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additional changes needed to merge with current master

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This commit is contained in:
Steve Plimpton
2021-01-11 17:26:00 -07:00
parent 0b14770468
commit bddd26ba6c
3 changed files with 201 additions and 95 deletions
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283
src/library.cpp
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@ -2650,9 +2650,10 @@ void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count,
see gather_concat() to return data for all atoms, unordered see gather_concat() to return data for all atoms, unordered
see gather_subset() to return data for only a subset of atoms see gather_subset() to return data for only a subset of atoms
name = "x" , "f" or other atom properties name = "x" , "f" or other atom properties
"d_name" or "i_name" for fix property/atom quantities "f_fix", "c_compute" for fixes / computes
"f_fix", "c_compute" for fixes / computes "d_name" or "i_name" for fix property/atom vectors with count = 1
will return error if fix/compute doesn't isn't atom-based "d2_name" or "i2_name" for fix property/atom arrays with count > 1
will return error if fix/compute isn't atom-based
type = 0 for integer values, 1 for double values type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" if want single image flag unpacked into xyz use count = 3 with "image" if want single image flag unpacked into xyz
@ -2673,12 +2674,13 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
BEGIN_CAPTURE BEGIN_CAPTURE
{ {
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)
lmp->error->all(FLERR,"Library function lammps_gather" lmp->error->all(FLERR,"Library function lammps_gather"
" not compatible with -DLAMMPS_BIGBIG"); " not compatible with -DLAMMPS_BIGBIG");
#else #else
int i,j,offset,fcid,ltype; int i,j,offset,fcid,ltype,icol;
// error if tags are not defined or not consecutive // error if tags are not defined or not consecutive
int flag = 0; int flag = 0;
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0)
flag = 1; flag = 1;
@ -2690,10 +2692,11 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
} }
int natoms = static_cast<int> (lmp->atom->natoms); int natoms = static_cast<int> (lmp->atom->natoms);
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr==nullptr && strstr(name,"f_") == name) { // fix // fix
if (vptr==nullptr && strstr(name,"f_") == name) {
fcid = lmp->modify->find_fix(&name[2]); fcid = lmp->modify->find_fix(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -2726,7 +2729,9 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
else vptr = (void *) lmp->modify->fix[fcid]->array_atom; else vptr = (void *) lmp->modify->fix[fcid]->array_atom;
} }
if (vptr==nullptr && strstr(name,"c_") == name) { // compute // compute
if (vptr==nullptr && strstr(name,"c_") == name) {
fcid = lmp->modify->find_compute(&name[2]); fcid = lmp->modify->find_compute(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -2753,41 +2758,58 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
if (count==1) vptr = (void *) lmp->modify->compute[fcid]->vector_atom; if (count==1) vptr = (void *) lmp->modify->compute[fcid]->vector_atom;
else vptr = (void *) lmp->modify->compute[fcid]->array_atom; else vptr = (void *) lmp->modify->compute[fcid]->array_atom;
} }
// property / atom
if ( (vptr == nullptr) && ((strstr(name,"d_") == name) // property/atom
|| (strstr(name,"i_") == name))) {
fcid = lmp->atom->find_custom(&name[2], ltype); if ((vptr == nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) { if (fcid < 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather: unknown property/atom id"); lmp->error->warning(FLERR,"lammps_gather: unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom type"); lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom type");
return; return;
} }
if (count != 1) { if (count == 1 && icol != 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather: property/atom has count=1"); lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
return; return;
} }
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid]; if (count > 1 && icol != count) {
else vptr = (void *) lmp->atom->dvector[fcid]; if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
return;
}
if (count == 1) {
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
} else {
if (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
} }
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather: unknown property name"); lmp->error->warning(FLERR,"lammps_gather: undefined property name");
return; return;
} }
// copy = Natom length vector of per-atom values // copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy // use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type==0) { if (type==0) {
int *vector = nullptr; int *vector = nullptr;
int **array = nullptr; int **array = nullptr;
@ -2829,7 +2851,6 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
lmp->memory->destroy(copy); lmp->memory->destroy(copy);
} else { } else {
double *vector = nullptr; double *vector = nullptr;
double **array = nullptr; double **array = nullptr;
if (count == 1) vector = (double *) vptr; if (count == 1) vector = (double *) vptr;
@ -2869,9 +2890,10 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
see gather() to return data ordered by consecutive atom IDs see gather() to return data ordered by consecutive atom IDs
see gather_subset() to return data for only a subset of atoms see gather_subset() to return data for only a subset of atoms
name = "x" , "f" or other atom properties name = "x" , "f" or other atom properties
"d_name" or "i_name" for fix property/atom quantities "f_fix", "c_compute" for fixes / computes
"f_fix", "c_compute" for fixes / computes "d_name" or "i_name" for fix property/atom vectors with count = 1
will return error if fix/compute doesn't isn't atom-based "d2_name" or "i2_name" for fix property/atom arrays with count > 1
will return error if fix/compute isn't atom-based
type = 0 for integer values, 1 for double values type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" if want single image flag unpacked into xyz use count = 3 with "image" if want single image flag unpacked into xyz
@ -2895,9 +2917,10 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
lmp->error->all(FLERR,"Library function lammps_gather_concat" lmp->error->all(FLERR,"Library function lammps_gather_concat"
" not compatible with -DLAMMPS_BIGBIG"); " not compatible with -DLAMMPS_BIGBIG");
#else #else
int i,offset,fcid,ltype; int i,offset,fcid,ltype,icol;
// error if tags are not defined or not consecutive // error if tags are not defined or not consecutive
int flag = 0; int flag = 0;
if (lmp->atom->tag_enable == 0) flag = 1; if (lmp->atom->tag_enable == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
@ -2907,12 +2930,12 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
return; return;
} }
int natoms = static_cast<int> (lmp->atom->natoms); int natoms = static_cast<int> (lmp->atom->natoms);
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr==nullptr && strstr(name,"f_") == name) { // fix // fix
if (vptr==nullptr && strstr(name,"f_") == name) {
fcid = lmp->modify->find_fix(&name[2]); fcid = lmp->modify->find_fix(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -2933,8 +2956,6 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
" count != values peratom for fix"); " count != values peratom for fix");
return; return;
} }
if (lmp->update->ntimestep % lmp->modify->fix[fcid]->peratom_freq) { if (lmp->update->ntimestep % lmp->modify->fix[fcid]->peratom_freq) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->all(FLERR,"lammps_gather_concat:" lmp->error->all(FLERR,"lammps_gather_concat:"
@ -2946,7 +2967,9 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
else vptr = (void *) lmp->modify->fix[fcid]->array_atom; else vptr = (void *) lmp->modify->fix[fcid]->array_atom;
} }
if (vptr==nullptr && strstr(name,"c_") == name) { // compute // compute
if (vptr==nullptr && strstr(name,"c_") == name) {
fcid = lmp->modify->find_compute(&name[2]); fcid = lmp->modify->find_compute(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -2973,39 +2996,55 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
if (count==1) vptr = (void *) lmp->modify->compute[fcid]->vector_atom; if (count==1) vptr = (void *) lmp->modify->compute[fcid]->vector_atom;
else vptr = (void *) lmp->modify->compute[fcid]->array_atom; else vptr = (void *) lmp->modify->compute[fcid]->array_atom;
} }
if (vptr==nullptr && strstr(name,"d_") == name) { // property / atom // property/atom
fcid = lmp->atom->find_custom(&name[2], ltype); if ((vptr==nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) { if (fcid < 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat: " lmp->error->warning(FLERR,"lammps_gather_concat: "
"unknown property/atom id"); "unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat: " lmp->error->warning(FLERR,"lammps_gather_concat: "
"mismatch property/atom type"); "mismatch property/atom type");
return; return;
} }
if (count != 1) { if (count == 1 && icol != 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat: " lmp->error->warning(FLERR,"lammps_gather_concat: "
"property/atom has count=1"); "mismatch property/atom count");
return;
}
if (count > 1 && icol != count) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat: "
"mismatch property/atom count");
return; return;
} }
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
if (count == 1) {
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
} else {
if (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
} }
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat: unknown property name"); lmp->error->warning(FLERR,"lammps_gather_concat: undefined property name");
return; return;
} }
@ -3020,6 +3059,7 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
if (type == 0) { if (type == 0) {
int *vector = nullptr; int *vector = nullptr;
int **array = nullptr; int **array = nullptr;
const int imgunpack = (count == 3) && (strcmp(name,"image") == 0); const int imgunpack = (count == 3) && (strcmp(name,"image") == 0);
if ((count == 1) || imgunpack) vector = (int *) vptr; if ((count == 1) || imgunpack) vector = (int *) vptr;
@ -3111,9 +3151,10 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
see gather() to return data ordered by consecutive atom IDs see gather() to return data ordered by consecutive atom IDs
see gather_concat() to return data for all atoms, unordered see gather_concat() to return data for all atoms, unordered
name = "x" , "f" or other atom properties name = "x" , "f" or other atom properties
"d_name" or "i_name" for fix property/atom quantities "f_fix", "c_compute" for fixes / computes
"f_fix", "c_compute" for fixes / computes "d_name" or "i_name" for fix property/atom vectors with count = 1
will return error if fix/compute doesn't isn't atom-based "d2_name" or "i2_name" for fix property/atom arrays with count > 1
will return error if fix/compute isn't atom-based
type = 0 for integer values, 1 for double values type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" if want single image flag unpacked into xyz use count = 3 with "image" if want single image flag unpacked into xyz
@ -3136,13 +3177,14 @@ void lammps_gather_subset(void *handle, char *name,
BEGIN_CAPTURE BEGIN_CAPTURE
{ {
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)
lmp->error->all(FLERR,"Library function lammps_gather_subset() " lmp->error->all(FLERR,"Library function lammps_gather_subset() "
"is not compatible with -DLAMMPS_BIGBIG"); "is not compatible with -DLAMMPS_BIGBIG");
#else #else
int i,j,m,offset,fcid,ltype; int i,j,m,offset,fcid,ltype,icol;
tagint id; tagint id;
// error if tags are not defined or not consecutive // error if tags are not defined or not consecutive
int flag = 0; int flag = 0;
if (lmp->atom->tag_enable == 0) flag = 1; if (lmp->atom->tag_enable == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
@ -3154,7 +3196,9 @@ void lammps_gather_subset(void *handle, char *name,
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr==nullptr && strstr(name,"f_") == name) { // fix // fix
if (vptr==nullptr && strstr(name,"f_") == name) {
fcid = lmp->modify->find_fix(&name[2]); fcid = lmp->modify->find_fix(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -3169,13 +3213,11 @@ void lammps_gather_subset(void *handle, char *name,
" fix does not return peratom data"); " fix does not return peratom data");
return; return;
} }
if (count>1 && lmp->modify->fix[fcid]->size_peratom_cols != count) { if (count>1 && lmp->modify->fix[fcid]->size_peratom_cols != count) {
lmp->error->warning(FLERR,"lammps_gather_subset:" lmp->error->warning(FLERR,"lammps_gather_subset:"
" count != values peratom for fix"); " count != values peratom for fix");
return; return;
} }
if (lmp->update->ntimestep % lmp->modify->fix[fcid]->peratom_freq) { if (lmp->update->ntimestep % lmp->modify->fix[fcid]->peratom_freq) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->all(FLERR,"lammps_gather_subset:" lmp->error->all(FLERR,"lammps_gather_subset:"
@ -3187,7 +3229,9 @@ void lammps_gather_subset(void *handle, char *name,
else vptr = (void *) lmp->modify->fix[fcid]->array_atom; else vptr = (void *) lmp->modify->fix[fcid]->array_atom;
} }
if (vptr==nullptr && strstr(name,"c_") == name) { // compute // compute
if (vptr==nullptr && strstr(name,"c_") == name) {
fcid = lmp->modify->find_compute(&name[2]); fcid = lmp->modify->find_compute(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -3214,39 +3258,56 @@ void lammps_gather_subset(void *handle, char *name,
if (count==1) vptr = (void *) lmp->modify->compute[fcid]->vector_atom; if (count==1) vptr = (void *) lmp->modify->compute[fcid]->vector_atom;
else vptr = (void *) lmp->modify->compute[fcid]->array_atom; else vptr = (void *) lmp->modify->compute[fcid]->array_atom;
} }
if (vptr==nullptr && strstr(name,"d_") == name) { // property / atom // property/atom
fcid = lmp->atom->find_custom(&name[2], ltype); if ((vptr == nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) { if (fcid < 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: " lmp->error->warning(FLERR,"lammps_gather_subset: "
"unknown property/atom id"); "unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: " lmp->error->warning(FLERR,"lammps_gather_subset: "
"mismatch property/atom type"); "mismatch property/atom type");
return; return;
} }
if (count != 1) { if (count == 1 && icol != 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: " lmp->error->warning(FLERR,"lammps_gather_subset: "
"property/atom has count=1"); "mismatch property/atom count");
return; return;
} }
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid]; if (count > 1 && icol != count) {
else vptr = (void *) lmp->atom->dvector[fcid]; if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: "
"mismatch property/atom count");
return;
}
if (count == 1) {
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
} else {
if (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
} }
if (vptr == nullptr) { if (vptr == nullptr) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: " lmp->error->warning(FLERR,"lammps_gather_subset: undefined property name");
"unknown property name");
return; return;
} }
@ -3304,6 +3365,7 @@ void lammps_gather_subset(void *handle, char *name,
} else { } else {
double *vector = nullptr; double *vector = nullptr;
double **array = nullptr; double **array = nullptr;
if (count == 1) vector = (double *) vptr; if (count == 1) vector = (double *) vptr;
else array = (double **) vptr; else array = (double **) vptr;
@ -3346,9 +3408,10 @@ void lammps_gather_subset(void *handle, char *name,
requirement for consecutive atom IDs (1 to N) requirement for consecutive atom IDs (1 to N)
see scatter_subset() to scatter data for some (or all) atoms, unordered see scatter_subset() to scatter data for some (or all) atoms, unordered
name = "x" , "f" or other atom properties name = "x" , "f" or other atom properties
"d_name" or "i_name" for fix property/atom quantities "f_fix", "c_compute" for fixes / computes
"f_fix", "c_compute" for fixes / computes "d_name" or "i_name" for fix property/atom vectors with count = 1
will return error if fix/compute doesn't isn't atom-based "d2_name" or "i2_name" for fix property/atom arrays with count > 1
will return error if fix/compute isn't atom-based
type = 0 for integer values, 1 for double values type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" if want single image flag unpacked into xyz use count = 3 with "image" if want single image flag unpacked into xyz
@ -3372,7 +3435,7 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data)
lmp->error->all(FLERR,"Library function lammps_scatter() " lmp->error->all(FLERR,"Library function lammps_scatter() "
"is not compatible with -DLAMMPS_BIGBIG"); "is not compatible with -DLAMMPS_BIGBIG");
#else #else
int i,j,m,offset,fcid,ltype; int i,j,m,offset,fcid,ltype,icol;
// error if tags are not defined or not consecutive or no atom map // error if tags are not defined or not consecutive or no atom map
// NOTE: test that name = image or ids is not a 64-bit int in code? // NOTE: test that name = image or ids is not a 64-bit int in code?
@ -3389,10 +3452,11 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data)
} }
int natoms = static_cast<int> (lmp->atom->natoms); int natoms = static_cast<int> (lmp->atom->natoms);
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr==nullptr && strstr(name,"f_") == name) { // fix // fix
if (vptr==nullptr && strstr(name,"f_") == name) {
fcid = lmp->modify->find_fix(&name[2]); fcid = lmp->modify->find_fix(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -3418,7 +3482,9 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data)
else vptr = (void *) lmp->modify->fix[fcid]->array_atom; else vptr = (void *) lmp->modify->fix[fcid]->array_atom;
} }
if (vptr==nullptr && strstr(name,"c_") == name) { // compute // compute
if (vptr==nullptr && strstr(name,"c_") == name) {
fcid = lmp->modify->find_compute(&name[2]); fcid = lmp->modify->find_compute(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -3445,31 +3511,46 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data)
if (count==1) vptr = (void *) lmp->modify->compute[fcid]->vector_atom; if (count==1) vptr = (void *) lmp->modify->compute[fcid]->vector_atom;
else vptr = (void *) lmp->modify->compute[fcid]->array_atom; else vptr = (void *) lmp->modify->compute[fcid]->array_atom;
} }
if (vptr==nullptr && strstr(name,"d_") == name) { // property / atom // property/atom
if ((vptr == nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
fcid = lmp->atom->find_custom(&name[2], ltype); if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) { if (fcid < 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_scatter: unknown property/atom id"); lmp->error->warning(FLERR,"lammps_scatter: unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom type"); lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom type");
return; return;
} }
if (count != 1) { if (count == 1 && icol != 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_scatter: property/atom has count=1"); lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom count");
return;
}
if (count > 1 && icol != count) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_scatter: mismatch property/atom count");
return; return;
} }
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
if (count == 1) {
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
} else {
if (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
} }
if (vptr == nullptr) { if (vptr == nullptr) {
@ -3548,7 +3629,10 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data)
data is ordered by provided atom IDs data is ordered by provided atom IDs
no requirement for consecutive atom IDs (1 to N) no requirement for consecutive atom IDs (1 to N)
see scatter_atoms() to scatter data for all atoms, ordered by consecutive IDs see scatter_atoms() to scatter data for all atoms, ordered by consecutive IDs
name = desired quantity, e.g. x or charge name = "x" , "f" or other atom properties
"d_name" or "i_name" for fix property/atom quantities
"f_fix", "c_compute" for fixes / computes
will return error if fix/compute doesn't isn't atom-based
type = 0 for integer values, 1 for double values type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" for xyz to be packed into single image flag use count = 3 with "image" for xyz to be packed into single image flag
@ -3572,7 +3656,7 @@ void lammps_scatter_subset(void *handle, char *name,int type, int count,
lmp->error->all(FLERR,"Library function lammps_scatter_subset() " lmp->error->all(FLERR,"Library function lammps_scatter_subset() "
"is not compatible with -DLAMMPS_BIGBIG"); "is not compatible with -DLAMMPS_BIGBIG");
#else #else
int i,j,m,offset,fcid,ltype; int i,j,m,offset,fcid,ltype,icol;
tagint id; tagint id;
// error if tags are not defined or no atom map // error if tags are not defined or no atom map
@ -3590,7 +3674,9 @@ void lammps_scatter_subset(void *handle, char *name,int type, int count,
void *vptr = lmp->atom->extract(name); void *vptr = lmp->atom->extract(name);
if (vptr==nullptr && strstr(name,"f_") == name) { // fix // fix
if (vptr==nullptr && strstr(name,"f_") == name) {
fcid = lmp->modify->find_fix(&name[2]); fcid = lmp->modify->find_fix(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -3616,7 +3702,9 @@ void lammps_scatter_subset(void *handle, char *name,int type, int count,
else vptr = (void *) lmp->modify->fix[fcid]->array_atom; else vptr = (void *) lmp->modify->fix[fcid]->array_atom;
} }
if (vptr==nullptr && strstr(name,"c_") == name) { // compute // compute
if (vptr==nullptr && strstr(name,"c_") == name) {
fcid = lmp->modify->find_compute(&name[2]); fcid = lmp->modify->find_compute(&name[2]);
if (fcid < 0) { if (fcid < 0) {
@ -3645,29 +3733,46 @@ void lammps_scatter_subset(void *handle, char *name,int type, int count,
else vptr = (void *) lmp->modify->compute[fcid]->array_atom; else vptr = (void *) lmp->modify->compute[fcid]->array_atom;
} }
if (vptr==nullptr && strstr(name,"d_") == name) { // property / atom // property/atom
if ((vptr == nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
fcid = lmp->atom->find_custom(&name[2], ltype); if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) { if (fcid < 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_scatter_subset: " lmp->error->warning(FLERR,"lammps_scatter_subset: "
"unknown property/atom id"); "unknown property/atom id");
return; return;
} }
if (ltype != type) { if (ltype != type) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_scatter_subset: " lmp->error->warning(FLERR,"lammps_scatter_subset: "
"mismatch property/atom type"); "mismatch property/atom type");
return; return;
} }
if (count != 1) { if (count == 1 && icol != 0) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_scatter_subset: " lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
"property/atom has count=1");
return; return;
} }
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid]; if (count > 1 && icol != count) {
else vptr = (void *) lmp->atom->dvector[fcid]; if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather: mismatch property/atom count");
return;
}
if (count == 1) {
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
} else {
if (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
} }
if (vptr == nullptr) { if (vptr == nullptr) {

8
src/set.cpp
View File

@ -579,8 +579,8 @@ void Set::command(int narg, char **arg)
int which = 0; int which = 0;
if (arg[iarg][0] == 'd') which = 1; if (arg[iarg][0] == 'd') which = 1;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else if (!which) ivalue = force->inumeric(FLERR,arg[iarg+1]); else if (!which) ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
else dvalue = force->numeric(FLERR,arg[iarg+1]); else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
int flag,cols; int flag,cols;
index_custom = atom->find_custom(&arg[iarg][2],flag,cols); index_custom = atom->find_custom(&arg[iarg][2],flag,cols);
@ -599,8 +599,8 @@ void Set::command(int narg, char **arg)
int which = 0; int which = 0;
if (arg[iarg][0] == 'd') which = 1; if (arg[iarg][0] == 'd') which = 1;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else if (!which) ivalue = force->inumeric(FLERR,arg[iarg+1]); else if (!which) ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
else dvalue = force->numeric(FLERR,arg[iarg+1]); else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
int n = strlen(arg[iarg]); int n = strlen(arg[iarg]);
char *suffix = new char[n]; char *suffix = new char[n];

5
src/utils.cpp
View File

@ -13,6 +13,7 @@
#include "utils.h" #include "utils.h"
#include "atom.h"
#include "comm.h" #include "comm.h"
#include "compute.h" #include "compute.h"
#include "error.h" #include "error.h"
@ -503,7 +504,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg,
} else if (arg[iarg][0] == 'i') { } else if (arg[iarg][0] == 'i') {
*ptr1 = '\0'; *ptr1 = '\0';
int flag,cols; int flag,cols;
int icustom = atom->find_custom(&arg[iarg][3],flag,cols); int icustom = lmp->atom->find_custom(&arg[iarg][3],flag,cols);
*ptr1 = '['; *ptr1 = '[';
// check for custom per-atom integer array // check for custom per-atom integer array
@ -518,7 +519,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg,
} else if (arg[iarg][0] == 'd') { } else if (arg[iarg][0] == 'd') {
*ptr1 = '\0'; *ptr1 = '\0';
int flag,cols; int flag,cols;
int icustom = atom->find_custom(&arg[iarg][3],flag,cols); int icustom = lmp->atom->find_custom(&arg[iarg][3],flag,cols);
*ptr1 = '['; *ptr1 = '[';
// check for custom per-atom floating point array // check for custom per-atom floating point array