Fixing bugs

docs/tutorial.rst

@@ -103,15 +103,15 @@ the drop-down menu as follows::
 Select the file and click on ``Import PLY``. You should now see something
 similar as to the image below.
 
-.. figure:: _static/img/tutorials/genus2_blender_01.jpg
+.. figure:: _static/img/tutorials/genus2_blender_01.JPG
    :alt: The imported Genus 2 isosurface in Blender.
 
 Finally, we assign a material to the object, tune the camera to bring the
 object fully into view, set the color of the background to black, add
 two sun-type light sources and set the film to transparent. For the material,
 we have used the settings as can be seen in the figure below.
 
-.. figure:: _static/img/tutorials/genus2_blender_02.jpg
+.. figure:: _static/img/tutorials/genus2_blender_02.JPG
    :alt: The imported Genus 2 isosurface in Blender.
 
 The only step that remains is to render the image, which will give the image
@@ -174,7 +174,7 @@ Observe that two isosurfaces are created and stored as ``.ply`` files:
 
 Importing these two files in Blender gives us the following result
 
-.. figure:: _static/img/tutorials/benzene_homo_blender_01.JPG
+.. figure:: _static/img/tutorials/benzene_homo_blender_01.jpg
    :alt: HOMO orbital of benzene imported into Blender
 
 Of course, this result is rather blend and we would like to add
@@ -253,7 +253,7 @@ This will generate all the atoms and bonds between them. Next,
 materials are assigned to all atoms and bonds and the final result
 looks as seen in the image below.
 
-.. figure:: _static/img/tutorials/benzene_homo_blender_02.JPG
+.. figure:: _static/img/tutorials/benzene_homo_blender_02.jpg
    :alt: HOMO orbital of benzene together with the atoms and bonds
 
 Finally, we can render the scene to create a nice picture of the molecular orbital.

src/CMakeLists.txt

@@ -52,7 +52,7 @@ execute_process(
 SET(PROGNAME "DEN2OBJ")
 SET(VERSION_MAJOR "1")
 SET(VERSION_MINOR "2")
-SET(VERSION_MICRO "0")
+SET(VERSION_MICRO "1")
 message(STATUS "Writing configuration file in: ${CMAKE_CURRENT_SOURCE_DIR}/config.h")
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config.h.in ${CMAKE_CURRENT_SOURCE_DIR}/config.h @ONLY)
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/den2obj.pc.in ${CMAKE_BINARY_DIR}/den2obj.pc @ONLY)

src/den2obj.cpp

@@ -62,8 +62,8 @@ int main(int argc, char* argv[]) {
         TCLAP::ValueArg<std::string> arg_generator("g","dataset","Dataset name",false,"","string");
         cmd.add(arg_generator);
 
-        // select compression algorithm
-        TCLAP::ValueArg<std::string> arg_algo("a","algo","Compression algorithm",false,"","string");
+        // select algorithm for either compression or for tesselation
+        TCLAP::ValueArg<std::string> arg_algo("a","algo","Algorithm selection",false,"","string");
         cmd.add(arg_algo);
 
         cmd.parse(argc, argv);
@@ -237,7 +237,13 @@ int main(int argc, char* argv[]) {
                     output_filename = stem.string().substr(0,stem.string().size()-4) + "_neg" + ext.string();
 
                     IsoSurface is_neg(sf.get());
-                    is_neg.marching_cubes(-isovalue);
+                    if(arg_algo.getValue().empty() || arg_algo.getValue() == "marching-cubes") {
+                        is_neg.marching_cubes(-isovalue);    
+                    } else if(arg_algo.getValue() == "marching-tetrahedra") {
+                        is_neg.marching_tetrahedra(-isovalue);
+                    } else {
+                        throw std::runtime_error("Invalid isosurface generation algo: " + arg_algo.getValue());
+                    }
 
                     IsoSurfaceMesh ism_neg(sf.get(), &is_neg);
                     ism_neg.construct_mesh(arg_c.getValue());

src/generator.cpp

@@ -67,7 +67,7 @@ void Generator::build_dataset(const std::string& name,
                     mo_id = 21;
                 }
 
-                const unsigned int npts = 150;
+                const unsigned int npts = 100;
                 const fpt sz = 6.0f;
                 std::array<unsigned int, 3> grid_dimensions = {npts, npts, npts};
                 std::vector<fpt> grid = this->benzene_molecular_orbital(sz, npts, mo_id);
@@ -103,19 +103,22 @@ std::vector<fpt> Generator::genus2(fpt sz, size_t npts) const {
 
     // build grid
     std::vector<fpt> f(npts*npts*npts);
-    #pragma omp parallel for schedule(static)
     for(unsigned int i=0; i<npts; i++) { // loop over z
         const float z = xx[i];
+        boost::timer::progress_display progress(npts);
         for(unsigned int j=0; j<npts; j++) { // loop over y
             const float y = xx[j];
+            #pragma omp parallel for schedule(static)
             for(unsigned int k=0; k<npts; k++) { // loop over x
                 const float x = xx[k];
                 const unsigned int idx = i * npts * npts + j * npts + k;
                 f[idx] = 2 * y * (y*y - 3 * x*x) * (1 - z*z) +
                          (x*x + y*y) * (x*x + y*y) - (9*z*z - 1) * (1 - z*z);
             }
         }
+        ++progress;
     }
+    std::cout << std::endl;
 
     return f;
 }
@@ -140,18 +143,21 @@ std::vector<fpt> Generator::benzene_molecular_orbital(fpt sz, size_t npts,
 
     // build grid
     std::vector<fpt> f(npts*npts*npts);
-    #pragma omp parallel for schedule(static)
+    boost::timer::progress_display progress(npts);
     for(unsigned int i=0; i<npts; i++) { // loop over z
         const float z = xx[i];
         for(unsigned int j=0; j<npts; j++) { // loop over y
             const float y = xx[j];
+            #pragma omp parallel for schedule(static)
             for(unsigned int k=0; k<npts; k++) { // loop over x
                 const float x = xx[k];
-                const unsigned int idx = i * npts * npts + j * npts + k;
+                const unsigned int idx = (i * npts * npts) + (j * npts) + k;
                 f[idx] = this->calculate_mo_amp(Vec3(x,y,z), mo_id);
             }
         }
+        ++progress;
     }
+    std::cout << std::endl;
 
     return f;
 }

src/generator.h

@@ -23,6 +23,7 @@
 
 #include <boost/math/constants/constants.hpp>
 #include <boost/math/special_functions/factorials.hpp>
+#include <boost/timer/progress_display.hpp>
 
 #include "d2o_format.h"
 #include "generator_benzene_data.h"