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).
The variable expression is being evaluated with a thermodynamic
diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt
index 1e01153094..448987d39f 100644
--- a/doc/Section_errors.txt
+++ b/doc/Section_errors.txt
@@ -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
diff --git a/doc/Section_history.html b/doc/Section_history.html
index 72be59bf56..c45f64fedf 100644
--- a/doc/Section_history.html
+++ b/doc/Section_history.html
@@ -23,22 +23,21 @@ molecular dynamics codes I've distributed.
10.1 Coming attractions
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
diff --git a/doc/Section_history.txt b/doc/Section_history.txt
index 0df99b6169..441e6c69d9 100644
--- a/doc/Section_history.txt
+++ b/doc/Section_history.txt
@@ -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
diff --git a/doc/Section_howto.html b/doc/Section_howto.html
index 3dd033b0a3..fdc91cf5f5 100644
--- a/doc/Section_howto.html
+++ b/doc/Section_howto.html
@@ -167,6 +167,10 @@ commands like pair_coeff or
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
+See (MacKerell) for a description of the CHARMM force
+field. See (Cornell) for a description of the AMBER force
+field.
+
@@ -577,6 +581,11 @@ back into LAMMPS.
+
+
+(Cornell) Corenll, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+
(Horn) Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt
index 2b44097e84..46622b3e9c 100644
--- a/doc/Section_howto.txt
+++ b/doc/Section_howto.txt
@@ -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).
diff --git a/doc/Section_start.html b/doc/Section_start.html
index 26541a71c0..6c2b634739 100644
--- a/doc/Section_start.html
+++ b/doc/Section_start.html
@@ -224,16 +224,17 @@ list of packages is as follows:
| 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
|
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
diff --git a/doc/Section_start.txt b/doc/Section_start.txt
index 1a1fe9d687..2334834a64 100644
--- a/doc/Section_start.txt
+++ b/doc/Section_start.txt
@@ -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
diff --git a/doc/angle_style.html b/doc/angle_style.html
index 3e2edf80b3..a6b7311ecc 100644
--- a/doc/angle_style.html
+++ b/doc/angle_style.html
@@ -67,8 +67,9 @@ specified by the associated angle_coeff 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 for more info.
Related commands:
diff --git a/doc/angle_style.txt b/doc/angle_style.txt
index beca2044bb..ddedf0a0fe 100644
--- a/doc/angle_style.txt
+++ b/doc/angle_style.txt
@@ -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:]
diff --git a/doc/angle_style_charmm.html b/doc/angle_style_charmm.html
index 94b63ae3bd..e5b3cc2705 100644
--- a/doc/angle_style_charmm.html
+++ b/doc/angle_style_charmm.html
@@ -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.
+See (MacKerell) for a description of the CHARMM force
+field.
+
The following coefficients must be defined for each angle type via the
angle_coeff command as in the example above, or in
the data file or restart files read by the read_data
@@ -43,14 +46,7 @@ or read_restart commands:
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 for more info.
+
Restrictions: none
Related commands:
@@ -58,4 +54,11 @@ LAMMPS section for more info.
Default: none
+
+
+
+
+(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+