to_silo() rewrite

src/libs/blueprint/conduit_blueprint_mesh.hpp

@@ -966,6 +966,7 @@ namespace specset
     //-------------------------------------------------------------------------
     bool CONDUIT_BLUEPRINT_API is_uni_buffer(const conduit::Node &specset);
 
+    //-------------------------------------------------------------------------
     void CONDUIT_BLUEPRINT_API to_multi_buffer_full(const conduit::Node &src_matset,
                                                     const conduit::Node &src_specset,
                                                     const std::string &dest_matset_name,
@@ -1008,7 +1009,11 @@ namespace specset
     // https://silo.readthedocs.io/en/latest/
     void CONDUIT_BLUEPRINT_API to_silo(const conduit::Node &specset,
                                        const conduit::Node &matset,
-                                       conduit::Node &dest);
+                                       conduit::Node &dest,
+                                       const float64 epsilon = CONDUIT_EPSILON);
+
+    //-------------------------------------------------------------------------
+    index_t CONDUIT_BLUEPRINT_API count_materials_from_specset(const conduit::Node &specset);
 
     //-------------------------------------------------------------------------
     // blueprint::mesh::specset::index protocol interface

src/libs/blueprint/conduit_blueprint_mesh_matset_accessor.cpp

@@ -256,7 +256,7 @@ MatsetAccessor::init(const Node &matset,
 
                 // For sparse by element material sets, the matset accessor uses the following
                 // ranges:
-                //     0 <= elem_idx < num elems
+                //     0 <= elem_idx < num elements
                 //     0 <= mat_idx < num mats for element elem_idx
                 //     0 <= spec_idx < num species for material mat_idx in element elem_idx
                 // To know which species mass fraction to fetch for a given (elem_idx, mat_idx, spec_idx),
@@ -768,7 +768,7 @@ MatsetAccessor::get_sbe_mass_frac(const index_t elem_idx,
     const index_t data_index = m_sbe_o2m_idx.index(elem_idx, mat_idx);
     const index_t nmatspec_offset = m_nmatspec_offsets_acc[data_index];
 
-    // We need an index that is between 0 and the number of species in this elem.
+    // We need an index that is between 0 and the number of species in this element.
     // The way to calculate this is to add out num material species offset
     // with the current species value index, which ranges between 0 and the
     // number of species for this material.
@@ -862,7 +862,7 @@ index_t
 MatsetAccessor::get_error_nmats_for_elem(const index_t elem_idx) const
 {
     (void) elem_idx;
-    CONDUIT_ERROR("Impossible to fetch number of materials for elem from "
+    CONDUIT_ERROR("Impossible to fetch number of materials for element from "
                   "non-sparse by element material set.");
     return 0;
 }
@@ -872,7 +872,7 @@ index_t
 MatsetAccessor::get_error_nelems_for_mat(const index_t mat_idx) const
 {
     (void) mat_idx;
-    CONDUIT_ERROR("Impossible to fetch number of elems for a material from "
+    CONDUIT_ERROR("Impossible to fetch number of elements for a material from "
                   "non-sparse by material material set.");
     return 0;
 }
@@ -886,7 +886,7 @@ MatsetAccessor::get_error_nspec_for_mat(const index_t elem_idx, const index_t ma
     // CONDUIT_ERROR("Impossible to fetch number of species for a material from "
     //               "specset.");
     // no need to error in this case, as we wish to support looping over 
-    // elems/materials and then species in the case that species
+    // elements/materials and then species in the case that species
     // do not exist. Then loops can be more general with minimal performance
     // costs.
     return 0;

src/libs/blueprint/conduit_blueprint_mesh_matset_accessor.hpp

@@ -242,7 +242,7 @@ using GetNMatSpecPtr     = index_t (MatsetAccessor::*)(index_t, index_t) const;
     //
 
     // multi-buffer by element (full)
-    // 0 <= elem_idx < num elems
+    // 0 <= elem_idx < num elements
     // 0 <= mat_idx < num mats
     // 0 <= spec_idx < num species for material mat_idx
     index_t get_full_mat_id(const index_t elem_idx, const index_t mat_idx) const;
@@ -256,12 +256,12 @@ using GetNMatSpecPtr     = index_t (MatsetAccessor::*)(index_t, index_t) const;
     // materials to iterate over in a sparse representation
     // index_t get_full_nmats_for_elem(const index_t elem_idx) const;
     // omitted because this method is used for knowing how many
-    // elems to iterate over in a sparse representation
+    // elements to iterate over in a sparse representation
     // index_t get_full_nelems_for_mat(const index_t mat_idx) const;
     index_t get_full_nspec_for_mat(const index_t elem_idx, const index_t mat_idx) const;
 
     // multi-buffer by material (sparse by material)
-    // 0 <= elem_idx < num elems for material mat_idx
+    // 0 <= elem_idx < num elements for material mat_idx
     // 0 <= mat_idx < num mats
     // 0 <= spec_idx < num species for material mat_idx
     index_t get_sbm_mat_id(const index_t elem_idx, const index_t mat_idx) const;
@@ -278,9 +278,9 @@ using GetNMatSpecPtr     = index_t (MatsetAccessor::*)(index_t, index_t) const;
     index_t get_sbm_nspec_for_mat(const index_t elem_idx, const index_t mat_idx) const;
 
     // uni-buffer by element (sparse by element)
-    // 0 <= elem_idx < num elems
-    // 0 <= mat_idx < num mats for elem elem_idx
-    // 0 <= spec_idx < num species for material mat_idx in elem elem_idx
+    // 0 <= elem_idx < num elements
+    // 0 <= mat_idx < num mats for element elem_idx
+    // 0 <= spec_idx < num species for material mat_idx in element elem_idx
     index_t get_sbe_mat_id(const index_t elem_idx, const index_t mat_idx) const;
     index_t get_sbe_elem_id(const index_t elem_idx, const index_t mat_idx) const;
     float64 get_sbe_vol_frac(const index_t elem_idx, const index_t mat_idx) const;
@@ -289,7 +289,7 @@ using GetNMatSpecPtr     = index_t (MatsetAccessor::*)(index_t, index_t) const;
                               const index_t mat_idx,
                               const index_t spec_idx) const;
     // omitted because this method is used for knowing how many
-    // elems to iterate over in a sparse representation
+    // elements to iterate over in a sparse representation
     // index_t get_sbe_nelems_for_mat(const index_t mat_idx) const;
     index_t get_sbe_nmats_for_elem(const index_t elem_idx) const;
     index_t get_sbe_nspec_for_mat(const index_t elem_idx, const index_t mat_idx) const;
@@ -305,7 +305,7 @@ using GetNMatSpecPtr     = index_t (MatsetAccessor::*)(index_t, index_t) const;
     index_t get_error_elem_id(const index_t elem_idx, const index_t mat_idx) const;
     float64 get_error_vol_frac(const index_t elem_idx, const index_t mat_idx) const;
     float64 get_error_mset_val(const index_t elem_idx, const index_t mat_idx) const;
-    float64 get_error_mass_frac(const index_t elem_idx, 
+    float64 get_error_mass_frac(const index_t elem_idx,
                                 const index_t mat_idx,
                                 const index_t spec_idx) const;
     index_t get_error_nmats_for_elem(const index_t elem_idx) const;