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84666543d1fb674ff9916780387603311ff5daa6
lammps/src/VTK/dump_vtk.cpp

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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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 "dump_vtk.h"
#include "arg_info.h"
#include "atom.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "fix_store.h"
#include "force.h"
#include "group.h"
#include "input.h"
#include "memory.h"
#include "modify.h"
#include "region.h"
#include "update.h"
#include "variable.h"
#include <cmath>
#include <cstring>
#include <sstream>
#include <vector>
#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,
COMPUTE,FIX,VARIABLE,IVEC,DVEC,IARRAY,DARRAY,
ATTRIBUTES}; // must come last
enum{LT,LE,GT,GE,EQ,NEQ,XOR};
enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats
#define ONEFIELD 32
#define DELTA 1048576
#if (VTK_MAJOR_VERSION < 5) || (VTK_MAJOR_VERSION > 8)
#error This code has only been tested with VTK 5, 6, 7, and 8
#elif VTK_MAJOR_VERSION > 6
#define InsertNextTupleValue InsertNextTypedTuple
#endif
/* ---------------------------------------------------------------------- */
DumpVTK::DumpVTK(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
if (narg == 5) error->all(FLERR,"No dump 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(nargnew,earg);
if (ioptional < nargnew)
error->all(FLERR,"Invalid attribute {} in dump vtk command", earg[ioptional]);
size_one = pack_choice.size();
current_pack_choice_key = -1;
if (filewriter) reset_vtk_data_containers();
label = nullptr;
{
// parallel vtp/vtu requires proc number to be preceded by underscore '_'
multiname_ex = nullptr;
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 = nullptr;
domainfilecurrent = nullptr;
parallelfilecurrent = nullptr;
header_choice = nullptr;
write_choice = nullptr;
boxcorners = nullptr;
}
/* ---------------------------------------------------------------------- */
DumpVTK::~DumpVTK()
{
delete [] filecurrent;
delete [] domainfilecurrent;
delete [] parallelfilecurrent;
delete [] multiname_ex;
delete [] label;
}
/* ---------------------------------------------------------------------- */
void DumpVTK::init_style()
{
// default for element names = C
if (typenames == nullptr) {
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 = &DumpVTK::header_vtk;
if (vtk_file_format == VTP || vtk_file_format == PVTP)
write_choice = &DumpVTK::write_vtp;
else if (vtk_file_format == VTU || vtk_file_format == PVTU)
write_choice = &DumpVTK::write_vtu;
else
write_choice = &DumpVTK::write_vtk;
// find current ptr for each compute,fix,variable and custom atom property
// check that fix frequency is acceptable
for (int i = 0; i < ncompute; i++) {
int icompute = modify->find_compute(id_compute[i]);
if (icompute < 0) error->all(FLERR,"Could not find dump vtk compute ID");
compute[i] = modify->compute[icompute];
}
for (int i = 0; i < nfix; i++) {
int ifix = modify->find_fix(id_fix[i]);
if (ifix < 0) error->all(FLERR,"Could not find dump vtk fix ID");
fix[i] = modify->fix[ifix];
if (nevery % modify->fix[ifix]->peratom_freq)
error->all(FLERR,"Dump vtk and fix not computed at compatible times");
}
for (int i = 0; i < nvariable; i++) {
int ivariable = input->variable->find(id_variable[i]);
if (ivariable < 0)
error->all(FLERR,"Could not find dump vtk variable name");
variable[i] = ivariable;
}
int icustom,flag,cols;
for (int i = 0; i < ncustom; i++) {
icustom = atom->find_custom(id_custom[i],flag,cols);
if (icustom < 0)
error->all(FLERR,"Could not find custom per-atom property ID");
custom[i] = icustom;
if (!flag && !cols) custom_flag[i] = IVEC;
else if (flag && !cols) custom_flag[i] = DVEC;
else if (!flag && cols) custom_flag[i] = IARRAY;
else if (flag && cols) custom_flag[i] = DARRAY;
}
// 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 vtk does not exist");
}
}
/* ---------------------------------------------------------------------- */
void DumpVTK::write_header(bigint)
{
}
/* ---------------------------------------------------------------------- */
void DumpVTK::header_vtk(bigint)
{
}
/* ---------------------------------------------------------------------- */
int DumpVTK::count()
{
n_calls_ = 0;
int i;
// grow choose and variable vbuf arrays if needed
const 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 & Compute::INVOKED_PERATOM)) {
compute[i]->compute_peratom();
compute[i]->invoked_flag |= Compute::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,*ptrhold;
double *values;
double value;
int nstride,lastflag;
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] == IVEC) {
i = ATTRIBUTES + nfield + ithresh;
int iwhich = custom[field2index[i]];
int *ivector = atom->ivector[iwhich];
for (i = 0; i < nlocal; i++)
dchoose[i] = ivector[i];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == DVEC) {
i = ATTRIBUTES + nfield + ithresh;
int iwhich = custom[field2index[i]];
ptr = atom->dvector[iwhich];
nstride = 1;
} else if (thresh_array[ithresh] == IARRAY) {
i = ATTRIBUTES + nfield + ithresh;
int iwhich = custom[field2index[i]];
int **iarray = atom->iarray[iwhich];
int icol = argindex[i] - 1;
for (i = 0; i < nlocal; i++)
dchoose[i] = iarray[i][icol];
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == DARRAY) {
i = ATTRIBUTES + nfield + ithresh;
int iwhich = custom[field2index[i]];
double **darray = atom->darray[iwhich];
ptr = &darray[0][argindex[i]-1];
nstride = atom->dcols[iwhich];
}
// unselect atoms that don't meet threshold criterion
// compare to single value or values stored in threshfix
// copy ptr attribute into thresh_fix if this is first comparison
if (thresh_last[ithresh] < 0) {
lastflag = 0;
value = thresh_value[ithresh];
} else {
lastflag = 1;
int ilast = thresh_last[ithresh];
values = thresh_fix[ilast]->vstore;
ptrhold = ptr;
if (thresh_first[ilast]) {
thresh_first[ilast] = 0;
for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
ptr = ptrhold;
}
}
if (thresh_op[ithresh] == LT) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr >= values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr >= value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == LE) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr > values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr > value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == GT) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr <= values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr <= value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == GE) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr < values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr < value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == EQ) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr != values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr != value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == NEQ) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr == values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr == value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == XOR) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if ((choose[i] && *ptr == 0.0 && values[i] == 0.0) ||
(*ptr != 0.0 && values[i] != 0.0))
choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if ((choose[i] && *ptr == 0.0 && value == 0.0) ||
(*ptr != 0.0 && value != 0.0))
choose[i] = 0;
}
}
// update values stored in threshfix
if (lastflag) {
ptr = ptrhold;
for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
}
}
}
// 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 DumpVTK::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(nullptr);
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 DumpVTK::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 DumpVTK::write_data(int n, double *mybuf)
{
(this->*write_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
void DumpVTK::setFileCurrent() {
delete [] filecurrent;
filecurrent = nullptr;
char *filestar = filename;
if (multiproc) {
if (multiproc > 1) { // if dump_modify fileper or nfile was used
delete [] multiname_ex;
multiname_ex = nullptr;
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 = nullptr;
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 = nullptr;
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 = nullptr;
} 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 = nullptr;
// 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 = nullptr;
}
}
/* ---------------------------------------------------------------------- */
void DumpVTK::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 Dump::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 Dump::DOUBLE:
{
vtkDoubleArray *pda = static_cast<vtkDoubleArray*>(paa);
pda->InsertNextTupleValue(&mybuf[iatom*size_one+j]);
break;
}
}
j+=3;
} else {
switch (vtype[it->first]) {
case Dump::INT:
{
vtkIntArray *pia = static_cast<vtkIntArray*>(paa);
pia->InsertNextValue(mybuf[iatom*size_one+j]);
break;
}
case Dump::DOUBLE:
{
vtkDoubleArray *pda = static_cast<vtkDoubleArray*>(paa);
pda->InsertNextValue(mybuf[iatom*size_one+j]);
break;
}
case Dump::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 DumpVTK::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 DumpVTK::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 DumpVTK::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 DumpVTK::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 DumpVTK::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 DumpVTK::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 DumpVTK::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 DumpVTK::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 DumpVTK::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 DumpVTK::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 Dump::INT:
myarrays[it->first] = vtkSmartPointer<vtkIntArray>::New();
break;
case Dump::DOUBLE:
myarrays[it->first] = vtkSmartPointer<vtkDoubleArray>::New();
break;
case Dump::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 DumpVTK::parse_fields(int narg, char **arg)
{
pack_choice[X] = &DumpVTK::pack_x;
vtype[X] = Dump::DOUBLE;
name[X] = "x";
pack_choice[Y] = &DumpVTK::pack_y;
vtype[Y] = Dump::DOUBLE;
name[Y] = "y";
pack_choice[Z] = &DumpVTK::pack_z;
vtype[Z] = Dump::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] = &DumpVTK::pack_id;
vtype[ID] = Dump::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] = &DumpVTK::pack_molecule;
vtype[MOL] = Dump::INT;
name[MOL] = arg[iarg];
} else if (strcmp(arg[iarg],"proc") == 0) {
pack_choice[PROC] = &DumpVTK::pack_proc;
vtype[PROC] = Dump::INT;
name[PROC] = arg[iarg];
} else if (strcmp(arg[iarg],"procp1") == 0) {
pack_choice[PROCP1] = &DumpVTK::pack_procp1;
vtype[PROCP1] = Dump::INT;
name[PROCP1] = arg[iarg];
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[TYPE] = &DumpVTK::pack_type;
vtype[TYPE] = Dump::INT;
name[TYPE] =arg[iarg];
} else if (strcmp(arg[iarg],"element") == 0) {
pack_choice[ELEMENT] = &DumpVTK::pack_type;
vtype[ELEMENT] = Dump::STRING;
name[ELEMENT] = arg[iarg];
} else if (strcmp(arg[iarg],"mass") == 0) {
pack_choice[MASS] = &DumpVTK::pack_mass;
vtype[MASS] = Dump::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] = &DumpVTK::pack_xs_triclinic;
else pack_choice[XS] = &DumpVTK::pack_xs;
vtype[XS] = Dump::DOUBLE;
name[XS] = arg[iarg];
} else if (strcmp(arg[iarg],"ys") == 0) {
if (domain->triclinic) pack_choice[YS] = &DumpVTK::pack_ys_triclinic;
else pack_choice[YS] = &DumpVTK::pack_ys;
vtype[YS] = Dump::DOUBLE;
name[YS] = arg[iarg];
} else if (strcmp(arg[iarg],"zs") == 0) {
if (domain->triclinic) pack_choice[ZS] = &DumpVTK::pack_zs_triclinic;
else pack_choice[ZS] = &DumpVTK::pack_zs;
vtype[ZS] = Dump::DOUBLE;
name[ZS] = arg[iarg];
} else if (strcmp(arg[iarg],"xu") == 0) {
if (domain->triclinic) pack_choice[XU] = &DumpVTK::pack_xu_triclinic;
else pack_choice[XU] = &DumpVTK::pack_xu;
vtype[XU] = Dump::DOUBLE;
name[XU] = arg[iarg];
} else if (strcmp(arg[iarg],"yu") == 0) {
if (domain->triclinic) pack_choice[YU] = &DumpVTK::pack_yu_triclinic;
else pack_choice[YU] = &DumpVTK::pack_yu;
vtype[YU] = Dump::DOUBLE;
name[YU] = arg[iarg];
} else if (strcmp(arg[iarg],"zu") == 0) {
if (domain->triclinic) pack_choice[ZU] = &DumpVTK::pack_zu_triclinic;
else pack_choice[ZU] = &DumpVTK::pack_zu;
vtype[ZU] = Dump::DOUBLE;
name[ZU] = arg[iarg];
} else if (strcmp(arg[iarg],"xsu") == 0) {
if (domain->triclinic) pack_choice[XSU] = &DumpVTK::pack_xsu_triclinic;
else pack_choice[XSU] = &DumpVTK::pack_xsu;
vtype[XSU] = Dump::DOUBLE;
name[XSU] = arg[iarg];
} else if (strcmp(arg[iarg],"ysu") == 0) {
if (domain->triclinic) pack_choice[YSU] = &DumpVTK::pack_ysu_triclinic;
else pack_choice[YSU] = &DumpVTK::pack_ysu;
vtype[YSU] = Dump::DOUBLE;
name[YSU] = arg[iarg];
} else if (strcmp(arg[iarg],"zsu") == 0) {
if (domain->triclinic) pack_choice[ZSU] = &DumpVTK::pack_zsu_triclinic;
else pack_choice[ZSU] = &DumpVTK::pack_zsu;
vtype[ZSU] = Dump::DOUBLE;
name[ZSU] = arg[iarg];
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[IX] = &DumpVTK::pack_ix;
vtype[IX] = Dump::INT;
name[IX] = arg[iarg];
} else if (strcmp(arg[iarg],"iy") == 0) {
pack_choice[IY] = &DumpVTK::pack_iy;
vtype[IY] = Dump::INT;
name[IY] = arg[iarg];
} else if (strcmp(arg[iarg],"iz") == 0) {
pack_choice[IZ] = &DumpVTK::pack_iz;
vtype[IZ] = Dump::INT;
name[IZ] = arg[iarg];
} else if (strcmp(arg[iarg],"vx") == 0) {
pack_choice[VX] = &DumpVTK::pack_vx;
vtype[VX] = Dump::DOUBLE;
name[VX] = arg[iarg];
} else if (strcmp(arg[iarg],"vy") == 0) {
pack_choice[VY] = &DumpVTK::pack_vy;
vtype[VY] = Dump::DOUBLE;
name[VY] = arg[iarg];
} else if (strcmp(arg[iarg],"vz") == 0) {
pack_choice[VZ] = &DumpVTK::pack_vz;
vtype[VZ] = Dump::DOUBLE;
name[VZ] = arg[iarg];
} else if (strcmp(arg[iarg],"fx") == 0) {
pack_choice[FX] = &DumpVTK::pack_fx;
vtype[FX] = Dump::DOUBLE;
name[FX] = arg[iarg];
} else if (strcmp(arg[iarg],"fy") == 0) {
pack_choice[FY] = &DumpVTK::pack_fy;
vtype[FY] = Dump::DOUBLE;
name[FY] = arg[iarg];
} else if (strcmp(arg[iarg],"fz") == 0) {
pack_choice[FZ] = &DumpVTK::pack_fz;
vtype[FZ] = Dump::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] = &DumpVTK::pack_q;
vtype[Q] = Dump::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] = &DumpVTK::pack_mux;
vtype[MUX] = Dump::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] = &DumpVTK::pack_muy;
vtype[MUY] = Dump::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] = &DumpVTK::pack_muz;
vtype[MUZ] = Dump::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] = &DumpVTK::pack_mu;
vtype[MU] = Dump::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] = &DumpVTK::pack_radius;
vtype[RADIUS] = Dump::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] = &DumpVTK::pack_diameter;
vtype[DIAMETER] = Dump::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] = &DumpVTK::pack_omegax;
vtype[OMEGAX] = Dump::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] = &DumpVTK::pack_omegay;
vtype[OMEGAY] = Dump::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] = &DumpVTK::pack_omegaz;
vtype[OMEGAZ] = Dump::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] = &DumpVTK::pack_angmomx;
vtype[ANGMOMX] = Dump::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] = &DumpVTK::pack_angmomy;
vtype[ANGMOMY] = Dump::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] = &DumpVTK::pack_angmomz;
vtype[ANGMOMZ] = Dump::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] = &DumpVTK::pack_tqx;
vtype[TQX] = Dump::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] = &DumpVTK::pack_tqy;
vtype[TQY] = Dump::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] = &DumpVTK::pack_tqz;
vtype[TQZ] = Dump::DOUBLE;
name[TQZ] = arg[iarg];
} else {
int n,flag,cols;
ArgInfo argi(arg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE
|ArgInfo::DNAME|ArgInfo::INAME);
argindex[ATTRIBUTES+i] = argi.get_index1();
auto aname = argi.get_name();
switch (argi.get_type()) {
case ArgInfo::UNKNOWN:
error->all(FLERR,"Invalid attribute in dump vtk command: {}",arg[iarg]);
break;
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is int between []
case ArgInfo::COMPUTE:
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_compute;
vtype[ATTRIBUTES+i] = Dump::DOUBLE;
n = modify->find_compute(aname);
if (n < 0) error->all(FLERR,"Could not find dump vtk compute ID: {}",aname);
if (modify->compute[n]->peratom_flag == 0)
error->all(FLERR,"Dump vtk compute {} does not compute per-atom info",aname);
if (argi.get_dim() == 0 && modify->compute[n]->size_peratom_cols > 0)
error->all(FLERR,"Dump vtk compute {} does not calculate per-atom vector",aname);
if (argi.get_dim() > 0 && modify->compute[n]->size_peratom_cols == 0)
error->all(FLERR,"Dump vtk compute {} does not calculate per-atom array",aname);
if (argi.get_dim() > 0 &&
argi.get_index1() > modify->compute[n]->size_peratom_cols)
error->all(FLERR,"Dump vtk compute {} vector is accessed out-of-range",aname);
field2index[ATTRIBUTES+i] = add_compute(aname);
name[ATTRIBUTES+i] = arg[iarg];
break;
// fix value = f_ID
// if no trailing [], then arg is set to 0, else arg is between []
case ArgInfo::FIX:
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_fix;
vtype[ATTRIBUTES+i] = Dump::DOUBLE;
n = modify->find_fix(aname);
if (n < 0) error->all(FLERR,"Could not find dump vtk fix ID: {}",aname);
if (modify->fix[n]->peratom_flag == 0)
error->all(FLERR,"Dump vtk fix {} does not compute per-atom info",aname);
if (argi.get_dim() == 0 && modify->fix[n]->size_peratom_cols > 0)
error->all(FLERR,"Dump vtk fix {} does not compute per-atom vector",aname);
if (argi.get_dim() > 0 && modify->fix[n]->size_peratom_cols == 0)
error->all(FLERR,"Dump vtk fix {} does not compute per-atom array",aname);
if (argi.get_dim() > 0 &&
argi.get_index1() > modify->fix[n]->size_peratom_cols)
error->all(FLERR,"Dump vtk fix {} vector is accessed out-of-range",aname);
field2index[ATTRIBUTES+i] = add_fix(aname);
name[ATTRIBUTES+i] = arg[iarg];
break;
// variable value = v_name
case ArgInfo::VARIABLE:
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_variable;
vtype[ATTRIBUTES+i] = Dump::DOUBLE;
n = input->variable->find(aname);
if (n < 0) error->all(FLERR,"Could not find dump vtk variable name {}",aname);
if (input->variable->atomstyle(n) == 0)
error->all(FLERR,"Dump vtk variable {} is not atom-style variable",aname);
field2index[ATTRIBUTES+i] = add_variable(aname);
name[ATTRIBUTES+i] = arg[iarg];
break;
// custom per-atom floating point vector or array = d_ID d2_ID
case ArgInfo::DNAME:
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
vtype[ATTRIBUTES+i] = Dump::DOUBLE;
n = atom->find_custom(aname,flag,cols);
if (n < 0)
error->all(FLERR,"Could not find custom per-atom property ID: {}", aname);
if (argindex[ATTRIBUTES+i] == 0) {
if (!flag || cols)
error->all(FLERR,"Property double vector {} for dump vtk does not exist",aname);
} else {
if (!flag || !cols)
error->all(FLERR,"Property double array {} for dump vtk does not exist",aname);
if (argindex[ATTRIBUTES+i] > atom->dcols[n])
error->all(FLERR,"Dump vtk property array {} is accessed out-of-range",aname);
}
field2index[ATTRIBUTES+i] = add_custom(aname,1);
name[ATTRIBUTES+i] = arg[iarg];
break;
// custom per-atom integer vector or array = i_ID or i2_ID
case ArgInfo::INAME:
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
vtype[ATTRIBUTES+i] = Dump::INT;
n = atom->find_custom(aname,flag,cols);
if (n < 0)
error->all(FLERR,"Could not find custom per-atom property ID: {}", aname);
if (argindex[ATTRIBUTES+i] == 0) {
if (flag || cols)
error->all(FLERR,"Property integer vector {} for dump vtk does not exist",aname);
} else {
if (flag || !cols)
error->all(FLERR,"Property integer array {} for dump vtk does not exist",aname);
if (argindex[ATTRIBUTES+i] > atom->icols[n])
error->all(FLERR,"Dump vtk property array {} is accessed out-of-range",aname);
}
field2index[ATTRIBUTES+i] = add_custom(aname,0);
name[ATTRIBUTES+i] = arg[iarg];
break;
// no match
default:
return iarg;
break;
}
}
}
identify_vectors();
return narg;
}
/* ---------------------------------------------------------------------- */
void DumpVTK::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 DumpVTK::add_compute(const 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];
id_compute[ncompute] = utils::strdup(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 DumpVTK::add_fix(const 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];
id_fix[nfix] = utils::strdup(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 DumpVTK::add_variable(const 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] = nullptr;
id_variable[nvariable] = utils::strdup(id);
nvariable++;
return nvariable-1;
}
/* ----------------------------------------------------------------------
add custom atom property to list used by dump
return index of where this property is in Atom class custom lists
if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
int DumpVTK::add_custom(const char *id, int flag)
{
int icustom;
for (icustom = 0; icustom < ncustom; icustom++)
if (strcmp(id,id_custom[icustom]) == 0) break;
if (icustom < ncustom) return icustom;
id_custom = (char **) memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom");
custom = (int *) memory->srealloc(custom,(ncustom+1)*sizeof(int),"dump:custom");
custom_flag = (int *) memory->srealloc(custom_flag,(ncustom+1)*sizeof(int),"dump:custom_flag");
id_custom[ncustom] = utils::strdup(id);
custom_flag[ncustom] = flag;
ncustom++;
return ncustom-1;
}
/* ---------------------------------------------------------------------- */
int DumpVTK::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",arg[1]);
delete[] idregion;
idregion = utils::strdup(arg[1]);
}
return 2;
}
if (strcmp(arg[0],"label") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command [label]");
delete[] label;
label = utils::strdup(arg[1]);
return 2;
}
if (strcmp(arg[0],"binary") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command [binary]");
binary = utils::logical(FLERR,arg[1],false,lmp);
return 2;
}
if (strcmp(arg[0],"element") == 0) {
if (narg < ntypes+1)
error->all(FLERR,"Number of dump_modify element names does not match number of atom types");
for (int i = 1; i <= ntypes; i++) delete[] typenames[i];
delete[] typenames;
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
typenames[itype] = utils::strdup(arg[itype]);
}
return ntypes+1;
}
if (strcmp(arg[0],"refresh") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
ArgInfo argi(arg[1],ArgInfo::COMPUTE);
if ((argi.get_type() != ArgInfo::COMPUTE) || (argi.get_dim() != 0))
error->all(FLERR,"Illegal dump_modify command");
if (refreshflag) error->all(FLERR,"Dump_modify can only have one refresh");
refreshflag = 1;
refresh = argi.copy_name();
return 2;
}
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 = nullptr;
thresh_op = nullptr;
thresh_value = nullptr;
thresh_last = nullptr;
for (int i = 0; i < nthreshlast; i++) {
modify->delete_fix(thresh_fixID[i]);
delete[] thresh_fixID[i];
}
thresh_fix = nullptr;
thresh_fixID = nullptr;
thresh_first = nullptr;
}
nthresh = nthreshlast = 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");
memory->grow(thresh_last,(nthresh+1),"dump:thresh_last");
// 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 or fix or variable or custom vector/array
else {
int n,flag,cols;
ArgInfo argi(arg[1],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE
|ArgInfo::DNAME|ArgInfo::INAME);
argindex[ATTRIBUTES+nfield+nthresh] = argi.get_index1();
auto aname = argi.get_name();
switch (argi.get_type()) {
case ArgInfo::UNKNOWN:
error->all(FLERR,"Invalid attribute in dump modify command");
break;
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
case ArgInfo::COMPUTE:
thresh_array[nthresh] = COMPUTE;
n = modify->find_compute(aname);
if (n < 0) error->all(FLERR,"Could not find dump modify compute ID: {}",aname);
if (modify->compute[n]->peratom_flag == 0)
error->all(FLERR,"Dump modify compute ID {} does not compute per-atom info",aname);
if (argi.get_dim() == 0 && modify->compute[n]->size_peratom_cols > 0)
error->all(FLERR,"Dump modify compute ID {} does not compute per-atom vector",aname);
if (argi.get_index1() > 0 && modify->compute[n]->size_peratom_cols == 0)
error->all(FLERR,"Dump modify compute ID {} does not compute per-atom array",aname);
if (argi.get_index1() > 0 &&
argi.get_index1() > modify->compute[n]->size_peratom_cols)
error->all(FLERR,"Dump modify compute ID {} vector is not large enough",aname);
field2index[ATTRIBUTES+nfield+nthresh] = add_compute(aname);
break;
// fix value = f_ID
// if no trailing [], then arg is set to 0, else arg is between []
case ArgInfo::FIX:
thresh_array[nthresh] = FIX;
n = modify->find_fix(aname);
if (n < 0) error->all(FLERR,"Could not find dump modify fix ID: {}",aname);
if (modify->fix[n]->peratom_flag == 0)
error->all(FLERR,"Dump modify fix ID {} does not compute per-atom info",aname);
if (argi.get_dim() == 0 && modify->fix[n]->size_peratom_cols > 0)
error->all(FLERR,"Dump modify fix ID {} does not compute per-atom vector",aname);
if (argi.get_index1() > 0 && modify->fix[n]->size_peratom_cols == 0)
error->all(FLERR,"Dump modify fix ID {} does not compute per-atom array",aname);
if (argi.get_index1() > 0 && argi.get_index1() > modify->fix[n]->size_peratom_cols)
error->all(FLERR,"Dump modify fix ID {} vector is not large enough",aname);
field2index[ATTRIBUTES+nfield+nthresh] = add_fix(aname);
break;
// variable value = v_ID
case ArgInfo::VARIABLE:
thresh_array[nthresh] = VARIABLE;
n = input->variable->find(aname);
if (n < 0) error->all(FLERR,"Could not find dump modify variable name: {}",aname);
if (input->variable->atomstyle(n) == 0)
error->all(FLERR,"Dump modify variable {} is not atom-style variable",aname);
field2index[ATTRIBUTES+nfield+nthresh] = add_variable(aname);
break;
// custom per atom floating point vector or array
case ArgInfo::DNAME:
n = atom->find_custom(aname,flag,cols);
if (n < 0)
error->all(FLERR,"Could not find custom per-atom property ID: {}", aname);
if (argindex[ATTRIBUTES+nfield+nthresh] == 0) {
if (!flag || cols)
error->all(FLERR,"Property double vector for dump custom does not exist");
thresh_array[nthresh] = DVEC;
} else {
if (!flag || !cols)
error->all(FLERR,"Property double array for dump custom does not exist");
if (argindex[ATTRIBUTES+nfield+nthresh] > atom->dcols[n])
error->all(FLERR,"Dump custom property array is accessed out-of-range");
thresh_array[nthresh] = DARRAY;
}
field2index[ATTRIBUTES+nfield+nthresh] = add_custom(aname,thresh_array[nthresh]);
break;
// custom per atom integer vector or array
case ArgInfo::INAME:
n = atom->find_custom(aname,flag,cols);
if (n < 0)
error->all(FLERR,"Could not find custom per-atom property ID: {}", aname);
if (argindex[ATTRIBUTES+nfield+nthresh] == 0) {
if (flag || cols)
error->all(FLERR,"Property integer vector for dump custom does not exist");
thresh_array[nthresh] = IVEC;
} else {
if (flag || !cols)
error->all(FLERR,"Property integer array for dump custom does not exist");
if (argindex[ATTRIBUTES+nfield+nthresh] > atom->icols[n])
error->all(FLERR,"Dump custom property array is accessed out-of-range");
thresh_array[nthresh] = IARRAY;
}
field2index[ATTRIBUTES+nfield+nthresh] = add_custom(aname,thresh_array[nthresh]);
break;
// no match
default:
error->all(FLERR,"Invalid dump_modify thresh attribute: {}",aname);
break;
}
}
// 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 if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR;
else error->all(FLERR,"Invalid dump_modify thresh operator");
// set threshold value as number or special LAST keyword
// create FixStore to hold LAST values, should work with restart
// id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group
if (strcmp(arg[3],"LAST") != 0) {
thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp);
thresh_last[nthresh] = -1;
} else {
thresh_fix = (FixStore **)
memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),"dump:thresh_fix");
thresh_fixID = (char **)
memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),"dump:thresh_fixID");
memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
thresh_fixID[nthreshlast] = utils::strdup(threshid);
threshid += fmt::format(" {} STORE peratom 1 1", group->names[igroup]);
thresh_fix[nthreshlast] = (FixStore *) modify->add_fix(threshid);
thresh_last[nthreshlast] = nthreshlast;
thresh_first[nthreshlast] = 1;
nthreshlast++;
}
nthresh++;
return 4;
}
return 0;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf, choose, variable arrays
------------------------------------------------------------------------- */
double DumpVTK::memory_usage()
{
double 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 DumpVTK::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 DumpVTK::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 DumpVTK::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 DumpVTK::pack_custom(int n)
{
int flag = custom_flag[field2index[current_pack_choice_key]];
int iwhich = custom[field2index[current_pack_choice_key]];
int index = argindex[current_pack_choice_key];
if (flag == IVEC) {
int *ivector = atom->ivector[iwhich];
for (int i = 0; i < nchoose; i++) {
buf[n] = ivector[clist[i]];
n += size_one;
}
} else if (flag == DVEC) {
double *dvector = atom->dvector[iwhich];
for (int i = 0; i < nchoose; i++) {
buf[n] = dvector[clist[i]];
n += size_one;
}
} else if (flag == IARRAY) {
index--;
int **iarray = atom->iarray[iwhich];
for (int i = 0; i < nchoose; i++) {
buf[n] = iarray[clist[i]][index];
n += size_one;
}
} else if (flag == DARRAY) {
index--;
double **darray = atom->darray[iwhich];
for (int i = 0; i < nchoose; i++) {
buf[n] = darray[clist[i]][index];
n += size_one;
}
}
}
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