Visualizer bugfixes (espressomd#4686)

Closes espressomd#4663

Description of changes:
- the `*_arrows_type_materials` options of the visualizer now have an effect on arrow materials
- the visualizer `freeglut` dependency has been added to the user guide
- issues with the exception handling mechanism have been addressed
- undefined behavior in OpenMPI triggered by the visualizer (espressomd#4663) now has a workaround for simulations that use only 1 MPI rank

doc/sphinx/installation.rst

@@ -88,7 +88,7 @@ To compile |es| on Ubuntu 22.04 LTS, install the following dependencies:
 
     sudo apt install build-essential cmake cython3 python3-pip python3-numpy \
       libboost-all-dev openmpi-common fftw3-dev libhdf5-dev libhdf5-openmpi-dev \
-      python3-scipy python3-opengl libgsl-dev
+      python3-scipy python3-opengl libgsl-dev freeglut3
 
 Optionally the ccmake utility can be installed for easier configuration:
 

src/core/bond_breakage/bond_breakage.cpp

@@ -107,8 +107,10 @@ void clear_queue() { queue.clear(); }
 /** @brief Gathers combined queue from all mpi ranks */
 Queue gather_global_queue(Queue const &local_queue) {
   Queue res = local_queue;
-  Utils::Mpi::gather_buffer(res, comm_cart);
-  boost::mpi::broadcast(comm_cart, res, 0);
+  if (comm_cart.size() > 1) {
+    Utils::Mpi::gather_buffer(res, comm_cart);
+    boost::mpi::broadcast(comm_cart, res, 0);
+  }
   return res;
 }
 

src/core/collision.cpp

@@ -406,9 +406,10 @@ void glue_to_surface_bind_part_to_vs(const Particle *const p1,
 
 std::vector<CollisionPair> gather_global_collision_queue() {
   std::vector<CollisionPair> res = local_collision_queue;
-  Utils::Mpi::gather_buffer(res, comm_cart);
-  boost::mpi::broadcast(comm_cart, res, 0);
-
+  if (comm_cart.size() > 1) {
+    Utils::Mpi::gather_buffer(res, comm_cart);
+    boost::mpi::broadcast(comm_cart, res, 0);
+  }
   return res;
 }
 

src/python/espressomd/visualization.py

@@ -592,17 +592,9 @@ def screenshot(self, path):
 
         # read the pixels
         OpenGL.GL.glReadBuffer(OpenGL.GL.GL_COLOR_ATTACHMENT0)
-        data = OpenGL.GL.glReadPixels(
-            0,
-            0,
-            self.specs['window_size'][0],
-            self.specs['window_size'][1],
-            OpenGL.GL.GL_RGB,
-            OpenGL.GL.GL_FLOAT)
 
         # save image
-        data = np.flipud(data.reshape((data.shape[1], data.shape[0], 3)))
-        matplotlib.pyplot.imsave(path, data)
+        self._make_screenshot(path)
 
     def run(self, integration_steps=1):
         """Convenience method with a simple integration thread.
@@ -1007,14 +999,12 @@ def _draw_constraints(self):
 
     def _determine_radius(self, part_type):
         def radius_by_lj(part_type):
-            try:
-                radius = self.system.non_bonded_inter[part_type, part_type].lennard_jones.get_params()[
-                    'sigma'] * 0.5
-                if radius == 0.0:
-                    radius = self.system.non_bonded_inter[part_type, part_type].wca.get_params()[
-                        'sigma'] * 0.5
-            except Exception:
-                radius = 0.5
+            ia = self.system.non_bonded_inter[part_type, part_type]
+            radius = 0.5
+            if hasattr(ia, "lennard_jones"):
+                radius = ia.lennard_jones.sigma * 0.5
+            if radius == 0.0 and hasattr(ia, "wca"):
+                radius = ia.wca.sigma * 0.5
             if radius == 0.0:
                 radius = 0.5
             return radius
@@ -1041,8 +1031,9 @@ def _draw_system_particles(self, color_by_id=False):
 
             # Only change material if type/charge has changed, color_by_id or
             # material was reset by arrows
-            if reset_material or color_by_id or not part_type == part_type_last or \
-                    part_id == self.drag_id or part_id == self.info_id or self.specs['particle_coloring'] == 'node':
+            if reset_material or color_by_id or part_type != part_type_last or \
+                    part_id == self.drag_id or part_id == self.info_id or \
+                    self.specs['particle_coloring'] == 'node':
                 reset_material = False
 
                 radius = self._determine_radius(part_type)
@@ -1074,6 +1065,9 @@ def _draw_system_particles(self, color_by_id=False):
                     elif self.specs['particle_coloring'] == 'node':
                         color = self._modulo_indexing(
                             self.specs['particle_type_colors'], self.particles['node'][index])
+                    else:
+                        raise ValueError(
+                            f"Cannot process particle_coloring={self.specs['particle_coloring']}")
 
                     # Invert color of highlighted particle
                     if part_id == self.drag_id or part_id == self.info_id:
@@ -1120,33 +1114,37 @@ def _draw_system_particles(self, color_by_id=False):
                 self._draw_arrow_property(
                     part_id, part_type, self.specs['velocity_arrows_type_scale'],
                     self.specs['velocity_arrows_type_colors'],
+                    self.specs['velocity_arrows_type_materials'],
                     self.specs['velocity_arrows_type_radii'], 'velocity')
                 reset_material = True
 
             if self.specs['force_arrows']:
                 self._draw_arrow_property(
                     part_id, part_type, self.specs['force_arrows_type_scale'],
                     self.specs['force_arrows_type_colors'],
+                    self.specs['force_arrows_type_materials'],
                     self.specs['force_arrows_type_radii'], 'force')
                 reset_material = True
 
             if self.specs['director_arrows']:
                 self._draw_arrow_property(
                     part_id, part_type, self.specs['director_arrows_type_scale'],
                     self.specs['director_arrows_type_colors'],
+                    self.specs['director_arrows_type_materials'],
                     self.specs['director_arrows_type_radii'], 'director')
                 reset_material = True
 
-    def _draw_arrow_property(self, part_id, part_type,
-                             type_scale, type_colors, type_radii, prop):
+    def _draw_arrow_property(self, part_id, part_type, type_scale,
+                             type_colors, type_materials, type_radii, prop):
         sc = self._modulo_indexing(type_scale, part_type)
         if sc > 0:
             v = self.particles[prop][self.index_from_id[part_id]]
             col = self._modulo_indexing(type_colors, part_type)
             radius = self._modulo_indexing(type_radii, part_type)
+            material = self._modulo_indexing(type_materials, part_type)
             draw_arrow(self.particles['pos'][self.index_from_id[part_id]],
                        np.array(v, dtype=float) * sc, radius, col,
-                       self.materials['chrome'], self.specs['quality_arrows'])
+                       self.materials[material], self.specs['quality_arrows'])
 
     def _draw_bonds(self):
         half_box_l = self.system.box_l / 2.0
@@ -1163,8 +1161,9 @@ def _draw_bonds(self):
             try:
                 x_a = self.particles['pos'][self.index_from_id[b[0]]]
                 x_b = self.particles['pos'][self.index_from_id[b[1]]]
-            except BaseException:
-                pass
+            except Exception:
+                # skip this bond
+                continue
             dx = x_b - x_a
 
             if np.all(np.abs(dx) < half_box_l):
@@ -1281,23 +1280,26 @@ def _update_charge_color_range(self):
     def _handle_screenshot(self):
         if self.take_screenshot:
             self.take_screenshot = False
-            data = OpenGL.GL.glReadPixels(0, 0, self.specs['window_size'][0],
-                                          self.specs['window_size'][1],
-                                          OpenGL.GL.GL_RGB, OpenGL.GL.GL_FLOAT)
             script_name = os.path.splitext(sys.argv[0])[0]
 
             i = 0
             while os.path.exists(f"{script_name}_{i:04d}.png"):
                 i += 1
             file_name = f"{script_name}_{i:04d}.png"
 
-            data = np.flipud(data.reshape((data.shape[1], data.shape[0], 3)))
-            matplotlib.pyplot.imsave(file_name, data)
+            self._make_screenshot(file_name)
 
             self.screenshot_captured = True
             self.screenshot_capture_time = time.time()
             self.screenshot_capture_txt = f"Saved screenshot {file_name}"
 
+    def _make_screenshot(self, filepath):
+        data = OpenGL.GL.glReadPixels(0, 0, self.specs['window_size'][0],
+                                      self.specs['window_size'][1],
+                                      OpenGL.GL.GL_RGB, OpenGL.GL.GL_FLOAT)
+        data = np.flipud(data.reshape((data.shape[1], data.shape[0], 3)))
+        matplotlib.pyplot.imsave(filepath, data)
+
     def _display_all(self):
 
         OpenGL.GL.glClear(
@@ -1405,36 +1407,30 @@ def _init_OpenGL_callbacks(self):
         def display():
             if self.hasParticleData and self.glut_main_loop_started:
                 self._display_all()
-            return
 
         # pylint: disable=unused-argument
         def keyboard_up(button, x, y):
             if isinstance(button, bytes):
                 button = button.decode("utf-8")
             self.keyboard_manager.keyboard_up(button)
-            return
 
         # pylint: disable=unused-argument
         def keyboard_down(button, x, y):
             if isinstance(button, bytes):
                 button = button.decode("utf-8")
             self.keyboard_manager.keyboard_down(button)
-            return
 
         def mouse(button, state, x, y):
             self.mouse_manager.mouse_click(button, state, x, y)
-            return
 
         def motion(x, y):
             self.mouse_manager.mouse_move(x, y)
-            return
 
         def redraw_on_idle():
             # don't repost faster than 60 fps
             if (time.time() - self.last_draw) > 1.0 / 60.0:
                 OpenGL.GLUT.glutPostRedisplay()
                 self.last_draw = time.time()
-            return
 
         def reshape_callback(w, h):
             self._reshape_window(w, h)
@@ -1451,7 +1447,6 @@ def close_window():
         OpenGL.GLUT.glutReshapeFunc(reshape_callback)
         OpenGL.GLUT.glutMotionFunc(motion)
         OpenGL.GLUT.glutWMCloseFunc(close_window)
-
         OpenGL.GLUT.glutIdleFunc(redraw_on_idle)
 
     def _init_timers(self):
@@ -1548,10 +1543,9 @@ def _id_to_fcolor(part_id):
     def _fcolor_to_id(fcolor):
         if (fcolor == [0, 0, 0]).all():
             return -1
-        else:
-            return int(fcolor[0] * 255) * 256 ** 2 + \
-                int(fcolor[1] * 255) * 256 + \
-                int(fcolor[2] * 255) - 1
+        return int(fcolor[0] * 255) * 256 ** 2 + \
+            int(fcolor[1] * 255) * 256 + \
+            int(fcolor[2] * 255) - 1
 
     # pylint: disable=unused-argument
     def _set_particle_drag(self, pos, pos_old):
@@ -1900,7 +1894,6 @@ def __init__(self, shape, particle_type, color, material,
         self.box_l = box_l
         self.rasterize_resolution = rasterize_resolution
         self.pointsize = rasterize_pointsize
-
         self.rasterized_surface_points = None
 
     def draw(self):
@@ -1930,16 +1923,15 @@ def _rasterize_shape(self):
         for i in range(int(resolution[0])):
             for j in range(int(resolution[1])):
                 for k in range(int(resolution[2])):
-                    # some shapes may not have a well-defined distance function in the whole domain
-                    # and may throw upon asking for a distance
+                    # some shapes may not have a well-defined distance function
+                    # in the whole domain and may throw a ValueError
                     try:
                         p = np.array([i, j, k]) * spacing
                         dist, vec = self.shape.call_method(
                             "calc_distance", position=p.tolist())
-                        if not np.isnan(vec).any() and not np.isnan(
-                                dist) and abs(dist) < spacing:
+                        if not (np.isnan(vec).any() or np.isnan(dist)) \
+                                and abs(dist) < spacing:
                             points.append((p - vec).tolist())
-                    # domain error translates to ValueError (cython)
                     except ValueError:
                         continue
         return points
@@ -2478,7 +2470,6 @@ def draw_cylinder(posA, posB, radius, color, material, quality,
 
     d = posB - posA
 
-    # angle,t,length = calcAngle(d)
     length = np.linalg.norm(d)
     OpenGL.GL.glTranslatef(posA[0], posA[1], posA[2])