more work on dump image
This commit is contained in:
Steve Plimpton
@ -14,6 +14,7 @@
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#include "dump_image.h"
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#include "arg_info.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "atom_vec_body.h"
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@ -124,6 +125,8 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
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atomflag = YES;
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gridflag = NO;
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lineflag = triflag = bodyflag = fixflag = NO;
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id_grid_compute = id_grid_fix = nullptr;
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if (atom->nbondtypes == 0) bondflag = NO;
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else {
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bondflag = YES;
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@ -188,8 +191,16 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
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int igrid,idata,index;
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int iflag =
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utils::check_grid_reference((char *) "Dump image",
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arg[iarg+1],igrid,idata,index,lmp);
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arg[iarg+1],nevery,id,
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igrid,idata,index,lmp);
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if (iflag < 0) error->all(FLERR,"Invalid grid reference in dump image command");
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if (iflag == ArgInfo::COMPUTE) id_grid_compute = utils::strdup(id);
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else if (iflag == ArgInfo::FIX) id_grid_fix = utils::strdup(id);
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delete [] id;
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grid_igrid = igrid;
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grid_idata = idata;
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grid_index = index;
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iarg += 2;
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} else if (strcmp(arg[iarg],"line") == 0) {
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@ -432,6 +443,9 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
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maxbufcopy = 0;
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chooseghost = nullptr;
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bufcopy = nullptr;
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maxgrid = 0;
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gbuf = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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@ -448,6 +462,7 @@ DumpImage::~DumpImage()
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delete [] bcolortype;
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memory->destroy(chooseghost);
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memory->destroy(bufcopy);
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memory->destroy(gbuf);
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}
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/* ---------------------------------------------------------------------- */
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@ -609,21 +624,33 @@ void DumpImage::write()
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}
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// pack grid gbuf with grid cell values
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// ngrid_mine = # of grid cells this proc owns
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// ngrid = # of grid cells this proc owns
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if (gridflag) {
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if (domain->dimension == 2) {
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if (grid_compute)
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grid2d = (Grid2d *) grid_compute->get_grid_by_index(grid_index);
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grid2d = (Grid2d *) grid_compute->get_grid_by_index(grid_igrid);
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else if (grid_fix)
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grid2d = (Grid2d *) grid_fix->get_grid_by_index(grid_index);
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grid2d = (Grid2d *) grid_fix->get_grid_by_index(grid_igrid);
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grid2d->get_size(nxgrid,nygrid);
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grid2d->get_bounds_owned(nxlo_in,nxhi_in,nylo_in,nyhi_in);
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ngrid = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1);
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} else {
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if (grid_compute)
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grid3d = (Grid3d *) grid_compute->get_grid_by_index(grid_index);
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grid3d = (Grid3d *) grid_compute->get_grid_by_index(grid_igrid);
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else if (grid_fix)
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grid3d = (Grid3d *) grid_fix->get_grid_by_index(grid_index);
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grid3d = (Grid3d *) grid_fix->get_grid_by_index(grid_igrid);
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grid3d->get_size(nxgrid,nygrid,nzgrid);
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grid3d->get_bounds_owned(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in);
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ngrid = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * (nzhi_in-nzlo_in+1);
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}
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// insure gbuf is large enough
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if (ngrid > maxgrid) {
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memory->destroy(gbuf);
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maxgrid = ngrid;
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memory->create(gbuf,maxgrid,"dump/image:gbuf");
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}
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// invoke Compute for per-grid quantities
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@ -646,37 +673,65 @@ void DumpImage::write()
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// access grid data and load gbuf
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/*
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if (index == 0) {
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double **vec2d;
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if (field2source[n] == COMPUTE)
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vec2d = (double **)
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compute[field2index[n]]->get_griddata_by_index(field2data[n]);
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else if (field2source[n] == FIX)
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vec2d = (double **)
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fix[field2index[n]]->get_griddata_by_index(field2data[n]);
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
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buf[n] = vec2d[iy][ix];
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n += size_one;
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if (domain->dimension == 2) {
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if (grid_index == 0) {
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double **vec2d;
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if (grid_compute)
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vec2d = (double **)
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grid_compute->get_griddata_by_index(grid_idata);
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else if (grid_fix)
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vec2d = (double **)
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grid_fix->get_griddata_by_index(grid_idata);
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int n = 0;
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++)
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gbuf[n++] = vec2d[iy][ix];
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} else {
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double ***array2d;
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if (grid_compute)
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array2d = (double ***)
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grid_compute->get_griddata_by_index(grid_idata);
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else if (grid_fix)
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array2d = (double ***)
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grid_fix->get_griddata_by_index(grid_idata);
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int index = grid_index - 1;
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int n = 0;
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++)
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gbuf[n++] = array2d[iy][ix][index];
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}
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} else if (domain->dimension == 3) {
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if (grid_index == 0) {
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double ***vec3d;
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if (grid_compute)
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vec3d = (double ***)
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grid_compute->get_griddata_by_index(grid_idata);
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else if (grid_fix)
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vec3d = (double ***)
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grid_fix->get_griddata_by_index(grid_idata);
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int n = 0;
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for (int iz = nzlo_in; iz <= nzhi_in; iz++)
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++)
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gbuf[n++] = vec3d[iz][iy][ix];
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}
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} else {
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double ***array2d;
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if (field2source[n] == COMPUTE)
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array2d = (double ***)
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compute[field2index[n]]->get_griddata_by_index(field2data[n]);
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else if (field2source[n] == FIX)
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array2d = (double ***)
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fix[field2index[n]]->get_griddata_by_index(field2data[n]);
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index--;
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
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buf[n] = array2d[iy][ix][index];
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n += size_one;
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}
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}
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*/
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double ****array3d;
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if (grid_compute)
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array3d = (double ****)
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grid_compute->get_griddata_by_index(grid_idata);
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else if (grid_fix)
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array3d = (double ****)
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grid_fix->get_griddata_by_index(grid_idata);
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int index = grid_index - 1;
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int n = 0;
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for (int iz = nzlo_in; iz <= nzhi_in; iz++)
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++)
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gbuf[n++] = array3d[iz][iy][ix][index];
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}
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}
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// set minmax color range if using dynamic grid color map
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@ -685,7 +740,7 @@ void DumpImage::write()
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double two[2],twoall[2];
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double lo = BIG;
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double hi = -BIG;
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for (int i = 0; i < ngrid_owned; i++) {
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for (int i = 0; i < ngrid; i++) {
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lo = MIN(lo,gbuf[i]);
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hi = MAX(hi,gbuf[i]);
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}
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@ -861,13 +916,46 @@ void DumpImage::create_image()
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}
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// render my grid cells
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// 2 triangles for 2d rectangle, 12 triangles for 3d cube surface
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// grid_cell_corners_2d/3d calculates orthogonal vs triclinic corner pts
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// for 3d, outward normals on all 6 faces
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if (gridflag) {
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// draw 2 or 12 triangles
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//image->draw_triangle(x,y,z,color);
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int n = 0;
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if (domain->dimension == 2) {
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
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grid_cell_corners_2d(ix,iy);
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color = image->map_value2color(1,gbuf[n++]);
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image->draw_triangle(gcorners[0],gcorners[1],gcorners[3],color);
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image->draw_triangle(gcorners[0],gcorners[3],gcorners[2],color);
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}
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} else {
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for (int iz = nzlo_in; iz <= nzhi_in; iz++)
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
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grid_cell_corners_3d(ix,iy,iz);
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color = image->map_value2color(1,gbuf[n++]);
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// lower x face
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image->draw_triangle(gcorners[0],gcorners[4],gcorners[6],color);
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image->draw_triangle(gcorners[0],gcorners[6],gcorners[2],color);
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// upper x face
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image->draw_triangle(gcorners[1],gcorners[5],gcorners[7],color);
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image->draw_triangle(gcorners[1],gcorners[7],gcorners[3],color);
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// lower y face
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image->draw_triangle(gcorners[0],gcorners[1],gcorners[5],color);
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image->draw_triangle(gcorners[0],gcorners[5],gcorners[4],color);
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// upper y face
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image->draw_triangle(gcorners[2],gcorners[6],gcorners[7],color);
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image->draw_triangle(gcorners[2],gcorners[7],gcorners[3],color);
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// lower z face
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image->draw_triangle(gcorners[0],gcorners[2],gcorners[3],color);
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image->draw_triangle(gcorners[0],gcorners[3],gcorners[1],color);
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// upper z face
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image->draw_triangle(gcorners[4],gcorners[5],gcorners[7],color);
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image->draw_triangle(gcorners[4],gcorners[7],gcorners[6],color);
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}
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}
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}
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// render atoms that are lines
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@ -1266,6 +1354,83 @@ void DumpImage::create_image()
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/* ---------------------------------------------------------------------- */
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void DumpImage::grid_cell_corners_2d(int ix, int iy)
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{
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double *boxlo = domain->boxlo;
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double *prd = domain->prd;
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if (!domain->triclinic) {
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double xdelta = prd[0] / nxgrid;
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double ydelta = prd[1] / nygrid;
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int n = 0;
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for (int y = 0; y < 2; y++)
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for (int x = 0; x < 2; x++) {
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gcorners[n][0] = boxlo[0] + (ix+x) * xdelta;
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gcorners[n][1] = boxlo[1] + (iy+y) * ydelta;
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n++;
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}
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} else {
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double lamda[3],xone[3];
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lamda[2] = 0.0;
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double dx = 1.0 / nxgrid;
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double dy = 1.0 / nygrid;
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int n = 0;
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for (int y = 0; y < 2; y++)
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for (int x = 0; x < 2; x++) {
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lamda[0] = (ix+x) * dx;
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lamda[1] = (iy+y) * dy;
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domain->lamda2x(lamda,gcorners[n++]);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpImage::grid_cell_corners_3d(int ix, int iy, int iz)
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{
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double *boxlo = domain->boxlo;
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double *prd = domain->prd;
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if (!domain->triclinic) {
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double xdelta = prd[0] / nxgrid;
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double ydelta = prd[1] / nygrid;
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double zdelta = prd[2] / nzgrid;
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int n = 0;
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for (int z = 0; z < 2; z++)
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for (int y = 0; y < 2; y++)
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for (int x = 0; x < 2; x++) {
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gcorners[n][0] = boxlo[0] + (ix+x) * xdelta;
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gcorners[n][1] = boxlo[1] + (iy+y) * ydelta;
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gcorners[n][2] = boxlo[2] + (iz+z) * zdelta;
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n++;
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}
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} else {
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double lamda[3],xone[3];
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double dx = 1.0 / nxgrid;
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double dy = 1.0 / nygrid;
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double dz = 1.0 / nzgrid;
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int n = 0;
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for (int z = 0; z < 2; z++)
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for (int y = 0; y < 2; y++)
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for (int x = 0; x < 2; x++) {
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lamda[0] = (ix+x) * dx;
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lamda[1] = (iy+y) * dy;
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lamda[2] = (iz+z) * dz;
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domain->lamda2x(lamda,gcorners[n++]);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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int DumpImage::pack_forward_comm(int n, int *list, double *buf,
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int /*pbc_flag*/, int * /*pbc*/)
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{
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Block a user