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start adding support for dump image of grid cell values

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This commit is contained in:
Steve Plimpton
2022-11-16 15:35:21 -07:00
parent a2435ea200
commit df5cfd18eb
4 changed files with 92 additions and 41 deletions
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45
doc/src/dump_image.rst
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@ -24,7 +24,7 @@ Syntax
* color = atom attribute that determines color of each atom
* diameter = atom attribute that determines size of each atom
* zero or more keyword/value pairs may be appended
* keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *ssao*
* keyword = *atom* or *adiam* or *bond* or *grid* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *ssao*
.. parsed-literal::
@ -34,6 +34,14 @@ Syntax
color = *atom* or *type* or *none*
width = number or *atom* or *type* or *none*
number = numeric value for bond width (distance units)
*grid* = per-grid value to use when coloring each grid cell
per-grid value = c_ID:gname:dname, c_ID:gname:dname[I], f_ID:gname:dname, f_ID:gname:dname[I]
gname = name of grid defined by compute or fix
dname = name of data field defined by compute or fix
c_ID = per-grid vector calculated by a compute with ID
c_ID[I] = Ith column of per-grid array calculated by a compute with ID
f_ID = per-grid vector calculated by a fix with ID
f_ID[I] = Ith column of per-grid array calculated by a fix with ID
*line* = color width
color = *type*
width = numeric value for line width (distance units)
@ -95,7 +103,7 @@ Syntax
dump_modify dump-ID keyword values ...
* these keywords apply only to the *image* and *movie* styles and are documented on this page
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
* keyword = *acolor* or *adiam* or *amap* or *gmap* or *backcolor* or *bcolor* or *bdiam* or *bitrate* or *boxcolor* or *color* or *framerate* or *gmap*
* see the :doc:`dump modify <dump_modify>` doc page for more general keywords
.. parsed-literal::
@ -134,15 +142,16 @@ Syntax
*bdiam* args = type diam
type = bond type or range of types (see below)
diam = diameter of bonds of that type (distance units)
*bitrate* arg = rate
rate = target bitrate for movie in kbps
*boxcolor* arg = color
color = name of color for simulation box lines and processor sub-domain lines
*color* args = name R G B
name = name of color
R,G,B = red/green/blue numeric values from 0.0 to 1.0
*bitrate* arg = rate
rate = target bitrate for movie in kbps
*framerate* arg = fps
fps = frames per second for movie
*gmap* args = identical to *amap* args
Examples
""""""""
@ -214,7 +223,7 @@ Similarly, the format of the resulting movie is chosen with the
and thus details have to be looked up in the `FFmpeg documentation
<https://ffmpeg.org/ffmpeg.html>`_. Typical examples are: .avi, .mpg,
.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie
compression like bitrate and framerate can be set using the
compression like *bitrate* and *framerate* can be set using the
dump_modify command as described below.
To write out JPEG and PNG format files, you must build LAMMPS with
@ -300,13 +309,13 @@ settings, they are interpreted in the following way.
If "vx", for example, is used as the *color* setting, then the color
of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by
a "color map", which can be specified via the dump_modify command, as
described below. The basic idea is that the atom-attribute will be
within a range of values, and every value within the range is mapped
to a specific color. Depending on how the color map is defined, that
mapping can take place via interpolation so that a value of -3.2 is
halfway between "red" and "blue", or discretely so that the value of
-3.2 is "orange".
a "color map", which can be specified via the dump_modify amap
command, as described below. The basic idea is that the
atom-attribute will be within a range of values, and every value
within the range is mapped to a specific color. Depending on how the
color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between "red" and "blue", or
discretely so that the value of -3.2 is "orange".
If "vx", for example, is used as the *diameter* setting, then the atom
will be rendered using the x-component of its velocity as the
@ -948,6 +957,17 @@ frequently.
----------
The *gmap* keyword can be used with the dump image command, with its
*grid* keyword, to setup a color map. The color map is used to assign
a specific RGB (red/green/blue) color value to an individual grid cell
when it is drawn, based on the grid cell value, which is a numeric
quantity specified with the *grid* keyword.
The arguments for the *gmap* keyword are identical to those for the
*amap* keyword (for atom coloring) described above.
----------
Restrictions
""""""""""""
@ -1031,6 +1051,7 @@ The defaults for the dump_modify keywords specific to dump image and dump movie
* boxcolor = yellow
* color = 140 color names are pre-defined as listed below
* framerate = 24
* gmap = min max cf 0.0 2 min blue max red
----------

46
src/dump_grid_vtk.cpp
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@ -66,9 +66,9 @@ void DumpGridVTK::init_style()
if (binary) error->all(FLERR,"Dump grid/vtk cannot write binary files\n");
if (!xcoord) {
memory->create(xcoord,nxgrid,"dumpgridVTK:xcoord");
memory->create(ycoord,nygrid,"dumpgridVTK:ycoord");
memory->create(zcoord,nzgrid,"dumpgridVTK:zcoord");
memory->create(xcoord,nxgrid+1,"dumpgridVTK:xcoord");
memory->create(ycoord,nygrid+1,"dumpgridVTK:ycoord");
memory->create(zcoord,nzgrid+1,"dumpgridVTK:zcoord");
}
}
@ -81,7 +81,7 @@ void DumpGridVTK::write_header(bigint ndump)
xyz_grid();
fprintf(fp,"<?xml version=\"1.0\"\?>\n");
fprintf(fp,"<VTKFile type=\"RectilinearGrid\"\n");
fprintf(fp,"<VTKFile type=\"RectilinearGrid\">\n");
fprintf(fp,"<RectilinearGrid WholeExtent=\"0 %d 0 %d 0 %d\" "
"Origin=\"0 0 0\" Spacing=\"1 1 1\">\n",nxgrid,nygrid,nzgrid);
fprintf(fp,"<Piece Extent=\"0 %d 0 %d 0 %d\">\n",nxgrid,nygrid,nzgrid);
@ -91,29 +91,27 @@ void DumpGridVTK::write_header(bigint ndump)
// coords of center point of grid cells in each of xyz dimensions
fprintf(fp,"<DataArray type=\"Float32\"\n");
for (int i = 0; i < nxgrid; i++)
fprintf(fp,"<DataArray type=\"Float32\" format=\"ascii\">\n");
for (int i = 0; i <= nxgrid; i++)
fprintf(fp,"%g ",xcoord[i]);
fprintf(fp,"\n");
fprintf(fp,"</DataArray>\n");
fprintf(fp,"<DataArray type=\"Float32\"\n");
for (int i = 0; i < nygrid; i++)
fprintf(fp,"\n</DataArray>\n");
fprintf(fp,"<DataArray type=\"Float32\" format=\"ascii\">\n");
for (int i = 0; i <= nygrid; i++)
fprintf(fp,"%g ",ycoord[i]);
fprintf(fp,"\n");
fprintf(fp,"</DataArray>\n");
fprintf(fp,"<DataArray type=\"Float32\"\n");
for (int i = 0; i < nzgrid; i++)
fprintf(fp,"\n</DataArray>\n");
fprintf(fp,"<DataArray type=\"Float32\" format=\"ascii\">\n");
for (int i = 0; i <= nzgrid; i++)
fprintf(fp,"%g ",zcoord[i]);
fprintf(fp,"\n");
fprintf(fp,"</DataArray>\n");
fprintf(fp,"\n</DataArray>\n");
fprintf(fp,"</Coordinates>\n");
fprintf(fp,"<CellData>\n");
if (mode == SCALAR)
fprintf(fp,"<DataArray type=\"Float32\" Name=\"Scalar\"\n");
fprintf(fp,"<DataArray type=\"Float32\" Name=\"Scalar\" format=\"ascii\">\n");
else if (mode == VECTOR)
fprintf(fp,"<DataArray type=\"Float32\" Name=\"Vector\" NumberOfComponents=\"3\"\n");
fprintf(fp,"<DataArray type=\"Float32\" Name=\"Vector\" "
"NumberOfComponents=\"3\" format=\"ascii\">\n");
}
/* ---------------------------------------------------------------------- */
@ -158,12 +156,12 @@ void DumpGridVTK::xyz_grid()
double dy = domain->prd[1] / nygrid;
double dz = domain->prd[2] / nzgrid;
for (int ix = 0; ix < nxgrid; ix++)
xcoord[ix] = boxlo[0] + (ix + 0.5) * dx;
for (int ix = 0; ix <= nxgrid; ix++)
xcoord[ix] = boxlo[0] + ix*dx;
for (int iy = 0; iy < nygrid; iy++)
ycoord[iy] = boxlo[1] + (iy + 0.5) * dy;
for (int iy = 0; iy <= nygrid; iy++)
ycoord[iy] = boxlo[1] + iy*dy;
for (int iz = 0; iz < nzgrid; iz++)
zcoord[iz] = boxlo[2] + (iz + 0.5) * dz;
for (int iz = 0; iz <= nzgrid; iz++)
zcoord[iz] = boxlo[2] + iz*dz;
}

38
src/dump_image.cpp
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@ -104,10 +104,10 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
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
// create Image class with two colormaps for atoms and grid cells
// change defaults for 2d
image = new Image(lmp,1);
image = new Image(lmp,2);
if (domain->dimension == 2) {
image->theta = 0.0;
@ -118,6 +118,7 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
// set defaults for optional args
atomflag = YES;
gridflag = NO;
lineflag = triflag = bodyflag = fixflag = NO;
if (atom->nbondtypes == 0) bondflag = NO;
else {
@ -175,6 +176,14 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
else error->all(FLERR,"Illegal dump image command");
iarg += 3;
} 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);
iarg += 2;
} else if (strcmp(arg[iarg],"line") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
@ -576,6 +585,25 @@ void DumpImage::write()
if (flag) error->all(FLERR,"Invalid color map min/max values");
}
// set minmax color range if using dynamic grid color map
if (acolor == ATTRIBUTE && 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;
}
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();
@ -1217,7 +1245,7 @@ int DumpImage::modify_param(int narg, char **arg)
return 3;
}
if (strcmp(arg[0],"amap") == 0) {
if ((strcmp(arg[0],"amap") == 0) || (strcmp(arg[0],"gmap") == 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 = 0;
@ -1229,7 +1257,9 @@ int DumpImage::modify_param(int narg, char **arg)
if (nentry < 1) error->all(FLERR,"Illegal dump_modify command");
n = 6 + factor*nentry;
if (narg < n) error->all(FLERR,"Illegal dump_modify command");
int flag = image->map_reset(0,n-1,&arg[1]);
int flag;
if (strcmp(arg[0],"amap") == 0) flag = image->map_reset(0,n-1,&arg[1]);
if (strcmp(arg[0],"gmap") == 0) flag = image->map_reset(1,n-1,&arg[1]);
if (flag) error->all(FLERR,"Illegal dump_modify command");
return n;
}

2
src/dump_image.h
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@ -41,6 +41,8 @@ class DumpImage : public DumpCustom {
int acolor, adiam; // what determines color/diam of atoms
double adiamvalue; // atom diameter value
int gridflag; // 0/1 for draw grid cells
int lineflag; // 0/1 for draw atoms as lines
int lcolor, ldiam; // what determines color/diam of lines
double ldiamvalue; // line diameter value