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removed changes to atom.cpp

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This commit is contained in:
Tom Swinburne
2020-04-20 19:42:04 +02:00
parent 1709bc3f83
commit 4da1ba749f
4 changed files with 106 additions and 50 deletions
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4
src/.gitignore vendored
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@ -47,6 +47,10 @@
/meam*.cpp
/pair_meamc.cpp
/pair_meamc.h
/pair_coul_slater*.cpp
/pair_coul_slater*.h
/fix_propel*.cpp
/fix_propel*.h
/ptm_*.cpp
/ptm_*.h

8
src/atom.cpp
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@ -2290,17 +2290,9 @@ void *Atom::extract(char *name)
if (strcmp(name, "eff_plastic_strain_rate") == 0)
return (void *) eff_plastic_strain_rate;
if (strcmp(name, "damage") == 0) return (void *) damage;
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
int vector_index, vector_type;
vector_index = lmp->atom->find_custom(name, vector_type);
if(vector_index>=0) return (void *) dvector[vector_index];
return NULL;
}

137
src/library.cpp
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@ -832,16 +832,6 @@ void lammps_gather_atoms(void *ptr, char *name,
void *vptr = lmp->atom->extract(name);
// look for property/atom if NULL
/*int vector_index, vector_type=type;
if (vptr == NULL) {
vector_index = lmp->atom->find_custom(name, vector_type);
if(vector_index>=0 && vector_type == type) {
if(type==0) vptr = (void *) lmp->atom->ivector[vector_index];
else vptr = (void *) lmp->atom->dvector[vector_index];
}
}*/
if (vptr == NULL) {
lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name");
return;
@ -1293,6 +1283,23 @@ void lammps_scatter_atoms(void *ptr, char *name,
int natoms = static_cast<int> (lmp->atom->natoms);
void *vptr = lmp->atom->extract(name);
// try to find property/atom vectors
if (vptr == NULL) {
int vector_type;
int vector_index = lmp->atom->find_custom(name, vector_type);
if(vector_index>=0) {
if(vector_type == type) {
if(type==0) vptr = (void *) lmp->atom->ivector[vector_index];
else vptr = (void *) lmp->atom->dvector[vector_index];
} else {
lmp->error->warning(FLERR,"lammps_scatter_atoms:"
" property/atom vector has wrong type");
return;
}
}
}
if(vptr == NULL) {
lmp->error->warning(FLERR,
"lammps_scatter_atoms: unknown property name");
@ -1421,9 +1428,26 @@ void lammps_scatter_atoms_subset(void *ptr, char *name,
}
void *vptr = lmp->atom->extract(name);
// try to find property/atom vectors
if (vptr == NULL) {
int vector_type;
int vector_index = lmp->atom->find_custom(name, vector_type);
if(vector_index>=0) {
if(vector_type == type) {
if(type==0) vptr = (void *) lmp->atom->ivector[vector_index];
else vptr = (void *) lmp->atom->dvector[vector_index];
} else {
lmp->error->warning(FLERR,"lammps_scatter_atoms_subset:"
" property/atom vector has wrong type");
return;
}
}
}
if(vptr == NULL) {
lmp->error->warning(FLERR,
"lammps_scatter_atoms_subset: unknown property name");
lmp->error->warning(FLERR,"lammps_scatter_atoms_subset: "
"unknown property name");
return;
}
@ -1501,17 +1525,33 @@ void lammps_scatter_atoms_subset(void *ptr, char *name,
#endif
/* ----------------------------------------------------------------------
Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France)
gather the named fix and return it in user-allocated data
gather_fix : extract_fix == gather_atoms : extract_atoms
error raised if fix doesn't return peratom data
data will be ordered by atom ID
requirement for consecutive atom IDs (1 to N)
id = fix ID
count: number of entries per atom
method:
alloc and zero count*Natom length vector
loop over Nlocal to fill vector with my values
Allreduce to sum vector into data across all procs
------------------------------------------------------------------------- */
#if defined(LAMMPS_BIGBIG)
void lammps_gather_peratom_fix(void *ptr, char * /*id */, int /*type*/, int /*count*/, void * /*data*/)
void lammps_gather_fix(void *ptr, char * /*id*/, int /*type*/,
int /*count*/, void * /*data*/)
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
lmp->error->all(FLERR,"Library function lammps_gather_peratom_fix() not compatible with -DLAMMPS_BIGBIG");
lmp->error->all(FLERR,"Library function lammps_gather_peratom_fix()"
" not compatible with -DLAMMPS_BIGBIG");
END_CAPTURE
}
#else
void lammps_gather_peratom_fix(void *ptr, char *id, int type, int count, void *data)
void lammps_gather_fix(void *ptr, char *id, int type, int count, void *data)
{
LAMMPS *lmp = (LAMMPS *) ptr;
@ -1520,12 +1560,29 @@ void lammps_gather_peratom_fix(void *ptr, char *id, int type, int count, void *d
int i,j,offset;
int ifix = lmp->modify->find_fix(id);
if (ifix < 0) {
lmp->error->warning(FLERR,"lammps_gather_peratom_fix: unknown fix id");
lmp->error->warning(FLERR,"lammps_gather_fix: unknown fix id");
return;
}
Fix *fix = lmp->modify->fix[ifix];
int natoms = static_cast<int> (lmp->atom->natoms);
// if
if (fix->peratom_flag == 0) {
lmp->error->warning(FLERR,"lammps_gather_fix:"
" fix does not return peratom data");
return;
}
if (fix->size_peratom_cols != count) {
lmp->error->warning(FLERR,"lammps_gather_fix:"
" count != values peratom for fix");
return;
}
if (lmp->update->ntimestep % fix->peratom_freq) {
lmp->error->all(FLERR,"lammps_gather_fix:"
" fix not computed at compatible time");
return;
}
// error if tags are not defined or not consecutive
int flag = 0;
@ -1597,35 +1654,21 @@ void lammps_gather_peratom_fix(void *ptr, char *id, int type, int count, void *d
}
#endif
/* ----------------------------------------------------------------------
Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France)
gather the named per atom fix for a subset of atoms and return
it in user-allocated data
(extract_fix was found to give errors when running lammps in parallel)
data will be ordered by atom ID
requirement for consecutive atom IDs (1 to N)
id = fix ID
count: number of entries per atom
ndata = # of atoms to return data for (could be all atoms)
ids = list of ndata atom IDs to return data for
Fills 1d data, which must be pre-allocated to length of count * ndata, where Natoms is as queried by get_natoms()
method:
alloc and zero count*Natom length vector
loop over Nlocal to fill vector with my values
Allreduce to sum vector into data across all procs
------------------------------------------------------------------------- */
#if defined(LAMMPS_BIGBIG)
void lammps_gather_peratom_fix_subset(void *ptr, char * /*id */, int /*type*/,
int /*count*/, int /*ndata*/, int * /*ids*/, void * /*data*/)
void lammps_gather_fix_subset(void *ptr, char * /*id */, int /*type*/,
int /*count*/, int /*ndata*/,
int * /*ids*/, void * /*data*/)
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
lmp->error->all(FLERR,"Library function lammps_gather_peratom_fix_subset() not compatible with -DLAMMPS_BIGBIG");
lmp->error->all(FLERR,"Library function lammps_gather_peratom_fix_subset() "
"not compatible with -DLAMMPS_BIGBIG");
END_CAPTURE
}
#else
void lammps_gather_peratom_fix_subset(void *ptr, char *id, int type, int count,
void lammps_gather_fix_subset(void *ptr, char *id,
int type, int count,
int ndata, int *ids, void *data)
{
LAMMPS *lmp = (LAMMPS *) ptr;
@ -1637,12 +1680,28 @@ void lammps_gather_peratom_fix_subset(void *ptr, char *id, int type, int count,
int ifix = lmp->modify->find_fix(id);
if (ifix < 0) {
lmp->error->warning(FLERR,"lammps_gather_peratom_fix_subset: unknown fix id");
lmp->error->warning(FLERR,"lammps_gather_fix_subset: unknown fix id");
return;
}
Fix *fix = lmp->modify->fix[ifix];
int natoms = static_cast<int> (lmp->atom->natoms);
if (fix->peratom_flag == 0) {
lmp->error->warning(FLERR,"lammps_gather_fix_subset:"
" fix does not return peratom data");
return;
}
if (fix->size_peratom_cols != count) {
lmp->error->warning(FLERR,"lammps_gather_fix_subset:"
" count != values peratom for fix");
return;
}
if (lmp->update->ntimestep % fix->peratom_freq) {
lmp->error->all(FLERR,"lammps_gather_fix_subset:"
" fix not computed at compatible time");
return;
}
// error if tags are not defined or not consecutive
int flag = 0;
@ -1651,7 +1710,7 @@ void lammps_gather_peratom_fix_subset(void *ptr, char *id, int type, int count,
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_gather_peratom_fix_subset");
lmp->error->warning(FLERR,"Library error in lammps_gather_fix_subset");
return;
}

5
src/library.h
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@ -66,11 +66,12 @@ void lammps_reset_box(void *, double *, double *, double, double, double);
void lammps_gather_atoms(void *, char *, int, int, void *);
void lammps_gather_atoms_concat(void *, char *, int, int, void *);
void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
void lammps_scatter_atoms(void *, char *, int, int, void *);
void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
void lammps_gather_peratom_fix(void *, char *, int, int, void *);
void lammps_gather_peratom_fix_subset(void *, char *, int, int, int, int *, void *);
void lammps_gather_fix(void *, char *, int, int, void *);
void lammps_gather_fix_subset(void *, char *, int, int, int, int *, void *);
#if defined(LAMMPS_BIGBIG)
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);