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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11381 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-01-29 22:22:56 +00:00
parent 9fe494cc6a
commit 89a4708824
27 changed files with 208 additions and 598 deletions
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5
src/GPU/fix_gpu.cpp
View File

@ -174,9 +174,10 @@ void FixGPU::init()
if (_particle_split < 0)
if (force->pair_match("hybrid",1) != NULL ||
force->pair_match("hybrid/overlay",1) != NULL)
error->all(FLERR,"GPU 'split' must be positive for hybrid pair styles");
error->all(FLERR,"GPU split param must be positive "
"for hybrid pair styles");
// Make sure fdotr virial is not accumulated multiple times
// make sure fdotr virial is not accumulated multiple times
if (force->pair_match("hybrid",1) != NULL) {
PairHybrid *hybrid = (PairHybrid *) force->pair;

20
src/GPU/fix_gpu.h
View File

@ -77,31 +77,19 @@ OpenMP support.
E: GPU package does not (yet) work with atom_style template
UNDOCUMENTED
Self-explanatory.
E: Cannot use pair hybrid with GPU neighbor list builds
UNDOCUMENTED
Neighbor list builds must be done on the CPU for this pair style.
E: GPU 'split' must be positive for hybrid pair styles
E: GPU split param must be positive for hybrid pair styles
UNDOCUMENTED
See the package gpu command.
E: Cannot use neigh_modify exclude with GPU neighbor builds
This is a current limitation of the GPU implementation
in LAMMPS.
U: Cannot use pair hybrid with GPU neighbor builds
See documentation for fix gpu.
U: Fix GPU split must be positive for hybrid pair styles
Self-explanatory.
U: GPU styles must be on the outmost r-RESPA level
Self-explanatory.
*/

2
src/GRANULAR/fix_pour.cpp
View File

@ -100,7 +100,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
zlo = ((RegCylinder *) domain->regions[iregion])->lo;
zhi = ((RegCylinder *) domain->regions[iregion])->hi;
if (axis != 'z')
error->all(FLERR,"Must use a z-axis cylinder with fix pour");
error->all(FLERR,"Must use a z-axis cylinder region with fix pour");
if (xc-rc < domain->boxlo[0] || xc+rc > domain->boxhi[0] ||
yc-rc < domain->boxlo[1] || yc+rc > domain->boxhi[1] ||
zlo < domain->boxlo[2] || zhi > domain->boxhi[2])

468
src/GRANULAR/fix_pour.h
View File

@ -88,478 +88,146 @@ command-line option when running LAMMPS to see the offending line.
E: Fix pour requires atom attributes radius, rmass
UNDOCUMENTED
The atom style defined does not have these attributes.
E: Invalid atom type in fix pour command
UNDOCUMENTED
Self-explanatory.
E: Must specify a region in fix pour
UNDOCUMENTED
Self-explanatory.
E: Fix pour region does not support a bounding box
UNDOCUMENTED
Not all regions represent bounded volumes. You cannot use
such a region with the fix pour command.
E: Fix pour region cannot be dynamic
UNDOCUMENTED
Only static regions can be used with fix pour.
E: Insertion region extends outside simulation box
UNDOCUMENTED
Self-explanatory.
E: Must use a z-axis cylinder with fix pour
UNDOCUMENTED
E: Must use a block or cylinder region with fix pour
UNDOCUMENTED
E: Must use a block region with fix pour for 2d simulations
UNDOCUMENTED
E: Cannot use fix_pour unless atoms have IDs
UNDOCUMENTED
E: Fix pour molecule must have coordinates
UNDOCUMENTED
E: Fix pour molecule must have atom types
UNDOCUMENTED
E: Invalid atom type in fix pour mol command
UNDOCUMENTED
E: Fix pour molecule template ID must be same as atom style template ID
UNDOCUMENTED
E: Cannot use fix pour rigid and not molecule
UNDOCUMENTED
E: Cannot use fix pour shake and not molecule
UNDOCUMENTED
E: Cannot use fix pour rigid and shake
UNDOCUMENTED
E: No fix gravity defined for fix pour
UNDOCUMENTED
E: Cannot use fix pour with triclinic box
UNDOCUMENTED
E: Gravity must point in -z to use with fix pour in 3d
UNDOCUMENTED
E: Gravity must point in -y to use with fix pour in 2d
UNDOCUMENTED
E: Gravity changed since fix pour was created
UNDOCUMENTED
E: Fix pour rigid fix does not exist
UNDOCUMENTED
E: Fix pour and fix rigid/small not using same molecule template ID
UNDOCUMENTED
E: Fix pour shake fix does not exist
UNDOCUMENTED
E: Fix pour and fix shake not using same molecule template ID
UNDOCUMENTED
W: Less insertions than requested
UNDOCUMENTED
E: Too many total atoms
UNDOCUMENTED
E: New atom IDs exceed maximum allowed ID
UNDOCUMENTED
E: Fix pour region ID does not exist
UNDOCUMENTED
E: Molecule template ID for fix pour does not exist
UNDOCUMENTED
W: Molecule template for fix pour has multiple molecules
UNDOCUMENTED
E: Fix pour polydisperse fractions do not sum to 1.0
UNDOCUMENTED
E: Cannot change timestep with fix pour
UNDOCUMENTED
U: Cannot read_data after simulation box is defined
The read_data command cannot be used after a read_data,
read_restart, or create_box command.
U: Cannot run 2d simulation with nonperiodic Z dimension
Use the boundary command to make the z dimension periodic in order to
run a 2d simulation.
U: Fix ID for read_data does not exist
E: Must use a z-axis cylinder region with fix pour
Self-explanatory.
U: Must read Atoms before Velocities
E: Must use a block or cylinder region with fix pour
The Atoms section of a data file must come before a Velocities
section.
Self-explanatory.
U: Invalid data file section: Bonds
E: Must use a block region with fix pour for 2d simulations
Atom style does not allow bonds.
Self-explanatory.
U: Must read Atoms before Bonds
E: Cannot use fix_pour unless atoms have IDs
The Atoms section of a data file must come before a Bonds section.
Self-explanatory.
U: Invalid data file section: Angles
E: Fix pour molecule must have coordinates
Atom style does not allow angles.
The defined molecule does not specify coordinates.
U: Must read Atoms before Angles
E: Fix pour molecule must have atom types
The Atoms section of a data file must come before an Angles section.
The defined molecule does not specify atom types.
U: Invalid data file section: Dihedrals
E: Invalid atom type in fix pour mol command
Atom style does not allow dihedrals.
The atom types in the defined molecule are added to the value
specified in the create_atoms command, as an offset. The final value
for each atom must be between 1 to N, where N is the number of atom
types.
U: Must read Atoms before Dihedrals
E: Fix pour molecule template ID must be same as atom style template ID
The Atoms section of a data file must come before a Dihedrals section.
When using atom_style template, you cannot pour molecules that are
not in that template.
U: Invalid data file section: Impropers
E: Cannot use fix pour rigid and not molecule
Atom style does not allow impropers.
Self-explanatory.
U: Must read Atoms before Impropers
E: Cannot use fix pour shake and not molecule
The Atoms section of a data file must come before an Impropers
section.
Self-explanatory.
U: Invalid data file section: Ellipsoids
E: Cannot use fix pour rigid and shake
Atom style does not allow ellipsoids.
These two attributes are conflicting.
U: Must read Atoms before Ellipsoids
E: No fix gravity defined for fix pour
The Atoms section of a data file must come before a Ellipsoids
section.
Gravity is required to use fix pour.
U: Invalid data file section: Lines
E: Cannot use fix pour with triclinic box
Atom style does not allow lines.
This option is not yet supported.
U: Must read Atoms before Lines
E: Gravity must point in -z to use with fix pour in 3d
The Atoms section of a data file must come before a Lines section.
Self-explanatory.
U: Invalid data file section: Triangles
E: Gravity must point in -y to use with fix pour in 2d
Atom style does not allow triangles.
Self-explanatory.
U: Must read Atoms before Triangles
E: Gravity changed since fix pour was created
The Atoms section of a data file must come before a Triangles section.
The gravity vector defined by fix gravity must be static.
U: Invalid data file section: Bodies
E: Fix pour rigid fix does not exist
Atom style does not allow bodies.
Self-explanatory.
U: Must read Atoms before Bodies
E: Fix pour and fix rigid/small not using same molecule template ID
The Atoms section of a data file must come before a Bodies section.
Self-explanatory.
U: Must define pair_style before Pair Coeffs
E: Fix pour shake fix does not exist
Must use a pair_style command before reading a data file that defines
Pair Coeffs.
Self-explanatory.
U: Must define pair_style before PairIJ Coeffs
E: Fix pour and fix shake not using same molecule template ID
UNDOCUMENTED
Self-explanatory.
U: Invalid data file section: Bond Coeffs
W: Less insertions than requested
Atom style does not allow bonds.
The fix pour command was unsuccessful at finding open space
for as many particles as it tried to insert.
U: Must define bond_style before Bond Coeffs
Must use a bond_style command before reading a data file that
defines Bond Coeffs.
U: Invalid data file section: Angle Coeffs
Atom style does not allow angles.
U: Must define angle_style before Angle Coeffs
Must use an angle_style command before reading a data file that
defines Angle Coeffs.
U: Invalid data file section: Dihedral Coeffs
Atom style does not allow dihedrals.
U: Must define dihedral_style before Dihedral Coeffs
Must use a dihedral_style command before reading a data file that
defines Dihedral Coeffs.
U: Invalid data file section: Improper Coeffs
Atom style does not allow impropers.
U: Must define improper_style before Improper Coeffs
Must use an improper_style command before reading a data file that
defines Improper Coeffs.
U: Invalid data file section: BondBond Coeffs
Atom style does not allow angles.
U: Must define angle_style before BondBond Coeffs
Must use an angle_style command before reading a data file that
defines Angle Coeffs.
U: Invalid data file section: BondAngle Coeffs
Atom style does not allow angles.
U: Must define angle_style before BondAngle Coeffs
Must use an angle_style command before reading a data file that
defines Angle Coeffs.
U: Invalid data file section: MiddleBondTorsion Coeffs
Atom style does not allow dihedrals.
U: Must define dihedral_style before MiddleBondTorsion Coeffs
Must use a dihedral_style command before reading a data file that
defines MiddleBondTorsion Coeffs.
U: Invalid data file section: EndBondTorsion Coeffs
Atom style does not allow dihedrals.
U: Must define dihedral_style before EndBondTorsion Coeffs
Must use a dihedral_style command before reading a data file that
defines EndBondTorsion Coeffs.
U: Invalid data file section: AngleTorsion Coeffs
Atom style does not allow dihedrals.
U: Must define dihedral_style before AngleTorsion Coeffs
Must use a dihedral_style command before reading a data file that
defines AngleTorsion Coeffs.
U: Invalid data file section: AngleAngleTorsion Coeffs
Atom style does not allow dihedrals.
U: Must define dihedral_style before AngleAngleTorsion Coeffs
Must use a dihedral_style command before reading a data file that
defines AngleAngleTorsion Coeffs.
U: Invalid data file section: BondBond13 Coeffs
Atom style does not allow dihedrals.
U: Must define dihedral_style before BondBond13 Coeffs
Must use a dihedral_style command before reading a data file that
defines BondBond13 Coeffs.
U: Invalid data file section: AngleAngle Coeffs
Atom style does not allow impropers.
U: Must define improper_style before AngleAngle Coeffs
Must use an improper_style command before reading a data file that
defines AngleAngle Coeffs.
U: Unknown identifier in data file: %s
A section of the data file cannot be read by LAMMPS.
U: No atoms in data file
The header of the data file indicated that atoms would be included,
but they were not present.
U: Needed molecular topology not in data file
UNDOCUMENTED
U: Needed bonus data not in data file
Some atom styles require bonus data. See the read_data doc page for
details.
U: Unexpected end of data file
LAMMPS hit the end of the data file while attempting to read a
section. Something is wrong with the format of the data file.
U: No ellipsoids allowed with this atom style
Self-explanatory. Check data file.
U: No lines allowed with this atom style
Self-explanatory. Check data file.
U: No triangles allowed with this atom style
Self-explanatory. Check data file.
U: No bodies allowed with this atom style
Self-explanatory. Check data file.
U: System in data file is too big
E: Too many total atoms
See the setting for bigint in the src/lmptype.h file.
U: No bonds allowed with this atom style
E: New atom IDs exceed maximum allowed ID
Self-explanatory. Check data file.
See the setting for tagint in the src/lmptype.h file.
U: No angles allowed with this atom style
E: Fix pour region ID does not exist
Self-explanatory. Check data file.
Self-explanatory.
U: No dihedrals allowed with this atom style
E: Molecule template ID for fix pour does not exist
Self-explanatory. Check data file.
Self-explanatory.
U: No impropers allowed with this atom style
W: Molecule template for fix pour has multiple molecules
Self-explanatory. Check data file.
The fix pour command will only create molecules of a single type,
i.e. the first molecule in the template.
U: Bonds defined but no bond types
E: Fix pour polydisperse fractions do not sum to 1.0
The data file header lists bonds but no bond types.
Self-explanatory.
U: Angles defined but no angle types
E: Cannot change timestep with fix pour
The data file header lists angles but no angle types.
U: Dihedrals defined but no dihedral types
The data file header lists dihedrals but no dihedral types.
U: Impropers defined but no improper types
The data file header lists improper but no improper types.
U: No molecule topology allowed with atom style template
UNDOCUMENTED
U: Did not assign all atoms correctly
Atoms read in from a data file were not assigned correctly to
processors. This is likely due to some atom coordinates being
outside a non-periodic simulation box.
U: Bonds assigned incorrectly
Bonds read in from the data file were not assigned correctly to atoms.
This means there is something invalid about the topology definitions.
U: Angles assigned incorrectly
Angles read in from the data file were not assigned correctly to
atoms. This means there is something invalid about the topology
definitions.
U: Dihedrals assigned incorrectly
Dihedrals read in from the data file were not assigned correctly to
atoms. This means there is something invalid about the topology
definitions.
U: Impropers assigned incorrectly
Impropers read in from the data file were not assigned correctly to
atoms. This means there is something invalid about the topology
definitions.
U: Too many lines in one body in data file - boost MAXBODY
MAXBODY is a setting at the top of the src/read_data.cpp file.
Set it larger and re-compile the code.
U: Cannot open gzipped file
LAMMPS was compiled without support for reading and writing gzipped
files through a pipeline to the gzip program with -DLAMMPS_GZIP.
U: Cannot open file %s
The specified file cannot be opened. Check that the path and name are
correct. If the file is a compressed file, also check that the gzip
executable can be found and run.
U: Invalid atom ID in Atoms section of data file
Atom IDs must be positive integers.
U: Molecular data file has too many atoms
These kids of data files are currently limited to a number
of atoms that fits in a 32-bit integer.
U: Needed topology not in data file
The header of the data file indicated that bonds or angles or
dihedrals or impropers would be included, but they were not present.
This is because fix pour pre-computes the time delay for particles to
fall out of the insertion volume due to gravity.
*/

2
src/MANYBODY/fix_qeq_comb.h
View File

@ -77,7 +77,7 @@ An atom style with charge must be used to perform charge equilibration.
E: Must use pair_style comb or comb3 with fix qeq/comb
UNDOCUMENTED
Self-explanatory.
E: Fix qeq/comb group has no atoms

3
src/MC/fix_bond_break.h
View File

@ -73,7 +73,8 @@ Self-explanatory.
E: Cannot use fix bond/break with non-molecular systems
Self-explanatory.
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
E: Fix bond/break requires special_bonds = 0,1,1

3
src/MC/fix_bond_create.h
View File

@ -91,7 +91,8 @@ Self-explanatory.
E: Cannot use fix bond/create with non-molecular systems
Self-explanatory.
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
E: Inconsistent iparam/jparam values in fix bond/create command

3
src/MC/fix_bond_swap.h
View File

@ -72,7 +72,8 @@ command-line option when running LAMMPS to see the offending line.
E: Cannot use fix bond/swap with non-molecular systems
UNDOCUMENTED
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
E: Must use atom style with molecule IDs with fix bond/swap

7
src/MC/fix_gcmc.h
View File

@ -122,7 +122,7 @@ command-line option when running LAMMPS to see the offending line.
E: Fix gcmc does not (yet) work with atom_style template
UNDOCUMENTED
Self-explanatory.
E: Fix gcmc region does not support a bounding box
@ -195,10 +195,7 @@ enable the atom_modify first command.
E: Fix gcmc ran out of available molecule IDs
This is a code limitation where more than MAXSMALLINT (usually around
two billion) molecules have been created. The code needs to be
modified to either allow molecule ID recycling or use bigger ints for
molecule IDs. A work-around is to run shorter simulations.
See the setting for tagint in the src/lmptype.h file.
E: Fix gcmc could not find any atoms in the user-supplied template molecule

44
src/MISC/fix_deposit.h
View File

@ -77,7 +77,7 @@ command-line option when running LAMMPS to see the offending line.
E: Invalid atom type in fix deposit command
UNDOCUMENTED
Self-explanatory.
E: Must specify a region in fix deposit
@ -98,35 +98,39 @@ Self-explanatory.
E: Cannot use fix_deposit unless atoms have IDs
UNDOCUMENTED
Self-explanatory.
E: Fix deposit molecule must have coordinates
UNDOCUMENTED
The defined molecule does not specify coordinates.
E: Fix deposit molecule must have atom types
UNDOCUMENTED
The defined molecule does not specify atom types.
E: Invalid atom type in fix deposit mol command
UNDOCUMENTED
The atom types in the defined molecule are added to the value
specified in the create_atoms command, as an offset. The final value
for each atom must be between 1 to N, where N is the number of atom
types.
E: Fix deposit molecule template ID must be same as atom style template ID
E: Fix deposit molecule template ID must be same as atom_style template ID
UNDOCUMENTED
When using atom_style template, you cannot deposit molecules that are
not in that template.
E: Cannot use fix deposit rigid and not molecule
UNDOCUMENTED
Self-explanatory.
E: Cannot use fix deposit shake and not molecule
UNDOCUMENTED
Self-explanatory.
E: Cannot use fix deposit rigid and shake
UNDOCUMENTED
These two attributes are conflicting.
E: Region ID for fix deposit does not exist
@ -134,19 +138,19 @@ Self-explanatory.
E: Fix pour rigid fix does not exist
UNDOCUMENTED
Self-explanatory.
E: Fix deposit and fix rigid/small not using same molecule template ID
UNDOCUMENTED
Self-explanatory.
E: Fix deposit shake fix does not exist
UNDOCUMENTED
Self-explanatory.
E: Fix deposit and fix shake not using same molecule template ID
UNDOCUMENTED
Self-explanatory.
W: Particle deposition was unsuccessful
@ -160,19 +164,15 @@ See the setting for bigint in the src/lmptype.h file.
E: New atom IDs exceed maximum allowed ID
UNDOCUMENTED
See the setting for tagint in the src/lmptype.h file.
E: Molecule template ID for fix deposit does not exist
UNDOCUMENTED
Self-explanatory.
W: Molecule template for fix deposit has multiple molecules
UNDOCUMENTED
U: Use of fix deposit with undefined lattice
Must use lattice command with compute fix deposit command if units
option is set to lattice.
The fix deposit command will only create molecules of a single type,
i.e. the first molecule in the template.
*/

30
src/MISC/fix_efield.h
View File

@ -66,48 +66,46 @@ class FixEfield : public Fix {
E: Illegal ... command
UNDOCUMENTED
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Region ID for fix efield does not exist
UNDOCUMENTED
Self-explanatory.
E: Fix efield requires atom attribute q or mu
UNDOCUMENTED
The atom style defined does not have this attribute.
E: Variable name for fix efield does not exist
UNDOCUMENTED
Self-explanatory.
E: Variable for fix efield is invalid style
UNDOCUMENTED
The variable must be an equal- or atom-style variable.
E: Region ID for fix aveforce does not exist
UNDOCUMENTED
Self-explanatory.
E: Fix efield with dipoles cannot use atom-style variables
UNDOCUMENTED
This option is not supported.
W: The minimizer does not re-orient dipoles when using fix efield
UNDOCUMENTED
This means that only the atom coordinates will be minimized,
not the orientation of the dipoles.
E: Cannot use variable energy with constant efield in fix efield
UNDOCUMENTED
LAMMPS computes the energy itself when the E-field is constant.
E: Must use variable energy with fix efield
UNDOCUMENTED
U: Neighbor list overflow, boost neigh_modify one
There are too many neighbors of a single atom. Use the neigh_modify
command to increase the max number of neighbors allowed for one atom.
You may also want to boost the page size.
You must define an energy when performing a minimization with a
variable E-field.
*/

14
src/MISC/fix_gld.cpp
View File

@ -72,12 +72,11 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
if(strcmp(arg[7],"pprony") == 0) {
series_type = 1; // series type 1 is 'positive Prony series'
} else {
error->all(FLERR,"Fix gld series type must be pprony...for now");
error->all(FLERR,"Fix gld series type must be pprony for now");
}
// Error checking for the first set of required input arguments
if (seed <= 0)
error->all(FLERR,"Fix gld random seed must be > 0");
if (seed <= 0) error->all(FLERR,"Illegal fix gld command");
if (prony_terms <= 0)
error->all(FLERR,"Fix gld prony terms must be > 0");
if (t_start < 0)
@ -85,7 +84,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
if (t_stop < 0)
error->all(FLERR,"Fix gld stop temperature must be >= 0");
if (narg - narg_min < 2*(prony_terms) )
error->all(FLERR,"Fix gld not enough prony series coefficients");
error->all(FLERR,"Fix gld needs more prony series coefficients");
// allocate memory for Prony series force coefficients
memory->create(prony_c, prony_terms, "gld:prony_c");
@ -127,12 +126,13 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
// optional arguments
freezeflag = 0;
zeroflag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"zero") == 0) {
if (iarg+2 > narg) {
error->all(FLERR, "Illegal fix gld command");
}
if (strcmp(arg[iarg+1],"no") == 0) { /* do nothing, default is zeroflag=0 */ }
if (strcmp(arg[iarg+1],"no") == 0)
else if (strcmp(arg[iarg+1],"yes") == 0) {
zeroflag = 1;
} else {
@ -144,7 +144,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
if (iarg+2 > narg) {
error->all(FLERR, "Illegal fix gld command");
}
if (strcmp(arg[iarg+1],"no") == 0) { /* do nothing, default is unfrozen */ }
if (strcmp(arg[iarg+1],"no") == 0)
else if (strcmp(arg[iarg+1],"yes") == 0) {
freezeflag = 1;
for (int i = 0; i < atom->nlocal; i++) {
@ -359,7 +359,7 @@ void FixGLD::initial_integrate(int vflag)
// correct the random force, if zeroflag is set
if (zeroflag) {
count = group->count(igroup);
if (count == 0) error->all(FLERR,"Cannot zero gld force of 0 atoms");
if (count == 0) error->all(FLERR,"Cannot zero gld force for zero atoms");
MPI_Allreduce(fsum,fsumall,3,MPI_DOUBLE,MPI_SUM,world);
fsumall[0] /= (count*prony_terms);

26
src/MISC/fix_gld.h
View File

@ -78,40 +78,36 @@ Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Fix gld series type must be pprony...for now
E: Fix gld series type must be pprony for now
UNDOCUMENTED
E: Fix gld random seed must be > 0
UNDOCUMENTED
Self-explanatory.
E: Fix gld prony terms must be > 0
UNDOCUMENTED
Self-explanatory.
E: Fix gld start temperature must be >= 0
UNDOCUMENTED
Self-explanatory.
E: Fix gld stop temperature must be >= 0
UNDOCUMENTED
Self-explanatory.
E: Fix gld not enough prony series coefficients
E: Fix gld needs more prony series coefficients
UNDOCUMENTED
Self-explanatory.
E: Fix gld c coefficients must be >= 0
UNDOCUMENTED
Self-explanatory.
E: Fix gld tau coefficients must be > 0
UNDOCUMENTED
Self-explanatory.
E: Cannot zero gld force of 0 atoms
E: Cannot zero gld force for zero atoms
UNDOCUMENTED
There are no atoms currently in the group.
*/

2
src/POEMS/fix_poems.h
View File

@ -132,7 +132,7 @@ Self-explanatory.
E: Too many molecules for fix poems
UNDOCUMENTED
The limit is 2^31 = ~2 billion molecules.
E: No rigid bodies defined

10
src/RIGID/fix_rigid.h
View File

@ -160,7 +160,7 @@ Self-explanatory.
E: Too many molecules for fix rigid
UNDOCUMENTED
The limit is 2^31 = ~2 billion molecules.
E: Could not find fix rigid group ID
@ -208,7 +208,8 @@ incorrect.
W: Cannot count rigid body degrees-of-freedom before bodies are fully initialized
UNDOCUMENTED
This means the temperature associated with the rigid bodies may be
incorrect on this timestep.
W: Computing temperature of portions of rigid bodies
@ -241,7 +242,7 @@ A read operation from the file failed.
E: Fix rigid file has no lines
UNDOCUMENTED
Self-explanatory.
E: Incorrect rigid body format in fix rigid file
@ -254,6 +255,7 @@ that are defined by the fix rigid command.
E: Cannot open fix rigid restart file %s
UNDOCUMENTED
The specified file cannot be opened. Check that the path and name are
correct.
*/

41
src/RIGID/fix_rigid_small.h
View File

@ -203,7 +203,7 @@ Self-explanatory.
E: Fix rigid/small requires an atom map, see atom_modify
UNDOCUMENTED
Self-explanatory.
E: Fix rigid/small langevin period must be > 0.0
@ -211,19 +211,20 @@ Self-explanatory.
E: Molecule template ID for fix rigid/small does not exist
UNDOCUMENTED
Self-explanatory.
W: Molecule template for fix rigid/small has multiple molecules
UNDOCUMENTED
The fix rigid/small command will only recoginze molecules of a single
type, i.e. the first molecule in the template.
E: Fix rigid/small molecule must have coordinates
UNDOCUMENTED
The defined molecule does not specify coordinates.
E: Fix rigid/small molecule must have atom types
UNDOCUMENTED
The defined molecule does not specify atom types.
W: More than one fix rigid
@ -237,7 +238,8 @@ incorrect.
W: Cannot count rigid body degrees-of-freedom before bodies are fully initialized
UNDOCUMENTED
This means the temperature associated with the rigid bodies may be
incorrect on this timestep.
W: Computing temperature of portions of rigid bodies
@ -261,42 +263,33 @@ are not within the required tolerances.
E: Cannot open fix rigid/small infile %s
UNDOCUMENTED
The specified file cannot be opened. Check that the path and name are
correct.
E: Unexpected end of fix rigid/small file
UNDOCUMENTED
A read operation from the file failed.
E: Fix rigid file has no lines
UNDOCUMENTED
Self-explanatory.
E: Incorrect rigid body format in fix rigid/small file
UNDOCUMENTED
The number of fields per line is not what expected.
E: Invalid rigid body ID in fix rigid/small file
UNDOCUMENTED
The ID does not match the number or an existing ID of rigid bodies
that are defined by the fix rigid/small command.
E: Cannot open fix rigid restart file %s
UNDOCUMENTED
The specified file cannot be opened. Check that the path and name are
correct.
E: Rigid body atoms %ld %ld missing on proc %d at step %ld
UNDOCUMENTED
U: Rigid body atoms missing on proc %d at step %ld
UNDOCUMENTED
U: No rigid bodies defined
The fix specification did not end up defining any rigid bodies.
U: Rigid body atoms %d %d missing on proc %d at step %ld
This means that an atom cannot find the atom that owns the rigid body
it is part of, or vice versa. The solution is to use the communicate
cutoff command to insure ghost atoms are acquired from far enough away

49
src/RIGID/fix_shake.h
View File

@ -167,15 +167,16 @@ types.
E: Molecule template ID for fix shake does not exist
UNDOCUMENTED
Self-explanatory.
W: Molecule template for fix shake has multiple molecules
UNDOCUMENTED
The fix shake command will only recoginze molecules of a single
type, i.e. the first molecule in the template.
E: Fix shake molecule template must have shake info
UNDOCUMENTED
The defined molecule does not specify SHAKE information.
E: More than one fix shake
@ -207,15 +208,21 @@ types for the 2 bonds in the angle.
E: Shake atoms %ld %ld missing on proc %d at step %ld
UNDOCUMENTED
The 2 atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
E: Shake atoms %ld %ld %ld missing on proc %d at step %ld
UNDOCUMENTED
The 3 atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
E: Shake atoms %ld %ld %ld %ld missing on proc %d at step %ld
UNDOCUMENTED
The 4 atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
E: Did not find fix shake partner info
@ -245,34 +252,4 @@ E: Shake determinant = 0.0
The determinant of the matrix being solved for a single cluster
specified by the fix shake command is numerically invalid.
U: Shake atoms missing on proc %d at step %ld
UNDOCUMENTED
U: Shake atoms missing on proc %d at step %ld
UNDOCUMENTED
U: Shake atoms missing on proc %d at step %ld
UNDOCUMENTED
U: Shake atoms %d %d missing on proc %d at step %ld
The 2 atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
U: Shake atoms %d %d %d missing on proc %d at step %ld
The 3 atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
U: Shake atoms %d %d %d %d missing on proc %d at step %ld
The 4 atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
*/

8
src/SHOCK/fix_append_atoms.h
View File

@ -84,7 +84,9 @@ f_.
E: Invalid basis setting in fix append/atoms command
UNDOCUMENTED
The basis index must be between 1 to N where N is the number of basis
atoms in the lattice. The type index must be between 1 to N where N
is the number of atom types.
E: Cannot use append/atoms in periodic dimension
@ -104,8 +106,4 @@ E: Too many total atoms
See the setting for bigint in the src/lmptype.h file.
U: Use of fix append/atoms with undefined lattice
A lattice must be defined before using this fix.
*/

4
src/compute.h
View File

@ -170,9 +170,7 @@ want.
E: Too many molecules for compute
The compute molecule commands store a list of all molecules in the
system. The size of that list must fit in a 32-bit integer, i.e. be
less than ~2 billion molecules.
The limit is 2^31 = ~2 billion molecules.
W: One or more compute molecules has atoms not in group

4
src/create_box.h
View File

@ -57,8 +57,8 @@ Self-explanatory.
E: Create_box region does not support a bounding box
Not all region styles define a bounding box which is required for use
with the create_box command. See the region command for details.
Not all regions represent bounded volumes. You cannot use
such a region with the create_box command.
E: No bonds allowed with this atom style

13
src/fix_ave_spatial.h
View File

@ -162,7 +162,8 @@ Self-explanatory.
E: Fix ave/spatial settings invalid with changing box size
UNDOCUMENTED
If the box size changes, only the units reduced option can be
used.
E: Fix for fix ave/spatial not computed at compatible time
@ -174,14 +175,4 @@ E: Fix ave/spatial missed timestep
You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
U: Fix ave/spatial settings invalid with changing box
If the ave setting is "running" or "window" and the box size/shape
changes during the simulation, then the units setting must be
"reduced", else the number of bins may change.
U: Use of fix ave/spatial with undefined lattice
A lattice must be defined to use fix ave/spatial with units = lattice.
*/

2
src/fix_nve_limit.h
View File

@ -58,6 +58,6 @@ command-line option when running LAMMPS to see the offending line.
W: Should not use fix nve/limit with fix shake
UNDOCUMENTED
This will lead to invalid constraint forces in the SHAKE computation.
*/

18
src/fix_property_atom.h
View File

@ -74,34 +74,36 @@ command-line option when running LAMMPS to see the offending line.
E: Fix property/atom mol when atom_style already has molecule attribute
UNDOCUMENTED
Self-explanatory.
E: Fix property/atom cannot specify mol twice
UNDOCUMENTED
Self-explanatory.
E: Fix property/atom q when atom_style already has charge attribute
UNDOCUMENTED
Self-explanatory.
E: Fix property/atom cannot specify q twice
UNDOCUMENTED
Self-explanatory.
E: Fix property/atom vector name already exists
UNDOCUMENTED
The name for an integer or floating-point vector must be unique.
E: Atom style was redefined after using fix property/atom
UNDOCUMENTED
This is not allowed.
E: Incorrect %s format in data file
UNDOCUMENTED
A section of the data file being read by fix property/atom does
not have the correct number of values per line.
E: Invalid atom ID in %s section of data file
UNDOCUMENTED
An atom in a section of the data file being read by fix property/atom
has an invalid atom ID that is <= 0 or > the maximum existing atom ID.
*/

8
src/fix_restrain.h
View File

@ -88,14 +88,6 @@ atom has moved too far.
W: Restrain problem: %d %ld %ld %ld %ld %ld
UNDOCUMENTED
U: Restrain problem: %d %ld
UNDOCUMENTED
U: Restrain problem: %d %ld %d %d %d %d
Conformation of the 4 listed dihedral atoms is extreme; you may want
to check your simulation geometry.

4
src/fix_shear_history.h
View File

@ -80,7 +80,9 @@ cannot be tracked by the granular pair potential.
E: Shear history overflow, boost neigh_modify one
UNDOCUMENTED
There are too many neighbors of a single atom. Use the neigh_modify
command to increase the max number of neighbors allowed for one atom.
You may also want to boost the page size.
U: Too many touching neighbors - boost MAXTOUCH

8
src/min_fire.cpp
View File

@ -86,7 +86,7 @@ int MinFire::iterate(int maxiter)
bigint ntimestep;
double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall;
double scale1,scale2;
double dtvone,dtv,dtfm;
double dtvone,dtv,dtf,dtfm;
int flag,flagall;
alpha_final = 0.0;
@ -195,13 +195,15 @@ int MinFire::iterate(int maxiter)
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
}
dtf = dtv * force->ftm2v;
// Euler integration step
double **x = atom->x;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtv / rmass[i];
dtfm = dtf / rmass[i];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
@ -211,7 +213,7 @@ int MinFire::iterate(int maxiter)
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtv / mass[type[i]];
dtfm = dtf / mass[type[i]];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];

8
src/min_quickmin.cpp
View File

@ -82,7 +82,7 @@ int MinQuickMin::iterate(int maxiter)
{
bigint ntimestep;
double vmax,vdotf,vdotfall,fdotf,fdotfall,scale;
double dtvone,dtv,dtfm;
double dtvone,dtv,dtf,dtfm;
int flag,flagall;
alpha_final = 0.0;
@ -162,13 +162,15 @@ int MinQuickMin::iterate(int maxiter)
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
}
dtf = dtv * force->ftm2v;
// Euler integration step
double **x = atom->x;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtv / rmass[i];
dtfm = dtf / rmass[i];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
@ -178,7 +180,7 @@ int MinQuickMin::iterate(int maxiter)
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtv / mass[type[i]];
dtfm = dtf / mass[type[i]];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];