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dump_local.cpp
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Sun, May 26, 05:36

dump_local.cpp
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/* ----------------------------------------------------------------------
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 "input.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
enum{INT,DOUBLE};
#define INVOKED_LOCAL 16
#define ONEFIELD 32
#define DELTA 1048576
/* ---------------------------------------------------------------------- */
DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) :
Dump(lmp, narg, arg),
label(NULL), vtype(NULL), vformat(NULL), columns(NULL), field2index(NULL),
argindex(NULL), id_compute(NULL), compute(NULL), id_fix(NULL), fix(NULL),
pack_choice(NULL)
{
if (narg == 5) error->all(FLERR,"No dump local arguments specified");
clearstep = 1;
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal dump local command");
if (binary)
error->all(FLERR,"Binary files are not supported with dump local");
nfield = narg - 5;
// expand args if any have wildcard character "*"
int expand = 0;
char **earg;
nfield = input->expand_args(nfield,&arg[5],1,earg);
if (earg != &arg[5]) expand = 1;
// allocate field vectors
pack_choice = new FnPtrPack[nfield];
vtype = new int[nfield];
buffer_allow = 1;
buffer_flag = 1;
// 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 attributes
parse_fields(nfield,earg);
size_one = nfield;
// 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) strcat(format_default,"%d ");
else if (vtype[i] == DOUBLE) strcat(format_default,"%g ");
vformat[i] = NULL;
}
format_column_user = new char*[size_one];
for (int i = 0; i < size_one; i++) format_column_user[i] = NULL;
// setup column string
int n = 0;
for (int iarg = 0; iarg < nfield; iarg++) n += strlen(earg[iarg]) + 2;
columns = new char[n];
columns[0] = '\0';
for (int iarg = 0; iarg < nfield; iarg++) {
strcat(columns,earg[iarg]);
strcat(columns," ");
}
// setup default label string
char *str = (char *) "ENTRIES";
n = strlen(str) + 1;
label = new char[n];
strcpy(label,str);
// if wildcard expansion occurred, free earg memory from exapnd_args()
if (expand) {
for (int i = 0; i < nfield; i++) delete [] earg[i];
memory->sfree(earg);
}
}
/* ---------------------------------------------------------------------- */
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;
for (int i = 0; i < size_one; i++) delete [] format_column_user[i];
delete [] format_column_user;
delete [] columns;
delete [] label;
}
/* ---------------------------------------------------------------------- */
void DumpLocal::init_style()
{
if (sort_flag && sortcol == 0)
error->all(FLERR,"Dump local cannot sort by atom ID");
// format = copy of default or user-specified line format
delete [] format;
char *str;
if (format_line_user) str = format_line_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
// if user-specified int/float format exists, use it instead
// if user-specified column format exists, use it instead
// lo priority = line, medium priority = int/float, hi priority = column
char *ptr;
for (int i = 0; i < size_one; i++) {
if (i == 0) ptr = strtok(format," \0");
else ptr = strtok(NULL," \0");
if (ptr == NULL) error->all(FLERR,"Dump_modify format line is too short");
delete [] vformat[i];
if (format_column_user[i]) {
vformat[i] = new char[strlen(format_column_user[i]) + 2];
strcpy(vformat[i],format_column_user[i]);
} else if (vtype[i] == INT && format_int_user) {
vformat[i] = new char[strlen(format_int_user) + 2];
strcpy(vformat[i],format_int_user);
} else if (vtype[i] == DOUBLE && format_float_user) {
vformat[i] = new char[strlen(format_float_user) + 2];
strcpy(vformat[i],format_float_user);
} else {
vformat[i] = new char[strlen(ptr) + 2];
strcpy(vformat[i],ptr);
}
vformat[i] = strcat(vformat[i]," ");
}
// setup boundary string
domain->boundary_string(boundstr);
// setup function ptrs
if (buffer_flag == 1) write_choice = &DumpLocal::write_string;
else write_choice = &DumpLocal::write_lines;
// 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(FLERR,"Could not find dump local 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(FLERR,"Could not find dump local fix ID");
fix[i] = modify->fix[ifix];
if (nevery % modify->fix[ifix]->local_freq)
error->all(FLERR,"Dump local and fix not computed at compatible times");
}
// open single file, one time only
if (multifile == 0) openfile();
}
/* ---------------------------------------------------------------------- */
int DumpLocal::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"label") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
delete [] label;
int n = strlen(arg[1]) + 1;
label = new char[n];
strcpy(label,arg[1]);
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void DumpLocal::write_header(bigint ndump)
{
if (me == 0) {
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF %s\n",label);
fprintf(fp,BIGINT_FORMAT "\n",ndump);
if (domain->triclinic) {
fprintf(fp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
fprintf(fp,"%g %g %g\n",boxxlo,boxxhi,boxxy);
fprintf(fp,"%g %g %g\n",boxylo,boxyhi,boxxz);
fprintf(fp,"%g %g %g\n",boxzlo,boxzhi,boxyz);
} else {
fprintf(fp,"ITEM: BOX BOUNDS %s\n",boundstr);
fprintf(fp,"%g %g\n",boxxlo,boxxhi);
fprintf(fp,"%g %g\n",boxylo,boxyhi);
fprintf(fp,"%g %g\n",boxzlo,boxzhi);
}
fprintf(fp,"ITEM: %s %s\n",label,columns);
}
}
/* ---------------------------------------------------------------------- */
int DumpLocal::count()
{
int i;
// invoke Computes for local quantities
// only if within a run or minimize
// else require that computes are current
// this prevents a compute from being invoked by the WriteDump class
if (ncompute) {
if (update->whichflag == 0) {
for (i = 0; i < ncompute; i++)
if (compute[i]->invoked_local != update->ntimestep)
error->all(FLERR,"Compute used in dump between runs is not current");
} else {
for (i = 0; i < ncompute; i++) {
if (!(compute[i]->invoked_flag & INVOKED_LOCAL)) {
compute[i]->compute_local();
compute[i]->invoked_flag |= INVOKED_LOCAL;
}
}
}
}
// nmine = # of local values I contribute
// must be consistent for all input fields
nmine = -1;
for (int i = 0; i < ncompute; i++) {
if (nmine < 0) nmine = compute[i]->size_local_rows;
else if (nmine != compute[i]->size_local_rows)
error->one(FLERR,
"Dump local count is not consistent across input fields");
}
for (int i = 0; i < nfix; i++) {
if (nmine < 0) nmine = fix[i]->size_local_rows;
else if (nmine != fix[i]->size_local_rows)
error->one(FLERR,
"Dump local count is not consistent across input fields");
}
return nmine;
}
/* ---------------------------------------------------------------------- */
void DumpLocal::pack(tagint *dummy)
{
for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n);
}
/* ----------------------------------------------------------------------
convert mybuf of doubles to one big formatted string in sbuf
return -1 if strlen exceeds an int, since used as arg in MPI calls in Dump
------------------------------------------------------------------------- */
int DumpLocal::convert_string(int n, double *mybuf)
{
int i,j;
int offset = 0;
int m = 0;
for (i = 0; i < n; i++) {
if (offset + size_one*ONEFIELD > maxsbuf) {
if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1;
maxsbuf += DELTA;
memory->grow(sbuf,maxsbuf,"dump:sbuf");
}
for (j = 0; j < size_one; j++) {
if (vtype[j] == INT)
offset += sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
else
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
m++;
}
offset += sprintf(&sbuf[offset],"\n");
}
return offset;
}
/* ---------------------------------------------------------------------- */
void DumpLocal::write_data(int n, double *mybuf)
{
(this->*write_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
void DumpLocal::write_string(int n, double *mybuf)
{
fwrite(mybuf,sizeof(char),n,fp);
}
/* ---------------------------------------------------------------------- */
void DumpLocal::write_lines(int n, double *mybuf)
{
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> (mybuf[m]));
else fprintf(fp,vformat[j],mybuf[m]);
m++;
}
fprintf(fp,"\n");
}
}
/* ---------------------------------------------------------------------- */
void DumpLocal::parse_fields(int narg, char **arg)
{
int computefixflag = 0;
// customize by adding to if statement
int i;
for (int iarg = 0; iarg < narg; iarg++) {
i = iarg;
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) {
computefixflag = 1;
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(FLERR,"Invalid attribute 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(FLERR,"Could not find dump local compute ID");
if (modify->compute[n]->local_flag == 0)
error->all(FLERR,"Dump local compute does not compute local info");
if (argindex[i] == 0 && modify->compute[n]->size_local_cols > 0)
error->all(FLERR,"Dump local compute does not calculate local vector");
if (argindex[i] > 0 && modify->compute[n]->size_local_cols == 0)
error->all(FLERR,"Dump local compute does not calculate local array");
if (argindex[i] > 0 &&
argindex[i] > modify->compute[n]->size_local_cols)
error->all(FLERR,"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) {
computefixflag = 1;
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(FLERR,"Invalid attribute 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(FLERR,"Could not find dump local fix ID");
if (modify->fix[n]->local_flag == 0)
error->all(FLERR,"Dump local fix does not compute local info");
if (argindex[i] == 0 && modify->fix[n]->size_local_cols > 0)
error->all(FLERR,"Dump local fix does not compute local vector");
if (argindex[i] > 0 && modify->fix[n]->size_local_cols == 0)
error->all(FLERR,"Dump local fix does not compute local array");
if (argindex[i] > 0 &&
argindex[i] > modify->fix[n]->size_local_cols)
error->all(FLERR,"Dump local fix vector is accessed out-of-range");
field2index[i] = add_fix(suffix);
delete [] suffix;
} else error->all(FLERR,"Invalid attribute in dump local command");
}
if (computefixflag == 0)
error->all(FLERR,"Dump local attributes contain no compute or fix");
}
/* ----------------------------------------------------------------------
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 attribute dump local can output
the local value is packed into buf starting at n with stride size_one
customize a new attribute 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;
}
}

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