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add support for optionally including unit information in standard dump files

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This commit is contained in:
Axel Kohlmeyer
2019-09-12 14:37:42 -04:00
parent 4bbe4c73aa
commit e413aaf217
7 changed files with 51 additions and 24 deletions
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19
src/COMPRESS/dump_atom_gz.cpp
View File

@ -108,27 +108,26 @@ void DumpAtomGZ::openfile()
void DumpAtomGZ::write_header(bigint ndump)
{
if ((multiproc) || (!multiproc && me == 0)) {
if (unit_flag && !unit_count) {
++unit_count;
gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
}
gzprintf(gzFp,"ITEM: TIMESTEP\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
if (domain->triclinic == 0) {
gzprintf(gzFp,"ITEM: TIMESTEP\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
gzprintf(gzFp,"%g %g\n",boxxlo,boxxhi);
gzprintf(gzFp,"%g %g\n",boxylo,boxyhi);
gzprintf(gzFp,"%g %g\n",boxzlo,boxzhi);
gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
} else {
gzprintf(gzFp,"ITEM: TIMESTEP\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
gzprintf(gzFp,"%g %g %g\n",boxxlo,boxxhi,boxxy);
gzprintf(gzFp,"%g %g %g\n",boxylo,boxyhi,boxxz);
gzprintf(gzFp,"%g %g %g\n",boxzlo,boxzhi,boxyz);
gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
}
gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
}
}

19
src/COMPRESS/dump_custom_gz.cpp
View File

@ -108,27 +108,26 @@ void DumpCustomGZ::openfile()
void DumpCustomGZ::write_header(bigint ndump)
{
if ((multiproc) || (!multiproc && me == 0)) {
if (unit_flag && !unit_count) {
++unit_count;
gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
}
gzprintf(gzFp,"ITEM: TIMESTEP\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
if (domain->triclinic == 0) {
gzprintf(gzFp,"ITEM: TIMESTEP\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
} else {
gzprintf(gzFp,"ITEM: TIMESTEP\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
}
gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
}
}

11
src/dump.cpp
View File

@ -87,6 +87,8 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
buffer_flag = 0;
padflag = 0;
pbcflag = 0;
unit_flag = 0;
unit_count = 0;
delay_flag = 0;
maxfiles = -1;
@ -545,6 +547,8 @@ void Dump::openfile()
if (singlefile_opened) return;
if (multifile == 0) singlefile_opened = 1;
unit_count = 0;
// if one file per timestep, replace '*' with current timestep
char *filecurrent = filename;
@ -1119,6 +1123,13 @@ void Dump::modify_params(int narg, char **arg)
}
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) unit_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) unit_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else {
int n = modify_param(narg-iarg,&arg[iarg]);
if (n == 0) error->all(FLERR,"Illegal dump_modify command");

2
src/dump.h
View File

@ -75,6 +75,8 @@ class Dump : protected Pointers {
int sortcol; // 0 to sort on ID, 1-N on columns
int sortcolm1; // sortcol - 1
int sortorder; // ASCEND or DESCEND
int unit_flag; // 1 if dump should contain unit information
int unit_count; // # of times the unit information was written
int delay_flag; // 1 if delay output until delaystep
bigint delaystep;

10
src/dump_atom.cpp
View File

@ -209,7 +209,10 @@ void DumpAtom::header_binary_triclinic(bigint ndump)
void DumpAtom::header_item(bigint ndump)
{
fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
if (unit_flag && !unit_count) {
++unit_count;
fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
}
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
@ -225,7 +228,10 @@ void DumpAtom::header_item(bigint ndump)
void DumpAtom::header_item_triclinic(bigint ndump)
{
fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
if (unit_flag && !unit_count) {
++unit_count;
fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
}
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF ATOMS\n");

9
src/dump_custom.cpp
View File

@ -420,7 +420,10 @@ void DumpCustom::header_binary_triclinic(bigint ndump)
void DumpCustom::header_item(bigint ndump)
{
fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
if (unit_flag && !unit_count) {
++unit_count;
fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
}
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
@ -436,6 +439,10 @@ void DumpCustom::header_item(bigint ndump)
void DumpCustom::header_item_triclinic(bigint ndump)
{
if (unit_flag && !unit_count) {
++unit_count;
fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
}
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF ATOMS\n");

5
src/dump_local.cpp
View File

@ -256,7 +256,10 @@ int DumpLocal::modify_param(int narg, char **arg)
void DumpLocal::write_header(bigint ndump)
{
if (me == 0) {
fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
if (unit_flag && !unit_count) {
++unit_count;
fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style);
}
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF %s\n",label);