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more work on dump image

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This commit is contained in:
Steve Plimpton
2022-11-17 15:56:15 -07:00
parent df5cfd18eb
commit c9b431214c
6 changed files with 294 additions and 32 deletions
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138
src/dump_image.cpp
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@ -21,10 +21,13 @@
#include "atom_vec_tri.h"
#include "body.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "force.h"
#include "grid2d.h"
#include "grid3d.h"
#include "image.h"
#include "input.h"
#include "math_const.h"
@ -33,6 +36,7 @@
#include "modify.h"
#include "molecule.h"
#include "tokenizer.h"
#include "update.h"
#include "variable.h"
#include <cmath>
@ -179,10 +183,14 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"grid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
gridflag = YES;
if (strcmp(arg[iarg+1],"type") == 0) lcolor = TYPE;
else error->all(FLERR,"Illegal dump image command");
ldiam = NUMERIC;
ldiamvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
char *id;
int igrid,idata,index;
int iflag =
utils::check_grid_reference(igrid,idata,index,lmp);
// utils::check_grid_reference((char *) "Dump image",
// arg[iarg+1],igrid,idata,index,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"line") == 0) {
@ -453,7 +461,23 @@ void DumpImage::init_style()
DumpCustom::init_style();
// check variables
// for grid output, find current ptr for compute or fix
// check that fix frequency is acceptable
if (gridflag) {
if (id_grid_compute) {
grid_compute = modify->get_compute_by_id(id_grid_compute);
if (!grid_compute)
error->all(FLERR,"Could not find dump image grid compute ID {}",id_grid_compute);
} else if (id_grid_fix) {
grid_fix = modify->get_fix_by_id(id_grid_fix);
if (!grid_fix) error->all(FLERR,"Could not find dump image fix ID {}",id_grid_fix);
if (nevery % grid_fix->peratom_freq)
error->all(FLERR,"Dump image and grid fix not computed at compatible times");
}
}
// check image variables
if (thetastr) {
thetavar = input->variable->find(thetastr);
@ -562,7 +586,7 @@ void DumpImage::write()
memory->create(buf,maxbuf*size_one,"dump:buf");
}
// pack buf with color & diameter
// pack atom buf with color & diameter
pack(nullptr);
@ -582,26 +606,95 @@ void DumpImage::write()
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");
if (flag) error->all(FLERR,"Invalid atom color map min/max values");
}
// pack grid gbuf with grid cell values
// ngrid_mine = # of grid cells this proc owns
if (gridflag) {
if (domain->dimension == 2) {
if (grid_compute)
grid2d = (Grid2d *) grid_compute->get_grid_by_index(grid_index);
else if (grid_fix)
grid2d = (Grid2d *) grid_fix->get_grid_by_index(grid_index);
grid2d->get_bounds_owned(nxlo_in,nxhi_in,nylo_in,nyhi_in);
} else {
if (grid_compute)
grid3d = (Grid3d *) grid_compute->get_grid_by_index(grid_index);
else if (grid_fix)
grid3d = (Grid3d *) grid_fix->get_grid_by_index(grid_index);
grid3d->get_bounds_owned(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in);
}
// invoke Compute for per-grid quantities
// only if within a run or minimize
// else require the compute is current
// this prevents the compute from being invoked by the WriteDump class
if (grid_compute) {
if (update->whichflag == 0) {
if (grid_compute->invoked_pergrid != update->ntimestep)
error->all(FLERR,"Grid compute {} used in dump image between runs is not current",
grid_compute->id);
} else {
if (!(grid_compute->invoked_flag & Compute::INVOKED_PERGRID)) {
grid_compute->compute_pergrid();
grid_compute->invoked_flag |= Compute::INVOKED_PERGRID;
}
}
}
// access grid data and load gbuf
/*
if (index == 0) {
double **vec2d;
if (field2source[n] == COMPUTE)
vec2d = (double **)
compute[field2index[n]]->get_griddata_by_index(field2data[n]);
else if (field2source[n] == FIX)
vec2d = (double **)
fix[field2index[n]]->get_griddata_by_index(field2data[n]);
for (int iy = nylo_in; iy <= nyhi_in; iy++)
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
buf[n] = vec2d[iy][ix];
n += size_one;
}
} else {
double ***array2d;
if (field2source[n] == COMPUTE)
array2d = (double ***)
compute[field2index[n]]->get_griddata_by_index(field2data[n]);
else if (field2source[n] == FIX)
array2d = (double ***)
fix[field2index[n]]->get_griddata_by_index(field2data[n]);
index--;
for (int iy = nylo_in; iy <= nyhi_in; iy++)
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
buf[n] = array2d[iy][ix][index];
n += size_one;
}
}
*/
}
// set minmax color range if using dynamic grid color map
if (acolor == ATTRIBUTE && image->map_dynamic(1)) {
if (gridflag && image->map_dynamic(1)) {
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;
for (int i = 0; i < ngrid_owned; i++) {
lo = MIN(lo,gbuf[i]);
hi = MAX(hi,gbuf[i]);
}
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");
int flag = image->map_minmax(1,-twoall[0],twoall[1]);
if (flag) error->all(FLERR,"Invalid grid color map min/max values");
}
// create image on each proc, then merge them
@ -702,8 +795,9 @@ void DumpImage::view_params()
}
/* ----------------------------------------------------------------------
create image for atoms on this proc
every pixel has depth
create image for all data this proc owns
all procs draw simulation box edges if requested
every drawn pixel has depth so merge can decide which to keep
------------------------------------------------------------------------- */
void DumpImage::create_image()
@ -767,6 +861,16 @@ void DumpImage::create_image()
}
}
// render my grid cells
if (gridflag) {
// draw 2 or 12 triangles
//image->draw_triangle(x,y,z,color);
}
// render atoms that are lines
if (lineflag) {