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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10324 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-07-24 15:58:48 +00:00
parent ab1488daba
commit 5b0af4dedb
3 changed files with 118 additions and 247 deletions
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332
src/read_data.cpp
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@ -164,7 +164,7 @@ void ReadData::command(int narg, char **arg)
if (me == 0) {
if (screen) fprintf(screen,"Reading data file ...\n");
open(arg[0]);
}
} else fp = NULL;
header(1);
domain->box_exist = 1;
@ -561,28 +561,15 @@ void ReadData::header(int flag)
void ReadData::atoms()
{
int i,m,nchunk;
int i,m,nchunk,eof;
bigint nread = 0;
bigint natoms = atom->natoms;
while (nread < natoms) {
if (natoms-nread > CHUNK) nchunk = CHUNK;
else nchunk = natoms-nread;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
m++;
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_atoms(nchunk,buffer);
nread += nchunk;
}
@ -646,7 +633,7 @@ void ReadData::atoms()
void ReadData::velocities()
{
int i,m,nchunk;
int i,m,nchunk,eof;
int mapflag = 0;
if (atom->map_style == 0) {
@ -660,22 +647,9 @@ void ReadData::velocities()
bigint natoms = atom->natoms;
while (nread < natoms) {
if (natoms-nread > CHUNK) nchunk = CHUNK;
else nchunk = natoms-nread;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
m++;
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_vels(nchunk,buffer);
nread += nchunk;
}
@ -698,7 +672,7 @@ void ReadData::velocities()
void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
{
int i,m,nchunk;
int i,m,nchunk,eof;
int mapflag = 0;
if (atom->map_style == 0) {
@ -712,22 +686,9 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
bigint natoms = nbonus;
while (nread < natoms) {
if (natoms-nread > CHUNK) nchunk = CHUNK;
else nchunk = natoms-nread;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
m++;
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_bonus(nchunk,buffer,ptr);
nread += nchunk;
}
@ -763,14 +724,13 @@ void ReadData::bodies()
}
// nmax = max # of bodies to read in this chunk
// nchunk = actual # readr
// nchunk = actual # read
bigint nread = 0;
bigint natoms = nbodies;
while (nread < natoms) {
if (natoms-nread > CHUNK) nmax = CHUNK;
else nmax = natoms-nread;
nchunk = MIN(natoms-nread,CHUNK);
if (me == 0) {
nchunk = 0;
@ -827,27 +787,17 @@ void ReadData::bodies()
void ReadData::bonds()
{
int i,m,nchunk;
int i,m,nchunk,eof;
bigint nread = 0;
bigint nbonds = atom->nbonds;
bigint natoms = atom->natoms;
while (nread < nbonds) {
nchunk = MIN(nbonds-nread,CHUNK);
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
m++;
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
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);
nread += nchunk;
}
@ -874,27 +824,15 @@ void ReadData::bonds()
void ReadData::angles()
{
int i,m,nchunk;
int i,m,nchunk,eof;
bigint nread = 0;
bigint nangles = atom->nangles;
while (nread < nangles) {
nchunk = MIN(nangles-nread,CHUNK);
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
m++;
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
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);
nread += nchunk;
}
@ -921,27 +859,15 @@ void ReadData::angles()
void ReadData::dihedrals()
{
int i,m,nchunk;
int i,m,nchunk,eof;
bigint nread = 0;
bigint ndihedrals = atom->ndihedrals;
while (nread < ndihedrals) {
nchunk = MIN(ndihedrals-nread,CHUNK);
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
m++;
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
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);
nread += nchunk;
}
@ -968,27 +894,15 @@ void ReadData::dihedrals()
void ReadData::impropers()
{
int i,m,nchunk;
int i,m,nchunk,eof;
bigint nread = 0;
bigint nimpropers = atom->nimpropers;
while (nread < nimpropers) {
nchunk = MIN(nimpropers-nread,CHUNK);
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
m++;
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
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);
nread += nchunk;
}
@ -1016,25 +930,16 @@ void ReadData::impropers()
void ReadData::mass()
{
int i,m;
char *next;
char *buf = new char[atom->ntypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->ntypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->ntypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->ntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
atom->set_mass(buf);
buf += strlen(buf) + 1;
}
@ -1046,25 +951,16 @@ void ReadData::mass()
void ReadData::paircoeffs()
{
int i,m;
char *next;
char *buf = new char[atom->ntypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->ntypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->ntypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->ntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
m = strlen(buf) + 1;
parse_coeffs(buf,NULL,1);
force->pair->coeff(narg,arg);
@ -1078,27 +974,19 @@ void ReadData::paircoeffs()
void ReadData::pairIJcoeffs()
{
int i,j,m;
char *buf = new char[atom->ntypes*(atom->ntypes+1)/2 * MAXLINE];
char *next;
int nsq = atom->ntypes* (atom->ntypes+1) / 2;
char *buf = new char[nsq * MAXLINE];
int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->ntypes; i++)
for (j = i; j < atom->ntypes; j++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->ntypes; i++)
for (j = i; j < atom->ntypes; j++) {
next = strchr(buf,'\n');
*next = '\0';
m = strlen(buf) + 1;
parse_coeffs(buf,NULL,0);
force->pair->coeff(narg,arg);
@ -1112,25 +1000,16 @@ void ReadData::pairIJcoeffs()
void ReadData::bondcoeffs()
{
int i,m;
char *next;
char *buf = new char[atom->nbondtypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->nbondtypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->nbondtypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->nbondtypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
m = strlen(buf) + 1;
parse_coeffs(buf,NULL,0);
force->bond->coeff(narg,arg);
@ -1144,25 +1023,16 @@ void ReadData::bondcoeffs()
void ReadData::anglecoeffs(int which)
{
int i,m;
char *next;
char *buf = new char[atom->nangletypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->nangletypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->nangletypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->nangletypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
m = strlen(buf) + 1;
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"bb",0);
@ -1178,25 +1048,16 @@ void ReadData::anglecoeffs(int which)
void ReadData::dihedralcoeffs(int which)
{
int i,m;
char *next;
char *buf = new char[atom->ndihedraltypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->ndihedraltypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->ndihedraltypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->ndihedraltypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
m = strlen(buf) + 1;
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"mbt",0);
@ -1215,25 +1076,16 @@ void ReadData::dihedralcoeffs(int which)
void ReadData::impropercoeffs(int which)
{
int i,m;
char *next;
char *buf = new char[atom->nimpropertypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->nimpropertypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->nimpropertypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buf[m]);
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->nimpropertypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
m = strlen(buf) + 1;
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"aa",0);
@ -1250,27 +1102,13 @@ void ReadData::impropercoeffs(int which)
void ReadData::fix(int ifix, char *line, bigint nlines)
{
int i,m,nchunk;
int i,m,nchunk,eof;
bigint nread = 0;
while (nread < nlines) {
if (nlines-nread > CHUNK) nchunk = CHUNK;
else nchunk = nlines-nread;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
m += strlen(&buffer[m]);
}
if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
m++;
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
nchunk = MIN(nlines-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
modify->fix[ifix]->read_data_section(line,nchunk,buffer);
nread += nchunk;
}