git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3564 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
427
src/dump_local.cpp
Normal file
427
src/dump_local.cpp
Normal file
@ -0,0 +1,427 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
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
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "mpi.h"
|
||||
#include "string.h"
|
||||
#include "stdlib.h"
|
||||
#include "dump_local.h"
|
||||
#include "atom.h"
|
||||
#include "modify.h"
|
||||
#include "fix.h"
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
|
||||
#include "comm.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
enum{INDEX,COMPUTE,FIX};
|
||||
enum{INT,DOUBLE};
|
||||
|
||||
#define INVOKED_LOCAL 16
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) :
|
||||
Dump(lmp, narg, arg)
|
||||
{
|
||||
if (narg == 5) error->all("No dump local arguments specified");
|
||||
|
||||
nevery = atoi(arg[3]);
|
||||
|
||||
size_one = nfield = narg-5;
|
||||
pack_choice = new FnPtrPack[nfield];
|
||||
vtype = new int[nfield];
|
||||
|
||||
// computes & fixes which the dump accesses
|
||||
|
||||
field2index = new int[nfield];
|
||||
argindex = new int[nfield];
|
||||
|
||||
ncompute = 0;
|
||||
id_compute = NULL;
|
||||
compute = NULL;
|
||||
|
||||
nfix = 0;
|
||||
id_fix = NULL;
|
||||
fix = NULL;
|
||||
|
||||
// process keywords
|
||||
|
||||
parse_fields(narg,arg);
|
||||
|
||||
// setup format strings
|
||||
|
||||
vformat = new char*[size_one];
|
||||
|
||||
format_default = new char[3*size_one+1];
|
||||
format_default[0] = '\0';
|
||||
|
||||
for (int i = 0; i < size_one; i++) {
|
||||
if (vtype[i] == INT) format_default = strcat(format_default,"%d ");
|
||||
else format_default = strcat(format_default,"%g ");
|
||||
vformat[i] = NULL;
|
||||
}
|
||||
|
||||
// setup column string
|
||||
|
||||
int n = 0;
|
||||
for (int iarg = 5; iarg < narg; iarg++) n += strlen(arg[iarg]) + 2;
|
||||
columns = new char[n];
|
||||
columns[0] = '\0';
|
||||
for (int iarg = 5; iarg < narg; iarg++) {
|
||||
strcat(columns,arg[iarg]);
|
||||
strcat(columns," ");
|
||||
}
|
||||
|
||||
label = "BONDS";
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DumpLocal::~DumpLocal()
|
||||
{
|
||||
delete [] pack_choice;
|
||||
delete [] vtype;
|
||||
delete [] field2index;
|
||||
delete [] argindex;
|
||||
|
||||
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
|
||||
memory->sfree(id_compute);
|
||||
delete [] compute;
|
||||
|
||||
for (int i = 0; i < nfix; i++) delete [] id_fix[i];
|
||||
memory->sfree(id_fix);
|
||||
delete [] fix;
|
||||
|
||||
for (int i = 0; i < size_one; i++) delete [] vformat[i];
|
||||
delete [] vformat;
|
||||
|
||||
delete [] columns;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpLocal::init()
|
||||
{
|
||||
delete [] format;
|
||||
char *str;
|
||||
if (format_user) str = format_user;
|
||||
else str = format_default;
|
||||
|
||||
int n = strlen(str) + 1;
|
||||
format = new char[n];
|
||||
strcpy(format,str);
|
||||
|
||||
// tokenize the format string and add space at end of each format element
|
||||
|
||||
char *ptr;
|
||||
for (int i = 0; i < size_one; i++) {
|
||||
if (i == 0) ptr = strtok(format," \0");
|
||||
else ptr = strtok(NULL," \0");
|
||||
delete [] vformat[i];
|
||||
vformat[i] = new char[strlen(ptr) + 2];
|
||||
strcpy(vformat[i],ptr);
|
||||
vformat[i] = strcat(vformat[i]," ");
|
||||
}
|
||||
|
||||
// find current ptr for each compute,fix,variable
|
||||
// check that fix frequency is acceptable
|
||||
|
||||
int icompute;
|
||||
for (int i = 0; i < ncompute; i++) {
|
||||
icompute = modify->find_compute(id_compute[i]);
|
||||
if (icompute < 0) error->all("Could not find dump custom compute ID");
|
||||
compute[i] = modify->compute[icompute];
|
||||
}
|
||||
|
||||
int ifix;
|
||||
for (int i = 0; i < nfix; i++) {
|
||||
ifix = modify->find_fix(id_fix[i]);
|
||||
if (ifix < 0) error->all("Could not find dump custom fix ID");
|
||||
fix[i] = modify->fix[ifix];
|
||||
if (nevery % modify->fix[ifix]->peratom_freq)
|
||||
error->all("Dump custom and fix not computed at compatible times");
|
||||
}
|
||||
|
||||
// open single file, one time only
|
||||
|
||||
if (multifile == 0) openfile();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpLocal::write_header(int ndump)
|
||||
{
|
||||
if (me == 0) {
|
||||
fprintf(fp,"ITEM: TIMESTEP\n");
|
||||
fprintf(fp,"%d\n",update->ntimestep);
|
||||
fprintf(fp,"ITEM: NUMBER OF %s\n",label);
|
||||
fprintf(fp,"%d\n",ndump);
|
||||
fprintf(fp,"ITEM: %s\n",label);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int DumpLocal::count()
|
||||
{
|
||||
int i;
|
||||
|
||||
// invoke Computes for local quantities
|
||||
|
||||
if (ncompute) {
|
||||
int ntimestep = update->ntimestep;
|
||||
for (i = 0; i < ncompute; i++) {
|
||||
if (!(compute[i]->invoked_flag & INVOKED_LOCAL)) {
|
||||
compute[i]->compute_local();
|
||||
compute[i]->invoked_flag |= INVOKED_LOCAL;
|
||||
nmine = compute[i]->size_local_rows;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return nmine;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int DumpLocal::pack()
|
||||
{
|
||||
for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n);
|
||||
return nmine*size_one;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpLocal::write_data(int n, double *buf)
|
||||
{
|
||||
int i,j;
|
||||
|
||||
int m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
for (j = 0; j < size_one; j++) {
|
||||
if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (buf[m]));
|
||||
else fprintf(fp,vformat[j],buf[m]);
|
||||
m++;
|
||||
}
|
||||
fprintf(fp,"\n");
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpLocal::parse_fields(int narg, char **arg)
|
||||
{
|
||||
// customize by adding to if statement
|
||||
|
||||
int i;
|
||||
for (int iarg = 5; iarg < narg; iarg++) {
|
||||
i = iarg-5;
|
||||
|
||||
if (strcmp(arg[iarg],"index") == 0) {
|
||||
pack_choice[i] = &DumpLocal::pack_index;
|
||||
vtype[i] = INT;
|
||||
|
||||
// compute value = c_ID
|
||||
// if no trailing [], then arg is set to 0, else arg is int between []
|
||||
|
||||
} else if (strncmp(arg[iarg],"c_",2) == 0) {
|
||||
pack_choice[i] = &DumpLocal::pack_compute;
|
||||
vtype[i] = DOUBLE;
|
||||
|
||||
int n = strlen(arg[iarg]);
|
||||
char *suffix = new char[n];
|
||||
strcpy(suffix,&arg[iarg][2]);
|
||||
|
||||
char *ptr = strchr(suffix,'[');
|
||||
if (ptr) {
|
||||
if (suffix[strlen(suffix)-1] != ']')
|
||||
error->all("Invalid keyword in dump local command");
|
||||
argindex[i] = atoi(ptr+1);
|
||||
*ptr = '\0';
|
||||
} else argindex[i] = 0;
|
||||
|
||||
n = modify->find_compute(suffix);
|
||||
if (n < 0) error->all("Could not find dump local compute ID");
|
||||
if (modify->compute[n]->local_flag == 0)
|
||||
error->all("Dump local compute does not compute local info");
|
||||
if (argindex[i] == 0 && modify->compute[n]->size_local_cols > 0)
|
||||
error->all("Dump local compute does not calculate local vector");
|
||||
if (argindex[i] > 0 && modify->compute[n]->size_local_cols == 0)
|
||||
error->all("Dump local compute does not calculate local array");
|
||||
if (argindex[i] > 0 &&
|
||||
argindex[i] > modify->compute[n]->size_local_cols)
|
||||
error->all("Dump local compute vector is accessed out-of-range");
|
||||
|
||||
field2index[i] = add_compute(suffix);
|
||||
delete [] suffix;
|
||||
|
||||
// fix value = f_ID
|
||||
// if no trailing [], then arg is set to 0, else arg is between []
|
||||
|
||||
} else if (strncmp(arg[iarg],"f_",2) == 0) {
|
||||
pack_choice[i] = &DumpLocal::pack_fix;
|
||||
vtype[i] = DOUBLE;
|
||||
|
||||
int n = strlen(arg[iarg]);
|
||||
char *suffix = new char[n];
|
||||
strcpy(suffix,&arg[iarg][2]);
|
||||
|
||||
char *ptr = strchr(suffix,'[');
|
||||
if (ptr) {
|
||||
if (suffix[strlen(suffix)-1] != ']')
|
||||
error->all("Invalid keyword in dump local command");
|
||||
argindex[i] = atoi(ptr+1);
|
||||
*ptr = '\0';
|
||||
} else argindex[i] = 0;
|
||||
|
||||
n = modify->find_fix(suffix);
|
||||
if (n < 0) error->all("Could not find dump local fix ID");
|
||||
if (modify->fix[n]->local_flag == 0)
|
||||
error->all("Dump local fix does not compute local info");
|
||||
if (argindex[i] == 0 && modify->fix[n]->size_local_cols > 0)
|
||||
error->all("Dump local fix does not compute local vector");
|
||||
if (argindex[i] > 0 && modify->fix[n]->size_local_cols == 0)
|
||||
error->all("Dump local fix does not compute local array");
|
||||
if (argindex[i] > 0 &&
|
||||
argindex[i] > modify->fix[n]->size_local_cols)
|
||||
error->all("Dump local fix vector is accessed out-of-range");
|
||||
|
||||
field2index[i] = add_fix(suffix);
|
||||
delete [] suffix;
|
||||
|
||||
} else error->all("Invalid keyword in dump local command");
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add Compute to list of Compute objects used by dump
|
||||
return index of where this Compute is in list
|
||||
if already in list, do not add, just return index, else add to list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int DumpLocal::add_compute(char *id)
|
||||
{
|
||||
int icompute;
|
||||
for (icompute = 0; icompute < ncompute; icompute++)
|
||||
if (strcmp(id,id_compute[icompute]) == 0) break;
|
||||
if (icompute < ncompute) return icompute;
|
||||
|
||||
id_compute = (char **)
|
||||
memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute");
|
||||
delete [] compute;
|
||||
compute = new Compute*[ncompute+1];
|
||||
|
||||
int n = strlen(id) + 1;
|
||||
id_compute[ncompute] = new char[n];
|
||||
strcpy(id_compute[ncompute],id);
|
||||
ncompute++;
|
||||
return ncompute-1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add Fix to list of Fix objects used by dump
|
||||
return index of where this Fix is in list
|
||||
if already in list, do not add, just return index, else add to list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int DumpLocal::add_fix(char *id)
|
||||
{
|
||||
int ifix;
|
||||
for (ifix = 0; ifix < nfix; ifix++)
|
||||
if (strcmp(id,id_fix[ifix]) == 0) break;
|
||||
if (ifix < nfix) return ifix;
|
||||
|
||||
id_fix = (char **)
|
||||
memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix");
|
||||
delete [] fix;
|
||||
fix = new Fix*[nfix+1];
|
||||
|
||||
int n = strlen(id) + 1;
|
||||
id_fix[nfix] = new char[n];
|
||||
strcpy(id_fix[nfix],id);
|
||||
nfix++;
|
||||
return nfix-1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
extraction of Compute, Fix results
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DumpLocal::pack_compute(int n)
|
||||
{
|
||||
double *vector = compute[field2index[n]]->vector_local;
|
||||
double **array = compute[field2index[n]]->array_local;
|
||||
int ncount = compute[field2index[n]]->size_local_rows;
|
||||
int index = argindex[n];
|
||||
|
||||
if (index == 0) {
|
||||
for (int i = 0; i < ncount; i++) {
|
||||
buf[n] = vector[i];
|
||||
n += size_one;
|
||||
}
|
||||
} else {
|
||||
index--;
|
||||
for (int i = 0; i < ncount; i++) {
|
||||
buf[n] = array[i][index];
|
||||
n += size_one;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpLocal::pack_fix(int n)
|
||||
{
|
||||
double *vector = fix[field2index[n]]->vector_local;
|
||||
double **array = fix[field2index[n]]->array_local;
|
||||
int index = argindex[n];
|
||||
|
||||
if (index == 0) {
|
||||
for (int i = 0; i < nmine; i++) {
|
||||
buf[n] = vector[i];
|
||||
n += size_one;
|
||||
}
|
||||
} else {
|
||||
index--;
|
||||
for (int i = 0; i < nmine; i++) {
|
||||
buf[n] = array[i][index];
|
||||
n += size_one;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
one method for every keyword dump local can output
|
||||
the local value is packed into buf starting at n with stride size_one
|
||||
customize a new keyword by adding a method
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpLocal::pack_index(int n)
|
||||
{
|
||||
int index;
|
||||
MPI_Scan(&nmine,&index,1,MPI_INT,MPI_SUM,world);
|
||||
index -= nmine;
|
||||
|
||||
for (int i = 0; i < nmine; i++) {
|
||||
buf[n] = ++index;
|
||||
n += size_one;
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user