improve postprocessing

cxxfem/src/femDOF.h

@@ -53,7 +53,7 @@ class FEM_API DOFMask
     size_t v;         ///< mask
 public:
     /// create a mask from a single dof (implicitly if needed)
-    DOFMask(DOF const &dof) : dofs(dof.dofs), v(1 << dof.index()) {}
+    DOFMask(DOF const &dof) : dofs(dof.dofs), v(1ULL << dof.index()) {}
     /// combine masks & other dofs
     DOFMask operator|(DOFMask const &obj) const
     {

cxxfem/src/femPost.cpp

@@ -5,6 +5,7 @@
 #include "femGroup.h"
 #include "femEntity.h"
 #include <numeric>
+#include <fstream>
 
 namespace fem
 {
@@ -226,6 +227,7 @@ int Post::add_view(std::string const &name)
     // sview = 1 for the first view although it is named Views[0] in the GUI and the options!!
     views[name] = sview;
     configure(sview);
+    //set_viridis(sview); // <= already present in gmsh with 'F4' key (View.ColormapNumber=23)
     return sview;
 }
 
@@ -269,6 +271,9 @@ void Post::configure(int sview)
     gmsh::option::setNumber("View[" + std::to_string(sview - 1) + "].GlyphLocation", 2); // at the node (default=barycenter)
     gmsh::option::setNumber("View[" + std::to_string(sview - 1) + "].VectorType", 2);    // simple Arrow (default=3D arrow)
 
+    gmsh::option::setNumber("View[" + std::to_string(sview - 1) + "].ColormapNumber", 23);  // Viridis colormap   
+    gmsh::option::setNumber("View[" + std::to_string(sview - 1) + "].LightLines", 0);  // disable lighting for lines
+    gmsh::option::setNumber("View[" + std::to_string(sview - 1) + "].LightTwoSide", 0);  // disable 2-sided lighting
     gmsh::option::setNumber("View[" + std::to_string(sview - 1) + "].ShowElement", 1);  // view black mesh outline
     gmsh::option::setNumber("View[" + std::to_string(sview - 1) + "].DrawSkinOnly", 1); // display skin only (should be faster)
     gmsh::option::setNumber("View[" + std::to_string(sview - 1) + "].Visible", 0);      // hide all views
@@ -302,6 +307,11 @@ void Post::write()
 
     gmsh::write("mesh.opt"); //  save the options
     gmsh::write("mesh.msh"); //  only save the mesh
+
+    // save the views (without the mesh)
+    gmsh::option::setNumber("PostProcessing.SaveMesh", 0);
+    gmsh::option::setNumber("PostProcessing.SaveInterpolationMatrices", 0);
+
     for (auto const &[name, sview] : views)
     {
         // gmsh::view::write(sview, name+".pos"); // pos format: list-based data (indep. of any model)
@@ -406,4 +416,5 @@ operator<<(std::ostream &out, Post const &obj)
     return out;
 }
 
+
 } // namespace fem

cxxfem/src/femProblem.cpp

@@ -13,7 +13,8 @@ namespace fem
 
 Problem::Problem() : quadrature("Gauss2")
 {
-    gmsh::initialize();
+    if(!gmsh::isInitialized())
+        gmsh::initialize();
     // General.Verbosity
     // (0: silent except for fatal errors, 1: +errors, 2: +warnings, 3: +direct, 4: +information, 5: +status (default), 99: +debug)
     gmsh::option::setNumber("General.Verbosity", 2);

fossils.py

@@ -150,11 +150,12 @@ if __name__ == "__main__":
                 exec(open(testname, encoding='utf-8').read())
         elif action == 'post':
             import gmsh
-            gmsh.initialize()
-            # gmsh.merge('mesh.msh')
-            # print('loading options...')
-            # gmsh.merge('mesh.opt')
+            if not gmsh.isInitialized():
+                gmsh.initialize()
+            # load empty mesh
+            gmsh.merge('mesh.msh')
             gmsh.option.setNumber("General.Verbosity", 3)
+            # load views from the option file
             views = []
             with open('mesh.opt') as f:
                 import re
@@ -167,14 +168,7 @@ if __name__ == "__main__":
             for v in views:
                 print(f'loading "{v[1]}"')
                 gmsh.merge(v[1])
-
-            # gmsh.view.combine("elements",
-            #               "all",
-            #               True,
-            #               True)    
             print('loading options...')
             gmsh.merge('mesh.opt')
-            print('please wait...')
-            # for f in os.listdir():
-            #     print(f)
+            print('starting Gmsh GUI, please wait...')
             gmsh.fltk.run()

models/bonemodel2.py

@@ -85,8 +85,6 @@ def solve(p={}):
 
     pbl = fem.Problem()
 
-    gmsh.initialize()
-    gmsh.option.setNumber("General.Terminal", 1)
     # load main mandible mesh (volume or surface - it will be meshed in 3D)
     import_mesh(p['bone'])