Exporting and importing physical properties

docs/source/io_formats/index.rst

@@ -45,6 +45,7 @@ Output Files
    statepoint
    source
    summary
+   properties
    depletion_results
    particle_restart
    track

docs/source/io_formats/properties.rst

@@ -0,0 +1,36 @@
+.. _io_properties:
+
+======================
+Properties File Format
+======================
+
+The current version of the properties file format is 1.0.
+
+**/**
+
+:Attributes: - **filetype** (*char[]*) -- String indicating the type of file.
+             - **version** (*int[2]*) -- Major and minor version of the
+               statepoint file format.
+             - **openmc_version** (*int[3]*) -- Major, minor, and release
+               version number for OpenMC.
+             - **git_sha1** (*char[40]*) -- Git commit SHA-1 hash.
+             - **date_and_time** (*char[]*) -- Date and time the summary was
+               written.
+             - **path** (*char[]*) -- Path to directory containing input files.
+
+**/geometry/**
+
+:Attributes: - **n_cells** (*int*) -- Number of cells in the problem.
+
+**/geometry/cells/cell <uid>/**
+
+:Datasets: - **temperature** (*double[]*) -- Temperature of the cell in [K].
+
+**/materials/**
+
+:Attributes: - **n_materials** (*int*) -- Number of materials in the problem.
+
+**/materials/material <uid>/**
+
+:Attributes: - **atom_density** (*double*) -- Total density in [atom/b-cm].
+             - **mass_density** (*double*) -- Total density in [g/cm^3].

include/openmc/capi.h

@@ -15,6 +15,7 @@ extern "C" {
   int openmc_cell_get_id(int32_t index, int32_t* id);
   int openmc_cell_get_temperature(int32_t index, const int32_t* instance, double* T);
   int openmc_cell_get_name(int32_t index, const char** name);
+  int openmc_cell_get_num_instances(int32_t index, int32_t* num_instances);
   int openmc_cell_set_name(int32_t index, const char* name);
   int openmc_cell_set_fill(int32_t index, int type, int32_t n, const int32_t* indices);
   int openmc_cell_set_id(int32_t index, int32_t id);
@@ -144,13 +145,13 @@ extern "C" {
   //! \param[in] meshtyally_id id of CMFD Mesh Tally
   //! \param[in] cmfd_indices indices storing spatial and energy dimensions of CMFD problem
   //! \param[in] norm CMFD normalization factor
-  extern "C" void openmc_initialize_mesh_egrid(const int meshtally_id, const int* cmfd_indices,
-                                               const double norm);
+  void openmc_initialize_mesh_egrid(const int meshtally_id, const int* cmfd_indices,
+                                    const double norm);
 
   //! Sets the mesh and energy grid for CMFD reweight
   //! \param[in] feedback whether or not to run CMFD feedback
   //! \param[in] cmfd_src computed CMFD source
-  extern "C" void openmc_cmfd_reweight(const bool feedback, const double* cmfd_src);
+  void openmc_cmfd_reweight(const bool feedback, const double* cmfd_src);
 
   //! Sets the fixed variables that are used for CMFD linear solver
   //! \param[in] indptr CSR format index pointer array of loss matrix
@@ -161,10 +162,10 @@ extern "C" {
   //! \param[in] spectral spectral radius of CMFD matrices and tolerances
   //! \param[in] map coremap for problem, storing accelerated regions
   //! \param[in] use_all_threads whether to use all threads when running CMFD solver
-  extern "C" void openmc_initialize_linsolver(const int* indptr, int len_indptr,
-                                              const int* indices, int n_elements,
-                                              int dim, double spectral,
-                                              const int* map, bool use_all_threads);
+  void openmc_initialize_linsolver(const int* indptr, int len_indptr,
+                                   const int* indices, int n_elements,
+                                   int dim, double spectral,
+                                   const int* map, bool use_all_threads);
 
   //! Runs a Gauss Seidel linear solver to solve CMFD matrix equations
   //! linear solver
@@ -173,9 +174,19 @@ extern "C" {
   //! \param[out] x unknown vector
   //! \param[in] tol tolerance on final error
   //! \return number of inner iterations required to reach convergence
-  extern "C" int openmc_run_linsolver(const double* A_data, const double* b,
+  int openmc_run_linsolver(const double* A_data, const double* b,
                                       double* x, double tol);
 
+  //! Export physical properties for model
+  //! \param[in] filename Filename to write to
+  //! \return Error code
+  int openmc_properties_export(const char* filename);
+
+  //! Import physical properties for model
+  //! \param[in] filename Filename to read from
+  // \return Error code
+  int openmc_properties_import(const char* filename);
+
   // Error codes
   extern int OPENMC_E_UNASSIGNED;
   extern int OPENMC_E_ALLOCATE;

include/openmc/cell.h

@@ -130,6 +130,14 @@ class Cell {
 
   virtual void to_hdf5_inner(hid_t group_id) const = 0;
 
+  //! Export physical properties to HDF5
+  //! \param[in] group  HDF5 group to read from
+  void export_properties_hdf5(hid_t group) const;
+
+  //! Import physical properties from HDF5
+  //! \param[in] group  HDF5 group to write to
+  void import_properties_hdf5(hid_t group);
+
   //! Get the BoundingBox for this cell.
   virtual BoundingBox bounding_box() const = 0;
 

include/openmc/constants.h

@@ -31,6 +31,7 @@ constexpr array<int, 2> VERSION_SUMMARY {6, 0};
 constexpr array<int, 2> VERSION_VOLUME {1, 0};
 constexpr array<int, 2> VERSION_VOXEL {2, 0};
 constexpr array<int, 2> VERSION_MGXS_LIBRARY {1, 0};
+constexpr array<int, 2> VERSION_PROPERTIES {1, 0};
 
 // ============================================================================
 // ADJUSTABLE PARAMETERS

include/openmc/hdf5_interface.h

@@ -51,7 +51,7 @@ inline hid_t create_group(hid_t parent_id, const std::stringstream& name)
 
 
 hid_t file_open(const std::string& filename, char mode, bool parallel=false);
-
+hid_t open_group(hid_t group_id, const std::string& name);
 void write_string(hid_t group_id, const char* name, const std::string& buffer,
                   bool indep);
 

include/openmc/material.h

@@ -69,6 +69,14 @@ class Material
   //! Write material data to HDF5
   void to_hdf5(hid_t group) const;
 
+  //! Export physical properties to HDF5
+  //! \param[in] group  HDF5 group to write to
+  void export_properties_hdf5(hid_t group) const;
+
+  //! Import physical properties from HDF5
+  //! \param[in] group  HDF5 group to read from
+  void import_properties_hdf5(hid_t group);
+
   //! Add nuclide to the material
   //
   //! \param[in] nuclide Name of the nuclide

openmc/__init__.py

@@ -31,7 +31,7 @@
 from openmc.polynomial import *
 from . import examples
 
-# Import a few convencience functions that used to be here
-from openmc.model import rectangular_prism, hexagonal_prism
+# Import a few names from the model module
+from openmc.model import rectangular_prism, hexagonal_prism, Model
 
 __version__ = '0.13.0-dev'

openmc/lib/cell.py

@@ -25,6 +25,9 @@
     c_int32, POINTER(c_int), POINTER(POINTER(c_int32)), POINTER(c_int32)]
 _dll.openmc_cell_get_fill.restype = c_int
 _dll.openmc_cell_get_fill.errcheck = _error_handler
+_dll.openmc_cell_get_num_instances.argtypes = [c_int32, POINTER(c_int32)]
+_dll.openmc_cell_get_num_instances.restype = c_int
+_dll.openmc_cell_get_num_instances.errcheck = _error_handler
 _dll.openmc_cell_get_temperature.argtypes = [
     c_int32, POINTER(c_int32), POINTER(c_double)]
 _dll.openmc_cell_get_temperature.restype = c_int
@@ -78,6 +81,14 @@ class Cell(_FortranObjectWithID):
     ----------
     id : int
         ID of the cell
+    fill : openmc.lib.Material or list of openmc.lib.Material
+        Indicates what the region of space is filled with
+    name : str
+        Name of the cell
+    num_instances : int
+        Number of unique cell instances
+    bounding_box : 2-tuple of numpy.ndarray
+        Lower-left and upper-right coordinates of bounding box
 
     """
     __instances = WeakValueDictionary()
@@ -159,6 +170,12 @@ def fill(self, fill):
             indices = (c_int32*1)(-1)
             _dll.openmc_cell_set_fill(self._index, 0, 1, indices)
 
+    @property
+    def num_instances(self):
+        n = c_int32()
+        _dll.openmc_cell_get_num_instances(self._index, n)
+        return n.value
+
     def get_temperature(self, instance=None):
         """Get the temperature of a cell
 
@@ -211,6 +228,7 @@ def bounding_box(self):
 
         return llc, urc
 
+
 class _CellMapping(Mapping):
     def __getitem__(self, key):
         index = c_int32()

openmc/lib/core.py

@@ -62,7 +62,13 @@ class _SourceSite(Structure):
 _dll.openmc_next_batch.restype = c_int
 _dll.openmc_next_batch.errcheck = _error_handler
 _dll.openmc_plot_geometry.restype = c_int
-_dll.openmc_plot_geometry.restype = _error_handler
+_dll.openmc_plot_geometry.errcheck = _error_handler
+_dll.openmc_properties_export.argtypes = [c_char_p]
+_dll.openmc_properties_export.restype = c_int
+_dll.openmc_properties_export.errcheck = _error_handler
+_dll.openmc_properties_import.argtypes = [c_char_p]
+_dll.openmc_properties_import.restype = c_int
+_dll.openmc_properties_import.errcheck = _error_handler
 _dll.openmc_run.restype = c_int
 _dll.openmc_run.errcheck = _error_handler
 _dll.openmc_reset.restype = c_int
@@ -120,6 +126,24 @@ def current_batch():
     return c_int.in_dll(_dll, 'current_batch').value
 
 
+def export_properties(filename=None):
+    """Export physical properties.
+
+    Parameters
+    ----------
+    filename : str or None
+        Filename to export properties to (defaults to "properties.h5")
+
+    See Also
+    --------
+    openmc.lib.import_properties
+
+    """
+    if filename is not None:
+        filename = c_char_p(filename.encode())
+    _dll.openmc_properties_export(filename)
+
+
 def finalize():
     """Finalize simulation and free memory"""
     _dll.openmc_finalize()
@@ -178,6 +202,22 @@ def hard_reset():
     _dll.openmc_hard_reset()
 
 
+def import_properties(filename):
+    """Import physical properties.
+
+    Parameters
+    ----------
+    filename : str
+        Filename to import properties from
+
+    See Also
+    --------
+    openmc.lib.export_properties
+
+    """
+    _dll.openmc_properties_import(filename.encode())
+
+
 def init(args=None, intracomm=None):
     """Initialize OpenMC
 

openmc/lib/material.py

@@ -174,15 +174,6 @@ def nuclides(self):
         return self._get_densities()[0]
         return nuclides
 
-    @property
-    def density(self):
-      density = c_double()
-      try:
-          _dll.openmc_material_get_density(self._index, density)
-      except OpenMCError:
-          return None
-      return density.value
-
     @property
     def densities(self):
         return self._get_densities()[1]
@@ -224,6 +215,29 @@ def add_nuclide(self, name, density):
         """
         _dll.openmc_material_add_nuclide(self._index, name.encode(), density)
 
+    def get_density(self, units='atom/b-cm'):
+        """Get density of a material.
+
+        Parameters
+        ----------
+        units : {'atom/b-cm', 'g/cm3'}
+            Units for density
+
+        Returns
+        -------
+        float
+            Density in requested units
+
+        """
+        if units == 'atom/b-cm':
+            return self.densities.sum()
+        elif units == 'g/cm3':
+            density = c_double()
+            _dll.openmc_material_get_density(self._index, density)
+            return density.value
+        else:
+            raise ValueError("Units must be 'atom/b-cm' or 'g/cm3'")
+
     def set_density(self, density, units='atom/b-cm'):
         """Set density of a material.
 

openmc/lib/plot.py

@@ -228,11 +228,11 @@ def id_map(plot):
     Returns
     -------
     id_map : numpy.ndarray
-        A NumPy array with shape (vertical pixels, horizontal pixels, 2) of
+        A NumPy array with shape (vertical pixels, horizontal pixels, 3) of
         OpenMC property ids with dtype int32
 
     """
-    img_data = np.zeros((plot.v_res, plot.h_res, 2),
+    img_data = np.zeros((plot.v_res, plot.h_res, 3),
                         dtype=np.dtype('int32'))
     _dll.openmc_id_map(plot, img_data.ctypes.data_as(POINTER(c_int32)))
     return img_data