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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14163 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2015-10-22 21:48:05 +00:00
parent 1eeeb028f9
commit b229c719d0
6 changed files with 160 additions and 70 deletions
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105
src/read_data.cpp
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@ -279,7 +279,7 @@ void ReadData::command(int narg, char **arg)
// -----------------------------------------------------------------
// perform 1-pass read if no molecular topoogy in file
// perform 1-pass read if no molecular topology in file
// perform 2-pass read if molecular topology,
// first pass calculates max topology/atom
@ -301,7 +301,7 @@ void ReadData::command(int narg, char **arg)
triclinic = 0;
keyword[0] = '\0';
int nlocal_previous = atom->nlocal;
nlocal_previous = atom->nlocal;
int firstpass = 1;
while (1) {
@ -315,7 +315,7 @@ void ReadData::command(int narg, char **arg)
// read header info
header();
header(firstpass);
// problem setup using info from header
// only done once, if firstpass and first data file
@ -648,7 +648,7 @@ void ReadData::command(int narg, char **arg)
// will also observe extra settings even if bond/etc topology not in file
// leaves other atom arrays unchanged, since already nmax in length
atom->deallocate_topology();
if (addflag == NONE) atom->deallocate_topology();
atom->avec->grow(atom->nmax);
}
@ -788,7 +788,7 @@ void ReadData::command(int narg, char **arg)
some logic differs if adding atoms
------------------------------------------------------------------------- */
void ReadData::header()
void ReadData::header(int firstpass)
{
int n;
char *ptr;
@ -856,7 +856,7 @@ void ReadData::header()
if (strstr(line,"atoms")) {
sscanf(line,BIGINT_FORMAT,&natoms);
if (addflag == NONE) atom->natoms = natoms;
else atom->natoms += natoms;
else if (firstpass) atom->natoms += natoms;
// check for these first
// otherwise "triangles" will be matched as "angles"
@ -1093,6 +1093,8 @@ void ReadData::velocities()
void ReadData::bonds(int firstpass)
{
int nchunk,eof;
if (me == 0) {
if (firstpass) {
if (screen) fprintf(screen," scanning bonds ...\n");
@ -1114,32 +1116,38 @@ void ReadData::bonds(int firstpass)
// read and process bonds
int nchunk,eof;
bigint nread = 0;
bigint nbonds = atom->nbonds;
while (nread < nbonds) {
nchunk = MIN(nbonds-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_bonds(nchunk,buffer,count,id_offset);
atom->data_bonds(nchunk,buffer,count,id_offset,boffset);
nread += nchunk;
}
// if firstpass: tally max bond/atom and return
// if addflag = NONE, store max bond/atom with extra
// else just check actual max does not exceed existing max
if (firstpass) {
int max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]);
for (int i = nlocal_previous; i < nlocal; i++) max = MAX(max,count[i]);
int maxall;
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
maxall += atom->extra_bond_per_atom;
if (addflag == NONE) maxall += atom->extra_bond_per_atom;
if (me == 0) {
if (screen) fprintf(screen," %d = max bonds/atom\n",maxall);
if (logfile) fprintf(logfile," %d = max bonds/atom\n",maxall);
}
atom->bond_per_atom = maxall;
if (addflag != NONE) {
if (maxall > atom->bond_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many bonds per atom");
} else atom->bond_per_atom = maxall;
memory->destroy(count);
return;
}
@ -1147,7 +1155,7 @@ void ReadData::bonds(int firstpass)
// if 2nd pass: check that bonds were assigned correctly
bigint n = 0;
for (int i = 0; i < nlocal; i++) n += atom->num_bond[i];
for (int i = nlocal_previous; i < nlocal; i++) n += atom->num_bond[i];
bigint sum;
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
@ -1158,7 +1166,7 @@ void ReadData::bonds(int firstpass)
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",sum/factor);
}
if (sum != factor*atom->nbonds)
if (sum != factor*nbonds)
error->all(FLERR,"Bonds assigned incorrectly");
}
@ -1168,6 +1176,8 @@ void ReadData::bonds(int firstpass)
void ReadData::angles(int firstpass)
{
int nchunk,eof;
if (me == 0) {
if (firstpass) {
if (screen) fprintf(screen," scanning angles ...\n");
@ -1189,32 +1199,38 @@ void ReadData::angles(int firstpass)
// read and process angles
int nchunk,eof;
bigint nread = 0;
bigint nangles = atom->nangles;
while (nread < nangles) {
nchunk = MIN(nangles-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_angles(nchunk,buffer,count,id_offset);
atom->data_angles(nchunk,buffer,count,id_offset,aoffset);
nread += nchunk;
}
// if firstpass: tally max angle/atom and return
// if addflag = NONE, store max angle/atom with extra
// else just check actual max does not exceed existing max
if (firstpass) {
int max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]);
for (int i = nlocal_previous; i < nlocal; i++) max = MAX(max,count[i]);
int maxall;
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
maxall += atom->extra_angle_per_atom;
if (addflag == NONE) maxall += atom->extra_angle_per_atom;
if (me == 0) {
if (screen) fprintf(screen," %d = max angles/atom\n",maxall);
if (logfile) fprintf(logfile," %d = max angles/atom\n",maxall);
}
atom->angle_per_atom = maxall;
if (addflag != NONE) {
if (maxall > atom->angle_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many angles per atom");
} else atom->angle_per_atom = maxall;
memory->destroy(count);
return;
}
@ -1222,7 +1238,7 @@ void ReadData::angles(int firstpass)
// if 2nd pass: check that angles were assigned correctly
bigint n = 0;
for (int i = 0; i < nlocal; i++) n += atom->num_angle[i];
for (int i = nlocal_previous; i < nlocal; i++) n += atom->num_angle[i];
bigint sum;
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
@ -1233,7 +1249,7 @@ void ReadData::angles(int firstpass)
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",sum/factor);
}
if (sum != factor*atom->nangles)
if (sum != factor*nangles)
error->all(FLERR,"Angles assigned incorrectly");
}
@ -1243,6 +1259,8 @@ void ReadData::angles(int firstpass)
void ReadData::dihedrals(int firstpass)
{
int nchunk,eof;
if (me == 0) {
if (firstpass) {
if (screen) fprintf(screen," scanning dihedrals ...\n");
@ -1264,31 +1282,38 @@ void ReadData::dihedrals(int firstpass)
// read and process dihedrals
int nchunk,eof;
bigint nread = 0;
bigint ndihedrals = atom->ndihedrals;
while (nread < ndihedrals) {
nchunk = MIN(ndihedrals-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_dihedrals(nchunk,buffer,count,id_offset);
atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset);
nread += nchunk;
}
// if firstpass: tally max dihedral/atom and return
// if addflag = NONE, store max dihedral/atom with extra
// else just check actual max does not exceed existing max
if (firstpass) {
int max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]);
int maxall;
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
maxall += atom->extra_dihedral_per_atom;
if (addflag == NONE) maxall += atom->extra_dihedral_per_atom;
if (me == 0) {
if (screen) fprintf(screen," %d = max dihedrals/atom\n",maxall);
if (logfile) fprintf(logfile," %d = max dihedrals/atom\n",maxall);
}
if (addflag != NONE) {
if (maxall > atom->dihedral_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many dihedrals per atom");
} else atom->dihedral_per_atom = maxall;
atom->dihedral_per_atom = maxall;
memory->destroy(count);
return;
@ -1297,7 +1322,7 @@ void ReadData::dihedrals(int firstpass)
// if 2nd pass: check that dihedrals were assigned correctly
bigint n = 0;
for (int i = 0; i < nlocal; i++) n += atom->num_dihedral[i];
for (int i = nlocal_previous; i < nlocal; i++) n += atom->num_dihedral[i];
bigint sum;
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
@ -1308,7 +1333,7 @@ void ReadData::dihedrals(int firstpass)
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",sum/factor);
}
if (sum != factor*atom->ndihedrals)
if (sum != factor*ndihedrals)
error->all(FLERR,"Dihedrals assigned incorrectly");
}
@ -1318,6 +1343,8 @@ void ReadData::dihedrals(int firstpass)
void ReadData::impropers(int firstpass)
{
int nchunk,eof;
if (me == 0) {
if (firstpass) {
if (screen) fprintf(screen," scanning impropers ...\n");
@ -1339,32 +1366,38 @@ void ReadData::impropers(int firstpass)
// read and process impropers
int nchunk,eof;
bigint nread = 0;
bigint nimpropers = atom->nimpropers;
while (nread < nimpropers) {
nchunk = MIN(nimpropers-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_impropers(nchunk,buffer,count,id_offset);
atom->data_impropers(nchunk,buffer,count,id_offset,ioffset);
nread += nchunk;
}
// if firstpass: tally max improper/atom and return
// if addflag = NONE, store max improper/atom
// else just check it does not exceed existing max
if (firstpass) {
int max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]);
for (int i = nlocal_previous; i < nlocal; i++) max = MAX(max,count[i]);
int maxall;
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
maxall += atom->extra_improper_per_atom;
if (addflag == NONE) maxall += atom->extra_improper_per_atom;
if (me == 0) {
if (screen) fprintf(screen," %d = max impropers/atom\n",maxall);
if (logfile) fprintf(logfile," %d = max impropers/atom\n",maxall);
}
atom->improper_per_atom = maxall;
if (addflag != NONE) {
if (maxall > atom->improper_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many impropers per atom");
} else atom->improper_per_atom = maxall;
memory->destroy(count);
return;
}
@ -1372,7 +1405,7 @@ void ReadData::impropers(int firstpass)
// if 2nd pass: check that impropers were assigned correctly
bigint n = 0;
for (int i = 0; i < nlocal; i++) n += atom->num_improper[i];
for (int i = nlocal_previous; i < nlocal; i++) n += atom->num_improper[i];
bigint sum;
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
@ -1383,7 +1416,7 @@ void ReadData::impropers(int firstpass)
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",sum/factor);
}
if (sum != factor*atom->nimpropers)
if (sum != factor*nimpropers)
error->all(FLERR,"Impropers assigned incorrectly");
}