Sep bc (#764)

* adding global mass, penalty and separable boundary conditions

CMakeLists.txt

@@ -249,7 +249,11 @@ if (ASGARD_USE_PYTHON)
     endforeach()
     add_custom_target(asgard_python_testing ALL DEPENDS "${_pyasgard_buildstage}")
 
-    configure_file("${CMAKE_CURRENT_SOURCE_DIR}/python/plot.sh" "${CMAKE_CURRENT_BINARY_DIR}/plot.sh" @ONLY)
+    configure_file("${CMAKE_CURRENT_SOURCE_DIR}/python/asgardplot.sh" "${CMAKE_CURRENT_BINARY_DIR}/asgardplot.sh" @ONLY)
+    install(FILES "${CMAKE_CURRENT_BINARY_DIR}/asgardplot.sh" DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE)
+
+    configure_file("${CMAKE_CURRENT_SOURCE_DIR}/python/asgardrun.sh" "${CMAKE_CURRENT_BINARY_DIR}/asgardrun.sh" @ONLY)
+    install(FILES "${CMAKE_CURRENT_BINARY_DIR}/asgardrun.sh" DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE)
 
     # install the module without the testing files
     set(__pyasgard_libasgard_path__ "${__asgard_final_path}")
@@ -503,7 +507,8 @@ if (${ASGARD_USE_PCH})
     target_precompile_headers (asgard_exe REUSE_FROM libasgard)
 endif ()
 
-set (_asgard_pdes continuity diffusion two_stream)
+set (_asgard_pdes continuity diffusion elliptic sinwav two_stream
+                  mass_internal varcoeff_internal bound_internal)
 
 foreach (_asgexe ${_asgard_pdes})
     add_executable (${_asgexe} "${CMAKE_CURRENT_SOURCE_DIR}/src/${_asgexe}.cpp")

doxygen/CMakeLists.txt

@@ -55,6 +55,8 @@ doxygen_add_docs(asgard_doxygen
                  examples/inputs_1d.cpp
                  src/continuity.cpp
                  src/diffusion.cpp
+                 src/elliptic.cpp
+                 src/sinwav.cpp
                  src/two_stream.cpp
                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../
                  COMMENT "Building the ${PROJECT_NAME} documentation")

examples/continuity_2d.cpp

@@ -16,7 +16,7 @@
  *
  * \par Example 1
  * Solves the continuity partial differential equation
- * \f[ \frac{d}{dt} f + \nabla \cdot f = s \f]
+ * \f[ \frac{\partial}{\partial t} f + \nabla \cdot f = s \f]
  * where both \b f and \b s are defined over the two dimensional domain
  * \f[ (x, y) \in (-1, 1) \otimes (-2, 2) \f]
  *

examples/inputs_1d.cpp

@@ -16,7 +16,7 @@
  *
  * \par Example 2
  * Solves the continuity partial differential equation
- * \f[ \frac{d}{dt} f + \frac{d}{dx} f = s \f]
+ * \f[ \frac{\partial}{\partial t} f + \frac{\partial}{\partial x} f = s \f]
  * where both \b f and \b s are defined over domain
  * \f[ (-\pi N_w, \pi N_w) \f]
  * where N-w is the number of waves.

python/asgard.py

@@ -73,6 +73,8 @@ def __init__(self, filename, verbose = False):
             if 'ndims' in fdata: # using version 1
                 self.using_version_2 = False
 
+                self.default_view = ""
+
                 self.num_dimensions = fdata['ndims'][()]
 
                 self.cells = fdata['elements'][()]
@@ -321,11 +323,16 @@ def __str__(self):
         print("python -m asgard -s plt.data")
         print("   shows summary of the snapshot contained in the out.data")
         print("")
+        print("python -m asgard plt.data <-view string/-fig filename/-grid>")
+        print("   same as the first example but also adds more options,")
+        print("   set the view plane, save the figure to a file, add the grid entries")
+        print("")
         print("options:")
         print(" -h, -help, --help           : shows this help text")
         print(" -v, -version, --version     : shows the library version info")
         print(" -s, -stat, -stats, -summary : shows the summary of a snapshot")
         print(" -g, -grid                   : plot the grid")
+        print(" -view                       : adjust the view plane")
         print("")
         print("no file and no option provided, shows the version of the")
         print("")
@@ -367,6 +374,7 @@ def __str__(self):
         # we are plotting, consider extra options
         plotview = None
         savefig  = None
+        addgrid  = False
         if len(sys.argv) > 2:
             i = 2
             n = len(sys.argv)
@@ -377,6 +385,9 @@ def __str__(self):
                 elif sys.argv[i] == "-fig":
                     savefig = sys.argv[i + 1] if i + 1 < n else None
                     i += 2
+                elif sys.argv[i] == "-grid":
+                    addgrid = True
+                    i += 1
                 else:
                     savefig = sys.argv[i]
                     i += 1
@@ -387,6 +398,12 @@ def __str__(self):
             z, x = shot.plot_data1d(((),), num_points = 256)
             asgplot.plot(x, z)
             asgplot.xlabel(shot.dimension_names[0], fontsize = 'large')
+
+            if addgrid:
+                cc = shot.cell_centers()
+                ymin = np.min(z)
+                asgplot.plot(cc, ymin * np.ones(cc.shape), 'om')
+
         else:
             if plotview is None and shot.default_view != "":
                 plotview = shot.default_view
@@ -401,10 +418,11 @@ def __str__(self):
                 ss = plotview.split(':')
                 plist = []
                 dims = []
-                for s in ss:
+                for i in range(len(ss)):
+                    s = ss[i]
                     if '*' in s:
                         plist.append(())
-                        dims.append(ss.index(s))
+                        dims.append(i)
                     else:
                         plist.append(float(s))
 
@@ -415,13 +433,17 @@ def __str__(self):
             xmax = shot.dimension_max[dims[0]]
             ymax = shot.dimension_max[dims[1]]
 
-            #p = asgplot.pcolor(x, y, z, cmap='jet') # , extent=[xmin, xmax, ymin, ymax])
+            #p = asgplot.pcolor(x, y, z, cmap='jet')
             p = asgplot.imshow(np.flipud(z), cmap='jet', extent=[xmin, xmax, ymin, ymax])
 
             asgplot.colorbar(p, orientation='vertical')
 
             asgplot.gca().set_anchor('C')
 
+            if addgrid:
+                cc = shot.cell_centers()
+                asgplot.scatter(cc[:,0], cc[:,1], 5 * np.ones(cc[:,0].shape), color='purple')
+
             asgplot.xlabel(shot.dimension_names[dims[0]], fontsize='large')
             asgplot.ylabel(shot.dimension_names[dims[1]], fontsize='large')
 

python/asgardplot.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+set -e
+
+if [[ "$1" == "help" || "$1" == "-help" || "$1" == "--help" ]]; then
+
+    echo ""
+    echo "usage: asgardplot.sh <filename> <plot opts>"
+    echo ""
+    echo "calls the asgard python quick plot utility"
+    echo "for more details see:"
+    echo "@Python_EXECUTABLE@ -m asgard --help"
+    echo ""
+
+    exit 0;
+fi
+
+
+if [ ! -f $1 ]; then
+    echo "cannot find file '$1'"
+    exit 1
+fi
+
+@Python_EXECUTABLE@ -m asgard $@
+

python/asgardrun.sh

@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+
+set -e # exit on first error
+#set -x # plot every command (debugging purposes)
+
+if [[ "$1" == "help" || "$1" == "-help" || "$1" == "--help" ]]; then
+
+    echo ""
+    echo "usage: asgardrun.sh <executable> <options>"
+    echo "usage: asgardrun.sh -plt \"<plotter opts>\" <executable> <options>"
+    echo ""
+    echo "runs the executable file with the given options"
+    echo "adding '-of _plt.h5' to save the output in a temp-file"
+    echo "then calls the plotter on the temp file"
+    echo "starting with the -plt switch allows passing options to the final plotter"
+    echo "for example: asgardrun.sh -plt -grid continuity -dims 2 -l 5"
+    echo ""
+
+    exit 0;
+fi
+
+plt_opts=""
+
+if [[ "$1" == "-plt" ]]; then
+    plt_opts="$2"
+    shift
+    shift
+fi
+
+exename=$1
+
+shift
+
+echo $1
+
+./$exename $@ -of _plt.h5
+
+@Python_EXECUTABLE@ -m asgard _plt.h5 $plt_opts
+

src/asgard.hpp

@@ -55,7 +55,7 @@ void simulate_builtin(prog_opts const &options)
   discretization_manager discretization(make_PDE<precision>(options),
                                         verbosity_level::high);
 
-  advance_time(discretization);
+  discretization.advance_time();
 
   discretization.save_final_snapshot();
 
@@ -142,7 +142,7 @@ void simulate(prog_opts const &options, verbosity_level verbosity = verbosity_le
  */
 template<typename precision>
 void simulate(discretization_manager<precision> &disc) {
-  asgard::advance_time(disc); // integrate until num-steps or stop-time
+  disc.advance_time(); // integrate until num-steps or stop-time
 
   if (not disc.stop_verbosity())
     disc.progress_report();

src/asgard_adapt_tests.cpp

@@ -33,135 +33,7 @@ int main(int argc, char *argv[])
   return result;
 }
 
-template<typename P>
-void test_adapt(prog_opts const &opts, std::filesystem::path gold_base)
+TEMPLATE_TEST_CASE("no-test", "[none]", test_precs)
 {
-  auto const prefix = gold_base.filename().string();
-  gold_base.remove_filename();
-  auto const fval_orig_path    = gold_base / (prefix + "orig.dat");
-  auto const fval_refine_path  = gold_base / (prefix + "refine.dat");
-  auto const fval_coarse_path  = gold_base / (prefix + "coarse.dat");
-  auto const table_refine_path = gold_base / (prefix + "refine_table.dat");
-  auto const table_coarse_path = gold_base / (prefix + "coarse_table.dat");
-
-  auto const fval_orig   = read_vector_from_txt_file<P>(fval_orig_path);
-  auto const gold_coarse = read_vector_from_txt_file<P>(fval_coarse_path);
-  auto const gold_refine = [fval_refine_path]() {
-    auto gold = read_vector_from_txt_file<P>(fval_refine_path);
-    for (auto i = 0; i < gold.size(); ++i)
-    {
-      // matlab stores new refined coefficients as 1e-15 (0 deletes from sparse
-      // vect)
-      if (std::abs(gold(i)) < 1e-14)
-      {
-        gold(i) = 0.0;
-      }
-    }
-    return gold;
-  }();
-
-  auto const test_tables = [](elements::table const &test,
-                              fk::matrix<int> const &gold) {
-    REQUIRE(test.size() == gold.nrows());
-    for (int64_t i = 0; i < test.size(); ++i)
-    {
-      auto const &test_coords = test.get_coords(i);
-      fk::vector<int> const gold_coords =
-          gold.extract_submatrix(i, 0, 1, gold.ncols());
-      REQUIRE(test_coords == gold_coords);
-    }
-  };
-
-  auto const gold_coarse_table =
-      read_matrix_from_txt_file<int>(table_coarse_path);
-  auto const gold_refine_table =
-      fk::matrix<int>(read_matrix_from_txt_file<int>(table_refine_path));
-
-  auto const pde = make_PDE<P>(opts);
-  // using second opts after reset from the pde
-  auto const &opts2 = pde->options();
-
-  adapt::distributed_grid<P> refine_grid(*pde);
-  auto const my_subgrid   = refine_grid.get_subgrid(get_rank());
-  auto const segment_size = element_segment_size(*pde);
-  auto const my_fval_orig =
-      fval_orig.extract(my_subgrid.col_start * segment_size,
-                        (my_subgrid.col_stop + 1) * segment_size - 1);
-
-  auto const test_refine = refine_grid.refine(my_fval_orig, opts2);
-  adapt::distributed_grid<P> coarse_grid(*pde);
-  auto const test_coarse = coarse_grid.coarsen(my_fval_orig, opts2);
-  test_tables(coarse_grid.get_table(), gold_coarse_table);
-  test_tables(refine_grid.get_table(), gold_refine_table);
-
-  auto const refine_subgrid = refine_grid.get_subgrid(get_rank());
-  fk::vector<P, mem_type::const_view> const my_gold_refine(
-      gold_refine, refine_subgrid.col_start * segment_size,
-      (refine_subgrid.col_stop + 1) * segment_size - 1);
-  REQUIRE(test_refine == my_gold_refine);
-
-  auto const coarsen_subgrid = coarse_grid.get_subgrid(get_rank());
-  fk::vector<P, mem_type::const_view> const my_gold_coarse(
-      gold_coarse, coarsen_subgrid.col_start * segment_size,
-      (coarsen_subgrid.col_stop + 1) * segment_size - 1);
-  REQUIRE(test_coarse == my_gold_coarse);
-}
-
-template<typename P>
-void test_initial(prog_opts const &opts, std::string const &gold_filepath)
-{
-  auto const gold = [&gold_filepath]() {
-    auto raw = read_vector_from_txt_file<P>(gold_filepath);
-    // matlab stores new refined coefficients as 1e-15 (0 deletes from sparse
-    // vector)
-    std::replace_if(
-        raw.begin(), raw.end(),
-        [](P old_value) { return std::abs(old_value) < 1.e-14; }, 0.0);
-    return raw;
-  }();
-
-  discretization_manager<P> disc(make_PDE<P>(opts));
-
-  fk::vector<P> const test = disc.current_state();
-
-  REQUIRE(gold.size() >= test.size());
-
-  auto constexpr tol_factor = get_tolerance<P>(100);
-  auto const my_subgrid     = disc.get_grid().get_subgrid(get_rank());
-  auto const segment_size   = disc.get_hiermanip().block_size();
-  fk::vector<P, mem_type::const_view> const my_gold(
-      gold, my_subgrid.col_start * segment_size,
-      (my_subgrid.col_stop + 1) * segment_size - 1);
-  rmse_comparison(my_gold, test, tol_factor);
-}
-
-TEMPLATE_TEST_CASE("initial - diffusion 1d", "[adapt]", test_precs)
-{
-  auto opts = make_opts("-p diffusion_1 -d 3 -l 3 -m 8");
-
-  opts.adapt_threshold = adapt_threshold;
-  opts.anorm           = adapt_norm::linf;
-
-  // don't test this in the MPI case -- too small to split table
-  if (get_num_ranks() == 1)
-  {
-    test_initial<TestType>(opts,
-                           adapt_base_dir / "diffusion1_l3_d4_initial.dat");
-  }
-}
-
-TEMPLATE_TEST_CASE("initial - diffusion 2d", "[adapt]", test_precs)
-{
-  if (!is_active())
-  {
-    return;
-  }
-
-  auto opts = make_opts("-p diffusion_2 -d 2 -l 2 -m 8");
-
-  opts.adapt_threshold = adapt_threshold;
-  opts.anorm           = adapt_norm::linf;
-
-  test_initial<TestType>(opts,
-                         adapt_base_dir / "diffusion2_l2_d3_initial.dat");
+  REQUIRE(true);
 }