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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13282 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-03-24 15:34:07 +00:00
parent 421724aadc
commit 25b928b276
35 changed files with 179 additions and 137 deletions
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6
src/DIPOLE/pair_lj_long_dipole_long.cpp
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@ -251,14 +251,14 @@ void PairLJLongDipoleLong::init_style()
error->all(FLERR,"Pair style requires a KSpace style");
for (i=0; style3[i]&&strcmp(force->kspace_style, style3[i]); ++i);
if (!style3[i])
error->all(FLERR,"Pair style is incompatible with KSpace style");
error->all(FLERR,"Pair style requires use of kspace_style ewald/disp");
}
if (ewald_order&(1<<6)) { // r^-6 kspace
if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
error->all(FLERR,"Pair style requires a KSpace style");
for (i=0; style6[i]&&strcmp(force->kspace_style, style6[i]); ++i);
if (!style6[i])
error->all(FLERR,"Pair style is incompatible with KSpace style");
error->all(FLERR,"Pair style requires use of kspace_style ewald/disp");
}
if (force->kspace) g_ewald = force->kspace->g_ewald;
}

4
src/DIPOLE/pair_lj_long_dipole_long.h
View File

@ -110,6 +110,10 @@ E: Pair style requires a KSpace style
No kspace style is defined.
E: Pair style requires use of kspace_style ewald/disp
Self-explanatory.
E: Pair style lj/long/dipole/long does not currently support respa
This feature is not yet supported.

6
src/GPU/pair_lj_sf_dipole_sf_gpu.h
View File

@ -51,11 +51,11 @@ E: Insufficient memory on accelerator
There is insufficient memory on one of the devices specified for the gpu
package
E: Pair style dipole/cut/gpu requires atom attribute q
E: Pair dipole/sf/gpu requires atom attributes q, mu, torque
The atom style defined does not have this attribute.
The atom style defined does not one or more of these attributes.
E: Cannot use newton pair with dipole/cut/gpu pair style
E: Cannot use newton pair with dipole/sf/gpu pair style
Self-explanatory.

10
src/KOKKOS/bond_fene_kokkos.h
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@ -100,4 +100,14 @@ class BondFENEKokkos : public BondFENE {
/* ERROR/WARNING messages:
W: FENE bond too long
A FENE bond has stretched dangerously far. It's interaction strength
will be truncated to attempt to prevent the bond from blowing up.
E: Bad FENE bond
Two atoms in a FENE bond have become so far apart that the bond cannot
be computed.
*/

5
src/KOKKOS/dihedral_charmm_kokkos.h
View File

@ -183,4 +183,9 @@ class DihedralCharmmKokkos : public DihedralCharmm {
/* ERROR/WARNING messages:
W: Dihedral problem
Conformation of the 4 listed dihedral atoms is extreme; you may want
to check your simulation geometry.
*/

5
src/KOKKOS/dihedral_opls_kokkos.h
View File

@ -98,4 +98,9 @@ class DihedralOPLSKokkos : public DihedralOPLS {
/* ERROR/WARNING messages:
W: Dihedral problem
Conformation of the 4 listed dihedral atoms is extreme; you may want
to check your simulation geometry.
*/

5
src/KOKKOS/improper_harmonic_kokkos.h
View File

@ -94,4 +94,9 @@ class ImproperHarmonicKokkos : public ImproperHarmonic {
/* ERROR/WARNING messages:
W: Dihedral problem
Conformation of the 4 listed dihedral atoms is extreme; you may want
to check your simulation geometry.
*/

4
src/KOKKOS/neigh_bond_kokkos.cpp
View File

@ -199,7 +199,7 @@ void NeighBondKokkos<DeviceType>::build_topology_kk()
// don't yet have atom_map_kokkos routines, so move data from host to device
if (atom->map_style != 1)
error->all(FLERR,"Must use map style array with Kokkos for topology");
error->all(FLERR,"Must use atom map style array with Kokkos");
int* map_array_host = atom->get_map_array();
int map_size = atom->get_map_size();
@ -1281,4 +1281,4 @@ void NeighBondKokkos<DeviceType>::update_domain_variables()
template class NeighBondKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class NeighBondKokkos<LMPHostType>;
#endif
#endif

80
src/KOKKOS/neigh_bond_kokkos.h
View File

@ -173,4 +173,84 @@ class NeighBondKokkos : protected Pointers {
/* ERROR/WARNING messages:
E: Must use atom map style array with Kokkos
See the atom_modify map command.
E: Bond atoms missing on proc %d at step %ld
The 2nd atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
W: Bond atoms missing at step %ld
The 2nd atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
E: Cannot (yet) use molecular templates with Kokkos
Self-explanatory.
E: Bond extent > half of periodic box length
This error was detected by the neigh_modify check yes setting. It is
an error because the bond atoms are so far apart it is ambiguous how
it should be defined.
E: Angle atoms missing on proc %d at step %ld
One or more of 3 atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
W: Angle atoms missing at step %ld
One or more of 3 atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
E: Angle extent > half of periodic box length
This error was detected by the neigh_modify check yes setting. It is
an error because the angle atoms are so far apart it is ambiguous how
it should be defined.
E: Dihedral atoms missing on proc %d at step %ld
One or more of 4 atoms needed to compute a particular dihedral are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the dihedral has blown apart and an atom is
too far away.
W: Dihedral atoms missing at step %ld
One or more of 4 atoms needed to compute a particular dihedral are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the dihedral has blown apart and an atom is
too far away.
E: Dihedral/improper extent > half of periodic box length
This error was detected by the neigh_modify check yes setting. It is
an error because the dihedral atoms are so far apart it is ambiguous
how it should be defined.
E: Improper atoms missing on proc %d at step %ld
One or more of 4 atoms needed to compute a particular improper are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the improper has blown apart and an atom is
too far away.
W: Improper atoms missing at step %ld
One or more of 4 atoms needed to compute a particular improper are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the improper has blown apart and an atom is
too far away.
*/

6
src/KOKKOS/neighbor_kokkos.h
View File

@ -377,4 +377,10 @@ class NeighborKokkos : public Neighbor {
/* ERROR/WARNING messages:
E: Too many local+ghost atoms for neighbor list
The number of nlocal + nghost atoms on a processor
is limited by the size of a 32-bit integer with 2 bits
removed for masking 1-2, 1-3, 1-4 neighbors.
*/

14
src/KOKKOS/pair_lj_cut_coul_long_kokkos.h
View File

@ -144,4 +144,18 @@ class PairLJCutCoulLongKokkos : public PairLJCutCoulLong {
/* ERROR/WARNING messages:
E: Illegal ... command
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: Cannot use Kokkos pair style with rRESPA inner/middle
rRESPA inner/middle options are not yet supported by Kokkos.
E: Cannot use chosen neighbor list style with lj/cut/coul/long/kk
That style is not supported by Kokkos.
*/

2
src/PYTHON/python.cpp
View File

@ -154,7 +154,7 @@ void Python::command(int narg, char **arg)
//PySys_SetArgv(1,&arg);
//PyObject *pName = PyString_FromString("__main__");
//if (!pName) error->Xall(FLERR,"Bad pName");
//if (!pName) errorX->all(FLERR,"Bad pName");
//PyObject *pModule = PyImport_Import(pName);
//Py_DECREF(pName);

4
src/RIGID/fix_rattle.cpp
View File

@ -497,7 +497,7 @@ void FixRattle::solve3x3exactly(const double a[][3],
a[0][1]*a[1][0]*a[2][2] - a[0][2]*a[1][1]*a[2][0];
// check if matrix is actually invertible
if (determ == 0.0) error->one(FLERR,"Rattle determinant = 0.0");
if (determ == 0.0) error->one(FLERR,"RATTLE determinant = 0.0");
// calculate the inverse 3x3 matrix: A^(-1) = (ai_jk)
determinv = 1.0/determ;
@ -787,7 +787,7 @@ bool FixRattle::check3(double **v, int m, bool checkr, bool checkv)
fabs(MathExtra::dot3(r02,v02)) > tol));
if (!stat)
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
"up to desired tolerance!");
"up to desired tolerance");
return stat;
}

4
src/RIGID/fix_rattle.h
View File

@ -99,4 +99,8 @@ E: RATTLE velocity constraints are not satisfied up to desired tolerance
Self-explanatory.
E: RATTLE velocity constraints are not satisfied up to desired tolerance!
UNDOCUMENTED
*/

4
src/RIGID/fix_rigid_npt_small.h
View File

@ -58,10 +58,6 @@ E: Fix rigid npt/small t_chain should not be less than 1
Self-explanatory.
E: Fix rigid npt/small t_iter should not be less than 1
Self-explanatory.
E: Fix rigid npt/small t_order must be 3 or 5
Self-explanatory.

4
src/SRD/fix_srd.cpp
View File

@ -1347,7 +1347,7 @@ void FixSRD::collisions_single()
} else{
sprintf(str,
"SRD particle " TAGINT_FORMAT " started "
"inside wall %d on step " BIGINT_FORMAT " bounce %d",
"inside wall %d on step " BIGINT_FORMAT " bounce %d",
atom->tag[i],j,update->ntimestep,ibounce+1);
if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
error->warning(FLERR,str);
@ -1506,7 +1506,7 @@ void FixSRD::collisions_multi()
} else{
sprintf(str,
"SRD particle " TAGINT_FORMAT " started "
"inside wall %d on step " BIGINT_FORMAT " bounce %d",
"inside wall %d on step " BIGINT_FORMAT " bounce %d",
atom->tag[i],j,update->ntimestep,ibounce+1);
if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
error->warning(FLERR,str);

8
src/USER-MISC/fix_ave_spatial_sphere.cpp
View File

@ -1061,11 +1061,3 @@ double FixAveSpatialSphere::memory_usage()
bytes += nwindow*nbins*nvalues * sizeof(double); // values_list
return bytes;
}
/* ---------------------------------------------------------------------- */
void FixAveSpatialSphere::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid)
error->all(FLERR,"Fix ave/spatial/sphere missed timestep");
}

12
src/USER-MISC/fix_ave_spatial_sphere.h
View File

@ -37,7 +37,6 @@ class FixAveSpatialSphere : public Fix {
void end_of_step();
double memory_usage();
double compute_array(int,int);
void reset_timestep(bigint);
private:
int me; //rank of the MPI Process
@ -179,14 +178,9 @@ E: Fix ave/spatial/spherical requires reduced units if the box changes size.
If the box size changes, only the units reduced option can be
used.
E: Fix for fix ave/spatial/spherical not computed at compatible time
E: Invalid timestep reset for fix ave/spatial/sphere
Fixes generate their values on specific timesteps. Fix ave/spatial/spherical is
requesting a value on a non-allowed timestep.
E: Fix ave/spatial/spherical missed timestep
You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
Resetting the timestep has invalidated the sequence of timesteps this
fix needs to process.
*/

4
src/XTC/dump_xtc.h
View File

@ -108,11 +108,11 @@ E: Too big a timestep for dump xtc
The timestep must fit in a 32-bit integer to use this dump style.
E: Illegal dump_modify sfactor value (must be >0.0)
E: Illegal dump_modify sfactor value (must be > 0.0)
Self-explanatory.
E: Illegal dump_modify tfactor value (must be >0.0)
E: Illegal dump_modify tfactor value (must be > 0.0)
Self-explanatory.

1
src/fix.h
View File

@ -179,7 +179,6 @@ class Fix : protected Pointers {
virtual void deform(int) {}
virtual void reset_target(double) {}
virtual void reset_dt() {}
virtual void reset_timestep(bigint) {}
virtual void read_data_header(char *) {}
virtual void read_data_section(char *, int, char *) {}

9
src/fix_ave_atom.cpp
View File

@ -284,7 +284,7 @@ void FixAveAtom::end_of_step()
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep resets for fix ave/time");
error->all(FLERR,"Invalid timestep reset for fix ave/atom");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@ -457,10 +457,3 @@ bigint FixAveAtom::nextvalid()
if (nvalid < update->ntimestep) nvalid += peratom_freq;
return nvalid;
}
/* ---------------------------------------------------------------------- */
void FixAveAtom::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid) error->all(FLERR,"Fix ave/atom missed timestep");
}

11
src/fix_ave_atom.h
View File

@ -39,7 +39,6 @@ class FixAveAtom : public Fix {
void copy_arrays(int, int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
void reset_timestep(bigint);
private:
int nvalues;
@ -118,13 +117,9 @@ E: Fix ave/atom variable is not atom-style variable
A variable used by fix ave/atom must generate per-atom values.
E: Invalid timestep resets for fix ave/time
E: Invalid timestep reset for fix ave/atom
UNDOCUMENTED
E: Fix ave/atom missed timestep
You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
Resetting the timestep has invalidated the sequence of timesteps this
fix needs to process.
*/

9
src/fix_ave_chunk.cpp
View File

@ -511,7 +511,7 @@ void FixAveChunk::end_of_step()
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep resets for fix ave/time");
error->all(FLERR,"Invalid timestep reset for fix ave/chunk");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@ -1041,10 +1041,3 @@ double FixAveChunk::memory_usage()
bytes += nwindow*maxchunk*nvalues * sizeof(double); // values_list
return bytes;
}
/* ---------------------------------------------------------------------- */
void FixAveChunk::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid) error->all(FLERR,"Fix ave/chunk missed timestep");
}

10
src/fix_ave_chunk.h
View File

@ -35,7 +35,6 @@ class FixAveChunk : public Fix {
void end_of_step();
double compute_array(int,int);
double memory_usage();
void reset_timestep(bigint);
private:
int me,nvalues;
@ -164,12 +163,9 @@ E: Fix for fix ave/chunk not computed at compatible time
Fixes generate their values on specific timesteps. Fix ave/chunk is
requesting a value on a non-allowed timestep.
E: Invalid timestep resets for fix ave/time
E: Invalid timestep reset for fix ave/chunk
UNDOCUMENTED
E: Fix ave/chunk missed timestep
UNDOCUMENTED
Resetting the timestep has invalidated the sequence of timesteps this
fix needs to process.
*/

9
src/fix_ave_correlate.cpp
View File

@ -395,7 +395,7 @@ void FixAveCorrelate::end_of_step()
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep resets for fix ave/time");
error->all(FLERR,"Invalid timestep reset for fix ave/correlate");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@ -610,10 +610,3 @@ bigint FixAveCorrelate::nextvalid()
if (nvalid % nevery) nvalid = (nvalid/nevery)*nevery + nevery;
return nvalid;
}
/* ---------------------------------------------------------------------- */
void FixAveCorrelate::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid) error->all(FLERR,"Fix ave/correlate missed timestep");
}

11
src/fix_ave_correlate.h
View File

@ -34,7 +34,6 @@ class FixAveCorrelate : public Fix {
void setup(int);
void end_of_step();
double compute_array(int,int);
void reset_timestep(bigint);
private:
int me,nvalues;
@ -126,13 +125,9 @@ E: Fix ave/correlate variable is not equal-style variable
Self-explanatory.
E: Invalid timestep resets for fix ave/time
E: Invalid timestep reset for fix ave/correlate
UNDOCUMENTED
E: Fix ave/correlate missed timestep
You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
Resetting the timestep has invalidated the sequence of timesteps this
fix needs to process.
*/

9
src/fix_ave_histo.cpp
View File

@ -593,7 +593,7 @@ void FixAveHisto::end_of_step()
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep resets for fix ave/time");
error->all(FLERR,"Invalid timestep reset for fix ave/histo");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@ -1031,10 +1031,3 @@ bigint FixAveHisto::nextvalid()
if (nvalid < update->ntimestep) nvalid += nfreq;
return nvalid;
}
/* ---------------------------------------------------------------------- */
void FixAveHisto::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid) error->all(FLERR,"Fix ave/histo missed timestep");
}

11
src/fix_ave_histo.h
View File

@ -35,7 +35,6 @@ class FixAveHisto : public Fix {
void end_of_step();
double compute_vector(int);
double compute_array(int,int);
void reset_timestep(bigint);
private:
int me,nvalues;
@ -214,18 +213,14 @@ E: Variable name for fix ave/histo does not exist
Self-explanatory.
E: Invalid timestep resets for fix ave/time
E: Invalid timestep reset for fix ave/histo
UNDOCUMENTED
Resetting the timestep has invalidated the sequence of timesteps this
fix needs to process.
E: Cannot open fix ave/histo file %s
The specified file cannot be opened. Check that the path and name are
correct.
E: Fix ave/histo missed timestep
You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
*/

9
src/fix_ave_spatial.cpp
View File

@ -553,7 +553,7 @@ void FixAveSpatial::end_of_step()
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep resets for fix ave/time");
error->all(FLERR,"Invalid timestep reset for fix ave/spatial");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@ -1536,10 +1536,3 @@ double FixAveSpatial::memory_usage()
bytes += nwindow*nbins*nvalues * sizeof(double); // values_list
return bytes;
}
/* ---------------------------------------------------------------------- */
void FixAveSpatial::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid) error->all(FLERR,"Fix ave/spatial missed timestep");
}

11
src/fix_ave_spatial.h
View File

@ -35,7 +35,6 @@ class FixAveSpatial : public Fix {
void end_of_step();
double compute_array(int,int);
double memory_usage();
void reset_timestep(bigint);
private:
int me,nvalues;
@ -181,17 +180,13 @@ E: Fix for fix ave/spatial not computed at compatible time
Fixes generate their values on specific timesteps. Fix ave/spatial is
requesting a value on a non-allowed timestep.
E: Invalid timestep resets for fix ave/time
E: Invalid timestep reset for fix ave/spatial
UNDOCUMENTED
Resetting the timestep has invalidated the sequence of timesteps this
fix needs to process.
E: Invalid bin bounds in fix ave/spatial
The lo/hi values are inconsistent.
E: Fix ave/spatial missed timestep
You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
*/

9
src/fix_ave_time.cpp
View File

@ -554,7 +554,7 @@ void FixAveTime::end_of_step()
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep resets for fix ave/time");
error->all(FLERR,"Invalid timestep reset for fix ave/time");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@ -1121,10 +1121,3 @@ bigint FixAveTime::nextvalid()
if (nvalid < update->ntimestep) nvalid += nfreq;
return nvalid;
}
/* ---------------------------------------------------------------------- */
void FixAveTime::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid) error->all(FLERR,"Fix ave/time missed timestep");
}

11
src/fix_ave_time.h
View File

@ -36,7 +36,6 @@ class FixAveTime : public Fix {
double compute_scalar();
double compute_vector(int);
double compute_array(int,int);
void reset_timestep(bigint);
private:
int me,nvalues;
@ -170,9 +169,10 @@ One of more of the vector inputs has individual elements which are
flagged as intensive or extensive. Such an input cannot be flagged as
all intensive/extensive when turned into an array by fix ave/time.
E: Invalid timestep resets for fix ave/time
E: Invalid timestep reset for fix ave/time
UNDOCUMENTED
Resetting the timestep has invalidated the sequence of timesteps this
fix needs to process.
E: Fix ave/time columns are inconsistent lengths
@ -183,9 +183,4 @@ E: Cannot open fix ave/time file %s
The specified file cannot be opened. Check that the path and name are
correct.
E: Fix ave/time missed timestep
You cannot reset the timestep to a value beyond where the fix
expects to next perform averaging.
*/

2
src/pair.cpp
View File

@ -306,7 +306,7 @@ void Pair::init_tables(double cut_coul, double *cut_respa)
double qqrd2e = force->qqrd2e;
if (force->kspace == NULL)
error->all(FLERR,"Pair style requres a KSpace style");
error->all(FLERR,"Pair style requires a KSpace style");
double g_ewald = force->kspace->g_ewald;
double cut_coulsq = cut_coul * cut_coul;

4
src/pair.h
View File

@ -277,9 +277,9 @@ E: Fix adapt interface to this pair style not supported
New coding for the pair style would need to be done.
E: Pair style requres a KSpace style
E: Pair style requires a KSpace style
Self-explanatory.
No kspace style is defined.
E: Pair style does not support pair_write

3
src/update.cpp
View File

@ -428,7 +428,7 @@ void Update::reset_timestep(bigint newstep)
atimestep = ntimestep;
// trigger reset of timestep for output and for fixes that require it
// trigger reset of timestep for output
// do not allow any timestep-dependent fixes to be already defined
output->reset_timestep(ntimestep);
@ -437,7 +437,6 @@ void Update::reset_timestep(bigint newstep)
if (modify->fix[i]->time_depend)
error->all(FLERR,
"Cannot reset timestep with a time-dependent fix defined");
modify->fix[i]->reset_timestep(ntimestep);
}
// reset eflag/vflag global so no commands will think eng/virial are current