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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5457 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-01-04 19:12:58 +00:00
parent f3300e9536
commit d5aa03447b
27 changed files with 580 additions and 487 deletions
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48
src/read_data.cpp
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@ -16,6 +16,7 @@
#include "string.h"
#include "stdlib.h"
#include "read_data.h"
#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
@ -335,7 +336,7 @@ void ReadData::header(int flag)
// search line for header keyword and set corresponding variable
if (strstr(line,"atoms")) sscanf(line,"%lg",&atom->natoms);
if (strstr(line,"atoms")) sscanf(line,"%lu",&atom->natoms);
else if (strstr(line,"bonds")) sscanf(line,"%d",&atom->nbonds);
else if (strstr(line,"angles")) sscanf(line,"%d",&atom->nangles);
else if (strstr(line,"dihedrals")) sscanf(line,"%d",&atom->ndihedrals);
@ -402,19 +403,18 @@ void ReadData::header(int flag)
/* ----------------------------------------------------------------------
read all atoms
accumulate nread in double precision to allow natoms > 2^31
------------------------------------------------------------------------- */
void ReadData::atoms()
{
int i,m,nchunk;
double nread = 0.0;
double natoms = atom->natoms;
bigint nread = 0;
bigint natoms = atom->natoms;
while (nread < natoms) {
if (natoms-nread > CHUNK) nchunk = CHUNK;
else nchunk = static_cast<int> (natoms - nread);
else nchunk = natoms-nread;
if (me == 0) {
char *eof;
m = 0;
@ -449,24 +449,27 @@ void ReadData::atoms()
// if any atom ID > 0, error if any atom ID == 0
// not checking if atom IDs > natoms or are unique
int nlocal = atom->nlocal;
int *tag = atom->tag;
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if (atom->tag[i] < 0) flag = 1;
for (int i = 0; i < nlocal; i++)
if (tag[i] < 0) flag = 1;
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all)
error->all("Invalid atom ID in Atoms section of data file");
flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if (atom->tag[i] > 0) flag = 1;
for (int i = 0; i < nlocal; i++)
if (tag[i] > 0) flag = 1;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all == 0) atom->tag_enable = 0;
if (atom->tag_enable) {
flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if (atom->tag[i] == 0) flag = 1;
for (int i = 0; i < nlocal; i++)
if (tag[i] == 0) flag = 1;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all)
error->all("Invalid atom ID in Atoms section of data file");
@ -483,7 +486,6 @@ void ReadData::atoms()
/* ----------------------------------------------------------------------
read all velocities
to find atoms, must build atom map if not a molecular system
accumulate nread in double precision to allow natoms > 2^31
------------------------------------------------------------------------- */
void ReadData::velocities()
@ -498,12 +500,12 @@ void ReadData::velocities()
atom->map_set();
}
double nread = 0.0;
double natoms = atom->natoms;
bigint nread = 0;
bigint natoms = atom->natoms;
while (nread < natoms) {
if (natoms-nread > CHUNK) nchunk = CHUNK;
else nchunk = static_cast<int> (natoms - nread);
else nchunk = natoms-nread;
if (me == 0) {
char *eof;
m = 0;
@ -560,9 +562,11 @@ void ReadData::bonds()
// check that bonds were assigned correctly
int nlocal = atom->nlocal;
int sum;
int n = 0;
for (i = 0; i < atom->nlocal; i++) n += atom->num_bond[i];
for (i = 0; i < nlocal; i++) n += atom->num_bond[i];
MPI_Allreduce(&n,&sum,1,MPI_INT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 2;
@ -602,9 +606,11 @@ void ReadData::angles()
// check that angles were assigned correctly
int nlocal = atom->nlocal;
int sum;
int n = 0;
for (i = 0; i < atom->nlocal; i++) n += atom->num_angle[i];
for (i = 0; i < nlocal; i++) n += atom->num_angle[i];
MPI_Allreduce(&n,&sum,1,MPI_INT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 3;
@ -644,9 +650,11 @@ void ReadData::dihedrals()
// check that dihedrals were assigned correctly
int nlocal = atom->nlocal;
int sum;
int n = 0;
for (i = 0; i < atom->nlocal; i++) n += atom->num_dihedral[i];
for (i = 0; i < nlocal; i++) n += atom->num_dihedral[i];
MPI_Allreduce(&n,&sum,1,MPI_INT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 4;
@ -687,9 +695,11 @@ void ReadData::impropers()
// check that impropers were assigned correctly
int nlocal = atom->nlocal;
int sum;
int n = 0;
for (i = 0; i < atom->nlocal; i++) n += atom->num_improper[i];
for (i = 0; i < nlocal; i++) n += atom->num_improper[i];
MPI_Allreduce(&n,&sum,1,MPI_INT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 4;