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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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32
src/comm.cpp
View File

@ -1548,6 +1548,38 @@ void Comm::ring(int n, int nper, void *inbuf, int messtag,
memory->destroy(bufcopy);
}
/* ----------------------------------------------------------------------
proc 0 reads Nlines from file into buf and bcasts buf to all procs
caller allocates buf to max size needed
each line is terminated by newline, even if last line in file is not
return 0 if successful, 1 if get EOF error before read is complete
------------------------------------------------------------------------- */
int Comm::read_lines_from_file(FILE *fp, int nlines, int maxline, char *buf)
{
int m;
if (me == 0) {
m = 0;
for (int i = 0; i < nlines; i++) {
if (!fgets(&buf[m],maxline,fp)) {
m = 0;
break;
}
m += strlen(&buf[m]);
}
if (m) {
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
m++;
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
if (m == 0) return 1;
MPI_Bcast(buf,m,MPI_CHAR,0,world);
return 0;
}
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
if flag = 1, realloc

1
src/comm.h
View File

@ -63,6 +63,7 @@ class Comm : protected Pointers {
void ring(int, int, void *, int, void (*)(int, char *), // ring comm
void *, int self = 1);
int read_lines_from_file(FILE *, int, int, char *); // read/bcast file lines
virtual void set(int, char **); // set communication style
void set_processors(int, char **); // set 3d processor grid attributes

332
src/read_data.cpp
View File

@ -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;
}