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lammps/src/dump_custom.cpp
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dump_custom.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 "stdlib.h"
#include "string.h"
#include "dump_custom.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "region.h"
#include "group.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
// customize by adding keyword to 1st enum
enum{TAG,MOL,TYPE,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,
VX,VY,VZ,FX,FY,FZ,
Q,MUX,MUY,MUZ,TQX,TQY,TQZ,
EPAIR,KE,ETOTAL,CENTRO,SXX,SYY,SZZ,SXY,SXZ,SYZ,
COMPUTE};
enum{LT,LE,GT,GE,EQ,NEQ};
enum{INT,DOUBLE};
/* ---------------------------------------------------------------------- */
DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
Dump(lmp, narg, arg)
{
if (narg == 5) error->all("No dump custom arguments specified");
size_one = nfield = narg-5;
pack_choice = new FnPtrPack[nfield];
vtype = new int[nfield];
iregion = -1;
nthresh = 0;
thresh_array = NULL;
thresh_op = NULL;
thresh_value = NULL;
// flags, IDs, and memory for compute objects dump may create
index_epair = index_ke = index_etotal = index_centro = index_stress = -1;
style_epair = "epair/atom";
style_ke = "ke/atom";
style_etotal = "etotal/atom";
style_centro = "centro/atom";
style_stress = "stress/atom";
ncompute = 0;
id_compute = NULL;
compute = NULL;
field2compute = (int *) memory->smalloc(nfield*sizeof(int),
"dump:field2compute");
arg_compute = (int *) memory->smalloc(nfield*sizeof(int),"dump:arg_compute");
// process keywords
parse_fields(narg,arg);
// create the requested Computes
if (index_epair >= 0) create_compute(style_epair,NULL);
if (index_ke >= 0) create_compute(style_ke,NULL);
if (index_etotal >= 0) create_compute(style_etotal,style_epair);
if (index_centro >= 0) create_compute(style_centro,NULL);
if (index_stress >= 0) create_compute(style_stress,NULL);
// atom selection arrays
maxlocal = 0;
choose = NULL;
dchoose = NULL;
// 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;
}
// one-time file open
if (multifile == 0) openfile();
}
/* ---------------------------------------------------------------------- */
DumpCustom::~DumpCustom()
{
delete [] pack_choice;
delete [] vtype;
memory->sfree(thresh_array);
memory->sfree(thresh_op);
memory->sfree(thresh_value);
// delete Compute classes if dump custom created them
if (index_epair >= 0) modify->delete_compute(id_compute[index_epair]);
if (index_ke >= 0) modify->delete_compute(id_compute[index_ke]);
if (index_etotal >= 0) modify->delete_compute(id_compute[index_etotal]);
if (index_centro >= 0) modify->delete_compute(id_compute[index_centro]);
if (index_stress >= 0) modify->delete_compute(id_compute[index_stress]);
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
memory->sfree(id_compute);
memory->sfree(compute);
memory->sfree(field2compute);
memory->sfree(arg_compute);
delete [] choose;
delete [] dchoose;
for (int i = 0; i < size_one; i++) delete [] vformat[i];
delete [] vformat;
}
/* ---------------------------------------------------------------------- */
void DumpCustom::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]," ");
}
// setup function ptrs
if (binary) header_choice = &DumpCustom::header_binary;
else header_choice = &DumpCustom::header_item;
if (binary) write_choice = &DumpCustom::write_binary;
else write_choice = &DumpCustom::write_text;
// find current ptr for each Compute ID
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];
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::write_header(int ndump)
{
(this->*header_choice)(ndump);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::header_binary(int ndump)
{
fwrite(&update->ntimestep,sizeof(int),1,fp);
fwrite(&ndump,sizeof(int),1,fp);
fwrite(&domain->boxxlo,sizeof(double),1,fp);
fwrite(&domain->boxxhi,sizeof(double),1,fp);
fwrite(&domain->boxylo,sizeof(double),1,fp);
fwrite(&domain->boxyhi,sizeof(double),1,fp);
fwrite(&domain->boxzlo,sizeof(double),1,fp);
fwrite(&domain->boxzhi,sizeof(double),1,fp);
fwrite(&size_one,sizeof(int),1,fp);
if (multiproc) {
int one = 1;
fwrite(&one,sizeof(int),1,fp);
} else fwrite(&nprocs,sizeof(int),1,fp);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::header_item(int ndump)
{
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,"%d\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF ATOMS\n");
fprintf(fp,"%d\n",ndump);
fprintf(fp,"ITEM: BOX BOUNDS\n");
fprintf(fp,"%g %g\n",domain->boxxlo,domain->boxxhi);
fprintf(fp,"%g %g\n",domain->boxylo,domain->boxyhi);
fprintf(fp,"%g %g\n",domain->boxzlo,domain->boxzhi);
fprintf(fp,"ITEM: ATOMS\n");
}
/* ---------------------------------------------------------------------- */
int DumpCustom::count()
{
int i;
// grow choose arrays if needed
int nlocal = atom->nlocal;
if (nlocal > maxlocal) {
delete [] choose;
delete [] dchoose;
maxlocal = atom->nmax;
choose = new int[maxlocal];
dchoose = new double[maxlocal];
}
// invoke Computes for per-atom dump quantities
if (ncompute)
for (i = 0; i < ncompute; i++) compute[i]->compute_peratom();
// choose all local atoms for output
for (i = 0; i < nlocal; i++) choose[i] = 1;
nmine = nlocal;
// un-choose if not in group
if (igroup) {
int *mask = atom->mask;
for (i = 0; i < nlocal; i++)
if (!(mask[i] & groupbit)) {
choose[i] = 0;
nmine--;
}
}
// un-choose if not in region
if (iregion >= 0) {
Region *region = domain->regions[iregion];
double **x = atom->x;
for (i = 0; i < nlocal; i++)
if (choose[i] && region->match(x[i][0],x[i][1],x[i][2]) == 0) {
choose[i] = 0;
nmine--;
}
}
// un-choose if any threshhold criterion isn't met
if (nthresh) {
double *ptr;
double value;
int nstride;
int nlocal = atom->nlocal;
for (int ithresh = 0; ithresh < nthresh; ithresh++) {
// customize by adding to if statement
if (thresh_array[ithresh] == TAG) {
int *tag = atom->tag;
for (i = 0; i < nlocal; i++) dchoose[i] = tag[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == MOL) {
int *molecule = atom->molecule;
for (i = 0; i < nlocal; i++) dchoose[i] = molecule[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == TYPE) {
int *type = atom->type;
for (i = 0; i < nlocal; i++) dchoose[i] = type[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == X) {
ptr = &atom->x[0][0];
nstride = 3;
} else if (thresh_array[ithresh] == Y) {
ptr = &atom->x[0][1];
nstride = 3;
} else if (thresh_array[ithresh] == Z) {
ptr = &atom->x[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == XS) {
double **x = atom->x;
double boxxlo = domain->boxxlo;
double invxprd = 1.0/domain->xprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][0] - boxxlo) * invxprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YS) {
double **x = atom->x;
double boxylo = domain->boxylo;
double invyprd = 1.0/domain->yprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][1] - boxylo) * invyprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZS) {
double **x = atom->x;
double boxzlo = domain->boxzlo;
double invzprd = 1.0/domain->zprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][2] - boxzlo) * invzprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == XU) {
double **x = atom->x;
int *image = atom->image;
double xprd = domain->xprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YU) {
double **x = atom->x;
int *image = atom->image;
double yprd = domain->yprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZU) {
double **x = atom->x;
int *image = atom->image;
double zprd = domain->zprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IX) {
int *image = atom->image;
for (i = 0; i < nlocal; i++)
dchoose[i] = (image[i] & 1023) - 512;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IY) {
int *image = atom->image;
for (i = 0; i < nlocal; i++)
dchoose[i] = (image[i] >> 10 & 1023) - 512;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IX) {
int *image = atom->image;
for (i = 0; i < nlocal; i++)
dchoose[i] = (image[i] >> 20) - 512;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == VX) {
ptr = &atom->v[0][0];
nstride = 3;
} else if (thresh_array[ithresh] == VY) {
ptr = &atom->v[0][1];
nstride = 3;
} else if (thresh_array[ithresh] == VZ) {
ptr = &atom->v[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == FX) {
ptr = &atom->f[0][0];
nstride = 3;
} else if (thresh_array[ithresh] == FY) {
ptr = &atom->f[0][1];
nstride = 3;
} else if (thresh_array[ithresh] == FZ) {
ptr = &atom->f[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == Q) {
ptr = atom->q;
nstride = 1;
} else if (thresh_array[ithresh] == MUX) {
ptr = &atom->mu[0][0];
nstride = 3;
} else if (thresh_array[ithresh] == MUY) {
ptr = &atom->mu[0][1];
nstride = 3;
} else if (thresh_array[ithresh] == MUZ) {
ptr = &atom->mu[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == TQX) {
ptr = &atom->torque[0][0];
nstride = 3;
} else if (thresh_array[ithresh] == TQY) {
ptr = &atom->torque[0][1];
nstride = 3;
} else if (thresh_array[ithresh] == TQZ) {
ptr = &atom->torque[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == EPAIR) {
ptr = compute[index_epair]->scalar_atom;
nstride = 1;
} else if (thresh_array[ithresh] == KE) {
ptr = compute[index_ke]->scalar_atom;
nstride = 1;
} else if (thresh_array[ithresh] == ETOTAL) {
ptr = compute[index_etotal]->scalar_atom;
nstride = 1;
} else if (thresh_array[ithresh] == CENTRO) {
ptr = compute[index_centro]->scalar_atom;
nstride = 1;
} else if (thresh_array[ithresh] == SXX) {
ptr = &compute[index_stress]->vector_atom[0][0];
nstride = 6;
} else if (thresh_array[ithresh] == SYY) {
ptr = &compute[index_stress]->vector_atom[0][1];
nstride = 6;
} else if (thresh_array[ithresh] == SZZ) {
ptr = &compute[index_stress]->vector_atom[0][2];
nstride = 6;
} else if (thresh_array[ithresh] == SXY) {
ptr = &compute[index_stress]->vector_atom[0][3];
nstride = 6;
} else if (thresh_array[ithresh] == SXZ) {
ptr = &compute[index_stress]->vector_atom[0][4];
nstride = 6;
} else if (thresh_array[ithresh] == SYZ) {
ptr = &compute[index_stress]->vector_atom[0][5];
nstride = 6;
} else if (thresh_array[ithresh] == COMPUTE) {
i = nfield + ithresh;
if (arg_compute[i] == 0) {
ptr = compute[field2compute[i]]->scalar_atom;
nstride = 1;
} else {
ptr = &compute[field2compute[i]]->vector_atom[0][arg_compute[i]-1];
nstride = compute[field2compute[i]]->size_peratom;
}
}
value = thresh_value[ithresh];
if (thresh_op[ithresh] == GE) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr >= value) {
choose[i] = 0;
nmine--;
}
} else if (thresh_op[ithresh] == GT) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr > value) {
choose[i] = 0;
nmine--;
}
} else if (thresh_op[ithresh] == LE) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr <= value) {
choose[i] = 0;
nmine--;
}
} else if (thresh_op[ithresh] == LT) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr < value) {
choose[i] = 0;
nmine--;
}
} else if (thresh_op[ithresh] == EQ) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr == value) {
choose[i] = 0;
nmine--;
}
} else if (thresh_op[ithresh] == NEQ) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr != value) {
choose[i] = 0;
nmine--;
}
}
}
}
return nmine;
}
/* ---------------------------------------------------------------------- */
int DumpCustom::pack()
{
for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n);
return nmine*size_one;
}
/* ---------------------------------------------------------------------- */
void DumpCustom::write_data(int n, double *buf)
{
(this->*write_choice)(n,buf);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::write_binary(int n, double *buf)
{
n *= size_one;
fwrite(&n,sizeof(int),1,fp);
fwrite(buf,sizeof(double),n,fp);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::write_text(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 DumpCustom::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],"tag") == 0) {
pack_choice[i] = &DumpCustom::pack_tag;
vtype[i] = INT;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (atom->molecule == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_molecule;
vtype[i] = INT;
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[i] = &DumpCustom::pack_type;
vtype[i] = INT;
} else if (strcmp(arg[iarg],"x") == 0) {
pack_choice[i] = &DumpCustom::pack_x;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"y") == 0) {
pack_choice[i] = &DumpCustom::pack_y;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"z") == 0) {
pack_choice[i] = &DumpCustom::pack_z;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"xs") == 0) {
pack_choice[i] = &DumpCustom::pack_xs;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"ys") == 0) {
pack_choice[i] = &DumpCustom::pack_ys;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"zs") == 0) {
pack_choice[i] = &DumpCustom::pack_zs;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"xu") == 0) {
pack_choice[i] = &DumpCustom::pack_xu;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"yu") == 0) {
pack_choice[i] = &DumpCustom::pack_yu;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"zu") == 0) {
pack_choice[i] = &DumpCustom::pack_zu;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[i] = &DumpCustom::pack_ix;
vtype[i] = INT;
} else if (strcmp(arg[iarg],"iy") == 0) {
pack_choice[i] = &DumpCustom::pack_iy;
vtype[i] = INT;
} else if (strcmp(arg[iarg],"iz") == 0) {
pack_choice[i] = &DumpCustom::pack_iz;
vtype[i] = INT;
} else if (strcmp(arg[iarg],"vx") == 0) {
pack_choice[i] = &DumpCustom::pack_vx;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"vy") == 0) {
pack_choice[i] = &DumpCustom::pack_vy;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"vz") == 0) {
pack_choice[i] = &DumpCustom::pack_vz;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"fx") == 0) {
pack_choice[i] = &DumpCustom::pack_fx;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"fy") == 0) {
pack_choice[i] = &DumpCustom::pack_fy;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"fz") == 0) {
pack_choice[i] = &DumpCustom::pack_fz;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"q") == 0) {
if (atom->q == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_q;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"mux") == 0) {
if (atom->mu == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_mux;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"muy") == 0) {
if (atom->mu == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_muy;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"muz") == 0) {
if (atom->mu == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_muz;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (atom->torque == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqx;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (atom->torque == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqy;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (atom->torque == NULL)
error->all("Dumping an atom quantity that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqz;
vtype[i] = DOUBLE;
} else if (strcmp(arg[iarg],"epair") == 0) {
pack_choice[i] = &DumpCustom::pack_epair;
vtype[i] = DOUBLE;
index_epair = add_compute(style_epair,1);
} else if (strcmp(arg[iarg],"ke") == 0) {
pack_choice[i] = &DumpCustom::pack_ke;
vtype[i] = DOUBLE;
index_ke = add_compute(style_ke,1);
} else if (strcmp(arg[iarg],"etotal") == 0) {
pack_choice[i] = &DumpCustom::pack_etotal;
vtype[i] = DOUBLE;
index_epair = add_compute(style_epair,1);
index_etotal = add_compute(style_etotal,1);
} else if (strcmp(arg[iarg],"centro") == 0) {
pack_choice[i] = &DumpCustom::pack_centro;
vtype[i] = DOUBLE;
index_centro = add_compute(style_centro,1);
} else if (strcmp(arg[iarg],"sxx") == 0) {
pack_choice[i] = &DumpCustom::pack_sxx;
vtype[i] = DOUBLE;
index_stress = add_compute(style_stress,1);
} else if (strcmp(arg[iarg],"syy") == 0) {
pack_choice[i] = &DumpCustom::pack_syy;
vtype[i] = DOUBLE;
index_stress = add_compute(style_stress,1);
} else if (strcmp(arg[iarg],"szz") == 0) {
pack_choice[i] = &DumpCustom::pack_szz;
vtype[i] = DOUBLE;
index_stress = add_compute(style_stress,1);
} else if (strcmp(arg[iarg],"sxy") == 0) {
pack_choice[i] = &DumpCustom::pack_sxy;
vtype[i] = DOUBLE;
index_stress = add_compute(style_stress,1);
} else if (strcmp(arg[iarg],"sxz") == 0) {
pack_choice[i] = &DumpCustom::pack_sxz;
vtype[i] = DOUBLE;
index_stress = add_compute(style_stress,1);
} else if (strcmp(arg[iarg],"syz") == 0) {
pack_choice[i] = &DumpCustom::pack_syz;
vtype[i] = DOUBLE;
index_stress = add_compute(style_stress,1);
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
// if Compute has pre-compute, first add it to list
} else if (strncmp(arg[iarg],"c_",2) == 0) {
pack_choice[i] = &DumpCustom::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 custom command");
arg_compute[i] = atoi(ptr+1);
*ptr = '\0';
} else arg_compute[i] = 0;
n = modify->find_compute(suffix);
if (n < 0) error->all("Could not find dump custom compute ID");
if (modify->compute[n]->peratom_flag == 0)
error->all("Dump custom compute ID does not compute peratom info");
if (arg_compute[i] == 0 && modify->compute[n]->size_peratom > 0)
error->all("Dump custom compute ID does not compute scalar per atom");
if (arg_compute[i] > 0 && modify->compute[n]->size_peratom == 0)
error->all("Dump custom compute ID does not compute vector per atom");
if (arg_compute[i] > 0 &&
arg_compute[i] > modify->compute[n]->size_peratom)
error->all("Dump custom compute ID vector is not large enough");
if (modify->compute[n]->id_pre)
int tmp = add_compute(modify->compute[n]->id_pre,0);
field2compute[i] = add_compute(suffix,0);
delete [] suffix;
} else error->all("Invalid keyword in dump custom command");
}
}
/* ----------------------------------------------------------------------
add Compute to list of Compute objects to call
return index of where this Compute is in call list
compute ID = dump-ID + "_" + keyword if appendflag is set, else just keyword
if already in call list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
int DumpCustom::add_compute(char *keyword, int appendflag)
{
int n = strlen(id) + strlen(keyword) + 2;
char *name = new char[n];
if (appendflag) {
strcpy(name,id);
strcat(name,"_");
strcat(name,keyword);
} else strcpy(name,keyword);
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(name,id_compute[icompute]) == 0) break;
if (icompute < ncompute) {
delete [] name;
return icompute;
}
id_compute = (char **)
memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute");
compute = (Compute **)
memory->srealloc(compute,(ncompute+1)*sizeof(Compute *),"dump:compute");
n = strlen(name) + 1;
id_compute[ncompute] = new char[n];
strcpy(id_compute[ncompute],name);
delete [] name;
ncompute++;
return ncompute-1;
}
/* ----------------------------------------------------------------------
create a compute
compute ID = dump-ID + "_" + keyword, compute style = keyword
pass additional extra args to Modify::add_compute() if defined
------------------------------------------------------------------------- */
void DumpCustom::create_compute(char *keyword, char *extra)
{
int n = strlen(id) + strlen(keyword) + 2;
char *name = new char[n];
strcpy(name,id);
strcat(name,"_");
strcat(name,keyword);
char **newarg = new char*[4];
newarg[0] = name;
newarg[1] = group->names[igroup];
newarg[2] = keyword;
if (extra) newarg[3] = extra;
if (extra) modify->add_compute(4,newarg);
else modify->add_compute(3,newarg);
delete [] name;
delete [] newarg;
}
/* ---------------------------------------------------------------------- */
int DumpCustom::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"region") == 0) {
if (narg < 2) error->all("Illegal dump_modify command");
if (strcmp(arg[1],"none") == 0) iregion = -1;
else {
for (iregion = 0; iregion < domain->nregion; iregion++)
if (strcmp(arg[1],domain->regions[iregion]->id) == 0) break;
if (iregion == domain->nregion)
error->all("Dump_modify region ID does not exist");
}
return 2;
} else if (strcmp(arg[0],"thresh") == 0) {
if (narg < 2) error->all("Illegal dump_modify command");
if (strcmp(arg[1],"none") == 0) {
if (nthresh) {
memory->sfree(thresh_array);
memory->sfree(thresh_op);
memory->sfree(thresh_value);
thresh_array = NULL;
thresh_op = NULL;
thresh_value = NULL;
}
nthresh = 0;
return 2;
}
if (narg < 4) error->all("Illegal dump_modify command");
// grow threshhold arrays
thresh_array = (int *)
memory->srealloc(thresh_array,(nthresh+1)*sizeof(int),
"dump:thresh_array");
thresh_op = (int *)
memory->srealloc(thresh_op,(nthresh+1)*sizeof(int),
"dump:thresh_op");
thresh_value = (double *)
memory->srealloc(thresh_value,(nthresh+1)*sizeof(double),
"dump:thresh_value");
// set keyword type of threshhold
// customize by adding to if statement
if (strcmp(arg[1],"tag") == 0) thresh_array[nthresh] = TAG;
else if (strcmp(arg[1],"mol") == 0) thresh_array[nthresh] = MOL;
else if (strcmp(arg[1],"type") == 0) thresh_array[nthresh] = TYPE;
else if (strcmp(arg[1],"x") == 0) thresh_array[nthresh] = X;
else if (strcmp(arg[1],"y") == 0) thresh_array[nthresh] = Y;
else if (strcmp(arg[1],"z") == 0) thresh_array[nthresh] = Z;
else if (strcmp(arg[1],"xs") == 0) thresh_array[nthresh] = XS;
else if (strcmp(arg[1],"ys") == 0) thresh_array[nthresh] = YS;
else if (strcmp(arg[1],"zs") == 0) thresh_array[nthresh] = ZS;
else if (strcmp(arg[1],"xu") == 0) thresh_array[nthresh] = XU;
else if (strcmp(arg[1],"yu") == 0) thresh_array[nthresh] = YU;
else if (strcmp(arg[1],"zu") == 0) thresh_array[nthresh] = ZU;
else if (strcmp(arg[1],"ix") == 0) thresh_array[nthresh] = IX;
else if (strcmp(arg[1],"iy") == 0) thresh_array[nthresh] = IY;
else if (strcmp(arg[1],"iz") == 0) thresh_array[nthresh] = IZ;
else if (strcmp(arg[1],"vx") == 0) thresh_array[nthresh] = VX;
else if (strcmp(arg[1],"vy") == 0) thresh_array[nthresh] = VY;
else if (strcmp(arg[1],"vz") == 0) thresh_array[nthresh] = VZ;
else if (strcmp(arg[1],"fx") == 0) thresh_array[nthresh] = FX;
else if (strcmp(arg[1],"fy") == 0) thresh_array[nthresh] = FY;
else if (strcmp(arg[1],"fz") == 0) thresh_array[nthresh] = FZ;
else if (strcmp(arg[1],"q") == 0) thresh_array[nthresh] = Q;
else if (strcmp(arg[1],"mux") == 0) thresh_array[nthresh] = MUX;
else if (strcmp(arg[1],"muy") == 0) thresh_array[nthresh] = MUY;
else if (strcmp(arg[1],"muz") == 0) thresh_array[nthresh] = MUZ;
else if (strcmp(arg[1],"tqx") == 0) thresh_array[nthresh] = TQX;
else if (strcmp(arg[1],"tqy") == 0) thresh_array[nthresh] = TQY;
else if (strcmp(arg[1],"tqz") == 0) thresh_array[nthresh] = TQZ;
else if (strcmp(arg[1],"epair") == 0) {
thresh_array[nthresh] = EPAIR;
if (index_epair < 0) {
index_epair = add_compute(style_epair,1);
create_compute(style_epair,NULL);
}
} else if (strcmp(arg[1],"ke") == 0) {
thresh_array[nthresh] = KE;
if (index_ke < 0) {
index_ke = add_compute(style_ke,1);
create_compute(style_ke,NULL);
}
} else if (strcmp(arg[1],"etotal") == 0) {
thresh_array[nthresh] = ETOTAL;
if (index_etotal < 0) {
if (index_epair < 0) {
index_epair = add_compute(style_epair,1);
create_compute(style_epair,NULL);
}
index_etotal = add_compute(style_etotal,1);
create_compute(style_etotal,style_epair);
}
} else if (strcmp(arg[1],"centro") == 0) {
thresh_array[nthresh] = CENTRO;
if (index_centro < 0) {
index_centro = add_compute(style_centro,1);
create_compute(style_stress,NULL);
}
} else if (strcmp(arg[1],"sxx") == 0) {
thresh_array[nthresh] = SXX;
if (index_stress < 0) {
index_stress = add_compute(style_stress,1);
create_compute(style_stress,NULL);
}
} else if (strcmp(arg[1],"syy") == 0) {
thresh_array[nthresh] = SYY;
if (index_stress < 0) {
index_stress = add_compute(style_stress,1);
create_compute(style_stress,NULL);
}
} else if (strcmp(arg[1],"szz") == 0) {
thresh_array[nthresh] = SZZ;
if (index_stress < 0) {
index_stress = add_compute(style_stress,1);
create_compute(style_stress,NULL);
}
} else if (strcmp(arg[1],"sxy") == 0) {
thresh_array[nthresh] = SXY;
if (index_stress < 0) {
index_stress = add_compute(style_stress,1);
create_compute(style_stress,NULL);
}
} else if (strcmp(arg[1],"sxz") == 0) {
thresh_array[nthresh] = SXZ;
if (index_stress < 0) {
index_stress = add_compute(style_stress,1);
create_compute(style_stress,NULL);
}
} else if (strcmp(arg[1],"syz") == 0) {
thresh_array[nthresh] = SYZ;
if (index_stress < 0) {
index_stress = add_compute(style_stress,1);
create_compute(style_stress,NULL);
}
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
// must grow field2compute and arg_compute arrays,
// since access is beyond nfield
// if Compute has pre-compute, first add it to list
} else if (strncmp(arg[1],"c_",2) == 0) {
thresh_array[nthresh] = COMPUTE;
field2compute = (int *) memory->srealloc(field2compute,
(nfield+nthresh+1)*sizeof(int),
"dump:field2compute");
arg_compute = (int *) memory->srealloc(arg_compute,
(nfield+nthresh+1)*sizeof(int),
"dump:arg_compute");
int n = strlen(arg[1]);
char *suffix = new char[n];
strcpy(suffix,&arg[1][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Invalid keyword in dump custom command");
arg_compute[nfield+nthresh] = atoi(ptr+1);
*ptr = '\0';
} else arg_compute[nfield+nthresh] = 0;
n = modify->find_compute(suffix);
if (n < 0) error->all("Could not find dump custom compute ID");
if (modify->compute[n]->peratom_flag == 0)
error->all("Dump custom compute ID does not compute peratom info");
if (arg_compute[nfield+nthresh] == 0 &&
modify->compute[n]->size_peratom > 0)
error->all("Dump custom compute ID does not compute scalar per atom");
if (arg_compute[nfield+nthresh] > 0 &&
modify->compute[n]->size_peratom == 0)
error->all("Dump custom compute ID does not compute vector per atom");
if (arg_compute[nfield+nthresh] > 0 &&
arg_compute[nfield+nthresh] > modify->compute[n]->size_peratom)
error->all("Dump custom compute ID vector is not large enough");
if (modify->compute[n]->id_pre)
int tmp = add_compute(modify->compute[n]->id_pre,0);
field2compute[nfield+nthresh] = add_compute(suffix,0);
delete [] suffix;
} else error->all("Invalid dump_modify threshhold operator");
// set operation type of threshhold
if (strcmp(arg[2],">=") == 0) thresh_op[nthresh] = LT;
else if (strcmp(arg[2],">") == 0) thresh_op[nthresh] = LE;
else if (strcmp(arg[2],"<=") == 0) thresh_op[nthresh] = GT;
else if (strcmp(arg[2],"<") == 0) thresh_op[nthresh] = GE;
else if (strcmp(arg[2],"=") == 0) thresh_op[nthresh] = NEQ;
else if (strcmp(arg[2],"<>") == 0) thresh_op[nthresh] = EQ;
else error->all("Invalid dump_modify threshhold operator");
// set threshhold value
thresh_value[nthresh] = atof(arg[3]);
nthresh++;
return 4;
}
return 0;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf and choose and local arrays
------------------------------------------------------------------------- */
int DumpCustom::memory_usage()
{
int bytes = maxbuf * sizeof(double);
bytes += maxlocal * sizeof(int);
bytes += maxlocal * sizeof(double);
return bytes;
}
// ----------------------------------------------------------------------
// one method for every keyword dump custom can output
// the atom quantity is packed into buf starting at n with stride size_one
// customize by adding a method
// ----------------------------------------------------------------------
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_compute(int n)
{
double *vector = compute[field2compute[n]]->scalar_atom;
double **array = compute[field2compute[n]]->vector_atom;
int index = arg_compute[n];
int nlocal = atom->nlocal;
if (index == 0) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = array[i][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_tag(int n)
{
int *tag = atom->tag;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = tag[i];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_molecule(int n)
{
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = molecule[i];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_type(int n)
{
int *type = atom->type;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = type[i];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_x(int n)
{
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = x[i][0];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_y(int n)
{
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = x[i][1];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_z(int n)
{
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = x[i][2];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_xs(int n)
{
double **x = atom->x;
int nlocal = atom->nlocal;
double boxxlo = domain->boxxlo;
double invxprd = 1.0/domain->xprd;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = (x[i][0] - boxxlo) * invxprd;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_ys(int n)
{
double **x = atom->x;
int nlocal = atom->nlocal;
double boxylo = domain->boxylo;
double invyprd = 1.0/domain->yprd;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = (x[i][1] - boxylo) * invyprd;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_zs(int n)
{
double **x = atom->x;
int nlocal = atom->nlocal;
double boxzlo = domain->boxzlo;
double invzprd = 1.0/domain->zprd;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = (x[i][2] - boxzlo) * invzprd;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_xu(int n)
{
double **x = atom->x;
int *image = atom->image;
double xprd = domain->xprd;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_yu(int n)
{
double **x = atom->x;
int *image = atom->image;
double yprd = domain->yprd;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_zu(int n)
{
double **x = atom->x;
int *image = atom->image;
double zprd = domain->zprd;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_ix(int n)
{
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = (image[i] & 1023) - 512;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_iy(int n)
{
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = (image[i] >> 10 & 1023) - 512;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_iz(int n)
{
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = (image[i] >> 20) - 512;
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_vx(int n)
{
double **v = atom->v;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = v[i][0];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_vy(int n)
{
double **v = atom->v;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = v[i][1];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_vz(int n)
{
double **v = atom->v;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = v[i][2];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_fx(int n)
{
double **f = atom->f;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = f[i][0];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_fy(int n)
{
double **f = atom->f;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = f[i][1];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_fz(int n)
{
double **f = atom->f;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = f[i][2];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_q(int n)
{
double *q = atom->q;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = q[i];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_mux(int n)
{
double **mu = atom->mu;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = mu[i][0];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_muy(int n)
{
double **mu = atom->mu;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = mu[i][1];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_muz(int n)
{
double **mu = atom->mu;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = mu[i][2];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_tqx(int n)
{
double **torque = atom->torque;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = torque[i][0];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_tqy(int n)
{
double **torque = atom->torque;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = torque[i][1];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_tqz(int n)
{
double **torque = atom->torque;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = torque[i][2];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_epair(int n)
{
double *epair = compute[index_epair]->scalar_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = epair[i];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_ke(int n)
{
double *ke = compute[index_ke]->scalar_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = ke[i];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_etotal(int n)
{
double *etotal = compute[index_etotal]->scalar_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = etotal[i];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_centro(int n)
{
double *centro = compute[index_centro]->scalar_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = centro[i];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_sxx(int n)
{
double **stress = compute[index_stress]->vector_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = stress[i][0];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_syy(int n)
{
double **stress = compute[index_stress]->vector_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = stress[i][1];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_szz(int n)
{
double **stress = compute[index_stress]->vector_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = stress[i][2];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_sxy(int n)
{
double **stress = compute[index_stress]->vector_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = stress[i][3];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_sxz(int n)
{
double **stress = compute[index_stress]->vector_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = stress[i][4];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_syz(int n)
{
double **stress = compute[index_stress]->vector_atom;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = stress[i][5];
n += size_one;
}
}
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