add support for reading binary STL files

doc/src/create_atoms.rst

@@ -21,7 +21,7 @@ Syntax
        *single* args = x y z
          x,y,z = coordinates of a single particle (distance units)
        *mesh* args = STL-file
-         STL-file = file with triangle mesh in ASCII STL format
+         STL-file = file with triangle mesh in STL format
        *random* args = N seed region-ID
          N = number of particles to create
          seed = random # seed (positive integer)
@@ -136,18 +136,20 @@ positions.
             :align: right
             :target: _images/marble_race.jpg
 
-For the *mesh* style, a file with a triangle mesh in `ASCII STL format
-<https://en.wikipedia.org/wiki/STL_(file_format)#ASCII_STL>`_ is read
-and one or more particles are placed into the area of each triangle.
-Binary STL files (e.g. as frequently offered for 3d-printing) can be
-converted to ASCII with the :ref:`stl_bin2txt tool <stlconvert>`.  The
-use of the *units box* option is required. There are two algorithms for
-placing atoms available: *bisect* and *qrand*. They can be selected via
-the *meshmode* option; *bisect* is the default.  If the atom style allows
-to set a per-atom radius this radius is set to the average
-distance of the triangle vertices from its center times the value of the
-*radscale* keyword (default: 1.0).  If the atom style supports it, the
-atoms created from the mesh are assigned a new molecule ID.
+For the *mesh* style, a file with a triangle mesh in `STL format
+<https://en.wikipedia.org/wiki/STL_(file_format)>`_ is read and one or
+more particles are placed into the area of each triangle.  The reader
+supports both ASCII and binary files conforming to the format on the
+Wikipedia page.  Binary STL files (e.g. as frequently offered for
+3d-printing) also be first converted to ASCII for editing with the
+:ref:`stl_bin2txt tool <stlconvert>`.  The use of the *units box* option
+is required. There are two algorithms for placing atoms available:
+*bisect* and *qrand*. They can be selected via the *meshmode* option;
+*bisect* is the default.  If the atom style allows to set a per-atom
+radius this radius is set to the average distance of the triangle
+vertices from its center times the value of the *radscale* keyword
+(default: 1.0).  If the atom style supports it, the atoms created from
+the mesh are assigned a new molecule ID.
 
 In *bisect* mode a particle is created at the center of each triangle
 unless the average distance of the triangle vertices from its center is

src/create_atoms.cpp

@@ -1036,9 +1036,11 @@ void CreateAtoms::add_mesh(const char *filename)
     molid = maxmol + 1;
   }
 
-  FILE *fp = fopen(filename, "r");
+  FILE *fp = fopen(filename, "rb");
   if (fp == nullptr) error->one(FLERR, "Cannot open file {}: {}", filename, utils::getsyserror());
 
+  // first try reading the file in ASCII format
+
   TextFileReader reader(fp, "STL mesh");
   try {
     char *line = reader.next_line();
@@ -1047,7 +1049,7 @@ void CreateAtoms::add_mesh(const char *filename)
 
     line += 6;
     if (comm->me == 0)
-      utils::logmesg(lmp, "Reading STL object {} from file {}\n", utils::trim(line), filename);
+      utils::logmesg(lmp, "Reading STL object {} from text file {}\n", utils::trim(line), filename);
 
     while ((line = reader.next_line())) {
 
@@ -1092,8 +1094,50 @@ void CreateAtoms::add_mesh(const char *filename)
       }
     }
   } catch (std::exception &e) {
+
+    // if ASCII failed for the first line, try reading as binary
+    if (utils::strmatch(e.what(), "^Invalid STL mesh file format")) {
+      char title[80];
+      float triangle[12];
+      uint32_t ntri;
+      uint16_t attr;
+      size_t count;
+
+      rewind(fp);
+      count = fread(title, sizeof(char), 80, fp);
+      title[79] = '\0';
+      count = fread(&ntri, sizeof(ntri), 1, fp);
+      if (count <= 0) {
+        error->all(FLERR, "Error reading STL file {}: {}", filename, utils::getsyserror());
+      } else {
+        if (comm->me == 0)
+          utils::logmesg(lmp, "Reading STL object {} from binary file {}\n", utils::trim(title),
+                         filename);
+      }
+
+      for (uint32_t i = 0U; i < ntri; ++i) {
+        count = fread(triangle, sizeof(float), 12, fp);
+        if (count != 12)
+          error->all(FLERR, "Error reading STL file {}: {}", filename, utils::getsyserror());
+        count = fread(&attr, sizeof(attr), 1, fp);
+
+        for (int j = 0; j < 3; ++j)
+          for (int k = 0; k < 3; ++k) vert[j][k] = triangle[3 * j + 3 + k];
+
+        ++ntriangle;
+        if (mesh_style == BISECTION) {
+          // add in center of triangle or bisecting recursively along longest edge
+          // as needed to get the desired atom density/radii
+          atomlocal += add_bisection(vert, molid);
+        } else if (mesh_style == QUASIRANDOM) {
+          // add quasi-random distribution of atoms
+          atomlocal += add_quasirandom(vert, molid);
+        }
+      }
+    } else {
       error->all(FLERR, "Error reading triangles from file {}: {}", filename, e.what());
     }
+  }
 
   if (ntriangle > 0) {
     MPI_Allreduce(&atomlocal, &atomall, 1, MPI_LMP_BIGINT, MPI_SUM, world);