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lammps/src/dump_image.cpp
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dump_image.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <math.h>
#include <ctype.h>
#include <stdlib.h>
#include <string.h>
#include "dump_image.h"
#include "image.h"
#include "atom.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "atom_vec_body.h"
#include "body.h"
#include "molecule.h"
#include "domain.h"
#include "group.h"
#include "force.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "math_const.h"
#include "math_extra.h"
#include "error.h"
#include "memory.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define BIG 1.0e20
enum{NUMERIC,ATOM,TYPE,ELEMENT,ATTRIBUTE};
enum{SPHERE,LINE}; // also in Body child classes
enum{STATIC,DYNAMIC};
enum{NO,YES};
/* ---------------------------------------------------------------------- */
DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
if (binary || multiproc) error->all(FLERR,"Invalid dump image filename");
// force binary flag on to avoid corrupted output on Windows
binary = 1;
multifile_override = 0;
// set filetype based on filename suffix
int n = strlen(filename);
if (strlen(filename) > 4 && strcmp(&filename[n-4],".jpg") == 0)
filetype = JPG;
else if (strlen(filename) > 4 && strcmp(&filename[n-4],".JPG") == 0)
filetype = JPG;
else if (strlen(filename) > 5 && strcmp(&filename[n-5],".jpeg") == 0)
filetype = JPG;
else if (strlen(filename) > 5 && strcmp(&filename[n-5],".JPEG") == 0)
filetype = JPG;
else if (strlen(filename) > 4 && strcmp(&filename[n-4],".png") == 0)
filetype = PNG;
else if (strlen(filename) > 4 && strcmp(&filename[n-4],".PNG") == 0)
filetype = PNG;
else filetype = PPM;
#ifndef LAMMPS_JPEG
if (filetype == JPG)
error->all(FLERR,"Support for writing images in JPEG format not included");
#endif
#ifndef LAMMPS_PNG
if (filetype == PNG)
error->all(FLERR,"Support for writing images in PNG format not included");
#endif
// atom color,diameter settings
if (nfield != 2) error->all(FLERR,"Illegal dump image command");
acolor = ATTRIBUTE;
if (strcmp(arg[5],"type") == 0) acolor = TYPE;
else if (strcmp(arg[5],"element") == 0) acolor = ELEMENT;
adiam = ATTRIBUTE;
if (strcmp(arg[6],"type") == 0) adiam = TYPE;
else if (strcmp(arg[6],"element") == 0) adiam = ELEMENT;
// create Image class with single colormap for atoms
// change defaults for 2d
image = new Image(lmp,1);
if (domain->dimension == 2) {
image->theta = 0.0;
image->phi = 0.0;
image->up[0] = 0.0; image->up[1] = 1.0; image->up[2] = 0.0;
}
// set defaults for optional args
atomflag = YES;
lineflag = triflag = bodyflag = NO;
if (atom->nbondtypes == 0) bondflag = NO;
else {
bondflag = YES;
bcolor = ATOM;
bdiam = NUMERIC;
bdiamvalue = 0.5;
}
thetastr = phistr = NULL;
cflag = STATIC;
cx = cy = cz = 0.5;
cxstr = cystr = czstr = NULL;
upxstr = upystr = upzstr = NULL;
zoomstr = NULL;
perspstr = NULL;
boxflag = YES;
boxdiam = 0.02;
axesflag = NO;
subboxflag = NO;
// parse optional args
int iarg = ioptional;
while (iarg < narg) {
if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
if (strcmp(arg[iarg+1],"yes") == 0) atomflag = YES;
else if (strcmp(arg[iarg+1],"no") == 0) atomflag = NO;
else error->all(FLERR,"Illegal dump image command");
iarg += 2;
} else if (strcmp(arg[iarg],"adiam") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
adiam = NUMERIC;
adiamvalue = force->numeric(FLERR,arg[iarg+1]);
if (adiamvalue <= 0.0) error->all(FLERR,"Illegal dump image command");
iarg += 2;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
if (atom->nbondtypes == 0)
error->all(FLERR,"Dump image bond not allowed with no bond types");
bondflag = YES;
if (strcmp(arg[iarg+1],"none") == 0) bondflag = NO;
else if (strcmp(arg[iarg+1],"atom") == 0) bcolor = ATOM;
else if (strcmp(arg[iarg+1],"type") == 0) bcolor = TYPE;
else error->all(FLERR,"Illegal dump image command");
if (!islower(arg[iarg+2][0])) {
bdiam = NUMERIC;
bdiamvalue = force->numeric(FLERR,arg[iarg+2]);
if (bdiamvalue <= 0.0) error->all(FLERR,"Illegal dump image command");
} else if (strcmp(arg[iarg+2],"atom") == 0) bdiam = ATOM;
else if (strcmp(arg[iarg+2],"type") == 0) bdiam = TYPE;
else if (strcmp(arg[iarg+2],"none") == 0) bondflag = NO;
else error->all(FLERR,"Illegal dump image command");
iarg += 3;
} else if (strcmp(arg[iarg],"line") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
lineflag = YES;
if (strcmp(arg[iarg+1],"type") == 0) lcolor = TYPE;
else error->all(FLERR,"Illegal dump image command");
ldiam = NUMERIC;
ldiamvalue = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"tri") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal dump image command");
triflag = YES;
if (strcmp(arg[iarg+1],"type") == 0) tcolor = TYPE;
else error->all(FLERR,"Illegal dump image command");
tstyle = force->inumeric(FLERR,arg[iarg+2]);
tdiamvalue = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"body") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal dump image command");
bodyflag = YES;
if (strcmp(arg[iarg+1],"type") == 0) bodycolor = TYPE;
else error->all(FLERR,"Illegal dump image command");
bodyflag1 = force->numeric(FLERR,arg[iarg+2]);
bodyflag2 = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"size") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
int width = force->inumeric(FLERR,arg[iarg+1]);
int height = force->inumeric(FLERR,arg[iarg+2]);
if (width <= 0 || height <= 0)
error->all(FLERR,"Illegal dump image command");
image->width = width;
image->height = height;
iarg += 3;
} else if (strcmp(arg[iarg],"view") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
thetastr = new char[n];
strcpy(thetastr,&arg[iarg+1][2]);
} else {
double theta = force->numeric(FLERR,arg[iarg+1]);
if (theta < 0.0 || theta > 180.0)
error->all(FLERR,"Invalid dump image theta value");
theta *= MY_PI/180.0;
image->theta = theta;
}
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
phistr = new char[n];
strcpy(phistr,&arg[iarg+2][2]);
} else {
double phi = force->numeric(FLERR,arg[iarg+2]);
phi *= MY_PI/180.0;
image->phi = phi;
}
iarg += 3;
} else if (strcmp(arg[iarg],"center") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal dump image command");
if (strcmp(arg[iarg+1],"s") == 0) cflag = STATIC;
else if (strcmp(arg[iarg+1],"d") == 0) cflag = DYNAMIC;
else error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
cxstr = new char[n];
strcpy(cxstr,&arg[iarg+2][2]);
cflag = DYNAMIC;
} else cx = force->numeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
cystr = new char[n];
strcpy(cystr,&arg[iarg+3][2]);
cflag = DYNAMIC;
} else cy = force->numeric(FLERR,arg[iarg+3]);
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) {
int n = strlen(&arg[iarg+4][2]) + 1;
czstr = new char[n];
strcpy(czstr,&arg[iarg+4][2]);
cflag = DYNAMIC;
} else cz = force->numeric(FLERR,arg[iarg+4]);
iarg += 5;
} else if (strcmp(arg[iarg],"up") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
upxstr = new char[n];
strcpy(upxstr,&arg[iarg+1][2]);
} else image->up[0] = force->numeric(FLERR,arg[iarg+1]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
upystr = new char[n];
strcpy(upystr,&arg[iarg+2][2]);
} else image->up[1] = force->numeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
upzstr = new char[n];
strcpy(upzstr,&arg[iarg+3][2]);
} else image->up[2] = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"zoom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
zoomstr = new char[n];
strcpy(zoomstr,&arg[iarg+1][2]);
} else {
double zoom = force->numeric(FLERR,arg[iarg+1]);
if (zoom <= 0.0) error->all(FLERR,"Illegal dump image command");
image->zoom = zoom;
}
iarg += 2;
} else if (strcmp(arg[iarg],"persp") == 0) {
error->all(FLERR,"Dump image persp option is not yet supported");
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
perspstr = new char[n];
strcpy(perspstr,&arg[iarg+1][2]);
} else {
double persp = force->numeric(FLERR,arg[iarg+1]);
if (persp < 0.0) error->all(FLERR,"Illegal dump image command");
image->persp = persp;
}
iarg += 2;
} else if (strcmp(arg[iarg],"box") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
if (strcmp(arg[iarg+1],"yes") == 0) boxflag = YES;
else if (strcmp(arg[iarg+1],"no") == 0) boxflag = NO;
else error->all(FLERR,"Illegal dump image command");
boxdiam = force->numeric(FLERR,arg[iarg+2]);
if (boxdiam < 0.0) error->all(FLERR,"Illegal dump image command");
iarg += 3;
} else if (strcmp(arg[iarg],"axes") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
if (strcmp(arg[iarg+1],"yes") == 0) axesflag = YES;
else if (strcmp(arg[iarg+1],"no") == 0) axesflag = NO;
else error->all(FLERR,"Illegal dump image command");
axeslen = force->numeric(FLERR,arg[iarg+2]);
axesdiam = force->numeric(FLERR,arg[iarg+3]);
if (axeslen < 0.0 || axesdiam < 0.0)
error->all(FLERR,"Illegal dump image command");
iarg += 4;
} else if (strcmp(arg[iarg],"subbox") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
if (strcmp(arg[iarg+1],"yes") == 0) subboxflag = YES;
else if (strcmp(arg[iarg+1],"no") == 0) subboxflag = NO;
else error->all(FLERR,"Illegal dump image command");
subboxdiam = force->numeric(FLERR,arg[iarg+2]);
if (subboxdiam < 0.0) error->all(FLERR,"Illegal dump image command");
iarg += 3;
} else if (strcmp(arg[iarg],"shiny") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
double shiny = force->numeric(FLERR,arg[iarg+1]);
if (shiny < 0.0 || shiny > 1.0)
error->all(FLERR,"Illegal dump image command");
image->shiny = shiny;
iarg += 2;
} else if (strcmp(arg[iarg],"ssao") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal dump image command");
if (strcmp(arg[iarg+1],"yes") == 0) image->ssao = YES;
else if (strcmp(arg[iarg+1],"no") == 0) image->ssao = NO;
else error->all(FLERR,"Illegal dump image command");
int seed = force->inumeric(FLERR,arg[iarg+2]);
if (seed <= 0) error->all(FLERR,"Illegal dump image command");
image->seed = seed;
double ssaoint = force->numeric(FLERR,arg[iarg+3]);
if (ssaoint < 0.0 || ssaoint > 1.0)
error->all(FLERR,"Illegal dump image command");
image->ssaoint = ssaoint;
iarg += 4;
} else error->all(FLERR,"Illegal dump image command");
}
// error checks and setup for lineflag, triflag, bodyflag
if (lineflag) {
avec_line = (AtomVecLine *) atom->style_match("line");
if (!avec_line)
error->all(FLERR,"Dump image line requires atom style line");
}
if (triflag) {
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_tri)
error->all(FLERR,"Dump image tri requires atom style tri");
}
if (bodyflag) {
avec_body = (AtomVecBody *) atom->style_match("body");
if (!avec_body)
error->all(FLERR,"Dump image body yes requires atom style body");
}
extraflag = 0;
if (lineflag || triflag || bodyflag) extraflag = 1;
// allocate image buffer now that image size is known
image->buffers();
// communication neede for bonds colored by atoms
if (bondflag) {
if (bcolor == ATOM || bdiam == ATOM) comm_forward = 3;
else comm_forward = 1;
}
// additional defaults for dump_modify options
diamtype = new double[ntypes+1];
diamelement = new double[ntypes+1];
colortype = new double*[ntypes+1];
colorelement = new double*[ntypes+1];
for (int i = 1; i <= ntypes; i++) {
diamtype[i] = 1.0;
if (i % 6 == 1) colortype[i] = image->color2rgb("red");
else if (i % 6 == 2) colortype[i] = image->color2rgb("green");
else if (i % 6 == 3) colortype[i] = image->color2rgb("blue");
else if (i % 6 == 4) colortype[i] = image->color2rgb("yellow");
else if (i % 6 == 5) colortype[i] = image->color2rgb("aqua");
else if (i % 6 == 0) colortype[i] = image->color2rgb("cyan");
}
if (bondflag) {
bdiamtype = new double[atom->nbondtypes+1];
bcolortype = new double*[atom->nbondtypes+1];
for (int i = 1; i <= atom->nbondtypes; i++) {
bdiamtype[i] = 0.5;
if (i % 6 == 1) bcolortype[i] = image->color2rgb("red");
else if (i % 6 == 2) bcolortype[i] = image->color2rgb("green");
else if (i % 6 == 3) bcolortype[i] = image->color2rgb("blue");
else if (i % 6 == 4) bcolortype[i] = image->color2rgb("yellow");
else if (i % 6 == 5) bcolortype[i] = image->color2rgb("aqua");
else if (i % 6 == 0) bcolortype[i] = image->color2rgb("cyan");
}
} else {
bdiamtype = NULL;
bcolortype = NULL;
}
// viewflag = DYNAMIC if any view parameter is dynamic
viewflag = STATIC;
if (thetastr || phistr || cflag == DYNAMIC ||
upxstr || upystr || upzstr || zoomstr || perspstr) viewflag = DYNAMIC;
box_bounds();
if (cflag == STATIC) box_center();
if (viewflag == STATIC) view_params();
// local data
maxbufcopy = 0;
chooseghost = NULL;
bufcopy = NULL;
}
/* ---------------------------------------------------------------------- */
DumpImage::~DumpImage()
{
delete image;
delete [] diamtype;
delete [] diamelement;
delete [] colortype;
delete [] colorelement;
delete [] bdiamtype;
delete [] bcolortype;
memory->destroy(chooseghost);
memory->destroy(bufcopy);
}
/* ---------------------------------------------------------------------- */
void DumpImage::init_style()
{
if (multifile == 0 && !multifile_override)
error->all(FLERR,"Dump image requires one snapshot per file");
if (sort_flag) error->all(FLERR,"Dump image cannot perform sorting");
DumpCustom::init_style();
// check variables
if (thetastr) {
thetavar = input->variable->find(thetastr);
if (thetavar < 0)
error->all(FLERR,"Variable name for dump image theta does not exist");
if (!input->variable->equalstyle(thetavar))
error->all(FLERR,"Variable for dump image theta is invalid style");
}
if (phistr) {
phivar = input->variable->find(phistr);
if (phivar < 0)
error->all(FLERR,"Variable name for dump image phi does not exist");
if (!input->variable->equalstyle(phivar))
error->all(FLERR,"Variable for dump image phi is invalid style");
}
if (cxstr) {
cxvar = input->variable->find(cxstr);
if (cxvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(cxvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (cystr) {
cyvar = input->variable->find(cystr);
if (cyvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(cyvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (czstr) {
czvar = input->variable->find(czstr);
if (czvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(czvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (upxstr) {
upxvar = input->variable->find(upxstr);
if (upxvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(upxvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (upystr) {
upyvar = input->variable->find(upystr);
if (upyvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(upyvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (upzstr) {
upzvar = input->variable->find(upzstr);
if (upzvar < 0)
error->all(FLERR,"Variable name for dump image center does not exist");
if (!input->variable->equalstyle(upzvar))
error->all(FLERR,"Variable for dump image center is invalid style");
}
if (zoomstr) {
zoomvar = input->variable->find(zoomstr);
if (zoomvar < 0)
error->all(FLERR,"Variable name for dump image zoom does not exist");
if (!input->variable->equalstyle(zoomvar))
error->all(FLERR,"Variable for dump image zoom is invalid style");
}
if (perspstr) {
perspvar = input->variable->find(perspstr);
if (perspvar < 0)
error->all(FLERR,"Variable name for dump image persp does not exist");
if (!input->variable->equalstyle(perspvar))
error->all(FLERR,"Variable for dump image persp is invalid style");
}
// set up type -> element mapping
if (atomflag && acolor == ELEMENT) {
for (int i = 1; i <= ntypes; i++) {
colorelement[i] = image->element2color(typenames[i]);
if (colorelement[i] == NULL)
error->all(FLERR,"Invalid dump image element name");
}
}
if (atomflag && adiam == ELEMENT) {
for (int i = 1; i <= ntypes; i++) {
diamelement[i] = image->element2diam(typenames[i]);
if (diamelement[i] == 0.0)
error->all(FLERR,"Invalid dump image element name");
}
}
}
/* ---------------------------------------------------------------------- */
void DumpImage::write()
{
// open new file
openfile();
// reset box center and view parameters if dynamic
box_bounds();
if (cflag == DYNAMIC) box_center();
if (viewflag == DYNAMIC) view_params();
// nme = # of atoms this proc will contribute to dump
nme = count();
if (nme > maxbuf) {
maxbuf = nme;
memory->destroy(buf);
memory->create(buf,maxbuf*size_one,"dump:buf");
}
// pack buf with color & diameter
pack(NULL);
// set minmax color range if using dynamic atom color map
if (acolor == ATTRIBUTE && image->map_dynamic(0)) {
double two[2],twoall[2];
double lo = BIG;
double hi = -BIG;
int m = 0;
for (int i = 0; i < nchoose; i++) {
lo = MIN(lo,buf[m]);
hi = MAX(hi,buf[m]);
m += size_one;
}
two[0] = -lo;
two[1] = hi;
MPI_Allreduce(two,twoall,2,MPI_DOUBLE,MPI_MAX,world);
int flag = image->map_minmax(0,-twoall[0],twoall[1]);
if (flag) error->all(FLERR,"Invalid color map min/max values");
}
// create image on each proc, then merge them
image->clear();
create_image();
image->merge();
// write image file
if (me == 0) {
if (filetype == JPG) image->write_JPG(fp);
else if (filetype == PNG) image->write_PNG(fp);
else image->write_PPM(fp);
if (multifile) {
fclose(fp);
fp = NULL;
}
}
}
/* ----------------------------------------------------------------------
simulation box bounds
------------------------------------------------------------------------- */
void DumpImage::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 {
boxxlo = domain->boxlo_bound[0];
boxxhi = domain->boxhi_bound[0];
boxylo = domain->boxlo_bound[1];
boxyhi = domain->boxhi_bound[1];
boxzlo = domain->boxlo_bound[2];
boxzhi = domain->boxhi_bound[2];
boxxy = domain->xy;
boxxz = domain->xz;
boxyz = domain->yz;
}
}
/* ----------------------------------------------------------------------
reset view parameters
called once from constructor if view is STATIC
called every snapshot from write() if view is DYNAMIC
------------------------------------------------------------------------- */
void DumpImage::box_center()
{
if (cxstr) cx = input->variable->compute_equal(cxvar);
if (cystr) cy = input->variable->compute_equal(cyvar);
if (czstr) cz = input->variable->compute_equal(czvar);
image->xctr = boxxlo + cx*(boxxhi-boxxlo);
image->yctr = boxylo + cy*(boxyhi-boxylo);
image->zctr = boxzlo + cz*(boxzhi-boxzlo);
}
/* ----------------------------------------------------------------------
reset view parameters in Image class
called once from constructor if view is STATIC
called every snapshot from write() if view is DYNAMIC
------------------------------------------------------------------------- */
void DumpImage::view_params()
{
// view direction theta and phi
if (thetastr) {
double theta = input->variable->compute_equal(thetavar);
if (theta < 0.0 || theta > 180.0)
error->all(FLERR,"Invalid dump image theta value");
theta *= MY_PI/180.0;
image->theta = theta;
}
if (phistr) {
double phi = input->variable->compute_equal(phivar);
phi *= MY_PI/180.0;
image->phi = phi;
}
// up vector
if (upxstr) image->up[0] = input->variable->compute_equal(upxvar);
if (upystr) image->up[1] = input->variable->compute_equal(upyvar);
if (upzstr) image->up[2] = input->variable->compute_equal(upzvar);
// zoom and perspective
if (zoomstr) image->zoom = input->variable->compute_equal(zoomvar);
if (image->zoom <= 0.0) error->all(FLERR,"Invalid dump image zoom value");
if (perspstr) image->persp = input->variable->compute_equal(perspvar);
if (image->persp < 0.0) error->all(FLERR,"Invalid dump image persp value");
// remainder of view setup is internal to Image class
image->view_params(boxxlo,boxxhi,boxylo,boxyhi,boxzlo,boxzhi);
}
/* ----------------------------------------------------------------------
create image for atoms on this proc
every pixel has depth
------------------------------------------------------------------------- */
void DumpImage::create_image()
{
int i,j,k,m,n,itype,atom1,atom2,imol,iatom,btype,ibonus,drawflag;
tagint tagprev;
double diameter,delx,dely,delz;
int *bodyvec;
double **bodyarray;
double *color,*color1,*color2;
double xmid[3],pt1[3],pt2[3],pt3[3];
double mat[3][3];
// render my atoms
if (atomflag) {
double **x = atom->x;
int *line = atom->line;
int *tri = atom->tri;
int *body = atom->body;
m = 0;
for (i = 0; i < nchoose; i++) {
j = clist[i];
if (acolor == TYPE) {
itype = static_cast<int> (buf[m]);
color = colortype[itype];
} else if (acolor == ELEMENT) {
itype = static_cast<int> (buf[m]);
color = colorelement[itype];
} else if (acolor == ATTRIBUTE) {
color = image->map_value2color(0,buf[m]);
} else color = image->color2rgb("white");
if (adiam == NUMERIC) {
diameter = adiamvalue;
} else if (adiam == TYPE) {
itype = static_cast<int> (buf[m+1]);
diameter = diamtype[itype];
} else if (adiam == ELEMENT) {
itype = static_cast<int> (buf[m+1]);
diameter = diamelement[itype];
} else if (adiam == ATTRIBUTE) {
diameter = buf[m+1];
}
// do not draw if line,tri,body keywords enabled and atom is one of those
drawflag = 1;
if (extraflag) {
if (lineflag && line[j] >= 0) drawflag = 0;
if (triflag && tri[j] >= 0) drawflag = 0;
if (bodyflag && body[j] >= 0) drawflag = 0;
}
if (drawflag) image->draw_sphere(x[j],color,diameter);
m += size_one;
}
}
// render atoms that are lines
if (lineflag) {
double length,theta,dx,dy;
double **x = atom->x;
int *line = atom->line;
int *type = atom->type;
for (i = 0; i < nchoose; i++) {
j = clist[i];
if (line[j] < 0) continue;
if (lcolor == TYPE) {
color = colortype[type[j]];
}
if (ldiam == NUMERIC) {
diameter = ldiamvalue;
}
length = avec_line->bonus[line[j]].length;
theta = avec_line->bonus[line[j]].theta;
dx = 0.5*length*cos(theta);
dy = 0.5*length*sin(theta);
pt1[0] = x[j][0] + dx;
pt1[1] = x[j][1] + dy;
pt1[2] = 0.0;
pt2[0] = x[j][0] - dx;
pt2[1] = x[j][1] - dy;
pt2[2] = 0.0;
image->draw_cylinder(pt1,pt2,color,ldiamvalue,3);
}
}
// render atoms that are triangles
// tstyle = 1 for tri only, 2 for edges only, 3 for both
if (triflag) {
int tridraw = 1;
if (tstyle == 2) tridraw = 0;
int edgedraw = 1;
if (tstyle == 1) edgedraw = 0;
double **x = atom->x;
int *tri = atom->tri;
int *type = atom->type;
for (i = 0; i < nchoose; i++) {
j = clist[i];
if (tri[j] < 0) continue;
if (tcolor == TYPE) {
color = colortype[type[j]];
}
MathExtra::quat_to_mat(avec_tri->bonus[tri[i]].quat,mat);
MathExtra::matvec(mat,avec_tri->bonus[tri[i]].c1,pt1);
MathExtra::matvec(mat,avec_tri->bonus[tri[i]].c2,pt2);
MathExtra::matvec(mat,avec_tri->bonus[tri[i]].c3,pt3);
MathExtra::add3(pt1,x[i],pt1);
MathExtra::add3(pt2,x[i],pt2);
MathExtra::add3(pt3,x[i],pt3);
if (tridraw) image->draw_triangle(pt1,pt2,pt3,color);
if (edgedraw) {
image->draw_cylinder(pt1,pt2,color,tdiamvalue,3);
image->draw_cylinder(pt2,pt3,color,tdiamvalue,3);
image->draw_cylinder(pt3,pt1,color,tdiamvalue,3);
}
}
}
// render atoms that are bodies
if (bodyflag) {
Body *bptr = avec_body->bptr;
int *body = atom->body;
m = 0;
for (i = 0; i < nchoose; i++) {
j = clist[i];
if (body[j] < 0) continue;
if (bodycolor == TYPE) {
itype = static_cast<int> (buf[m]);
color = colortype[itype];
}
ibonus = body[i];
n = bptr->image(ibonus,bodyflag1,bodyflag2,bodyvec,bodyarray);
for (k = 0; k < n; k++) {
if (bodyvec[k] == SPHERE)
image->draw_sphere(bodyarray[k],color,bodyarray[k][3]);
else if (bodyvec[k] == LINE)
image->draw_cylinder(&bodyarray[k][0],&bodyarray[k][3],
color,bodyarray[k][6],3);
}
m += size_one;
}
}
// render bonds for my atoms
// both atoms in bond must be selected for bond to be rendered
// if newton_bond is off, only render bond once
// render bond in 2 pieces if crosses periodic boundary
// if bond is deleted (type = 0), do not render
// if bond is turned off (type < 0), still render
if (bondflag) {
double **x = atom->x;
tagint *tag = atom->tag;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *num_bond = atom->num_bond;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int newton_bond = force->newton_bond;
int molecular = atom->molecular;
Molecule **onemols = atom->avec->onemols;
// communicate choose flag for ghost atoms to know if they are selected
// if bcolor/bdiam = ATOM, setup bufcopy to comm atom color/diam attributes
if (atom->nmax > maxbufcopy) {
maxbufcopy = atom->nmax;
memory->destroy(chooseghost);
memory->create(chooseghost,maxbufcopy,"dump:chooseghost");
if (comm_forward == 3) {
memory->destroy(bufcopy);
memory->create(bufcopy,maxbufcopy,2,"dump:bufcopy");
}
}
for (i = 0; i < nlocal; i++) chooseghost[i] = choose[i];
if (comm_forward == 3) {
for (i = 0; i < nlocal; i++) bufcopy[i][0] = bufcopy[i][1] = 0.0;
m = 0;
for (i = 0; i < nchoose; i++) {
j = clist[i];
bufcopy[j][0] = buf[m];
bufcopy[j][1] = buf[m+1];
m += size_one;
}
}
comm->forward_comm_dump(this);
for (i = 0; i < nchoose; i++) {
atom1 = clist[i];
if (molecular == 1) n = num_bond[atom1];
else {
if (molindex[atom1] < 0) continue;
imol = molindex[atom1];
iatom = molatom[atom1];
n = onemols[imol]->num_bond[iatom];
}
for (m = 0; m < n; m++) {
if (molecular == 1) {
btype = bond_type[atom1][m];
atom2 = atom->map(bond_atom[atom1][m]);
} else {
tagprev = tag[i] - iatom - 1;
btype = atom->map(onemols[imol]->bond_type[iatom][m]);
atom2 = atom->map(onemols[imol]->bond_atom[iatom][m]+tagprev);
}
if (atom2 < 0 || !chooseghost[atom2]) continue;
if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
if (btype == 0) continue;
if (bcolor == ATOM) {
if (acolor == TYPE) {
color1 = colortype[type[atom1]];
color2 = colortype[type[atom2]];
} else if (acolor == ELEMENT) {
color1 = colorelement[type[atom1]];
color2 = colorelement[type[atom2]];
} else if (acolor == ATTRIBUTE) {
color1 = image->map_value2color(0,bufcopy[atom1][0]);
color2 = image->map_value2color(0,bufcopy[atom2][0]);
} else {
color1 = image->color2rgb("white");
color2 = image->color2rgb("white");
}
} else if (bcolor == TYPE) {
itype = btype;
if (itype < 0) itype = -itype;
color = bcolortype[itype];
}
if (bdiam == NUMERIC) {
diameter = bdiamvalue;
} else if (bdiam == ATOM) {
if (adiam == NUMERIC) {
diameter = adiamvalue;
} else if (adiam == TYPE) {
diameter = MIN(diamtype[type[atom1]],diamtype[type[atom1]]);
} else if (adiam == ELEMENT) {
diameter = MIN(diamelement[type[atom1]],diamelement[type[atom1]]);
} else if (adiam == ATTRIBUTE) {
diameter = MIN(bufcopy[atom1][1],bufcopy[atom2][1]);
}
} else if (bdiam == TYPE) {
itype = btype;
if (itype < 0) itype = -itype;
diameter = bdiamtype[itype];
}
// draw cylinder in 2 pieces if bcolor = ATOM
// or bond crosses periodic boundary
delx = x[atom2][0] - x[atom1][0];
dely = x[atom2][1] - x[atom1][1];
delz = x[atom2][2] - x[atom1][2];
if (bcolor == ATOM || domain->minimum_image_check(delx,dely,delz)) {
domain->minimum_image(delx,dely,delz);
xmid[0] = x[atom1][0] + 0.5*delx;
xmid[1] = x[atom1][1] + 0.5*dely;
xmid[2] = x[atom1][2] + 0.5*delz;
if (bcolor == ATOM)
image->draw_cylinder(x[atom1],xmid,color1,diameter,3);
else image->draw_cylinder(x[atom1],xmid,color,diameter,3);
xmid[0] = x[atom2][0] - 0.5*delx;
xmid[1] = x[atom2][1] - 0.5*dely;
xmid[2] = x[atom2][2] - 0.5*delz;
if (bcolor == ATOM)
image->draw_cylinder(xmid,x[atom2],color2,diameter,3);
else image->draw_cylinder(xmid,x[atom2],color,diameter,3);
} else image->draw_cylinder(x[atom1],x[atom2],color,diameter,3);
}
}
}
// render outline of my sub-box, orthogonal or triclinic
if (subboxflag) {
double diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo);
if (domain->dimension == 3) diameter = MIN(diameter,boxzhi-boxzlo);
diameter *= subboxdiam;
double *sublo = domain->sublo;
double *subhi = domain->subhi;
double (*boxcorners)[3];
double box[8][3];
if (domain->triclinic == 0) {
box[0][0] = sublo[0]; box[0][1] = sublo[1]; box[0][2] = sublo[2];
box[1][0] = subhi[0]; box[1][1] = sublo[1]; box[1][2] = sublo[2];
box[2][0] = sublo[0]; box[2][1] = subhi[1]; box[2][2] = sublo[2];
box[3][0] = subhi[0]; box[3][1] = subhi[1]; box[3][2] = sublo[2];
box[4][0] = sublo[0]; box[4][1] = sublo[1]; box[4][2] = subhi[2];
box[5][0] = subhi[0]; box[5][1] = sublo[1]; box[5][2] = subhi[2];
box[6][0] = sublo[0]; box[6][1] = subhi[1]; box[6][2] = subhi[2];
box[7][0] = subhi[0]; box[7][1] = subhi[1]; box[7][2] = subhi[2];
boxcorners = box;
} else {
domain->subbox_corners();
boxcorners = domain->corners;
}
image->draw_box(boxcorners,diameter);
}
// render outline of simulation box, orthogonal or triclinic
if (boxflag) {
double diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo);
if (domain->dimension == 3) diameter = MIN(diameter,boxzhi-boxzlo);
diameter *= boxdiam;
double (*boxcorners)[3];
double box[8][3];
if (domain->triclinic == 0) {
box[0][0] = boxxlo; box[0][1] = boxylo; box[0][2] = boxzlo;
box[1][0] = boxxhi; box[1][1] = boxylo; box[1][2] = boxzlo;
box[2][0] = boxxlo; box[2][1] = boxyhi; box[2][2] = boxzlo;
box[3][0] = boxxhi; box[3][1] = boxyhi; box[3][2] = boxzlo;
box[4][0] = boxxlo; box[4][1] = boxylo; box[4][2] = boxzhi;
box[5][0] = boxxhi; box[5][1] = boxylo; box[5][2] = boxzhi;
box[6][0] = boxxlo; box[6][1] = boxyhi; box[6][2] = boxzhi;
box[7][0] = boxxhi; box[7][1] = boxyhi; box[7][2] = boxzhi;
boxcorners = box;
} else {
domain->box_corners();
boxcorners = domain->corners;
}
image->draw_box(boxcorners,diameter);
}
// render XYZ axes in red/green/blue
// offset by 10% of box size and scale by axeslen
if (axesflag) {
double diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo);
if (domain->dimension == 3) diameter = MIN(diameter,boxzhi-boxzlo);
diameter *= axesdiam;
double (*boxcorners)[3];
double axes[4][3];
if (domain->triclinic == 0) {
axes[0][0] = boxxlo; axes[0][1] = boxylo; axes[0][2] = boxzlo;
axes[1][0] = boxxhi; axes[1][1] = boxylo; axes[1][2] = boxzlo;
axes[2][0] = boxxlo; axes[2][1] = boxyhi; axes[2][2] = boxzlo;
axes[3][0] = boxxlo; axes[3][1] = boxylo; axes[3][2] = boxzhi;
} else {
domain->box_corners();
boxcorners = domain->corners;
axes[0][0] = boxcorners[0][0];
axes[0][1] = boxcorners[0][1];
axes[0][2] = boxcorners[0][2];
axes[1][0] = boxcorners[1][0];
axes[1][1] = boxcorners[1][1];
axes[1][2] = boxcorners[1][2];
axes[2][0] = boxcorners[2][0];
axes[2][1] = boxcorners[2][1];
axes[2][2] = boxcorners[2][2];
axes[3][0] = boxcorners[4][0];
axes[3][1] = boxcorners[4][1];
axes[3][2] = boxcorners[4][2];
}
double offset = MAX(boxxhi-boxxlo,boxyhi-boxylo);
if (domain->dimension == 3) offset = MAX(offset,boxzhi-boxzlo);
offset *= 0.1;
axes[0][0] -= offset; axes[0][1] -= offset; axes[0][2] -= offset;
axes[1][0] -= offset; axes[1][1] -= offset; axes[1][2] -= offset;
axes[2][0] -= offset; axes[2][1] -= offset; axes[2][2] -= offset;
axes[3][0] -= offset; axes[3][1] -= offset; axes[3][2] -= offset;
axes[1][0] = axes[0][0] + axeslen*(axes[1][0]-axes[0][0]);
axes[1][1] = axes[0][1] + axeslen*(axes[1][1]-axes[0][1]);
axes[1][2] = axes[0][2] + axeslen*(axes[1][2]-axes[0][2]);
axes[2][0] = axes[0][0] + axeslen*(axes[2][0]-axes[0][0]);
axes[2][1] = axes[0][1] + axeslen*(axes[2][1]-axes[0][1]);
axes[2][2] = axes[0][2] + axeslen*(axes[2][2]-axes[0][2]);
axes[3][0] = axes[0][0] + axeslen*(axes[3][0]-axes[0][0]);
axes[3][1] = axes[0][1] + axeslen*(axes[3][1]-axes[0][1]);
axes[3][2] = axes[0][2] + axeslen*(axes[3][2]-axes[0][2]);
image->draw_axes(axes,diameter);
}
}
/* ---------------------------------------------------------------------- */
int DumpImage::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
if (comm_forward == 1) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = chooseghost[j];
}
} else {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = chooseghost[j];
buf[m++] = bufcopy[j][0];
buf[m++] = bufcopy[j][1];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void DumpImage::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
if (comm_forward == 1)
for (i = first; i < last; i++) chooseghost[i] = static_cast<int> (buf[m++]);
else {
for (i = first; i < last; i++) {
chooseghost[i] = static_cast<int> (buf[m++]);
bufcopy[i][0] = buf[m++];
bufcopy[i][1] = buf[m++];
}
}
}
/* ---------------------------------------------------------------------- */
int DumpImage::modify_param(int narg, char **arg)
{
int n = DumpCustom::modify_param(narg,arg);
if (n) return n;
if (strcmp(arg[0],"acolor") == 0) {
if (narg < 3) error->all(FLERR,"Illegal dump_modify command");
int nlo,nhi;
force->bounds(arg[1],atom->ntypes,nlo,nhi);
// ptrs = list of ncount colornames separated by '/'
int ncount = 1;
char *nextptr;
char *ptr = arg[2];
while ((nextptr = strchr(ptr,'/'))) {
ptr = nextptr + 1;
ncount++;
}
char **ptrs = new char*[ncount+1];
ncount = 0;
ptrs[ncount++] = strtok(arg[2],"/");
while ((ptrs[ncount++] = strtok(NULL,"/")));
ncount--;
// assign each of ncount colors in round-robin fashion to types
int m = 0;
for (int i = nlo; i <= nhi; i++) {
colortype[i] = image->color2rgb(ptrs[m%ncount]);
if (colortype[i] == NULL)
error->all(FLERR,"Invalid color in dump_modify command");
m++;
}
delete [] ptrs;
return 3;
}
if (strcmp(arg[0],"adiam") == 0) {
if (narg < 3) error->all(FLERR,"Illegal dump_modify command");
int nlo,nhi;
force->bounds(arg[1],atom->ntypes,nlo,nhi);
double diam = force->numeric(FLERR,arg[2]);
if (diam <= 0.0) error->all(FLERR,"Illegal dump_modify command");
for (int i = nlo; i <= nhi; i++) diamtype[i] = diam;
return 3;
}
if (strcmp(arg[0],"amap") == 0) {
if (narg < 6) error->all(FLERR,"Illegal dump_modify command");
if (strlen(arg[3]) != 2) error->all(FLERR,"Illegal dump_modify command");
int factor;
if (arg[3][0] == 's') factor = 1;
else if (arg[3][0] == 'c') factor = 2;
else if (arg[3][0] == 'd') factor = 3;
else error->all(FLERR,"Illegal dump_modify command");
int nentry = force->inumeric(FLERR,arg[5]);
if (nentry < 1) error->all(FLERR,"Illegal dump_modify command");
int n = 6 + factor*nentry;
if (narg < n) error->all(FLERR,"Illegal dump_modify command");
int flag = image->map_reset(0,n-1,&arg[1]);
if (flag) error->all(FLERR,"Illegal dump_modify command");
return n;
}
if (strcmp(arg[0],"bcolor") == 0) {
if (narg < 3) error->all(FLERR,"Illegal dump_modify command");
if (atom->nbondtypes == 0)
error->all(FLERR,"Dump modify bcolor not allowed with no bond types");
int nlo,nhi;
force->bounds(arg[1],atom->nbondtypes,nlo,nhi);
// ptrs = list of ncount colornames separated by '/'
int ncount = 1;
char *nextptr;
char *ptr = arg[2];
while ((nextptr = strchr(ptr,'/'))) {
ptr = nextptr + 1;
ncount++;
}
char **ptrs = new char*[ncount+1];
ncount = 0;
ptrs[ncount++] = strtok(arg[2],"/");
while ((ptrs[ncount++] = strtok(NULL,"/")));
ncount--;
// assign each of ncount colors in round-robin fashion to types
int m = 0;
for (int i = nlo; i <= nhi; i++) {
bcolortype[i] = image->color2rgb(ptrs[m%ncount]);
if (bcolortype[i] == NULL)
error->all(FLERR,"Invalid color in dump_modify command");
m++;
}
delete [] ptrs;
return 3;
}
if (strcmp(arg[0],"bdiam") == 0) {
if (narg < 3) error->all(FLERR,"Illegal dump_modify command");
if (atom->nbondtypes == 0)
error->all(FLERR,"Dump modify bdiam not allowed with no bond types");
int nlo,nhi;
force->bounds(arg[1],atom->ntypes,nlo,nhi);
double diam = force->numeric(FLERR,arg[2]);
if (diam <= 0.0) error->all(FLERR,"Illegal dump_modify command");
for (int i = nlo; i <= nhi; i++) bdiamtype[i] = diam;
return 3;
}
if (strcmp(arg[0],"backcolor") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
double *color = image->color2rgb(arg[1]);
if (color == NULL) error->all(FLERR,"Invalid color in dump_modify command");
image->background[0] = static_cast<int> (color[0]*255.0);
image->background[1] = static_cast<int> (color[1]*255.0);
image->background[2] = static_cast<int> (color[2]*255.0);
return 2;
}
if (strcmp(arg[0],"boxcolor") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
image->boxcolor = image->color2rgb(arg[1]);
if (image->boxcolor == NULL)
error->all(FLERR,"Invalid color in dump_modify command");
return 2;
}
if (strcmp(arg[0],"color") == 0) {
if (narg < 5) error->all(FLERR,"Illegal dump_modify command");
int flag = image->addcolor(arg[1],force->numeric(FLERR,arg[2]),force->numeric(FLERR,arg[3]),force->numeric(FLERR,arg[4]));
if (flag) error->all(FLERR,"Illegal dump_modify command");
return 5;
}
return 0;
}
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