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more general tri support in dump atom and dump custom

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This commit is contained in:
Steve Plimpton
2023-09-06 10:11:04 -06:00
parent 4735534139
commit 1ab26e083a
3 changed files with 161 additions and 12 deletions
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147
src/dump_atom.cpp
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@ -36,6 +36,7 @@ DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) :
scale_flag = 1;
image_flag = 0;
triclinic_general = 0;
buffer_allow = 1;
buffer_flag = 1;
format_default = nullptr;
@ -90,12 +91,19 @@ void DumpAtom::init_style()
// setup function ptrs
if (scale_flag && triclinic_general)
error->all(FLERR,"Dump atom cannot use scale and triclinic/general settings");
if (binary && domain->triclinic == 0)
header_choice = &DumpAtom::header_binary;
else if (binary && triclinic_general == 1)
header_choice = &DumpAtom::header_binary_triclinic_general;
else if (binary && domain->triclinic == 1)
header_choice = &DumpAtom::header_binary_triclinic;
else if (!binary && domain->triclinic == 0)
header_choice = &DumpAtom::header_item;
else if (!binary && triclinic_general == 1)
header_choice = &DumpAtom::header_item_triclinic_general;
else if (!binary && domain->triclinic == 1)
header_choice = &DumpAtom::header_item_triclinic;
@ -103,10 +111,17 @@ void DumpAtom::init_style()
pack_choice = &DumpAtom::pack_scale_noimage;
else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0)
pack_choice = &DumpAtom::pack_scale_image;
else if (scale_flag == 0 && image_flag == 0 && triclinic_general == 1)
pack_choice = &DumpAtom::pack_noscale_noimage_triclinic_general;
else if (scale_flag == 0 && image_flag == 1 && triclinic_general == 1)
pack_choice = &DumpAtom::pack_noscale_image_triclinic_general;
else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1)
pack_choice = &DumpAtom::pack_scale_noimage_triclinic;
else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1)
pack_choice = &DumpAtom::pack_scale_image_triclinic;
else if (scale_flag == 0 && image_flag == 0)
pack_choice = &DumpAtom::pack_noscale_noimage;
else if (scale_flag == 0 && image_flag == 1)
@ -139,7 +154,14 @@ int DumpAtom::modify_param(int narg, char **arg)
image_flag = utils::logical(FLERR,arg[1],false,lmp);
for (auto &item : keyword_user) item.clear();
return 2;
} else if (strcmp(arg[0],"triclinic/general") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
triclinic_general = utils::logical(FLERR,arg[1],false,lmp);
if (triclinic_general && !domain->triclinic_general)
error->all(FLERR,"Dump_modify triclinic/general invalid b/c simulation box is not");
return 2;
}
return 0;
}
@ -306,6 +328,30 @@ void DumpAtom::header_binary_triclinic(bigint ndump)
/* ---------------------------------------------------------------------- */
void DumpAtom::header_binary_triclinic_general(bigint ndump)
{
header_format_binary();
fwrite(&update->ntimestep,sizeof(bigint),1,fp);
fwrite(&ndump,sizeof(bigint),1,fp);
int general_tri = 2;
fwrite(&general_tri,sizeof(int),1,fp);
fwrite(&domain->boundary[0][0],6*sizeof(int),1,fp);
fwrite(domain->avec,3*sizeof(double),1,fp);
fwrite(domain->bvec,3*sizeof(double),1,fp);
fwrite(domain->cvec,3*sizeof(double),1,fp);
fwrite(domain->boxlo,3*sizeof(double),1,fp);
header_unit_style_binary();
header_time_binary();
header_columns_binary();
if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);
else fwrite(&nprocs,sizeof(int),1,fp);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::header_item(bigint ndump)
{
if (unit_flag && !unit_count) {
@ -348,6 +394,32 @@ void DumpAtom::header_item_triclinic(bigint ndump)
/* ---------------------------------------------------------------------- */
void DumpAtom::header_item_triclinic_general(bigint ndump)
{
if (unit_flag && !unit_count) {
++unit_count;
fmt::print(fp,"ITEM: UNITS\n{}\n",update->unit_style);
}
if (time_flag) fmt::print(fp,"ITEM: TIME\n{:.16}\n",compute_time());
fmt::print(fp,"ITEM: TIMESTEP\n{}\n"
"ITEM: NUMBER OF ATOMS\n{}\n",
update->ntimestep, ndump);
fmt::print(fp,"ITEM: BOX BOUNDS abc origin {}\n"
"{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n"
"{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n"
"{:>1.16e} {:>1.16e} {:>1.16e} {:>1.16e}\n",
boundstr,
domain->avec[0],domain->avec[1],domain->avec[2],domain->boxlo[0],
domain->bvec[0],domain->bvec[1],domain->bvec[2],domain->boxlo[1],
domain->cvec[0],domain->cvec[1],domain->cvec[2],domain->boxlo[2]);
fmt::print(fp,"ITEM: ATOMS {}\n",columns);
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_scale_image(tagint *ids)
{
int m,n;
@ -406,6 +478,59 @@ void DumpAtom::pack_scale_noimage(tagint *ids)
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_noscale_image(tagint *ids)
{
int m,n;
tagint *tag = atom->tag;
int *type = atom->type;
imageint *image = atom->image;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = (image[i] & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMG2BITS) - IMGMAX;
if (ids) ids[n++] = tag[i];
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_noscale_noimage(tagint *ids)
{
int m,n;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
if (ids) ids[n++] = tag[i];
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_scale_image_triclinic(tagint *ids)
@ -466,7 +591,7 @@ void DumpAtom::pack_scale_noimage_triclinic(tagint *ids)
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_noscale_image(tagint *ids)
void DumpAtom::pack_noscale_image_triclinic_general(tagint *ids)
{
int m,n;
@ -477,14 +602,17 @@ void DumpAtom::pack_noscale_image(tagint *ids)
double **x = atom->x;
int nlocal = atom->nlocal;
double xtri[3];
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
domain->restricted_to_general_coords(x[i],xtri);
buf[m++] = xtri[0];
buf[m++] = xtri[1];
buf[m++] = xtri[2];
buf[m++] = (image[i] & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
buf[m++] = (image[i] >> IMG2BITS) - IMGMAX;
@ -494,7 +622,7 @@ void DumpAtom::pack_noscale_image(tagint *ids)
/* ---------------------------------------------------------------------- */
void DumpAtom::pack_noscale_noimage(tagint *ids)
void DumpAtom::pack_noscale_noimage_triclinic_general(tagint *ids)
{
int m,n;
@ -504,14 +632,17 @@ void DumpAtom::pack_noscale_noimage(tagint *ids)
double **x = atom->x;
int nlocal = atom->nlocal;
double xtri[3];
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
domain->restricted_to_general_coords(x[i],xtri);
buf[m++] = xtri[0];
buf[m++] = xtri[1];
buf[m++] = xtri[2];
if (ids) ids[n++] = tag[i];
}
}