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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-01-30 00:22:05 +00:00
parent 9cdbeaf9f2
commit 209f169cbc
414 changed files with 6935 additions and 10462 deletions
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60
src/write_restart.cpp
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@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -14,8 +14,9 @@
#include "mpi.h"
#include "string.h"
#include "write_restart.h"
#include "system.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_hybrid.h"
#include "group.h"
#include "force.h"
#include "pair.h"
@ -33,11 +34,13 @@
#include "memory.h"
#include "error.h"
enum {IGNORE,WARN,ERROR}; // same as thermo.cpp
using namespace LAMMPS_NS;
enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
/* ---------------------------------------------------------------------- */
WriteRestart::WriteRestart()
WriteRestart::WriteRestart(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
@ -69,7 +72,7 @@ void WriteRestart::command(int narg, char **arg)
if (comm->me == 0 && screen)
fprintf(screen,"System init for write_restart ...\n");
sys->init();
lmp->init();
// move atoms to new processors before writing file
// enforce PBC before in case atoms are outside box
@ -129,8 +132,8 @@ void WriteRestart::write(char *file)
if (me == 0) {
header();
group->write_restart(fp);
if (atom->mass_require) mass();
if (atom->dipole_require) dipole();
if (atom->mass) mass();
if (atom->dipole) dipole();
force_fields();
}
@ -140,7 +143,7 @@ void WriteRestart::write(char *file)
// max_size = largest buffer needed by any proc
int max_size;
int send_size = atom->size_restart();
int send_size = atom->avec->size_restart();
MPI_Allreduce(&send_size,&max_size,1,MPI_INT,MPI_MAX,world);
double *buf;
@ -153,8 +156,9 @@ void WriteRestart::write(char *file)
// pack my atom data into buf
AtomVec *avec = atom->avec;
int n = 0;
for (int i = 0; i < atom->nlocal; i++) n += atom->pack_restart(i,&buf[n]);
for (int i = 0; i < atom->nlocal; i++) n += avec->pack_restart(i,&buf[n]);
// if single file:
// write one chunk of atoms per proc to file
@ -235,22 +239,20 @@ void WriteRestart::header()
// atom_style must be written before atom class values
// so read_restart can create class before reading class values
// if style = hybrid, also write sub-class names (1 to nwords)
// if style = hybrid, also write sub-class styles
write_char(19,atom->style);
write_char(19,atom->atom_style);
if (strcmp(atom->style,"hybrid") == 0) {
char **words;
int nwords = atom->style2arg(words);
int nm1 = nwords - 1;
fwrite(&nm1,sizeof(int),1,fp);
for (int i = 1; i < nwords; i++) {
int n = strlen(words[i]) + 1;
if (strcmp(atom->atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) atom->avec;
int nstyles = avec_hybrid->nstyles;
char **keywords = avec_hybrid->keywords;
fwrite(&nstyles,sizeof(int),1,fp);
for (int i = 0; i < nstyles; i++) {
int n = strlen(keywords[i]) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(words[i],sizeof(char),n,fp);
fwrite(keywords[i],sizeof(char),n,fp);
}
for (int i = 0; i < nwords; i++) delete [] words[i];
delete [] words;
}
write_double(20,natoms);
@ -322,7 +324,7 @@ void WriteRestart::force_fields()
force->pair->write_restart(fp);
}
if (atom->bonds_allow) {
if (atom->avec->bonds_allow) {
if (force->bond) n = strlen(force->bond_style) + 1;
else n = 0;
fwrite(&n,sizeof(int),1,fp);
@ -332,7 +334,7 @@ void WriteRestart::force_fields()
}
}
if (atom->angles_allow) {
if (atom->avec->angles_allow) {
if (force->angle) n = strlen(force->angle_style) + 1;
else n = 0;
fwrite(&n,sizeof(int),1,fp);
@ -342,7 +344,7 @@ void WriteRestart::force_fields()
}
}
if (atom->dihedrals_allow) {
if (atom->avec->dihedrals_allow) {
if (force->dihedral) n = strlen(force->dihedral_style) + 1;
else n = 0;
fwrite(&n,sizeof(int),1,fp);
@ -352,7 +354,7 @@ void WriteRestart::force_fields()
}
}
if (atom->impropers_allow) {
if (atom->avec->impropers_allow) {
if (force->improper) n = strlen(force->improper_style) + 1;
else n = 0;
fwrite(&n,sizeof(int),1,fp);
@ -364,7 +366,7 @@ void WriteRestart::force_fields()
}
/* ----------------------------------------------------------------------
write_int - write a flag and an int into restart file
write a flag and an int into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_int(int flag, int value)
@ -374,7 +376,7 @@ void WriteRestart::write_int(int flag, int value)
}
/* ----------------------------------------------------------------------
write_double - write a flag and a double into restart file
write a flag and a double into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_double(int flag, double value)
@ -384,7 +386,7 @@ void WriteRestart::write_double(int flag, double value)
}
/* ----------------------------------------------------------------------
write_char - write a flag and a char str into restart file
write a flag and a char str into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_char(int flag, char *value)