tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update code

Browse Source
This commit is contained in:
Axel Kohlmeyer
2021-08-18 18:06:21 -04:00
parent f6874af7e5
commit b19a211d70
3 changed files with 101 additions and 145 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
src/atom.cpp
View File

@ -2774,13 +2774,10 @@ void *Atom::extract(const char *name)
// --------------------------------------------------------------------
// custom vectors and arrays
// OLDSTYLE code
if (strstr(name,"i_") == name || strstr(name,"d_") == name ||
strstr(name,"i2_") == name || strstr(name,"d2_") == name) {
int which = 0;
if (utils::strmatch(name,"^[id]2?_")) {
int which = 0, array = 0;
if (name[0] == 'd') which = 1;
int array = 0;
if (name[1] == '2') array = 1;
int index,flag,cols;
@ -2897,13 +2894,10 @@ int Atom::extract_datatype(const char *name)
// --------------------------------------------------------------------
// custom vectors and arrays
// OLDSTYLE code
if (strstr(name,"i_") == name || strstr(name,"d_") == name ||
strstr(name,"i2_") == name || strstr(name,"d2_") == name) {
int which = 0;
if (utils::strmatch(name,"^[id]2?_")) {
int which = 0, array = 0;
if (name[0] == 'd') which = 1;
int array = 0;
if (name[1] == '2') array = 1;
int index,flag,cols;

84
src/compute_property_atom.cpp
View File

@ -14,6 +14,7 @@
#include "compute_property_atom.h"
#include "arg_info.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_body.h"
@ -333,55 +334,52 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Compute property/atom for atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_nbonds;
// custom per-atom vector
// custom per-atom vector or array
} else if (utils::strmatch(arg[iarg],"^i_")) {
} else if (utils::strmatch(arg[iarg],"^[id]2?_")) {
int flag,cols;
index[i] = atom->find_custom(&arg[iarg][2],flag,cols);
if (index[i] < 0 || flag || cols)
error->all(FLERR,"Compute property/atom integer "
"vector does not exist");
pack_choice[i] = &ComputePropertyAtom::pack_iname;
ArgInfo argi(arg[iarg], ArgInfo::INAME| ArgInfo::DNAME);
const char *pname = argi.get_name();
} else if (utils::strmatch(arg[iarg],"^d_")) {
int flag,cols;
index[i] = atom->find_custom(&arg[iarg][2],flag,cols);
if (index[i] < 0 || flag || cols)
error->all(FLERR,"Compute property/atom floating point "
"vector does not exist");
pack_choice[i] = &ComputePropertyAtom::pack_dname;
index[i] = atom->find_custom(pname,flag,cols);
if (index[i] < 0)
error->all(FLERR,"Compute property/atom property {} does not exist", pname);
// custom per-atom arrays, must include bracketed index
// OLDSTYLE code
// handle vectors
if ((cols == 0) && (arg[iarg][1] == '_')) {
if (argi.get_dim() != 0)
error->all(FLERR,"Compute property/atom custom vector {} is incorrectly indexed",pname);
} else if (strstr(arg[iarg],"i2_") == arg[iarg] ||
strstr(arg[iarg],"d2_") == arg[iarg]) {
int which = 0;
if (arg[iarg][0] == 'd') which = 1;
if (arg[iarg][0] == 'i') {
if (argi.get_type() == ArgInfo::INAME)
pack_choice[i] = &ComputePropertyAtom::pack_iname;
else
error->all(FLERR,"Compute property/atom integer vector {} does not exist",pname);
} else if (arg[iarg][0] == 'd') {
if (argi.get_type() == ArgInfo::DNAME)
pack_choice[i] = &ComputePropertyAtom::pack_dname;
else
error->all(FLERR,"Compute property/atom floating-point vector {} does not exist",pname);
}
}
// handle arrays
else if ((cols > 0) && (arg[iarg][1] == '2')) {
if (argi.get_dim() != 1)
error->all(FLERR,"Compute property/atom custom array {} is not indexed",pname);
colindex[i] = argi.get_index1();
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][3]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Invalid attribute in set command");
suffix[strlen(suffix)-1] = '\0';
colindex[i] = utils::inumeric(FLERR,ptr+1,true,lmp);
*ptr = '\0';
} else error->all(FLERR,"Compute property/atom custom array is not indexed");
int flag,cols;
index[i] = atom->find_custom(suffix,flag,cols);
delete [] suffix;
if ((!which && (index[i] < 0 || flag || !cols)) ||
(which && (index[i] < 0 || !flag || !cols)))
error->all(FLERR,"Compute property/atom custom array does not exist");
if (!which) pack_choice[i] = &ComputePropertyAtom::pack_i2name;
else pack_choice[i] = &ComputePropertyAtom::pack_d2name;
if (arg[iarg][0] == 'i') {
if (argi.get_type() == ArgInfo::INAME)
pack_choice[i] = &ComputePropertyAtom::pack_i2name;
else
error->all(FLERR,"Compute property/atom integer array {} does not exist",pname);
} else if (arg[iarg][0] == 'd') {
if (argi.get_type() == ArgInfo::DNAME)
pack_choice[i] = &ComputePropertyAtom::pack_d2name;
else
error->all(FLERR,"Compute property/atom floating-point array {} does not exist",pname);
}
} else error->all(FLERR,"Inconsistent request for custom property {}", pname);
// anything else must be recognized by atom style

148
src/library.cpp
View File

@ -2829,7 +2829,7 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
{
#if defined(LAMMPS_BIGBIG)
lmp->error->all(FLERR,"Library function lammps_gather"
" not compatible with -DLAMMPS_BIGBIG");
" not compatible with -DLAMMPS_BIGBIG");
#else
int i,j,offset,fcid,ltype,icol;
@ -2915,14 +2915,10 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
}
// custom fix property/atom vector or array
// OLDSTYLE code
if ((vptr == nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) {
if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
if (utils::strmatch(name,"^[id]_")) fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) {
@ -2948,11 +2944,11 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
}
if (count == 1) {
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
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 (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
}
@ -2960,7 +2956,7 @@ void lammps_gather(void *handle, char *name, int type, int count, void *data)
if (vptr == nullptr) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather: undefined property name");
lmp->error->warning(FLERR,"lammps_gather: undefined property name");
return;
}
@ -3104,20 +3100,17 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
if (lmp->modify->fix[fcid]->peratom_flag == 0) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat:"
" fix does not return peratom data");
lmp->error->warning(FLERR,"lammps_gather_concat: fix does not return peratom data");
return;
}
if (count>1 && lmp->modify->fix[fcid]->size_peratom_cols != count) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat:"
" count != values peratom for fix");
lmp->error->warning(FLERR,"lammps_gather_concat: count != values peratom for fix");
return;
}
if (lmp->update->ntimestep % lmp->modify->fix[fcid]->peratom_freq) {
if (lmp->comm->me == 0)
lmp->error->all(FLERR,"lammps_gather_concat:"
" fix not computed at compatible time");
lmp->error->all(FLERR,"lammps_gather_concat: fix not computed at compatible time");
return;
}
@ -3138,14 +3131,12 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
if (lmp->modify->compute[fcid]->peratom_flag == 0) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat:"
" compute does not return peratom data");
lmp->error->warning(FLERR,"lammps_gather_concat: compute does not return peratom data");
return;
}
if (count>1 && lmp->modify->compute[fcid]->size_peratom_cols != count) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat:"
" count != values peratom for compute");
lmp->error->warning(FLERR,"lammps_gather_concat: count != values peratom for compute");
return;
}
@ -3157,48 +3148,40 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
}
// custom per-atom vector or array
// OLDSTYLE code
if ((vptr==nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
if ((vptr==nullptr) && utils::strmatch(name,"^[id]2?_")) {
if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
if (utils::strmatch(name,"^[id]_")) fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat: "
"unknown property/atom id");
lmp->error->warning(FLERR,"lammps_gather_concat: unknown property/atom id");
return;
}
if (ltype != type) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat: "
"mismatch property/atom type");
lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom type");
return;
}
if (count == 1 && icol != 0) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat: "
"mismatch property/atom count");
lmp->error->warning(FLERR,"lammps_gather_concat: 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");
lmp->error->warning(FLERR,"lammps_gather_concat: mismatch property/atom count");
return;
}
if (count == 1) {
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
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 (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
}
@ -3206,7 +3189,7 @@ void lammps_gather_concat(void *handle, char *name, int type, int count, void *d
if (vptr == nullptr) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_concat: undefined property name");
lmp->error->warning(FLERR,"lammps_gather_concat: undefined property name");
return;
}
@ -3375,14 +3358,12 @@ void lammps_gather_subset(void *handle, char *name,
return;
}
if (count>1 && lmp->modify->fix[fcid]->size_peratom_cols != count) {
lmp->error->warning(FLERR,"lammps_gather_subset:"
" count != values peratom for fix");
lmp->error->warning(FLERR,"lammps_gather_subset: count != values peratom for fix");
return;
}
if (lmp->update->ntimestep % lmp->modify->fix[fcid]->peratom_freq) {
if (lmp->comm->me == 0)
lmp->error->all(FLERR,"lammps_gather_subset:"
" fix not computed at compatible time");
lmp->error->all(FLERR,"lammps_gather_subset: fix not computed at compatible time");
return;
}
@ -3403,14 +3384,12 @@ void lammps_gather_subset(void *handle, char *name,
if (lmp->modify->compute[fcid]->peratom_flag == 0) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset:"
" compute does not return peratom data");
lmp->error->warning(FLERR,"lammps_gather_subset: compute does not return peratom data");
return;
}
if (count>1 && lmp->modify->compute[fcid]->size_peratom_cols != count) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset:"
" count != values peratom for compute");
lmp->error->warning(FLERR,"lammps_gather_subset: count != values peratom for compute");
return;
}
@ -3422,48 +3401,41 @@ void lammps_gather_subset(void *handle, char *name,
}
// custom fix property/atom vector or array
// OLDSTYLE code
if ((vptr == nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) {
if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
if (utils::strmatch(name,"^[id]_"))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: "
"unknown property/atom id");
lmp->error->warning(FLERR,"lammps_gather_subset: unknown property/atom id");
return;
}
if (ltype != type) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: "
"mismatch property/atom type");
lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom type");
return;
}
if (count == 1 && icol != 0) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: "
"mismatch property/atom count");
lmp->error->warning(FLERR,"lammps_gather_subset: mismatch property/atom count");
return;
}
if (count > 1 && icol != count) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: "
"mismatch property/atom count");
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];
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 (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
}
@ -3471,7 +3443,7 @@ void lammps_gather_subset(void *handle, char *name,
if (vptr == nullptr) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_gather_subset: undefined property name");
lmp->error->warning(FLERR,"lammps_gather_subset: undefined property name");
return;
}
@ -3678,14 +3650,11 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data)
}
// custom fix property/atom vector or array
// OLDSTYLE code
if ((vptr == nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) {
if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
if (utils::strmatch(name,"^[id]_"))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) {
@ -3711,11 +3680,11 @@ void lammps_scatter(void *handle, char *name, int type, int count, void *data)
}
if (count == 1) {
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
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 (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
}
@ -3902,27 +3871,22 @@ void lammps_scatter_subset(void *handle, char *name,int type, int count,
}
// custom fix property/atom vector or array
// OLDSTYLE code
if ((vptr == nullptr) &&
((strstr(name,"d_") == name) || (strstr(name,"i_") == name) ||
(strstr(name,"d2_") == name) || (strstr(name,"i2_") == name))) {
if ((vptr == nullptr) && utils::strmatch(name,"^[id]2?_")) {
if ((strstr(name,"d_") == name) || (strstr(name,"i_") == name))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
if (utils::strmatch(name,"^[id]_"))
fcid = lmp->atom->find_custom(&name[2],ltype,icol);
else fcid = lmp->atom->find_custom(&name[3],ltype,icol);
if (fcid < 0) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_scatter_subset: "
"unknown property/atom id");
lmp->error->warning(FLERR,"lammps_scatter_subset: unknown property/atom id");
return;
}
if (ltype != type) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"lammps_scatter_subset: "
"mismatch property/atom type");
lmp->error->warning(FLERR,"lammps_scatter_subset: mismatch property/atom type");
return;
}
if (count == 1 && icol != 0) {
@ -3937,11 +3901,11 @@ void lammps_scatter_subset(void *handle, char *name,int type, int count,
}
if (count == 1) {
if (ltype==0) vptr = (void *) lmp->atom->ivector[fcid];
else vptr = (void *) lmp->atom->dvector[fcid];
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 (ltype==0) vptr = (void *) lmp->atom->iarray[fcid];
else vptr = (void *) lmp->atom->darray[fcid];
}
}