>FS EAM files in the <I>potentials</I> directory of the LAMMPS distribution
have a ".eam.fs" suffix. Ther are formatted as follows:
</P>
<UL><LI>lines 1,2,3 = comments (ignored)
<LI>line 4: Nelements = # of elements in the file

52
doc/pair_style_eam.txt
View File

@ -52,13 +52,13 @@ Several DYNAMO potential files for different metals are included in
the "potentials" directory of the LAMMPS distribution.
IMPORTANT NOTE: The {eam} style reads single-element EAM potentials in
the DYNAMO {funcfl} format. Single element or alloy systems can be
modeled with {funcfl} files and style {eam}; for the alloy case LAMMPS
mixes the single-element potentials to produce alloy potentials the
same way that DYNAMO does. Alternatively, DYNAMO {setfl} files can be
used by LAMMPS to model alloy systems by invoking the {eam/alloy}
style as described below. {Setfl} files require no mixing as they
specify alloy interactions explicitly.
the DYNAMO {funcfl} format. Either single element or alloy systems
can be modeled with {funcfl} files and style {eam}. For the alloy
case LAMMPS mixes the single-element potentials to produce alloy
potentials the same way that DYNAMO does. Alternatively, DYNAMO
{setfl} files can be used by LAMMPS to model alloy systems by invoking
the {eam/alloy} style as described below. {Setfl} files require no
mixing since they specify alloy interactions explicitly.
For style {eam}, potential values are read from a file that is in the
DYNAMO single-element {funcfl} format. If the DYNAMO file was created
@ -88,8 +88,8 @@ same way that the serial DYANMO code originally did it; you do not
need to specify coefficients for these type pairs.
There are several {funcl} files in the {potentials} directory of the
LAMMPS distribution. A DYNAMO single-element {funcfl} file is
formatted as follows:
LAMMPS distribution, with the suffix ".eam". A DYNAMO single-element
{funcfl} file is formatted as follows:
line 1: comment (ignored)
line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
@ -147,13 +147,15 @@ pair_coeff * * nialhjea 1 1 1 2 :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three "1" values map LAMMPS atom types 1,2,3 to the 1st
element (Ni) in the {setfl} file. The final "2" value maps LAMMPS atom
type 4 to the 2nd element = Al. If a mapping value is "0", the
mapping is not performed. This is useful when EAM potentials are part
of the {hybrid} pair style, to represent non-EAM atom types.
element (Ni) in the {setfl} file. The final "2" value maps LAMMPS
atom type 4 to the 2nd element = Al. If a mapping value is "0", the
mapping is not performed. This can be used when an {eam/alloy}
potential is used as part of the {hybrid} pair style. The 0 values
are used as placeholders for atom types that will be used with other
potentials.
There is one {setfl} file (nialhjea) in the {potentials} directory of
the LAMMPS distribution. A DYNAMO multi-element {setfl} file is
{Setfl} files in the {potentials} directory of the LAMMPS distribution
have a ".eam.alloy" suffix. A DYNAMO multi-element {setfl} file is
formatted as follows:
lines 1,2,3 = comments (ignored)
@ -218,16 +220,20 @@ pair_coeff * * filename 1 1 1 2 :pre
where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. The N values determine the mapping
of LAMMPS atom types to EAM elements in the file, as described in
style {eam/alloy}.
of LAMMPS atom types to EAM elements in the file, as described above
for style {eam/alloy}. As with {eam/alloy}, if a mapping value is
"0", the mapping is not performed. This can be used when an {eam/fs}
potential is used as part of the {hybrid} pair style. The 0 values
are used as placeholders for atom types that will be used with other
potentials.
The difference is that files read by {eam/fs} are in a more general
format than the DYNAMO {setfl} format read by {eam/alloy}, so that the
i,j density functionals for all pairs of elements are included as
needed by the Finnis/Sinclair formulation of the EAM.
FS EAM files include more information than the DYNAMO {setfl} format
files read by {eam/alloy}, so that the i,j density functionals for all
pairs of elements are included as needed by the Finnis/Sinclair
formulation of the EAM.
There is one FS file (nialhjea_FS) in the {potentials} directory of
the LAMMPS distribution. It is formatted as follows:
FS EAM files in the {potentials} directory of the LAMMPS distribution
have a ".eam.fs" suffix. Ther are formatted as follows:
lines 1,2,3 = comments (ignored)
line 4: Nelements = # of elements in the file

40
doc/pair_style_hybrid.html
View File

@ -43,16 +43,31 @@ by its arguments, as illustrated in the example above.
and the remaining coefficients are those appropriate to that style.
For example, consider a simulation with 3 atom types: types 1 and 2
are Ni atoms, type 3 are LJ atoms with charges. The following
commands would set up the hybrid simulation:
commands would set up a hybrid simulation:
</P>
<PRE>atom_style hybrid eam charge
pair_style hybrid eam lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff 1*2 1*2 eam niu3
<PRE>pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff * * eam/alloy nialhjea 1 1 0
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.5 1.2
pair_coeff 1*2 3 lj/cut 0.8 1.1
</PRE>
<P>The <A HREF = "atom_style.html">atom_style</A> hybrid command is needed because
atoms in the simulation will have both EAM and charge attributes.
<P>Note that as with any pair_style, coeffs must be defined for all I,J
interactions. If the sub-style allows for mixing (see the
<A HREF = "pair_modify.html">pair_modify</A> command), then I,J interactions between
atom types which both are assigned to that sub-style do not need to be
specified. I.e. if atom types 1 and 2 are both computed with <I>lj/cut</I>
and coeffs for 1,1 and 2,2 interactions are specified, then coeffs for
1,2 interactions will be generated automatically via mixing.
</P>
<P>If the pair_coeff command for a sub-style requires the use of * * as
atom type arguments (e.g. the <I>eam/alloy</I> example above), then it will
also include trailing arguments which map atom types to elements in
the potential. These mapping arguments should be specified as 0 if
the sub-style is not being applied to certain atom types.
</P>
<P>Note that you may also need to use an <A HREF = "atom_style.html">atom_style</A>
hybrid command in your input script, if atoms in the simulation will
have attributes from several atom styles, due to using multiple pair
potentials.
</P>
<P><B>Restrictions:</B> none
</P>
@ -64,9 +79,16 @@ than one sub-style with a "long" component, but you must insure that
the short-range Coulombic cutoff used by each of these pair styles is
consistent. Else the long-range Coulombic solve will be inconsistent.
</P>
<P>A pair style of <I>none</I> can be specified as an argument to pair_style
hybrid and the corresponding pair_coeff commands, if you desire to
turn off pairwise interactions between certain pairs of atom types.
</P>
<P>The hybrid style cannot include any of the <I>granular</I> styles in its
list of styles to use. Only one <I>coul/long</I> style can be used in the
list of hybrid styles.
list of styles to use.
</P>
<P>If you use multiple <I>coul/long</I> pair styles along with a <A HREF = "kspace_style.html">kspace
style</A>, then you should make sure the pairwise
Coulombic cutoff is the same for all the pair styles.
</P>
<P><B>Related commands:</B>
</P>

40
doc/pair_style_hybrid.txt
View File

@ -40,16 +40,31 @@ In the pair_coeff command, the first coefficient sets the pair style
and the remaining coefficients are those appropriate to that style.
For example, consider a simulation with 3 atom types: types 1 and 2
are Ni atoms, type 3 are LJ atoms with charges. The following
commands would set up the hybrid simulation:
commands would set up a hybrid simulation:
atom_style hybrid eam charge
pair_style hybrid eam lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff 1*2 1*2 eam niu3
pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff * * eam/alloy nialhjea 1 1 0
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.5 1.2 :pre
pair_coeff 1*2 3 lj/cut 0.8 1.1 :pre
The "atom_style"_atom_style.html hybrid command is needed because
atoms in the simulation will have both EAM and charge attributes.
Note that as with any pair_style, coeffs must be defined for all I,J
interactions. If the sub-style allows for mixing (see the
"pair_modify"_pair_modify.html command), then I,J interactions between
atom types which both are assigned to that sub-style do not need to be
specified. I.e. if atom types 1 and 2 are both computed with {lj/cut}
and coeffs for 1,1 and 2,2 interactions are specified, then coeffs for
1,2 interactions will be generated automatically via mixing.
If the pair_coeff command for a sub-style requires the use of * * as
atom type arguments (e.g. the {eam/alloy} example above), then it will
also include trailing arguments which map atom types to elements in
the potential. These mapping arguments should be specified as 0 if
the sub-style is not being applied to certain atom types.
Note that you may also need to use an "atom_style"_atom_style.html
hybrid command in your input script, if atoms in the simulation will
have attributes from several atom styles, due to using multiple pair
potentials.
[Restrictions:] none
@ -61,9 +76,16 @@ than one sub-style with a "long" component, but you must insure that
the short-range Coulombic cutoff used by each of these pair styles is
consistent. Else the long-range Coulombic solve will be inconsistent.
A pair style of {none} can be specified as an argument to pair_style
hybrid and the corresponding pair_coeff commands, if you desire to
turn off pairwise interactions between certain pairs of atom types.
The hybrid style cannot include any of the {granular} styles in its
list of styles to use. Only one {coul/long} style can be used in the
list of hybrid styles.
list of styles to use.
If you use multiple {coul/long} pair styles along with a "kspace
style"_kspace_style.html, then you should make sure the pairwise
Coulombic cutoff is the same for all the pair styles.
[Related commands:]

6
doc/pair_style_morse.html
View File

@ -45,7 +45,11 @@ commands:
<P>The last coefficient is optional. If not specified, the global morse
cutoff is used.
</P>
<P><B>Restrictions:</B> none
<P><B>Restrictions:</B>
</P>
<P>The <I>morse</I> potential does not support the
<A HREF = "pair_modify.hmtl">pair_modify</A> <I>mix</I> option. Coefficients for all i,j
pairs must be specified explicitly.
</P>
<P><B>Related commands:</B>
</P>

6
doc/pair_style_morse.txt
View File

@ -42,7 +42,11 @@ cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global morse
cutoff is used.
[Restrictions:] none
[Restrictions:]
The {morse} potential does not support the
"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j
pairs must be specified explicitly.
[Related commands:]

6
doc/pair_style_table.html
View File

@ -140,7 +140,11 @@ from one line to the next (unless the BITMAP parameter is specified).
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.
</P>
<P><B>Restrictions:</B> none
<P><B>Restrictions:</B>
</P>
<P>The <I>table</I> potential does not support the
<A HREF = "pair_modify.hmtl">pair_modify</A> <I>mix</I> option. Coefficients for all i,j
pairs must be specified explicitly.
</P>
<P><B>Related commands:</B>
</P>

6
doc/pair_style_table.txt
View File

@ -137,7 +137,11 @@ Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.
[Restrictions:] none
[Restrictions:]
The {table} potential does not support the
"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j
pairs must be specified explicitly.
[Related commands:]

8
doc/read_data.html
View File

@ -245,8 +245,8 @@ quantity:
<P>Any quantity that is used by the atom style appears in the order
listed above. Thus if the atom style is <I>atomic</I>, an atom line should
have 5 quantities: atom-ID, type-ID, x, y, z. If the atom style is
<I>hybrid eam dipole molecular</I>, then an atom line should have 10
quantites: atom-ID, molecule-ID, type-ID, q, x, y, z, mux, muy, muz.
<I>hybrid dipole molecular</I>, then an atom line should have 10 quantites:
atom-ID, molecule-ID, type-ID, q, x, y, z, mux, muy, muz.
</P>
<P>The units for these quantities depend on the unit style; see the
<A HREF = "units.html">units</A> command for details.
@ -261,8 +261,8 @@ will cause extra memory to be allocated on each processor, if an atom
map array is used (see the <A HREF = "atom_modify.html">atom_modify</A> command).
If an atom map array is not used (e.g. an atomic system with no
bonds), velocities are not assigned in the data file, and you don't
care if unique atom IDs appear in dump files, then IDs can be set to
non-unique values > 0.
care if unique atom IDs appear in dump files, then the atom-IDs can all
be set to 0.
</P>
<P>The molecule ID is a 2nd identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs

8
doc/read_data.txt
View File

@ -224,8 +224,8 @@ nx,ny,nz = optional for all styles (see below) :ul
Any quantity that is used by the atom style appears in the order
listed above. Thus if the atom style is {atomic}, an atom line should
have 5 quantities: atom-ID, type-ID, x, y, z. If the atom style is
{hybrid eam dipole molecular}, then an atom line should have 10
quantites: atom-ID, molecule-ID, type-ID, q, x, y, z, mux, muy, muz.
{hybrid dipole molecular}, then an atom line should have 10 quantites:
atom-ID, molecule-ID, type-ID, q, x, y, z, mux, muy, muz.
The units for these quantities depend on the unit style; see the
"units"_units.html command for details.
@ -240,8 +240,8 @@ will cause extra memory to be allocated on each processor, if an atom
map array is used (see the "atom_modify"_atom_modify.html command).
If an atom map array is not used (e.g. an atomic system with no
bonds), velocities are not assigned in the data file, and you don't
care if unique atom IDs appear in dump files, then IDs can be set to
non-unique values > 0.
care if unique atom IDs appear in dump files, then the atom-IDs can all
be set to 0.
The molecule ID is a 2nd identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs

2
doc/variable.html
View File

@ -15,7 +15,7 @@
</P>
<PRE>variable name style args ...
</PRE>
<UL><LI>name = single lower-case character, 'a' thru 'z'
<UL><LI>name = name of variable to define
<LI>style = <I>index</I> or <I>loop</I> or <I>equal</I> or <I>world</I> or <I>universe</I>

Some files were not shown because too many files have changed in this diff Show More