[pull] develop from lammps:develop

doc/src/dump_image.rst

@@ -44,14 +44,14 @@ Syntax
            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*
+         color = *type* or *index* or *atom*
          width = numeric value for line width (distance units)
        *tri* = color tflag width
-         color = *type*
+         color = *type* or *index* or *atom*
          tflag = 1 for just triangle, 2 for just tri edges, 3 for both
          width = numeric value for triangle edge width (distance units)
        *ellipsoid* = color eflag level width
-         color = *type*
+         color = *type* or *index* or *atom*
          eflag = 1 for triangles, 2 for wireframe, 3 for both
          level = mesh refinement level, value between 1 (low resolution) and 6 (ultra high resolution)
          width = diameter of wireframe edges (distance units) (ignored for triangles)
@@ -494,10 +494,21 @@ as described below.
 The *line* keyword can be used when :doc:`atom_style line <atom_style>`
 is used to define particles as line segments, and will draw them as
 lines.  If this keyword is not used, such particles will be drawn as
-spheres, the same as if they were regular atoms.  The only setting
-currently allowed for the *color* value is *type*, which will color
-the lines according to the atom type of the particle.  By default the
-mapping of types to colors is as follows:
+spheres, the same as if they were regular atoms.
+
+.. versionchanged:: TBD
+
+   added *index* and *atom* color styles
+
+The there are currently three supported settings for the *color* value:
+*type*, *index*, or *atom*.  With the *type* setting the line particles
+will be colored according to the atom type of the particle.  With the
+*index* setting the coloring follows the line index instead.  With the
+*atom* setting, the color follows the coloring selected for coloring
+atoms (including using color maps).  For *type* and *index* settings,
+the value is mapped to the colors of atom types thus the coloring style
+for atoms **must** be set to *type*.  The list of colors is by default
+the list of atom type colors as follows:
 
 * type 1 = red
 * type 2 = green
@@ -506,8 +517,11 @@ mapping of types to colors is as follows:
 * type 5 = cyan
 * type 6 = magenta
 
-and repeats itself for types > 6.  There is not yet an option to
-change this via the dump_modify command.
+and repeats itself for types > 6.  This list can by changed with the
+:doc:`dump_modify acolor <dump_image>` command.  If more different
+colors than atom types are desired, the *number of atom types* must be
+*increased* correspondingly when using either the :doc:`create_box
+<create_box>` or the :doc:`read_data <read_data>` command.
 
 The line *width* can only be a numeric value, which specifies that all
 lines will be drawn as cylinders with that diameter, e.g. 1.0, which
@@ -521,10 +535,21 @@ used to define particles as triangles, and will draw them as triangles
 or edges (3 lines) or both, depending on the setting for *tflag*\ .  If
 edges are drawn, the *width* setting determines the diameters of the
 line segments.  If this keyword is not used, triangle particles will
-be drawn as spheres, the same as if they were regular atoms.  The only
-setting currently allowed for the *color* value is *type*, which will
-color the triangles according to the atom type of the particle.  By
-default the mapping of types to colors is as follows:
+be drawn as spheres, the same as if they were regular atoms.
+
+.. versionchanged:: TBD
+
+   added *index* and *atom* color styles
+
+The there are currently three supported settings for the *color* value:
+*type*, *index*, or *atom*.  With the *type* setting the triangles
+will be colored according to the atom type of the particle.  With the
+*index* setting the coloring follows the triangle index instead.  With the
+*atom* setting, the color follows the coloring selected for coloring
+atoms (including using color maps).  For *type* and *index* settings,
+the value is mapped to the colors of atom types thus the coloring style
+for atoms **must** be set to *type*.  The list of colors is by default
+the list of atom type colors as follows:
 
 * type 1 = red
 * type 2 = green
@@ -533,7 +558,11 @@ default the mapping of types to colors is as follows:
 * type 5 = cyan
 * type 6 = magenta
 
-and repeats itself for types > 6.
+and repeats itself for types > 6.  This list can by changed with the
+:doc:`dump_modify acolor <dump_image>` command.  If more different
+colors than atom types are desired, the *number of atom types* must be
+*increased* correspondingly when using either the :doc:`create_box
+<create_box>` or the :doc:`read_data <read_data>` command.
 
 ----------
 
@@ -545,9 +574,21 @@ them as a mesh of triangles or edges or both, depending on the setting
 for *eflag*\ .  If edges are drawn, the *width* setting determines the
 diameters of the line segments.  If this keyword is not used, ellipsoid
 particles will be drawn as spheres, the same as if they were regular
-atoms.  The only setting currently allowed for the *color* value is
-*type*, which will color the triangles according to the atom type of the
-particle.  By default the mapping of types to colors is as follows:
+atoms.
+
+.. versionchanged:: TBD
+
+   added *index* and *atom* color styles
+
+The there are currently three supported settings for the *color* value:
+*type*, *index*, or *atom*.  With the *type* setting the ellipsoids will
+be colored according to the atom type of the particle.  With the *index*
+setting the coloring follows the ellipsoid index instead.  With the
+*atom* setting, the color follows the coloring selected for coloring
+atoms (including using color maps).  For *type* and *index* settings,
+the value is mapped to the colors of atom types thus the coloring style
+for atoms **must** be set to *type*.  The list of colors is by default
+the list of atom type colors as follows:
 
 * type 1 = red
 * type 2 = green
@@ -556,7 +597,11 @@ particle.  By default the mapping of types to colors is as follows:
 * type 5 = cyan
 * type 6 = magenta
 
-and repeats itself for types > 6.
+and repeats itself for types > 6.  This list can by changed with the
+:doc:`dump_modify acolor <dump_image>` command.  If more different
+colors than atom types are desired, the *number of atom types* must be
+*increased* correspondingly when using either the :doc:`create_box
+<create_box>` or the :doc:`read_data <read_data>` command.
 
 The *level* setting determines the number of triangles in the mesh of
 triangles and thus the resolution of the representation of the
@@ -611,10 +656,10 @@ The there are currently three supported settings for the *color* value:
 the coloring selected for coloring atoms (including using color maps).
 With the *type* setting the body particles will be colored according to
 the atom type of the particle.  With the *index* setting the coloring
-follows the body index instead.  For both settings, the value (type or
-index) is mapped to the colors of atom types thus the coloring style for
-atoms **must** be set to *type*.  The list of colors is by default as
-follows:
+follows the body index instead.  For the *type* and *index* settings,
+the value (type or index) is mapped to the colors of atom types thus
+the coloring style for atoms **must** be set to *type*.  The list of
+colors is by default as follows:
 
 * type 1 = red
 * type 2 = green

src/GRAPHICS/dump_image.cpp

@@ -261,7 +261,13 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
       if (iarg+3 > narg) utils::missing_cmd_args(FLERR,"dump image line", error);
       lineflag = YES;
       if (strcmp(arg[iarg+1],"type") == 0) lcolor = TYPE;
-      else error->all(FLERR, iarg+1, "Dump image line only supports color by type");
+      else if (strcmp(arg[iarg+1],"atom") == 0) lcolor = ATOM;
+      else if (strcmp(arg[iarg+1],"index") == 0) lcolor = INDEX;
+      else
+        error->all(FLERR, iarg+1, "Dump image line only supports color by type, atom, or index");
+      if ((lcolor != ATOM) && (acolor != TYPE))
+        error->all(FLERR, iarg+1,
+                   "Must color atoms by type with line particles colored by type or index");
       ldiam = NUMERIC;
       ldiamvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
       iarg += 3;
@@ -270,7 +276,13 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
       if (iarg+4 > narg) utils::missing_cmd_args(FLERR,"dump image tri", error);
       triflag = YES;
       if (strcmp(arg[iarg+1],"type") == 0) tcolor = TYPE;
-      else error->all(FLERR, iarg+1, "Dump image tri only supports color by type");
+      else if (strcmp(arg[iarg+1],"atom") == 0) tcolor = ATOM;
+      else if (strcmp(arg[iarg+1],"index") == 0) tcolor = INDEX;
+      else
+        error->all(FLERR, iarg+1, "Dump image tri only supports color by type, atom, or index");
+      if ((tcolor != ATOM) && (acolor != TYPE))
+        error->all(FLERR, iarg+1,
+                   "Must color atoms by type with tri particles colored by type or index");
       tstyle = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
       tdiamvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp);
       iarg += 4;
@@ -279,14 +291,20 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
       if (iarg+5 > narg) utils::missing_cmd_args(FLERR,"dump image ellipsoid", error);
       ellipsoidflag = YES;
       if (strcmp(arg[iarg+1],"type") == 0) ecolor = TYPE;
-      else error->all(FLERR, iarg+1, "Dump image ellipsoid only supports color by type");
+      else if (strcmp(arg[iarg+1],"atom") == 0) ecolor = ATOM;
+      else if (strcmp(arg[iarg+1],"index") == 0) ecolor = INDEX;
+      else
+        error->all(FLERR, iarg+1, "Dump image ellipsoid only supports color by type, atom, or index");
+      if ((ecolor != ATOM) && (acolor != TYPE))
+        error->all(FLERR, iarg+1,
+                   "Must color atoms by type with ellipsoid particles colored by type or index");
       estyle = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
       if ((estyle < 0) || (estyle > 3))
         error->all(FLERR, iarg+2, "Dump image ellipsoid only supports style setting 1, 2, or 3");
       elevel = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
       if (elevel == 0) elevel = 4; // default setting
       if (elevel > 6)
-        error->all(FLERR, iarg+3, "Dump image ellipsoid mesh refinement level is too large");
+        error->all(FLERR, iarg+3, "Dump image ellipsoid mesh refinement level {} is too large", elevel);
       ediamvalue = utils::numeric(FLERR,arg[iarg+4],false,lmp);
       iarg += 5;
 
@@ -1230,12 +1248,30 @@ void DumpImage::create_image()
     int *line = atom->line;
     int *type = atom->type;
 
+    m = 0;
     for (i = 0; i < nchoose; i++) {
       j = clist[i];
       if (line[j] < 0) continue;
 
+      itype = type[j];
+      double opacity = aopacity[itype];
       if (lcolor == TYPE) {
-        color = colortype[type[j]];
+        color = colortype[itype];
+      } else if (lcolor == INDEX) {
+        itype = (line[j] % atom->ntypes) + 1;
+        color = colortype[itype];
+      } else if (lcolor == ATOM) {
+        if (acolor == TYPE) {
+          color = colortype[itype];
+        } else if (acolor == ELEMENT) {
+          color = colorelement[itype];
+        } else if (acolor == ATTRIBUTE) {
+          color = image->map_value2color(0,buf[m]);
+        } else {
+          color = image->color2rgb("white");
+        }
+      } else {
+        color = image->color2rgb("white");
       }
 
       if (ldiam == NUMERIC) {
@@ -1255,6 +1291,8 @@ void DumpImage::create_image()
       pt2[2] = 0.0;
 
       image->draw_cylinder(pt1,pt2,color,ldiamvalue,3,aopacity[atom->type[j]]);
+
+      m += size_one;
     }
   }
 
@@ -1271,14 +1309,31 @@ void DumpImage::create_image()
     int *tri = atom->tri;
     int *type = atom->type;
 
+    m = 0;
     for (i = 0; i < nchoose; i++) {
       j = clist[i];
       if (tri[j] < 0) continue;
 
+      itype = type[j];
+      double opacity = aopacity[itype];
       if (tcolor == TYPE) {
-        color = colortype[type[j]];
+        color = colortype[itype];
+      } else if (tcolor == INDEX) {
+        itype = (tri[j] % atom->ntypes) + 1;
+        color = colortype[itype];
+      } else if (tcolor == ATOM) {
+        if (acolor == TYPE) {
+          color = colortype[itype];
+        } else if (acolor == ELEMENT) {
+          color = colorelement[itype];
+        } else if (acolor == ATTRIBUTE) {
+          color = image->map_value2color(0,buf[m]);
+        } else {
+          color = image->color2rgb("white");
+        }
+      } else {
+        color = image->color2rgb("white");
       }
-      double opacity = aopacity[atom->type[j]];
 
       MathExtra::quat_to_mat(avec_tri->bonus[tri[j]].quat,mat);
       MathExtra::matvec(mat,avec_tri->bonus[tri[j]].c1,pt1);
@@ -1288,12 +1343,27 @@ void DumpImage::create_image()
       MathExtra::add3(pt2,x[j],pt2);
       MathExtra::add3(pt3,x[j],pt3);
 
-      if (tridraw) image->draw_triangle(pt1,pt2,pt3,color,opacity);
+      if (tridraw) {
+        // brighten flat surfaces a little bit
+        image->ambientColor[0] = image->ambientColor[1] = image->ambientColor[2] = 0.3;
+        image->keyLightColor[0] = image->keyLightColor[1] = image->keyLightColor[2] = 0.8;
+        image->fillLightColor[0] = image->fillLightColor[1] = image->fillLightColor[2] = 0.45;
+        image->backLightColor[0] = image->backLightColor[1] = image->backLightColor[2] = 0.8;
+
+        image->draw_triangle(pt1,pt2,pt3,color,opacity);
+
+        // restore previous settings
+        image->ambientColor[0] = image->ambientColor[1] = image->ambientColor[2] = 0.0;
+        image->keyLightColor[0] = image->keyLightColor[1] = image->keyLightColor[2] = 0.9;
+        image->fillLightColor[0] = image->fillLightColor[1] = image->fillLightColor[2] = 0.45;
+        image->backLightColor[0] = image->backLightColor[1] = image->backLightColor[2] = 0.9;
+      }
       if (edgedraw) {
         image->draw_cylinder(pt1,pt2,color,tdiamvalue,3,opacity);
         image->draw_cylinder(pt2,pt3,color,tdiamvalue,3,opacity);
         image->draw_cylinder(pt3,pt1,color,tdiamvalue,3,opacity);
       }
+      m += size_one;
     }
   }
 
@@ -1304,16 +1374,50 @@ void DumpImage::create_image()
     double **x = atom->x;
     int *ellipsoid = atom->ellipsoid;
     int *type = atom->type;
+    m = 0;
+
     for (i = 0; i < nchoose; i++) {
       j = clist[i];
       if (ellipsoid[j] < 0) continue;
 
+      itype = type[j];
+      double opacity = aopacity[itype];
       if (ecolor == TYPE) {
-        color = colortype[type[j]];
+        color = colortype[itype];
+      } else if (ecolor == INDEX) {
+        itype = (ellipsoid[j] % atom->ntypes) + 1;
+        color = colortype[itype];
+      } else if (ecolor == ATOM) {
+        if (acolor == TYPE) {
+          color = colortype[itype];
+        } else if (acolor == ELEMENT) {
+          color = colorelement[itype];
+        } else if (acolor == ATTRIBUTE) {
+          color = image->map_value2color(0,buf[m]);
+        } else {
+          color = image->color2rgb("white");
+        }
+      } else {
+        color = image->color2rgb("white");
+      }
+      if (estyle & 1) {
+        // brighten flat surfaces a little bit
+        image->ambientColor[0] = image->ambientColor[1] = image->ambientColor[2] = 0.3;
+        image->keyLightColor[0] = image->keyLightColor[1] = image->keyLightColor[2] = 0.8;
+        image->fillLightColor[0] = image->fillLightColor[1] = image->fillLightColor[2] = 0.45;
+        image->backLightColor[0] = image->backLightColor[1] = image->backLightColor[2] = 0.8;
       }
       EllipsoidObj e(elevel);
       e.draw(image, estyle, color, x[j], avec_ellipsoid->bonus[ellipsoid[j]].shape,
-             avec_ellipsoid->bonus[ellipsoid[j]].quat, ediamvalue, aopacity[type[j]]);
+             avec_ellipsoid->bonus[ellipsoid[j]].quat, ediamvalue, opacity);
+      if (estyle & 1) {
+        // restore previous settings
+        image->ambientColor[0] = image->ambientColor[1] = image->ambientColor[2] = 0.0;
+        image->keyLightColor[0] = image->keyLightColor[1] = image->keyLightColor[2] = 0.9;
+        image->fillLightColor[0] = image->fillLightColor[1] = image->fillLightColor[2] = 0.45;
+        image->backLightColor[0] = image->backLightColor[1] = image->backLightColor[2] = 0.9;
+      }
+      m += size_one;
     }
   }
 

src/dump_custom.cpp

@@ -108,9 +108,8 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
 
   ioptional = parse_fields(nfield,earg);
 
-  if (ioptional < nfield &&
-      strcmp(style,"image") != 0 && strcmp(style,"movie") != 0)
-    error->all(FLERR,"Invalid attribute {} in dump {} command",earg[ioptional],style);
+  if ((ioptional < nfield) && (strcmp(style,"image") != 0) && (strcmp(style,"movie") != 0))
+    error->all(FLERR, "Invalid attribute {} in dump {} command", earg[ioptional], style);
 
   // noptional = # of optional args
   // reset nfield to subtract off optional args
@@ -1455,6 +1454,10 @@ int DumpCustom::parse_fields(int narg, char **arg)
 
   for (int iarg = 0; iarg < narg; iarg++) {
     int errptr = iarg + argoff;
+
+    // only attempt to parse first two fields for dump image/movie
+    if ((iarg == 2) && ((strcmp(style,"image") == 0) || (strcmp(style,"movie") == 0))) return 2;
+
     if (strcmp(arg[iarg],"id") == 0) {
       pack_choice[iarg] = &DumpCustom::pack_id;
       if (sizeof(tagint) == sizeof(smallint)) vtype[iarg] = Dump::INT;