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dump_custom_vtk.cpp
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dump_custom_vtk.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.
This file initially came from LIGGGHTS (www.liggghts.com)
Copyright (2014) DCS Computing GmbH, Linz
Copyright (2015) Johannes Kepler University Linz
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Daniel Queteschiner (DCS, JKU)
Christoph Kloss (DCS)
Richard Berger (JKU)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "dump_custom_vtk.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "region.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
#include <vector>
#include <sstream>
#include <vtkVersion.h>
#ifndef VTK_MAJOR_VERSION
#include <vtkConfigure.h>
#endif
#include <vtkPointData.h>
#include <vtkCellData.h>
#include <vtkDoubleArray.h>
#include <vtkIntArray.h>
#include <vtkStringArray.h>
#include <vtkPolyData.h>
#include <vtkPolyDataWriter.h>
#include <vtkXMLPolyDataWriter.h>
#include <vtkXMLPPolyDataWriter.h>
#include <vtkRectilinearGrid.h>
#include <vtkRectilinearGridWriter.h>
#include <vtkXMLRectilinearGridWriter.h>
#include <vtkHexahedron.h>
#include <vtkUnstructuredGrid.h>
#include <vtkUnstructuredGridWriter.h>
#include <vtkXMLUnstructuredGridWriter.h>
#include <vtkXMLPUnstructuredGridWriter.h>
using namespace LAMMPS_NS;
// customize by
// * adding an enum constant (add vector components in consecutive order)
// * adding a pack_*(int) function for the value
// * adjusting parse_fields function to add the pack_* function to pack_choice
// (in case of vectors, adjust identify_vectors as well)
// * adjusting thresh part in modify_param and count functions
enum{X,Y,Z, // required for vtk, must come first
ID,MOL,PROC,PROCP1,TYPE,ELEMENT,MASS,
XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,
XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI,
IX,IY,IZ,
VX,VY,VZ,FX,FY,FZ,
Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
TQX,TQY,TQZ,
VARIABLE,COMPUTE,FIX,INAME,DNAME,
ATTRIBUTES}; // must come last
enum{LT,LE,GT,GE,EQ,NEQ};
enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCFG
enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats
#define INVOKED_PERATOM 8
#define ONEFIELD 32
#define DELTA 1048576
/* ---------------------------------------------------------------------- */
DumpCustomVTK::DumpCustomVTK(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
if (narg == 5) error->all(FLERR,"No dump custom/vtk arguments specified");
pack_choice.clear();
vtype.clear();
name.clear();
myarrays.clear();
n_calls_ = 0;
// process attributes
// ioptional = start of additional optional args
// only dump image and dump movie styles process optional args
ioptional = parse_fields(narg,arg);
if (ioptional < narg &&
strcmp(style,"image") != 0 && strcmp(style,"movie") != 0)
error->all(FLERR,"Invalid attribute in dump custom command");
size_one = pack_choice.size();
current_pack_choice_key = -1;
if (filewriter) reset_vtk_data_containers();
label = NULL;
{
// parallel vtp/vtu requires proc number to be preceded by underscore '_'
multiname_ex = NULL;
char *ptr = strchr(filename,'%');
if (ptr) {
multiname_ex = new char[strlen(filename) + 16];
*ptr = '\0';
sprintf(multiname_ex,"%s_%d%s",filename,me,ptr+1);
*ptr = '%';
}
}
vtk_file_format = VTK;
char *suffix = filename + strlen(filename) - strlen(".vtp");
if (suffix > filename && strcmp(suffix,".vtp") == 0) {
if (multiproc) vtk_file_format = PVTP;
else vtk_file_format = VTP;
} else if (suffix > filename && strcmp(suffix,".vtu") == 0) {
if (multiproc) vtk_file_format = PVTU;
else vtk_file_format = VTU;
}
if (vtk_file_format == VTK) { // no multiproc support for legacy vtk format
if (me != 0) filewriter = 0;
fileproc = 0;
multiproc = 0;
nclusterprocs = nprocs;
}
filecurrent = NULL;
domainfilecurrent = NULL;
parallelfilecurrent = NULL;
header_choice = NULL;
write_choice = NULL;
boxcorners = NULL;
}
/* ---------------------------------------------------------------------- */
DumpCustomVTK::~DumpCustomVTK()
{
delete [] filecurrent;
delete [] domainfilecurrent;
delete [] parallelfilecurrent;
delete [] multiname_ex;
delete [] label;
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::init_style()
{
// default for element names = C
if (typenames == NULL) {
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
typenames[itype] = new char[2];
strcpy(typenames[itype],"C");
}
}
// setup boundary string
domain->boundary_string(boundstr);
// setup function ptrs
header_choice = &DumpCustomVTK::header_vtk;
if (vtk_file_format == VTP || vtk_file_format == PVTP)
write_choice = &DumpCustomVTK::write_vtp;
else if (vtk_file_format == VTU || vtk_file_format == PVTU)
write_choice = &DumpCustomVTK::write_vtu;
else
write_choice = &DumpCustomVTK::write_vtk;
// 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 custom/vtk 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 custom/vtk fix ID");
fix[i] = modify->fix[ifix];
if (nevery % modify->fix[ifix]->peratom_freq)
error->all(FLERR,"Dump custom/vtk and fix not computed at compatible times");
}
int ivariable;
for (int i = 0; i < nvariable; i++) {
ivariable = input->variable->find(id_variable[i]);
if (ivariable < 0)
error->all(FLERR,"Could not find dump custom/vtk variable name");
variable[i] = ivariable;
}
int icustom;
for (int i = 0; i < ncustom; i++) {
icustom = atom->find_custom(id_custom[i],flag_custom[i]);
if (icustom < 0)
error->all(FLERR,"Could not find custom per-atom property ID");
}
// set index and check validity of region
if (iregion >= 0) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for dump custom/vtk does not exist");
}
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write_header(bigint)
{
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::header_vtk(bigint)
{
}
/* ---------------------------------------------------------------------- */
int DumpCustomVTK::count()
{
n_calls_ = 0;
int i;
// grow choose and variable vbuf arrays if needed
int nlocal = atom->nlocal;
if (atom->nmax > maxlocal) {
maxlocal = atom->nmax;
memory->destroy(choose);
memory->destroy(dchoose);
memory->destroy(clist);
memory->create(choose,maxlocal,"dump:choose");
memory->create(dchoose,maxlocal,"dump:dchoose");
memory->create(clist,maxlocal,"dump:clist");
for (i = 0; i < nvariable; i++) {
memory->destroy(vbuf[i]);
memory->create(vbuf[i],maxlocal,"dump:vbuf");
}
}
// invoke Computes for per-atom 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_peratom != 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_PERATOM)) {
compute[i]->compute_peratom();
compute[i]->invoked_flag |= INVOKED_PERATOM;
}
}
}
}
// evaluate atom-style Variables for per-atom quantities
if (nvariable)
for (i = 0; i < nvariable; i++)
input->variable->compute_atom(variable[i],igroup,vbuf[i],1,0);
// choose all local atoms for output
for (i = 0; i < nlocal; i++) choose[i] = 1;
// 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;
}
// un-choose if not in region
if (iregion >= 0) {
Region *region = domain->regions[iregion];
region->prematch();
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;
}
// un-choose if any threshold 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] == ID) {
tagint *tag = atom->tag;
for (i = 0; i < nlocal; i++) dchoose[i] = tag[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == MOL) {
if (!atom->molecule_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
tagint *molecule = atom->molecule;
for (i = 0; i < nlocal; i++) dchoose[i] = molecule[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == PROC) {
for (i = 0; i < nlocal; i++) dchoose[i] = me;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == PROCP1) {
for (i = 0; i < nlocal; i++) dchoose[i] = me;
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] == ELEMENT) {
int *type = atom->type;
for (i = 0; i < nlocal; i++) dchoose[i] = type[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == MASS) {
if (atom->rmass) {
ptr = atom->rmass;
nstride = 1;
} else {
double *mass = atom->mass;
int *type = atom->type;
for (i = 0; i < nlocal; i++) dchoose[i] = mass[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->boxlo[0];
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->boxlo[1];
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->boxlo[2];
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] == XSTRI) {
double **x = atom->x;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) +
h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YSTRI) {
double **x = atom->x;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) +
h_inv[3]*(x[i][2]-boxlo[2]);
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZSTRI) {
double **x = atom->x;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]);
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == XU) {
double **x = atom->x;
imageint *image = atom->image;
double xprd = domain->xprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = x[i][0] + ((image[i] & IMGMASK) - IMGMAX) * xprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YU) {
double **x = atom->x;
imageint *image = atom->image;
double yprd = domain->yprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = x[i][1] +
((image[i] >> IMGBITS & IMGMASK) - IMGMAX) * yprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZU) {
double **x = atom->x;
imageint *image = atom->image;
double zprd = domain->zprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = x[i][2] + ((image[i] >> IMG2BITS) - IMGMAX) * zprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == XUTRI) {
double **x = atom->x;
imageint *image = atom->image;
double *h = domain->h;
int xbox,ybox,zbox;
for (i = 0; i < nlocal; i++) {
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dchoose[i] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
}
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YUTRI) {
double **x = atom->x;
imageint *image = atom->image;
double *h = domain->h;
int ybox,zbox;
for (i = 0; i < nlocal; i++) {
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dchoose[i] = x[i][1] + h[1]*ybox + h[3]*zbox;
}
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZUTRI) {
double **x = atom->x;
imageint *image = atom->image;
double *h = domain->h;
int zbox;
for (i = 0; i < nlocal; i++) {
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dchoose[i] = x[i][2] + h[2]*zbox;
}
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == XSU) {
double **x = atom->x;
imageint *image = atom->image;
double boxxlo = domain->boxlo[0];
double invxprd = 1.0/domain->xprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][0] - boxxlo) * invxprd +
(image[i] & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YSU) {
double **x = atom->x;
imageint *image = atom->image;
double boxylo = domain->boxlo[1];
double invyprd = 1.0/domain->yprd;
for (i = 0; i < nlocal; i++)
dchoose[i] =
(x[i][1] - boxylo) * invyprd +
(image[i] >> IMGBITS & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZSU) {
double **x = atom->x;
imageint *image = atom->image;
double boxzlo = domain->boxlo[2];
double invzprd = 1.0/domain->zprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][2] - boxzlo) * invzprd +
(image[i] >> IMG2BITS) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == XSUTRI) {
double **x = atom->x;
imageint *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) +
h_inv[5]*(x[i][1]-boxlo[1]) +
h_inv[4]*(x[i][2]-boxlo[2]) +
(image[i] & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YSUTRI) {
double **x = atom->x;
imageint *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) +
h_inv[3]*(x[i][2]-boxlo[2]) +
(image[i] >> IMGBITS & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZSUTRI) {
double **x = atom->x;
imageint *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]) +
(image[i] >> IMG2BITS) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IX) {
imageint *image = atom->image;
for (i = 0; i < nlocal; i++)
dchoose[i] = (image[i] & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IY) {
imageint *image = atom->image;
for (i = 0; i < nlocal; i++)
dchoose[i] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IZ) {
imageint *image = atom->image;
for (i = 0; i < nlocal; i++)
dchoose[i] = (image[i] >> IMG2BITS) - IMGMAX;
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) {
if (!atom->q_flag)
error->all(FLERR,"Threshold for an atom property that isn't allocated");
ptr = atom->q;
nstride = 1;
} else if (thresh_array[ithresh] == MUX) {
if (!atom->mu_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->mu[0][0];
nstride = 4;
} else if (thresh_array[ithresh] == MUY) {
if (!atom->mu_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->mu[0][1];
nstride = 4;
} else if (thresh_array[ithresh] == MUZ) {
if (!atom->mu_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->mu[0][2];
nstride = 4;
} else if (thresh_array[ithresh] == MU) {
if (!atom->mu_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->mu[0][3];
nstride = 4;
} else if (thresh_array[ithresh] == RADIUS) {
if (!atom->radius_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = atom->radius;
nstride = 1;
} else if (thresh_array[ithresh] == DIAMETER) {
if (!atom->radius_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
double *radius = atom->radius;
for (i = 0; i < nlocal; i++) dchoose[i] = 2.0*radius[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == OMEGAX) {
if (!atom->omega_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->omega[0][0];
nstride = 3;
} else if (thresh_array[ithresh] == OMEGAY) {
if (!atom->omega_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->omega[0][1];
nstride = 3;
} else if (thresh_array[ithresh] == OMEGAZ) {
if (!atom->omega_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->omega[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == ANGMOMX) {
if (!atom->angmom_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->angmom[0][0];
nstride = 3;
} else if (thresh_array[ithresh] == ANGMOMY) {
if (!atom->angmom_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->angmom[0][1];
nstride = 3;
} else if (thresh_array[ithresh] == ANGMOMZ) {
if (!atom->angmom_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->angmom[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == TQX) {
if (!atom->torque_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->torque[0][0];
nstride = 3;
} else if (thresh_array[ithresh] == TQY) {
if (!atom->torque_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->torque[0][1];
nstride = 3;
} else if (thresh_array[ithresh] == TQZ) {
if (!atom->torque_flag)
error->all(FLERR,
"Threshold for an atom property that isn't allocated");
ptr = &atom->torque[0][2];
nstride = 3;
} else if (thresh_array[ithresh] == COMPUTE) {
i = ATTRIBUTES + nfield + ithresh;
if (argindex[i] == 0) {
ptr = compute[field2index[i]]->vector_atom;
nstride = 1;
} else {
ptr = &compute[field2index[i]]->array_atom[0][argindex[i]-1];
nstride = compute[field2index[i]]->size_peratom_cols;
}
} else if (thresh_array[ithresh] == FIX) {
i = ATTRIBUTES + nfield + ithresh;
if (argindex[i] == 0) {
ptr = fix[field2index[i]]->vector_atom;
nstride = 1;
} else {
ptr = &fix[field2index[i]]->array_atom[0][argindex[i]-1];
nstride = fix[field2index[i]]->size_peratom_cols;
}
} else if (thresh_array[ithresh] == VARIABLE) {
i = ATTRIBUTES + nfield + ithresh;
ptr = vbuf[field2index[i]];
nstride = 1;
} else if (thresh_array[ithresh] == DNAME) {
int iwhich,tmp;
i = ATTRIBUTES + nfield + ithresh;
iwhich = atom->find_custom(id_custom[field2index[i]],tmp);
ptr = atom->dvector[iwhich];
nstride = 1;
} else if (thresh_array[ithresh] == INAME) {
int iwhich,tmp;
i = ATTRIBUTES + nfield + ithresh;
iwhich = atom->find_custom(id_custom[field2index[i]],tmp);
int *ivector = atom->ivector[iwhich];
for (i = 0; i < nlocal; i++)
dchoose[i] = ivector[i];
ptr = dchoose;
nstride = 1;
}
// unselect atoms that don't meet threshold criterion
value = thresh_value[ithresh];
switch (thresh_op[ithresh]) {
case LT:
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr >= value) choose[i] = 0;
break;
case LE:
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr > value) choose[i] = 0;
break;
case GT:
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr <= value) choose[i] = 0;
break;
case GE:
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr < value) choose[i] = 0;
break;
case EQ:
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr != value) choose[i] = 0;
break;
case NEQ:
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr == value) choose[i] = 0;
break;
}
}
}
// compress choose flags into clist
// nchoose = # of selected atoms
// clist[i] = local index of each selected atom
nchoose = 0;
for (i = 0; i < nlocal; i++)
if (choose[i]) clist[nchoose++] = i;
return nchoose;
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write()
{
// simulation box bounds
if (domain->triclinic == 0) {
boxxlo = domain->boxlo[0];
boxxhi = domain->boxhi[0];
boxylo = domain->boxlo[1];
boxyhi = domain->boxhi[1];
boxzlo = domain->boxlo[2];
boxzhi = domain->boxhi[2];
} else {
domain->box_corners();
boxcorners = domain->corners;
}
// nme = # of dump lines this proc contributes to dump
nme = count();
// ntotal = total # of dump lines in snapshot
// nmax = max # of dump lines on any proc
bigint bnme = nme;
MPI_Allreduce(&bnme,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
int nmax;
if (multiproc != nprocs) MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
else nmax = nme;
// write timestep header
// for multiproc,
// nheader = # of lines in this file via Allreduce on clustercomm
bigint nheader = ntotal;
if (multiproc)
MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,clustercomm);
if (filewriter) write_header(nheader);
// insure buf is sized for packing and communicating
// use nmax to insure filewriter proc can receive info from others
// limit nmax*size_one to int since used as arg in MPI calls
if (nmax > maxbuf) {
if ((bigint) nmax * size_one > MAXSMALLINT)
error->all(FLERR,"Too much per-proc info for dump");
maxbuf = nmax;
memory->destroy(buf);
memory->create(buf,maxbuf*size_one,"dump:buf");
}
// insure ids buffer is sized for sorting
if (sort_flag && sortcol == 0 && nmax > maxids) {
maxids = nmax;
memory->destroy(ids);
memory->create(ids,maxids,"dump:ids");
}
// pack my data into buf
// if sorting on IDs also request ID list from pack()
// sort buf as needed
if (sort_flag && sortcol == 0) pack(ids);
else pack(NULL);
if (sort_flag) sort();
// filewriter = 1 = this proc writes to file
// ping each proc in my cluster, receive its data, write data to file
// else wait for ping from fileproc, send my data to fileproc
int tmp,nlines;
MPI_Status status;
MPI_Request request;
// comm and output buf of doubles
if (filewriter) {
for (int iproc = 0; iproc < nclusterprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,me+iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,me+iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&nlines);
nlines /= size_one;
} else nlines = nme;
write_data(nlines,buf);
}
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,&status);
MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,fileproc,0,world);
}
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::pack(tagint *ids)
{
int n = 0;
for (std::map<int,FnPtrPack>::iterator it=pack_choice.begin(); it!=pack_choice.end(); ++it, ++n) {
current_pack_choice_key = it->first; // work-around for pack_compute, pack_fix, pack_variable
(this->*(it->second))(n);
}
if (ids) {
tagint *tag = atom->tag;
for (int i = 0; i < nchoose; i++)
ids[i] = tag[clist[i]];
}
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write_data(int n, double *mybuf)
{
(this->*write_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::setFileCurrent() {
delete [] filecurrent;
filecurrent = NULL;
char *filestar = filename;
if (multiproc) {
if (multiproc > 1) { // if dump_modify fileper or nfile was used
delete [] multiname_ex;
multiname_ex = NULL;
char *ptr = strchr(filename,'%');
if (ptr) {
int id;
if (me + nclusterprocs == nprocs) // last filewriter
id = multiproc -1;
else
id = me/nclusterprocs;
multiname_ex = new char[strlen(filename) + 16];
*ptr = '\0';
sprintf(multiname_ex,"%s_%d%s",filename,id,ptr+1);
*ptr = '%';
}
} // else multiname_ex built in constructor is OK
filestar = multiname_ex;
}
if (multifile == 0) {
filecurrent = new char[strlen(filestar) + 1];
strcpy(filecurrent, filestar);
} else {
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0) {
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
} else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
// filename of domain box data file
delete [] domainfilecurrent;
domainfilecurrent = NULL;
if (multiproc) {
// remove '%' character
char *ptr = strchr(filename,'%');
domainfilecurrent = new char[strlen(filename)];
*ptr = '\0';
sprintf(domainfilecurrent,"%s%s",filename,ptr+1);
*ptr = '%';
// insert "_boundingBox" string
ptr = strrchr(domainfilecurrent,'.');
filestar = new char[strlen(domainfilecurrent)+16];
*ptr = '\0';
sprintf(filestar,"%s_boundingBox.%s",domainfilecurrent,ptr+1);
delete [] domainfilecurrent;
domainfilecurrent = NULL;
if (multifile == 0) {
domainfilecurrent = new char[strlen(filestar) + 1];
strcpy(domainfilecurrent, filestar);
} else {
domainfilecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0) {
sprintf(domainfilecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
} else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(domainfilecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
delete [] filestar;
filestar = NULL;
} else {
domainfilecurrent = new char[strlen(filecurrent) + 16];
char *ptr = strrchr(filecurrent,'.');
*ptr = '\0';
sprintf(domainfilecurrent,"%s_boundingBox.%s",filecurrent,ptr+1);
*ptr = '.';
}
// filename of parallel file
if (multiproc && me == 0) {
delete [] parallelfilecurrent;
parallelfilecurrent = NULL;
// remove '%' character and add 'p' to file extension
// -> string length stays the same
char *ptr = strchr(filename,'%');
filestar = new char[strlen(filename) + 1];
*ptr = '\0';
sprintf(filestar,"%s%s",filename,ptr+1);
*ptr = '%';
ptr = strrchr(filestar,'.');
ptr++;
*ptr++='p';
*ptr++='v';
*ptr++='t';
*ptr++= (vtk_file_format == PVTP)?'p':'u';
*ptr++= 0;
if (multifile == 0) {
parallelfilecurrent = new char[strlen(filestar) + 1];
strcpy(parallelfilecurrent, filestar);
} else {
parallelfilecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0) {
sprintf(parallelfilecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
} else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(parallelfilecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
delete [] filestar;
filestar = NULL;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::buf2arrays(int n, double *mybuf)
{
for (int iatom=0; iatom < n; ++iatom) {
vtkIdType pid[1];
pid[0] = points->InsertNextPoint(mybuf[iatom*size_one],mybuf[iatom*size_one+1],mybuf[iatom*size_one+2]);
int j=3; // 0,1,2 = x,y,z handled just above
for (std::map<int, vtkSmartPointer<vtkAbstractArray> >::iterator it=myarrays.begin(); it!=myarrays.end(); ++it) {
vtkAbstractArray *paa = it->second;
if (it->second->GetNumberOfComponents() == 3) {
switch (vtype[it->first]) {
case INT:
{
int iv3[3] = { static_cast<int>(mybuf[iatom*size_one+j ]),
static_cast<int>(mybuf[iatom*size_one+j+1]),
static_cast<int>(mybuf[iatom*size_one+j+2]) };
vtkIntArray *pia = static_cast<vtkIntArray*>(paa);
pia->InsertNextTupleValue(iv3);
break;
}
case DOUBLE:
{
vtkDoubleArray *pda = static_cast<vtkDoubleArray*>(paa);
pda->InsertNextTupleValue(&mybuf[iatom*size_one+j]);
break;
}
}
j+=3;
} else {
switch (vtype[it->first]) {
case INT:
{
vtkIntArray *pia = static_cast<vtkIntArray*>(paa);
pia->InsertNextValue(mybuf[iatom*size_one+j]);
break;
}
case DOUBLE:
{
vtkDoubleArray *pda = static_cast<vtkDoubleArray*>(paa);
pda->InsertNextValue(mybuf[iatom*size_one+j]);
break;
}
case STRING:
{
vtkStringArray *psa = static_cast<vtkStringArray*>(paa);
psa->InsertNextValue(typenames[static_cast<int>(mybuf[iatom*size_one+j])]);
break;
}
}
++j;
}
}
pointsCells->InsertNextCell(1,pid);
}
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::prepare_domain_data(vtkRectilinearGrid *rgrid)
{
vtkSmartPointer<vtkDoubleArray> xCoords = vtkSmartPointer<vtkDoubleArray>::New();
xCoords->InsertNextValue(boxxlo);
xCoords->InsertNextValue(boxxhi);
vtkSmartPointer<vtkDoubleArray> yCoords = vtkSmartPointer<vtkDoubleArray>::New();
yCoords->InsertNextValue(boxylo);
yCoords->InsertNextValue(boxyhi);
vtkSmartPointer<vtkDoubleArray> zCoords = vtkSmartPointer<vtkDoubleArray>::New();
zCoords->InsertNextValue(boxzlo);
zCoords->InsertNextValue(boxzhi);
rgrid->SetDimensions(2,2,2);
rgrid->SetXCoordinates(xCoords);
rgrid->SetYCoordinates(yCoords);
rgrid->SetZCoordinates(zCoords);
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::prepare_domain_data_triclinic(vtkUnstructuredGrid *hexahedronGrid)
{
vtkSmartPointer<vtkPoints> hexahedronPoints = vtkSmartPointer<vtkPoints>::New();
hexahedronPoints->SetNumberOfPoints(8);
hexahedronPoints->InsertPoint(0, boxcorners[0][0], boxcorners[0][1], boxcorners[0][2]);
hexahedronPoints->InsertPoint(1, boxcorners[1][0], boxcorners[1][1], boxcorners[1][2]);
hexahedronPoints->InsertPoint(2, boxcorners[3][0], boxcorners[3][1], boxcorners[3][2]);
hexahedronPoints->InsertPoint(3, boxcorners[2][0], boxcorners[2][1], boxcorners[2][2]);
hexahedronPoints->InsertPoint(4, boxcorners[4][0], boxcorners[4][1], boxcorners[4][2]);
hexahedronPoints->InsertPoint(5, boxcorners[5][0], boxcorners[5][1], boxcorners[5][2]);
hexahedronPoints->InsertPoint(6, boxcorners[7][0], boxcorners[7][1], boxcorners[7][2]);
hexahedronPoints->InsertPoint(7, boxcorners[6][0], boxcorners[6][1], boxcorners[6][2]);
vtkSmartPointer<vtkHexahedron> hexahedron = vtkSmartPointer<vtkHexahedron>::New();
hexahedron->GetPointIds()->SetId(0, 0);
hexahedron->GetPointIds()->SetId(1, 1);
hexahedron->GetPointIds()->SetId(2, 2);
hexahedron->GetPointIds()->SetId(3, 3);
hexahedron->GetPointIds()->SetId(4, 4);
hexahedron->GetPointIds()->SetId(5, 5);
hexahedron->GetPointIds()->SetId(6, 6);
hexahedron->GetPointIds()->SetId(7, 7);
hexahedronGrid->Allocate(1, 1);
hexahedronGrid->InsertNextCell(hexahedron->GetCellType(),
hexahedron->GetPointIds());
hexahedronGrid->SetPoints(hexahedronPoints);
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write_domain_vtk()
{
vtkSmartPointer<vtkRectilinearGrid> rgrid = vtkSmartPointer<vtkRectilinearGrid>::New();
prepare_domain_data(rgrid.GetPointer());
vtkSmartPointer<vtkRectilinearGridWriter> gwriter = vtkSmartPointer<vtkRectilinearGridWriter>::New();
if(label) gwriter->SetHeader(label);
else gwriter->SetHeader("Generated by LAMMPS");
if (binary) gwriter->SetFileTypeToBinary();
else gwriter->SetFileTypeToASCII();
#if VTK_MAJOR_VERSION < 6
gwriter->SetInput(rgrid);
#else
gwriter->SetInputData(rgrid);
#endif
gwriter->SetFileName(domainfilecurrent);
gwriter->Write();
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write_domain_vtk_triclinic()
{
vtkSmartPointer<vtkUnstructuredGrid> hexahedronGrid = vtkSmartPointer<vtkUnstructuredGrid>::New();
prepare_domain_data_triclinic(hexahedronGrid.GetPointer());
vtkSmartPointer<vtkUnstructuredGridWriter> gwriter = vtkSmartPointer<vtkUnstructuredGridWriter>::New();
if(label) gwriter->SetHeader(label);
else gwriter->SetHeader("Generated by LAMMPS");
if (binary) gwriter->SetFileTypeToBinary();
else gwriter->SetFileTypeToASCII();
#if VTK_MAJOR_VERSION < 6
gwriter->SetInput(hexahedronGrid);
#else
gwriter->SetInputData(hexahedronGrid);
#endif
gwriter->SetFileName(domainfilecurrent);
gwriter->Write();
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write_domain_vtr()
{
vtkSmartPointer<vtkRectilinearGrid> rgrid = vtkSmartPointer<vtkRectilinearGrid>::New();
prepare_domain_data(rgrid.GetPointer());
vtkSmartPointer<vtkXMLRectilinearGridWriter> gwriter = vtkSmartPointer<vtkXMLRectilinearGridWriter>::New();
if (binary) gwriter->SetDataModeToBinary();
else gwriter->SetDataModeToAscii();
#if VTK_MAJOR_VERSION < 6
gwriter->SetInput(rgrid);
#else
gwriter->SetInputData(rgrid);
#endif
gwriter->SetFileName(domainfilecurrent);
gwriter->Write();
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write_domain_vtu_triclinic()
{
vtkSmartPointer<vtkUnstructuredGrid> hexahedronGrid = vtkSmartPointer<vtkUnstructuredGrid>::New();
prepare_domain_data_triclinic(hexahedronGrid.GetPointer());
vtkSmartPointer<vtkXMLUnstructuredGridWriter> gwriter = vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
if (binary) gwriter->SetDataModeToBinary();
else gwriter->SetDataModeToAscii();
#if VTK_MAJOR_VERSION < 6
gwriter->SetInput(hexahedronGrid);
#else
gwriter->SetInputData(hexahedronGrid);
#endif
gwriter->SetFileName(domainfilecurrent);
gwriter->Write();
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write_vtk(int n, double *mybuf)
{
++n_calls_;
buf2arrays(n, mybuf);
if (n_calls_ < nclusterprocs)
return; // multiple processors but only proc 0 is a filewriter (-> nclusterprocs procs contribute to the filewriter's output data)
setFileCurrent();
{
#ifdef UNSTRUCTURED_GRID_VTK
vtkSmartPointer<vtkUnstructuredGrid> unstructuredGrid = vtkSmartPointer<vtkUnstructuredGrid>::New();
unstructuredGrid->SetPoints(points);
unstructuredGrid->SetCells(VTK_VERTEX, pointsCells);
for (std::map<int, vtkSmartPointer<vtkAbstractArray> >::iterator it=myarrays.begin(); it!=myarrays.end(); ++it) {
unstructuredGrid->GetPointData()->AddArray(it->second);
}
vtkSmartPointer<vtkUnstructuredGridWriter> writer = vtkSmartPointer<vtkUnstructuredGridWriter>::New();
#else
vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
polyData->SetPoints(points);
polyData->SetVerts(pointsCells);
for (std::map<int, vtkSmartPointer<vtkAbstractArray> >::iterator it=myarrays.begin(); it!=myarrays.end(); ++it) {
polyData->GetPointData()->AddArray(it->second);
}
vtkSmartPointer<vtkPolyDataWriter> writer = vtkSmartPointer<vtkPolyDataWriter>::New();
#endif
if(label) writer->SetHeader(label);
else writer->SetHeader("Generated by LAMMPS");
if (binary) writer->SetFileTypeToBinary();
else writer->SetFileTypeToASCII();
#ifdef UNSTRUCTURED_GRID_VTK
#if VTK_MAJOR_VERSION < 6
writer->SetInput(unstructuredGrid);
#else
writer->SetInputData(unstructuredGrid);
#endif
#else
#if VTK_MAJOR_VERSION < 6
writer->SetInput(polyData);
#else
writer->SetInputData(polyData);
#endif
#endif
writer->SetFileName(filecurrent);
writer->Write();
if (domain->triclinic == 0)
write_domain_vtk();
else
write_domain_vtk_triclinic();
}
reset_vtk_data_containers();
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write_vtp(int n, double *mybuf)
{
++n_calls_;
buf2arrays(n, mybuf);
if (n_calls_ < nclusterprocs)
return; // multiple processors but not all are filewriters (-> nclusterprocs procs contribute to the filewriter's output data)
setFileCurrent();
{
vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
polyData->SetPoints(points);
polyData->SetVerts(pointsCells);
for (std::map<int, vtkSmartPointer<vtkAbstractArray> >::iterator it=myarrays.begin(); it!=myarrays.end(); ++it) {
polyData->GetPointData()->AddArray(it->second);
}
vtkSmartPointer<vtkXMLPolyDataWriter> writer = vtkSmartPointer<vtkXMLPolyDataWriter>::New();
if (binary) writer->SetDataModeToBinary();
else writer->SetDataModeToAscii();
#if VTK_MAJOR_VERSION < 6
writer->SetInput(polyData);
#else
writer->SetInputData(polyData);
#endif
writer->SetFileName(filecurrent);
writer->Write();
if (me == 0) {
if (multiproc) {
vtkSmartPointer<vtkXMLPPolyDataWriter> pwriter = vtkSmartPointer<vtkXMLPPolyDataWriter>::New();
pwriter->SetFileName(parallelfilecurrent);
pwriter->SetNumberOfPieces((multiproc > 1)?multiproc:nprocs);
if (binary) pwriter->SetDataModeToBinary();
else pwriter->SetDataModeToAscii();
#if VTK_MAJOR_VERSION < 6
pwriter->SetInput(polyData);
#else
pwriter->SetInputData(polyData);
#endif
pwriter->Write();
}
if (domain->triclinic == 0) {
domainfilecurrent[strlen(domainfilecurrent)-1] = 'r'; // adjust filename extension
write_domain_vtr();
} else {
domainfilecurrent[strlen(domainfilecurrent)-1] = 'u'; // adjust filename extension
write_domain_vtu_triclinic();
}
}
}
reset_vtk_data_containers();
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::write_vtu(int n, double *mybuf)
{
++n_calls_;
buf2arrays(n, mybuf);
if (n_calls_ < nclusterprocs)
return; // multiple processors but not all are filewriters (-> nclusterprocs procs contribute to the filewriter's output data)
setFileCurrent();
{
vtkSmartPointer<vtkUnstructuredGrid> unstructuredGrid = vtkSmartPointer<vtkUnstructuredGrid>::New();
unstructuredGrid->SetPoints(points);
unstructuredGrid->SetCells(VTK_VERTEX, pointsCells);
for (std::map<int, vtkSmartPointer<vtkAbstractArray> >::iterator it=myarrays.begin(); it!=myarrays.end(); ++it) {
unstructuredGrid->GetPointData()->AddArray(it->second);
}
vtkSmartPointer<vtkXMLUnstructuredGridWriter> writer = vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
if (binary) writer->SetDataModeToBinary();
else writer->SetDataModeToAscii();
#if VTK_MAJOR_VERSION < 6
writer->SetInput(unstructuredGrid);
#else
writer->SetInputData(unstructuredGrid);
#endif
writer->SetFileName(filecurrent);
writer->Write();
if (me == 0) {
if (multiproc) {
vtkSmartPointer<vtkXMLPUnstructuredGridWriter> pwriter = vtkSmartPointer<vtkXMLPUnstructuredGridWriter>::New();
pwriter->SetFileName(parallelfilecurrent);
pwriter->SetNumberOfPieces((multiproc > 1)?multiproc:nprocs);
if (binary) pwriter->SetDataModeToBinary();
else pwriter->SetDataModeToAscii();
#if VTK_MAJOR_VERSION < 6
pwriter->SetInput(unstructuredGrid);
#else
pwriter->SetInputData(unstructuredGrid);
#endif
pwriter->Write();
}
if (domain->triclinic == 0) {
domainfilecurrent[strlen(domainfilecurrent)-1] = 'r'; // adjust filename extension
write_domain_vtr();
} else {
write_domain_vtu_triclinic();
}
}
}
reset_vtk_data_containers();
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::reset_vtk_data_containers()
{
points = vtkSmartPointer<vtkPoints>::New();
pointsCells = vtkSmartPointer<vtkCellArray>::New();
std::map<int,int>::iterator it=vtype.begin();
++it; ++it; ++it;
for (; it!=vtype.end(); ++it) {
switch(vtype[it->first]) {
case INT:
myarrays[it->first] = vtkSmartPointer<vtkIntArray>::New();
break;
case DOUBLE:
myarrays[it->first] = vtkSmartPointer<vtkDoubleArray>::New();
break;
case STRING:
myarrays[it->first] = vtkSmartPointer<vtkStringArray>::New();
break;
}
if (vector_set.find(it->first) != vector_set.end()) {
myarrays[it->first]->SetNumberOfComponents(3);
myarrays[it->first]->SetName(name[it->first].c_str());
++it; ++it;
} else {
myarrays[it->first]->SetName(name[it->first].c_str());
}
}
}
/* ---------------------------------------------------------------------- */
int DumpCustomVTK::parse_fields(int narg, char **arg)
{
pack_choice[X] = &DumpCustomVTK::pack_x;
vtype[X] = DOUBLE;
name[X] = "x";
pack_choice[Y] = &DumpCustomVTK::pack_y;
vtype[Y] = DOUBLE;
name[Y] = "y";
pack_choice[Z] = &DumpCustomVTK::pack_z;
vtype[Z] = DOUBLE;
name[Z] = "z";
// customize by adding to if statement
int i;
for (int iarg = 5; iarg < narg; iarg++) {
i = iarg-5;
if (strcmp(arg[iarg],"id") == 0) {
pack_choice[ID] = &DumpCustomVTK::pack_id;
vtype[ID] = INT;
name[ID] = arg[iarg];
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MOL] = &DumpCustomVTK::pack_molecule;
vtype[MOL] = INT;
name[MOL] = arg[iarg];
} else if (strcmp(arg[iarg],"proc") == 0) {
pack_choice[PROC] = &DumpCustomVTK::pack_proc;
vtype[PROC] = INT;
name[PROC] = arg[iarg];
} else if (strcmp(arg[iarg],"procp1") == 0) {
pack_choice[PROCP1] = &DumpCustomVTK::pack_procp1;
vtype[PROCP1] = INT;
name[PROCP1] = arg[iarg];
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[TYPE] = &DumpCustomVTK::pack_type;
vtype[TYPE] = INT;
name[TYPE] =arg[iarg];
} else if (strcmp(arg[iarg],"element") == 0) {
pack_choice[ELEMENT] = &DumpCustomVTK::pack_type;
vtype[ELEMENT] = STRING;
name[ELEMENT] = arg[iarg];
} else if (strcmp(arg[iarg],"mass") == 0) {
pack_choice[MASS] = &DumpCustomVTK::pack_mass;
vtype[MASS] = DOUBLE;
name[MASS] = arg[iarg];
} else if (strcmp(arg[iarg],"x") == 0) {
// required property
} else if (strcmp(arg[iarg],"y") == 0) {
// required property
} else if (strcmp(arg[iarg],"z") == 0) {
// required property
} else if (strcmp(arg[iarg],"xs") == 0) {
if (domain->triclinic) pack_choice[XS] = &DumpCustomVTK::pack_xs_triclinic;
else pack_choice[XS] = &DumpCustomVTK::pack_xs;
vtype[XS] = DOUBLE;
name[XS] = arg[iarg];
} else if (strcmp(arg[iarg],"ys") == 0) {
if (domain->triclinic) pack_choice[YS] = &DumpCustomVTK::pack_ys_triclinic;
else pack_choice[YS] = &DumpCustomVTK::pack_ys;
vtype[YS] = DOUBLE;
name[YS] = arg[iarg];
} else if (strcmp(arg[iarg],"zs") == 0) {
if (domain->triclinic) pack_choice[ZS] = &DumpCustomVTK::pack_zs_triclinic;
else pack_choice[ZS] = &DumpCustomVTK::pack_zs;
vtype[ZS] = DOUBLE;
name[ZS] = arg[iarg];
} else if (strcmp(arg[iarg],"xu") == 0) {
if (domain->triclinic) pack_choice[XU] = &DumpCustomVTK::pack_xu_triclinic;
else pack_choice[XU] = &DumpCustomVTK::pack_xu;
vtype[XU] = DOUBLE;
name[XU] = arg[iarg];
} else if (strcmp(arg[iarg],"yu") == 0) {
if (domain->triclinic) pack_choice[YU] = &DumpCustomVTK::pack_yu_triclinic;
else pack_choice[YU] = &DumpCustomVTK::pack_yu;
vtype[YU] = DOUBLE;
name[YU] = arg[iarg];
} else if (strcmp(arg[iarg],"zu") == 0) {
if (domain->triclinic) pack_choice[ZU] = &DumpCustomVTK::pack_zu_triclinic;
else pack_choice[ZU] = &DumpCustomVTK::pack_zu;
vtype[ZU] = DOUBLE;
name[ZU] = arg[iarg];
} else if (strcmp(arg[iarg],"xsu") == 0) {
if (domain->triclinic) pack_choice[XSU] = &DumpCustomVTK::pack_xsu_triclinic;
else pack_choice[XSU] = &DumpCustomVTK::pack_xsu;
vtype[XSU] = DOUBLE;
name[XSU] = arg[iarg];
} else if (strcmp(arg[iarg],"ysu") == 0) {
if (domain->triclinic) pack_choice[YSU] = &DumpCustomVTK::pack_ysu_triclinic;
else pack_choice[YSU] = &DumpCustomVTK::pack_ysu;
vtype[YSU] = DOUBLE;
name[YSU] = arg[iarg];
} else if (strcmp(arg[iarg],"zsu") == 0) {
if (domain->triclinic) pack_choice[ZSU] = &DumpCustomVTK::pack_zsu_triclinic;
else pack_choice[ZSU] = &DumpCustomVTK::pack_zsu;
vtype[ZSU] = DOUBLE;
name[ZSU] = arg[iarg];
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[IX] = &DumpCustomVTK::pack_ix;
vtype[IX] = INT;
name[IX] = arg[iarg];
} else if (strcmp(arg[iarg],"iy") == 0) {
pack_choice[IY] = &DumpCustomVTK::pack_iy;
vtype[IY] = INT;
name[IY] = arg[iarg];
} else if (strcmp(arg[iarg],"iz") == 0) {
pack_choice[IZ] = &DumpCustomVTK::pack_iz;
vtype[IZ] = INT;
name[IZ] = arg[iarg];
} else if (strcmp(arg[iarg],"vx") == 0) {
pack_choice[VX] = &DumpCustomVTK::pack_vx;
vtype[VX] = DOUBLE;
name[VX] = arg[iarg];
} else if (strcmp(arg[iarg],"vy") == 0) {
pack_choice[VY] = &DumpCustomVTK::pack_vy;
vtype[VY] = DOUBLE;
name[VY] = arg[iarg];
} else if (strcmp(arg[iarg],"vz") == 0) {
pack_choice[VZ] = &DumpCustomVTK::pack_vz;
vtype[VZ] = DOUBLE;
name[VZ] = arg[iarg];
} else if (strcmp(arg[iarg],"fx") == 0) {
pack_choice[FX] = &DumpCustomVTK::pack_fx;
vtype[FX] = DOUBLE;
name[FX] = arg[iarg];
} else if (strcmp(arg[iarg],"fy") == 0) {
pack_choice[FY] = &DumpCustomVTK::pack_fy;
vtype[FY] = DOUBLE;
name[FY] = arg[iarg];
} else if (strcmp(arg[iarg],"fz") == 0) {
pack_choice[FZ] = &DumpCustomVTK::pack_fz;
vtype[FZ] = DOUBLE;
name[FZ] = arg[iarg];
} else if (strcmp(arg[iarg],"q") == 0) {
if (!atom->q_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[Q] = &DumpCustomVTK::pack_q;
vtype[Q] = DOUBLE;
name[Q] = arg[iarg];
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MUX] = &DumpCustomVTK::pack_mux;
vtype[MUX] = DOUBLE;
name[MUX] = arg[iarg];
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MUY] = &DumpCustomVTK::pack_muy;
vtype[MUY] = DOUBLE;
name[MUY] = arg[iarg];
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MUZ] = &DumpCustomVTK::pack_muz;
vtype[MUZ] = DOUBLE;
name[MUZ] = arg[iarg];
} else if (strcmp(arg[iarg],"mu") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MU] = &DumpCustomVTK::pack_mu;
vtype[MU] = DOUBLE;
name[MU] = arg[iarg];
} else if (strcmp(arg[iarg],"radius") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[RADIUS] = &DumpCustomVTK::pack_radius;
vtype[RADIUS] = DOUBLE;
name[RADIUS] = arg[iarg];
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[DIAMETER] = &DumpCustomVTK::pack_diameter;
vtype[DIAMETER] = DOUBLE;
name[DIAMETER] = arg[iarg];
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[OMEGAX] = &DumpCustomVTK::pack_omegax;
vtype[OMEGAX] = DOUBLE;
name[OMEGAX] = arg[iarg];
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[OMEGAY] = &DumpCustomVTK::pack_omegay;
vtype[OMEGAY] = DOUBLE;
name[OMEGAY] = arg[iarg];
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[OMEGAZ] = &DumpCustomVTK::pack_omegaz;
vtype[OMEGAZ] = DOUBLE;
name[OMEGAZ] = arg[iarg];
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[ANGMOMX] = &DumpCustomVTK::pack_angmomx;
vtype[ANGMOMX] = DOUBLE;
name[ANGMOMX] = arg[iarg];
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[ANGMOMY] = &DumpCustomVTK::pack_angmomy;
vtype[ANGMOMY] = DOUBLE;
name[ANGMOMY] = arg[iarg];
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[ANGMOMZ] = &DumpCustomVTK::pack_angmomz;
vtype[ANGMOMZ] = DOUBLE;
name[ANGMOMZ] = arg[iarg];
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[TQX] = &DumpCustomVTK::pack_tqx;
vtype[TQX] = DOUBLE;
name[TQX] = arg[iarg];
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[TQY] = &DumpCustomVTK::pack_tqy;
vtype[TQY] = DOUBLE;
name[TQY] = arg[iarg];
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[TQZ] = &DumpCustomVTK::pack_tqz;
vtype[TQZ] = DOUBLE;
name[TQZ] = arg[iarg];
// 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[ATTRIBUTES+i] = &DumpCustomVTK::pack_compute;
vtype[ATTRIBUTES+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 custom/vtk command");
argindex[ATTRIBUTES+i] = atoi(ptr+1);
*ptr = '\0';
} else argindex[ATTRIBUTES+i] = 0;
n = modify->find_compute(suffix);
if (n < 0) error->all(FLERR,"Could not find dump custom/vtk compute ID");
if (modify->compute[n]->peratom_flag == 0)
error->all(FLERR,"Dump custom/vtk compute does not compute per-atom info");
if (argindex[ATTRIBUTES+i] == 0 && modify->compute[n]->size_peratom_cols > 0)
error->all(FLERR,
"Dump custom/vtk compute does not calculate per-atom vector");
if (argindex[ATTRIBUTES+i] > 0 && modify->compute[n]->size_peratom_cols == 0)
error->all(FLERR,\
"Dump custom/vtk compute does not calculate per-atom array");
if (argindex[ATTRIBUTES+i] > 0 &&
argindex[ATTRIBUTES+i] > modify->compute[n]->size_peratom_cols)
error->all(FLERR,"Dump custom/vtk compute vector is accessed out-of-range");
field2index[ATTRIBUTES+i] = add_compute(suffix);
name[ATTRIBUTES+i] = arg[iarg];
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[ATTRIBUTES+i] = &DumpCustomVTK::pack_fix;
vtype[ATTRIBUTES+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 custom/vtk command");
argindex[ATTRIBUTES+i] = atoi(ptr+1);
*ptr = '\0';
} else argindex[ATTRIBUTES+i] = 0;
n = modify->find_fix(suffix);
if (n < 0) error->all(FLERR,"Could not find dump custom/vtk fix ID");
if (modify->fix[n]->peratom_flag == 0)
error->all(FLERR,"Dump custom/vtk fix does not compute per-atom info");
if (argindex[ATTRIBUTES+i] == 0 && modify->fix[n]->size_peratom_cols > 0)
error->all(FLERR,"Dump custom/vtk fix does not compute per-atom vector");
if (argindex[ATTRIBUTES+i] > 0 && modify->fix[n]->size_peratom_cols == 0)
error->all(FLERR,"Dump custom/vtk fix does not compute per-atom array");
if (argindex[ATTRIBUTES+i] > 0 &&
argindex[ATTRIBUTES+i] > modify->fix[n]->size_peratom_cols)
error->all(FLERR,"Dump custom/vtk fix vector is accessed out-of-range");
field2index[ATTRIBUTES+i] = add_fix(suffix);
name[ATTRIBUTES+i] = arg[iarg];
delete [] suffix;
// variable value = v_name
} else if (strncmp(arg[iarg],"v_",2) == 0) {
pack_choice[ATTRIBUTES+i] = &DumpCustomVTK::pack_variable;
vtype[ATTRIBUTES+i] = DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
argindex[ATTRIBUTES+i] = 0;
n = input->variable->find(suffix);
if (n < 0) error->all(FLERR,"Could not find dump custom/vtk variable name");
if (input->variable->atomstyle(n) == 0)
error->all(FLERR,"Dump custom/vtk variable is not atom-style variable");
field2index[ATTRIBUTES+i] = add_variable(suffix);
name[ATTRIBUTES+i] = suffix;
delete [] suffix;
// custom per-atom floating point value = d_ID
} else if (strncmp(arg[iarg],"d_",2) == 0) {
pack_choice[ATTRIBUTES+i] = &DumpCustomVTK::pack_custom;
vtype[ATTRIBUTES+i] = DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
argindex[ATTRIBUTES+i] = 0;
int tmp = -1;
n = atom->find_custom(suffix,tmp);
if (n < 0)
error->all(FLERR,"Could not find custom per-atom property ID");
if (tmp != 1)
error->all(FLERR,"Custom per-atom property ID is not floating point");
field2index[ATTRIBUTES+i] = add_custom(suffix,1);
name[ATTRIBUTES+i] = suffix;
delete [] suffix;
// custom per-atom integer value = i_ID
} else if (strncmp(arg[iarg],"i_",2) == 0) {
pack_choice[ATTRIBUTES+i] = &DumpCustomVTK::pack_custom;
vtype[ATTRIBUTES+i] = INT;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
argindex[ATTRIBUTES+i] = 0;
int tmp = -1;
n = atom->find_custom(suffix,tmp);
if (n < 0)
error->all(FLERR,"Could not find custom per-atom property ID");
if (tmp != 0)
error->all(FLERR,"Custom per-atom property ID is not integer");
field2index[ATTRIBUTES+i] = add_custom(suffix,0);
name[ATTRIBUTES+i] = suffix;
delete [] suffix;
} else return iarg;
}
identify_vectors();
return narg;
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::identify_vectors()
{
// detect vectors
vector_set.insert(X); // required
int vector3_starts[] = {XS, XU, XSU, IX, VX, FX, MUX, OMEGAX, ANGMOMX, TQX};
int num_vector3_starts = sizeof(vector3_starts) / sizeof(int);
for (int v3s = 0; v3s < num_vector3_starts; v3s++) {
if(name.count(vector3_starts[v3s] ) &&
name.count(vector3_starts[v3s]+1) &&
name.count(vector3_starts[v3s]+2) )
{
std::string vectorName = name[vector3_starts[v3s]];
vectorName.erase(vectorName.find_first_of('x'));
name[vector3_starts[v3s]] = vectorName;
vector_set.insert(vector3_starts[v3s]);
}
}
// compute and fix vectors
for (std::map<int,std::string>::iterator it=name.begin(); it!=name.end(); ++it) {
if (it->first < ATTRIBUTES) // neither fix nor compute
continue;
if(argindex[it->first] == 0) // single value
continue;
// assume components are grouped together and in correct order
if(name.count(it->first + 1) && name.count(it->first + 2) ) { // more attributes?
if(it->second.compare(0,it->second.length()-3,name[it->first + 1],0,it->second.length()-3) == 0 && // same attributes?
it->second.compare(0,it->second.length()-3,name[it->first + 2],0,it->second.length()-3) == 0 )
{
it->second.erase(it->second.length()-1);
std::ostringstream oss;
oss << "-" << argindex[it->first+2] << "]";
it->second += oss.str();
vector_set.insert(it->first);
++it; ++it;
}
}
}
}
/* ----------------------------------------------------------------------
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 DumpCustomVTK::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 DumpCustomVTK::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;
}
/* ----------------------------------------------------------------------
add Variable to list of Variables used by dump
return index of where this Variable is in list
if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
int DumpCustomVTK::add_variable(char *id)
{
int ivariable;
for (ivariable = 0; ivariable < nvariable; ivariable++)
if (strcmp(id,id_variable[ivariable]) == 0) break;
if (ivariable < nvariable) return ivariable;
id_variable = (char **)
memory->srealloc(id_variable,(nvariable+1)*sizeof(char *),
"dump:id_variable");
delete [] variable;
variable = new int[nvariable+1];
delete [] vbuf;
vbuf = new double*[nvariable+1];
for (int i = 0; i <= nvariable; i++) vbuf[i] = NULL;
int n = strlen(id) + 1;
id_variable[nvariable] = new char[n];
strcpy(id_variable[nvariable],id);
nvariable++;
return nvariable-1;
}
/* ----------------------------------------------------------------------
add custom atom property to list used by dump
return index of where this property is in list
if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
int DumpCustomVTK::add_custom(char *id, int flag)
{
int icustom;
for (icustom = 0; icustom < ncustom; icustom++)
if ((strcmp(id,id_custom[icustom]) == 0)
&& (flag == flag_custom[icustom])) break;
if (icustom < ncustom) return icustom;
id_custom = (char **)
memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom");
flag_custom = (int *)
memory->srealloc(flag_custom,(ncustom+1)*sizeof(int),"dump:flag_custom");
int n = strlen(id) + 1;
id_custom[ncustom] = new char[n];
strcpy(id_custom[ncustom],id);
flag_custom[ncustom] = flag;
ncustom++;
return ncustom-1;
}
/* ---------------------------------------------------------------------- */
int DumpCustomVTK::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"region") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"none") == 0) iregion = -1;
else {
iregion = domain->find_region(arg[1]);
if (iregion == -1)
error->all(FLERR,"Dump_modify region ID does not exist");
delete [] idregion;
int n = strlen(arg[1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[1]);
}
return 2;
}
if (strcmp(arg[0],"label") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command [label]");
delete [] label;
int n = strlen(arg[1]) + 1;
label = new char[n];
strcpy(label,arg[1]);
return 2;
}
if (strcmp(arg[0],"binary") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command [binary]");
if (strcmp(arg[1],"yes") == 0) binary = 1;
else if (strcmp(arg[1],"no") == 0) binary = 0;
else error->all(FLERR,"Illegal dump_modify command [binary]");
return 2;
}
if (strcmp(arg[0],"element") == 0) {
if (narg < ntypes+1)
error->all(FLERR,"Dump modify: number of element names do not match atom types");
if (typenames) {
for (int i = 1; i <= ntypes; i++) delete [] typenames[i];
delete [] typenames;
typenames = NULL;
}
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
int n = strlen(arg[itype]) + 1;
typenames[itype] = new char[n];
strcpy(typenames[itype],arg[itype]);
}
return ntypes+1;
}
if (strcmp(arg[0],"thresh") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"none") == 0) {
if (nthresh) {
memory->destroy(thresh_array);
memory->destroy(thresh_op);
memory->destroy(thresh_value);
thresh_array = NULL;
thresh_op = NULL;
thresh_value = NULL;
}
nthresh = 0;
return 2;
}
if (narg < 4) error->all(FLERR,"Illegal dump_modify command");
// grow threshold arrays
memory->grow(thresh_array,nthresh+1,"dump:thresh_array");
memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
// set attribute type of threshold
// customize by adding to if statement
if (strcmp(arg[1],"id") == 0) thresh_array[nthresh] = ID;
else if (strcmp(arg[1],"mol") == 0) thresh_array[nthresh] = MOL;
else if (strcmp(arg[1],"proc") == 0) thresh_array[nthresh] = PROC;
else if (strcmp(arg[1],"procp1") == 0) thresh_array[nthresh] = PROCP1;
else if (strcmp(arg[1],"type") == 0) thresh_array[nthresh] = TYPE;
else if (strcmp(arg[1],"mass") == 0) thresh_array[nthresh] = MASS;
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 && domain->triclinic == 0)
thresh_array[nthresh] = XS;
else if (strcmp(arg[1],"xs") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = XSTRI;
else if (strcmp(arg[1],"ys") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = YS;
else if (strcmp(arg[1],"ys") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = YSTRI;
else if (strcmp(arg[1],"zs") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = ZS;
else if (strcmp(arg[1],"zs") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = ZSTRI;
else if (strcmp(arg[1],"xu") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = XU;
else if (strcmp(arg[1],"xu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = XUTRI;
else if (strcmp(arg[1],"yu") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = YU;
else if (strcmp(arg[1],"yu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = YUTRI;
else if (strcmp(arg[1],"zu") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = ZU;
else if (strcmp(arg[1],"zu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = ZUTRI;
else if (strcmp(arg[1],"xsu") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = XSU;
else if (strcmp(arg[1],"xsu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = XSUTRI;
else if (strcmp(arg[1],"ysu") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = YSU;
else if (strcmp(arg[1],"ysu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = YSUTRI;
else if (strcmp(arg[1],"zsu") == 0 && domain->triclinic == 0)
thresh_array[nthresh] = ZSU;
else if (strcmp(arg[1],"zsu") == 0 && domain->triclinic == 1)
thresh_array[nthresh] = ZSUTRI;
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],"mu") == 0) thresh_array[nthresh] = MU;
else if (strcmp(arg[1],"radius") == 0) thresh_array[nthresh] = RADIUS;
else if (strcmp(arg[1],"diameter") == 0) thresh_array[nthresh] = DIAMETER;
else if (strcmp(arg[1],"omegax") == 0) thresh_array[nthresh] = OMEGAX;
else if (strcmp(arg[1],"omegay") == 0) thresh_array[nthresh] = OMEGAY;
else if (strcmp(arg[1],"omegaz") == 0) thresh_array[nthresh] = OMEGAZ;
else if (strcmp(arg[1],"angmomx") == 0) thresh_array[nthresh] = ANGMOMX;
else if (strcmp(arg[1],"angmomy") == 0) thresh_array[nthresh] = ANGMOMY;
else if (strcmp(arg[1],"angmomz") == 0) thresh_array[nthresh] = ANGMOMZ;
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;
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
else if (strncmp(arg[1],"c_",2) == 0) {
thresh_array[nthresh] = 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(FLERR,"Invalid attribute in dump modify command");
argindex[ATTRIBUTES+nfield+nthresh] = atoi(ptr+1);
*ptr = '\0';
} else argindex[ATTRIBUTES+nfield+nthresh] = 0;
n = modify->find_compute(suffix);
if (n < 0) error->all(FLERR,"Could not find dump modify compute ID");
if (modify->compute[n]->peratom_flag == 0)
error->all(FLERR,
"Dump modify compute ID does not compute per-atom info");
if (argindex[ATTRIBUTES+nfield+nthresh] == 0 &&
modify->compute[n]->size_peratom_cols > 0)
error->all(FLERR,
"Dump modify compute ID does not compute per-atom vector");
if (argindex[ATTRIBUTES+nfield+nthresh] > 0 &&
modify->compute[n]->size_peratom_cols == 0)
error->all(FLERR,
"Dump modify compute ID does not compute per-atom array");
if (argindex[ATTRIBUTES+nfield+nthresh] > 0 &&
argindex[ATTRIBUTES+nfield+nthresh] > modify->compute[n]->size_peratom_cols)
error->all(FLERR,"Dump modify compute ID vector is not large enough");
field2index[ATTRIBUTES+nfield+nthresh] = 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[1],"f_",2) == 0) {
thresh_array[nthresh] = FIX;
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(FLERR,"Invalid attribute in dump modify command");
argindex[ATTRIBUTES+nfield+nthresh] = atoi(ptr+1);
*ptr = '\0';
} else argindex[ATTRIBUTES+nfield+nthresh] = 0;
n = modify->find_fix(suffix);
if (n < 0) error->all(FLERR,"Could not find dump modify fix ID");
if (modify->fix[n]->peratom_flag == 0)
error->all(FLERR,"Dump modify fix ID does not compute per-atom info");
if (argindex[ATTRIBUTES+nfield+nthresh] == 0 &&
modify->fix[n]->size_peratom_cols > 0)
error->all(FLERR,"Dump modify fix ID does not compute per-atom vector");
if (argindex[ATTRIBUTES+nfield+nthresh] > 0 &&
modify->fix[n]->size_peratom_cols == 0)
error->all(FLERR,"Dump modify fix ID does not compute per-atom array");
if (argindex[ATTRIBUTES+nfield+nthresh] > 0 &&
argindex[ATTRIBUTES+nfield+nthresh] > modify->fix[n]->size_peratom_cols)
error->all(FLERR,"Dump modify fix ID vector is not large enough");
field2index[ATTRIBUTES+nfield+nthresh] = add_fix(suffix);
delete [] suffix;
// variable value = v_ID
} else if (strncmp(arg[1],"v_",2) == 0) {
thresh_array[nthresh] = VARIABLE;
int n = strlen(arg[1]);
char *suffix = new char[n];
strcpy(suffix,&arg[1][2]);
argindex[ATTRIBUTES+nfield+nthresh] = 0;
n = input->variable->find(suffix);
if (n < 0) error->all(FLERR,"Could not find dump modify variable name");
if (input->variable->atomstyle(n) == 0)
error->all(FLERR,"Dump modify variable is not atom-style variable");
field2index[ATTRIBUTES+nfield+nthresh] = add_variable(suffix);
delete [] suffix;
} else error->all(FLERR,"Invalid dump_modify threshold operator");
// set operation type of threshold
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] = EQ;
else if (strcmp(arg[2],"!=") == 0) thresh_op[nthresh] = NEQ;
else error->all(FLERR,"Invalid dump_modify threshold operator");
// set threshold value
thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
nthresh++;
return 4;
}
return 0;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf, choose, variable arrays
------------------------------------------------------------------------- */
bigint DumpCustomVTK::memory_usage()
{
bigint bytes = Dump::memory_usage();
bytes += memory->usage(choose,maxlocal);
bytes += memory->usage(dchoose,maxlocal);
bytes += memory->usage(clist,maxlocal);
bytes += memory->usage(vbuf,nvariable,maxlocal);
return bytes;
}
/* ----------------------------------------------------------------------
extraction of Compute, Fix, Variable results
------------------------------------------------------------------------- */
void DumpCustomVTK::pack_compute(int n)
{
double *vector = compute[field2index[current_pack_choice_key]]->vector_atom;
double **array = compute[field2index[current_pack_choice_key]]->array_atom;
int index = argindex[current_pack_choice_key];
if (index == 0) {
for (int i = 0; i < nchoose; i++) {
buf[n] = vector[clist[i]];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nchoose; i++) {
buf[n] = array[clist[i]][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::pack_fix(int n)
{
double *vector = fix[field2index[current_pack_choice_key]]->vector_atom;
double **array = fix[field2index[current_pack_choice_key]]->array_atom;
int index = argindex[current_pack_choice_key];
if (index == 0) {
for (int i = 0; i < nchoose; i++) {
buf[n] = vector[clist[i]];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nchoose; i++) {
buf[n] = array[clist[i]][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::pack_variable(int n)
{
double *vector = vbuf[field2index[current_pack_choice_key]];
for (int i = 0; i < nchoose; i++) {
buf[n] = vector[clist[i]];
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustomVTK::pack_custom(int n)
{
int index = field2index[n];
if (flag_custom[index] == 0) { // integer
int iwhich,tmp;
iwhich = atom->find_custom(id_custom[index],tmp);
int *ivector = atom->ivector[iwhich];
for (int i = 0; i < nchoose; i++) {
buf[n] = ivector[clist[i]];
n += size_one;
}
} else if (flag_custom[index] == 1) { // double
int iwhich,tmp;
iwhich = atom->find_custom(id_custom[index],tmp);
double *dvector = atom->dvector[iwhich];
for (int i = 0; i < nchoose; i++) {
buf[n] = dvector[clist[i]];
n += size_one;
}
}
}

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