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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11388 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-01-30 17:06:17 +00:00
parent 677b11428e
commit 8a50725149
5 changed files with 127 additions and 225 deletions
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12
src/KSPACE/pppm_disp.cpp
View File

@ -274,7 +274,7 @@ void PPPMDisp::init()
else if (mixflag == 2) { k = 3; break; }
default:
sprintf(str, "Unsupported order in kspace_style "
"pppm/disp pair_style %s", force->pair_style);
"pppm/disp, pair_style %s", force->pair_style);
error->all(FLERR,str);
}
function[k] = 1;
@ -381,7 +381,7 @@ void PPPMDisp::init()
"b/c stencil extends beyond neighbor processor");
iteration++;
// set grid for dispersion interaction and coulomb interactions!
// set grid for dispersion interaction and coulomb interactions
set_grid();
@ -1292,7 +1292,7 @@ void PPPMDisp::init_coeffs() // local pair coeffs
err = bmax/amax;
if (err > 1.0e-4) {
char str[128];
sprintf(str, "Error in splitting of dispersion coeffs is estimated %g %.",err);
sprintf(str,"Error in splitting of dispersion coeffs is estimated %g%",err);
error->warning(FLERR, str);
}
// set B
@ -1337,7 +1337,7 @@ void PPPMDisp::init_coeffs() // local pair coeffs
if (screen) fprintf(screen," Using %d structure factors\n",nsplit);
if (logfile) fprintf(logfile," Using %d structure factors\n",nsplit);
}
if (nsplit > 9) error->warning(FLERR, "Simulations might be very slow because of large number of structure factors!");
if (nsplit > 9) error->warning(FLERR, "Simulations might be very slow because of large number of structure factors");
}
memory->destroy(A);
@ -1354,7 +1354,7 @@ void PPPMDisp::init_coeffs() // local pair coeffs
//cannot use sigma, because this has not been set yet
double **sigma = (double **) force->pair->extract("sigma",tmp);
if (!(epsilon&&sigma))
error->all(FLERR,"epsilon or sigma reference not set by pair style in PPPMDisp");
error->all(FLERR,"Epsilon or sigma reference not set by pair style in PPPMDisp");
double eps_i, sigma_i, sigma_n, *bi = B = new double[7*n+7];
double c[7] = {
1.0, sqrt(6.0), sqrt(15.0), sqrt(20.0), sqrt(15.0), sqrt(6.0), 1.0};
@ -2603,7 +2603,7 @@ void PPPMDisp::set_grid()
// break loop if the accuracy has been reached or too many loops have been performed
if (dfkspace <= accuracy) break;
if (count > 500) error->all(FLERR, "Could not compute grid size for Coulomb interaction!");
if (count > 500) error->all(FLERR, "Could not compute grid size for Coulomb interaction");
h *= 0.95;
h_x = h_y = h_z = h;
}

206
src/KSPACE/pppm_disp.h
View File

@ -383,32 +383,36 @@ command-line option when running LAMMPS to see the offending line.
E: Cannot use PPPMDisp with 2d simulation
UNDOCUMENTED
The kspace style pppm/disp cannot be used in 2d simulations. You can
use 2d pppm/disp in a 3d simulation; see the kspace_modify command.
E: Cannot use nonperiodic boundaries with PPPMDisp
UNDOCUMENTED
For kspace style pppm/disp, 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.
E: Incorrect boundaries with slab PPPMDisp
UNDOCUMENTED
Must have periodic x,y dimensions and non-periodic z dimension to use
2d slab option with pppm/disp.
E: PPPMDisp coulomb order cannot be greater than %d
UNDOCUMENTED
This is a limitation of the PPPM implementation in LAMMPS.
E: KSpace style is incompatible with Pair style
Setting a kspace style requires that a pair style with a long-range
Coulombic or dispersion component be used.
E: Unsupported order in kspace_style pppm/disp pair_style %s
E: Unsupported order in kspace_style pppm/disp, pair_style %s
UNDOCUMENTED
Only pair styles with 1/r and 1/r^6 dependence are currently supported.
W: Charges are set, but coulombic solver is not used
UNDOCUMENTED
Self-explanatory.
E: Kspace style with selected options requires atom attribute q
@ -432,35 +436,43 @@ are defined.
E: Bad TIP4P angle type for PPPMDisp/TIP4P
UNDOCUMENTED
Specified angle type is not valid.
E: Bad TIP4P bond type for PPPMDisp/TIP4P
UNDOCUMENTED
Specified bond type is not valid.
W: Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor
UNDOCUMENTED
This may lead to a larger grid than desired. See the kspace_modify overlap
command to prevent changing of the PPPM order.
E: PPPMDisp Coulomb grid is too large
UNDOCUMENTED
The global PPPM grid is larger than OFFSET in one or more dimensions.
OFFSET is currently set to 4096. You likely need to decrease the
requested accuracy.
E: Coulomb PPPMDisp order has been reduced below minorder
UNDOCUMENTED
The default minimum order is 2. This can be reset by the
kspace_modify minorder command.
W: Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor
UNDOCUMENTED
This may lead to a larger grid than desired. See the kspace_modify overlap
command to prevent changing of the PPPM order.
E: PPPMDisp Dispersion grid is too large
UNDOCUMENTED
The global PPPM grid is larger than OFFSET in one or more dimensions.
OFFSET is currently set to 4096. You likely need to decrease the
requested accuracy.
E: Dispersion PPPMDisp order has been reduced below minorder
UNDOCUMENTED
The default minimum order is 2. This can be reset by the
kspace_modify minorder command.
E: PPPM grid stencil extends beyond nearest neighbor processor
@ -468,28 +480,30 @@ This is not allowed if the kspace_modify overlap setting is no.
E: Matrix factorization to split dispersion coefficients failed
UNDOCUMENTED
This should not normally happen. Contact the developers.
W: Error in splitting of dispersion coeffs is estimated %g %.
W: Error in splitting of dispersion coeffs is estimated %g%
UNDOCUMENTED
Error is greater than 0.0001 percent.
W: Simulations might be very slow because of large number of structure factors!
W: Simulations might be very slow because of large number of structure factors
UNDOCUMENTED
Self-explanatory.
E: epsilon or sigma reference not set by pair style in PPPMDisp
E: Epsilon or sigma reference not set by pair style in PPPMDisp
UNDOCUMENTED
Self-explanatory.
E: KSpace accuracy too large to estimate G vector
Reduce the accuracy request or specify gwald explicitly
via the kspace_modify command.
E: Could not compute grid size for Coulomb interaction!
E: Could not compute grid size for Coulomb interaction
UNDOCUMENTED
The code is unable to compute a grid size consistent with the desired
accuracy. This error should not occur for typical problems. Please
send an email to the developers.
E: Could not compute g_ewald
@ -499,7 +513,9 @@ send an email to the developers.
E: Could not adjust g_ewald_6
UNDOCUMENTED
The Newton-Raphson solver failed to converge to a good value for
g_ewald. This error should not occur for typical problems. Please
send an email to the developers.
E: Cannot compute initial g_ewald_disp
@ -507,145 +523,15 @@ LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6
factor that partitions the computation between real space and k-space
for Disptersion interactions.
E: Could not compute grid size for Dispersion!
E: Could not compute grid size for Dispersion
UNDOCUMENTED
The code is unable to compute a grid size consistent with the desired
accuracy. This error should not occur for typical problems. Please
send an email to the developers.
E: Out of range atoms - cannot compute PPPMDisp
UNDOCUMENTED
U: Unsupported mixing rule in kspace_style pppm/disp for pair_style %s
UNDOCUMENTED
U: Cannot (yet) use PPPMDisp with triclinic box
UNDOCUMENTED
U: Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor.
UNDOCUMENTED
U: Reducing PPPMDisp dispersion order b/c stencil extends beyond
neighbor processor
UNDOCUMENTED
U: PPPMDisp dispersion grid is too large
UNDOCUMENTED
U: Could not compute grid size for dispersion
UNDOCUMENTED
U: Cannot (yet) use PPPM_disp with triclinic box
This feature is not yet supported.
U: Cannot use PPPM_disp with 2d simulation
The kspace style pppm_disp cannot be used in 2d simulations. You can use
2d PPPM_disp in a 3d simulation; see the kspace_modify command.
U: Cannot use nonperiodic boundaries with PPPM_disp
For kspace style pppm_disp, 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.
U: Incorrect boundaries with slab PPPM_disp
Must have periodic x,y dimensions and non-periodic z dimension to use
2d slab option with PPPM_disp.
U: PPPM_disp coulomb order cannot be greater than %d
Self-explanatory.
U: PPPM_disp dispersion order cannot be greater than %d
Self-explanatory.
U: Unsupported mixing rule in kspace_style pppm_disp for pair_style %s
PPPM_disp requires arithemtic or geometric mixing rules.
U: Unsupported order in kspace_style pppm_disp pair_style %s
PPPM_disp only works for 1/r and 1/r^6 potentials
U: Charges are set, but coulombic long-range solver is not used.
Charges have been specified, however, calculations are performed
as if they were zero.
U: Bad TIP4P angle type for PPPM_disp/TIP4P
Specified angle type is not valid.
U: Bad TIP4P bond type for PPPM_disp/TIP4P
Specified bond type is not valid.
U: Reducing PPPM_disp Coulomb order b/c stencil extends beyond neighbor processor
LAMMPS is attempting this in order to allow the simulation
to run. It should not effect the PPPM_disp accuracy.
U: Reducing PPPM_disp dispersion order b/c stencil extends beyond neighbor processor
LAMMPS is attempting this in order to allow the simulation
to run. It should not effect the PPPM_disp accuracy.
U: PPPM_disp Coulomb grid is too large
The global PPPM_disp grid for Coulomb interactions is larger than
OFFSET in one or more dimensions. OFFSET is currently set to 16384.
You likely need to decrease the requested precision.
U: PPPM_grid dispersion grid is too large
One of the PPPM_disp grids for dispersion interactions is larger than
OFFSET in one or more dimensions. OFFSET is currently set to 16384.
You likely need to decrease the requested precision.
U: Coulomb PPPM_disp order has been reduced to 0
LAMMPS has attempted to reduce the PPPM_disp coulomb order to enable
the simulation to run, but can reduce the order no further. Try
increasing the accuracy of PPPM_disp coulomb by reducing the tolerance
size, thus inducing a larger PPPM_disp coulomb grid.
U: Dispersion PPPM_disp order has been reduced to 0
LAMMPS has attempted to reduce the PPPM_disp dispersion order to
enable the simulation to run, but can reduce the order no further.
Try increasing the accuracy of PPPM_disp dispersion by reducing the
tolerance size, thus inducing a larger PPPM_disp dispersion grid.
U: Cannot compute PPPM_disp g_ewald
LAMMPS failed to compute a valid approximation for the PPPM_disp
g_ewald factor that partitions the computation between real space and
k-space for Coulomb interactions.
U: Cannot compute final g_ewald_disp
LAMMPS failed to compute a final value for the PPPM_disp g_ewald_6
factor that partitions the computation between real space and k-space
for Disptersion interactions.
U: Out of range atoms - cannot compute PPPM_disp
One or more atoms are attempting to map their charge to a PPPM_disp grid
One or more atoms are attempting to map their charge to a PPPM grid
point that is not owned by a processor. This is likely for one of two
reasons, both of them bad. First, it may mean that an atom near the
boundary of a processor's sub-domain has moved more than 1/2 the

83
src/molecule.h
View File

@ -150,154 +150,161 @@ class Molecule : protected Pointers {
E: Molecule template ID must be alphanumeric or underscore characters
UNDOCUMENTED
Self-explanatory.
E: Insufficient Jacobi rotations for rigid molecule
UNDOCUMENTED
Eigensolve for rigid body was not sufficiently accurate.
E: Unexpected end of molecule file
UNDOCUMENTED
Self-explanatory.
E: Molecule file z center-of-mass must be 0.0 for 2d
UNDOCUMENTED
Self-explanatory.
E: No atom count in molecule file
UNDOCUMENTED
Self-explanatory.
E: Molecule file has bonds but no nbonds setting
UNDOCUMENTED
Self-explanatory.
E: Molecule file has angles but no nangles setting
UNDOCUMENTED
Self-explanatory.
E: Molecule file has dihedrals but no ndihedrals setting
UNDOCUMENTED
Self-explanatory.
E: Molecule file has impropers but no nimpropers setting
UNDOCUMENTED
Self-explanatory.
E: Molecule file shake flags not before shake atoms
UNDOCUMENTED
The order of the two sections is important.
E: Molecule file shake flags not before shake bonds
UNDOCUMENTED
The order of the two sections is important.
E: Unknown section in molecule file
UNDOCUMENTED
Self-explanatory.
E: Molecule file needs both Special Bond sections
UNDOCUMENTED
Self-explanatory.
E: Molecule file has special flags but no bonds
UNDOCUMENTED
Self-explanatory.
E: Molecule file shake info is incomplete
UNDOCUMENTED
All 3 SHAKE sections are needed.
E: Molecule file z coord must be 0.0 for 2d
UNDOCUMENTED
Self-explanatory.
E: Invalid atom type in molecule file
UNDOCUMENTED
Atom types must range from 1 to specified # of types.
E: Invalid atom diameter in molecule file
UNDOCUMENTED
Diameters must be >= 0.0.
E: Invalid atom mass in molecule file
UNDOCUMENTED
Masses must be > 0.0.
E: Invalid atom ID in Bonds section of molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid bond type in Bonds section of molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid atom ID in Angles section of molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid angle type in Angles section of molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid atom ID in dihedrals section of molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid dihedral type in dihedrals section of molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid atom ID in impropers section of molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid improper type in impropers section of molecule file
UNDOCUMENTED
Self-explanatory.
E: Molecule file special list does not match special count
UNDOCUMENTED
The number of values in an atom's special list does not match count.
E: Invalid special atom index in molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid shake flag in molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid shake atom in molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid shake bond type in molecule file
UNDOCUMENTED
Self-explanatory.
E: Invalid shake angle type in molecule file
UNDOCUMENTED
Self-explanatory.
W: Molecule attributes do not match system attributes
UNDOCUMENTED
An attribute is specified (e.g. diameter, charge) that is
not defined for the specified atom style.
E: Molecule topology type exceeds system topology type
UNDOCUMENTED
The number of bond, angle, etc types in the molecule exceeds the
system setting. See the create_box command for how to specify these
values.
E: Molecule toplogy/atom exceeds system topology/atom
UNDOCUMENTED
The number of bonds, angles, etc per-atom in the molecule exceeds the
system setting. See the create_box command for how to specify these
values.
W: Molecule has bond topology but no special bond settings
UNDOCUMENTED
This means the bonded atoms will not be excluded in pair-wise
interactions.
E: Cannot open molecule file %s
UNDOCUMENTED
The specified file cannot be opened. Check that the path and name are
correct.
*/

36
src/read_restart.h
View File

@ -97,7 +97,7 @@ Self-explanatory.
E: Invalid flag in peratom section of restart file
UNDOCUMENTED
The format of this section of the file is not correct.
E: Did not assign all atoms correctly
@ -116,7 +116,10 @@ When using a "*" in the restart file name, no matching file was found.
E: Restart file incompatible with current version
UNDOCUMENTED
This is probably because you are trying to read a file created with a
version of LAMMPS that is too old compared to the current version.
Use your older version of LAMMPS and convert the restart file
to a data file.
E: Smallint setting in lmptype.h is not compatible
@ -125,17 +128,18 @@ you are running.
E: Imageint setting in lmptype.h is not compatible
UNDOCUMENTED
Format of imageint stored in restart file is not consistent with
LAMMPS version you are running. See the settings in src/lmptype.h
E: Tagint setting in lmptype.h is not compatible
Smallint stored in restart file is not consistent with LAMMPS version
you are running.
Format of tagint stored in restart file is not consistent with LAMMPS
version you are running. See the settings in src/lmptype.h
E: Bigint setting in lmptype.h is not compatible
Bigint stored in restart file is not consistent with LAMMPS version
you are running.
Format of bigint stored in restart file is not consistent with LAMMPS
version you are running. See the settings in src/lmptype.h
E: Cannot run 2d simulation with nonperiodic Z dimension
@ -182,30 +186,34 @@ Unrecognized entry in restart file.
E: Restart file is not a multi-proc file
UNDOCUMENTED
The file is inconsistent with the filename you specified for it.
E: Restart file is a multi-proc file
UNDOCUMENTED
The file is inconsistent with the filename you specified for it.
E: Restart file is a MPI-IO file
UNDOCUMENTED
The file is inconsistent with the filename you specified for it.
E: Restart file is not a MPI-IO file
UNDOCUMENTED
The file is inconsistent with the filename you specified for it.
E: Invalid LAMMPS restart file
UNDOCUMENTED
The file does not appear to be a LAMMPS restart file since
it doesn't contain the correct magic string at the beginning.
E: Restart file byte ordering is swapped
UNDOCUMENTED
The file was written on a machine with different byte-ordering than
the machine you are reading it on. Convert it to a text data file
instead, on the machine you wrote it on.
E: Restart file byte ordering is not recognized
UNDOCUMENTED
The file does not appear to be a LAMMPS restart file since it doesn't
contain a recognized byte-orderomg flag at the beginning.
*/

15
src/set.h
View File

@ -88,11 +88,11 @@ Self-explanatory.
E: Invalid density in set command
UNDOCUMENTED
Density must be > 0.0.
E: Invalid volume in set command
UNDOCUMENTED
Volume must be > 0.0.
E: Cannot set non-zero image flag for non-periodic dimension
@ -104,11 +104,11 @@ Self-explanatory.
E: Set command integer vector does not exist
UNDOCUMENTED
Self-explanatory.
E: Set command floating point vector does not exist
UNDOCUMENTED
Self-explanatory.
E: Cannot use set atom with no atom IDs defined
@ -152,7 +152,8 @@ Self-explanatory.
E: Cannot set bond topology types for atom style template
UNDOCUMENTED
The bond, angle, etc types cannot be changed for this atom style since
they are static settings in the molecule template files.
E: Bond atom missing in set command
@ -180,10 +181,10 @@ atoms are too far apart to make a valid improper.
E: Variable name for set command does not exist
UNDOCUMENTED
Self-explanatory.
E: Variable for set command is invalid style
UNDOCUMENTED
Only atom-style variables can be used.
*/