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‎src/docs/sphinx/blueprint_mesh.rst‎

Lines changed: 51 additions & 95 deletions
Original file line numberDiff line numberDiff line change
@@ -965,29 +965,11 @@ It is simple to ask what the layout representation is, and often code will branc
965965
The next tool in the tool box are material set conversions.
966966
A material set conforming to any of the material set layout types can be provided and converted into a material set with a different layout type:
967967

968-
.. code:: cpp
969-
970-
//-------------------------------------------------------------------------
971-
// creates a multi-buffer non-sparse case
972-
void CONDUIT_BLUEPRINT_API to_multi_buffer_by_element(const conduit::Node &src_matset,
973-
conduit::Node &dest_matset);
974-
975-
//-------------------------------------------------------------------------
976-
// creates a uni-buffer sparse case with 1st index into elements
977-
void CONDUIT_BLUEPRINT_API to_uni_buffer_by_element(const conduit::Node &src_matset,
978-
conduit::Node &dest_matset,
979-
const float64 epsilon = CONDUIT_EPSILON);
980-
981-
//-------------------------------------------------------------------------
982-
// creates a multi-buffer sparse case with 1st index into materials
983-
void CONDUIT_BLUEPRINT_API to_multi_buffer_by_material(const conduit::Node &src_matset,
984-
conduit::Node &dest_matset,
985-
const float64 epsilon = CONDUIT_EPSILON);
986-
//-------------------------------------------------------------------------
987-
// throws an error as this case is not supported
988-
void CONDUIT_BLUEPRINT_API to_uni_buffer_by_material(const conduit::Node &src_matset,
989-
conduit::Node &dest_matset,
990-
const float64 epsilon = CONDUIT_EPSILON);
968+
.. literalinclude:: ../../libs/blueprint/conduit_blueprint_mesh.hpp
969+
:start-after: _matset_layout_conversions_start
970+
:end-before: _matset_layout_conversions_end
971+
:language: cpp
972+
:dedent: 4
991973

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These are similarly simple to use:
993975

@@ -1015,13 +997,11 @@ These are similarly simple to use:
1015997
1016998
It is also possible to convert material sets to a `Silo <https://silo.readthedocs.io/en/latest/>`_-like mixed slot representation:
1017999

1018-
.. code:: cpp
1019-
1020-
//-------------------------------------------------------------------------
1021-
void CONDUIT_BLUEPRINT_API to_silo(const conduit::Node &matset,
1022-
conduit::Node &dest,
1023-
const float64 epsilon = CONDUIT_EPSILON);
1024-
1000+
.. literalinclude:: ../../libs/blueprint/conduit_blueprint_mesh.hpp
1001+
:start-after: _matset_to_silo_start
1002+
:end-before: _matset_to_silo_end
1003+
:language: cpp
1004+
:dedent: 4
10251005

10261006
This will create an output with the following information:
10271007

@@ -1054,49 +1034,27 @@ This will create an output with the following information:
10541034

10551035
Conduit also provides tools for creating/fetching material maps:
10561036

1057-
.. code:: cpp
1058-
1059-
//-------------------------------------------------------------------------
1060-
// this will use set external if the matmap already exists
1061-
void CONDUIT_BLUEPRINT_API create_or_reuse_material_map(const conduit::Node &matset,
1062-
conduit::Node &material_map);
1063-
//-------------------------------------------------------------------------
1064-
// this will use set if the matmap already exists
1065-
void CONDUIT_BLUEPRINT_API create_or_copy_material_map(const conduit::Node &matset,
1066-
conduit::Node &material_map);
1037+
.. literalinclude:: ../../libs/blueprint/conduit_blueprint_mesh.hpp
1038+
:start-after: _matset_create_matmap_methods_start
1039+
:end-before: _matset_create_matmap_methods_end
1040+
:language: cpp
1041+
:dedent: 4
10671042

10681043
And tools for renumbering material ids to be in the range ``[0, N-1]``, where ``N`` is the number of materials:
10691044

1070-
.. code:: cpp
1071-
1072-
//-------------------------------------------------------------------------
1073-
// renumbers material ids to run between 0 and N-1 where N is the number of
1074-
// materials.
1075-
void CONDUIT_BLUEPRINT_API renumber_material_ids(const conduit::Node &src_matset,
1076-
conduit::Node &dest_matset);
1077-
//-------------------------------------------------------------------------
1078-
// renumbers material ids to run between 0 and N-1 where N is the number of
1079-
// materials.
1080-
void CONDUIT_BLUEPRINT_API renumber_material_ids(conduit::Node &matset);
1081-
1082-
Conduit also provides some general information methods:
1083-
1084-
.. code:: cpp
1045+
.. literalinclude:: ../../libs/blueprint/conduit_blueprint_mesh.hpp
1046+
:start-after: _matset_renumber_mat_ids_start
1047+
:end-before: _matset_renumber_mat_ids_end
1048+
:language: cpp
1049+
:dedent: 4
10851050

1086-
//-------------------------------------------------------------------------
1087-
// renumbers material ids to run between 0 and N-1 where N is the number of
1088-
// materials.
1089-
void CONDUIT_BLUEPRINT_API renumber_material_ids(conduit::Node &matset);
1090-
//-------------------------------------------------------------------------
1091-
index_t CONDUIT_BLUEPRINT_API count_elements_from_matset(const conduit::Node &matset);
1092-
//-------------------------------------------------------------------------
1093-
index_t CONDUIT_BLUEPRINT_API count_materials_from_matset(const conduit::Node &matset);
1094-
//-------------------------------------------------------------------------
1095-
bool CONDUIT_BLUEPRINT_API is_material_in_element(const conduit::Node &matset,
1096-
const std::string &matname,
1097-
const index_t elem_id,
1098-
const float64 epsilon = CONDUIT_EPSILON);
1051+
Conduit Blueprint also provides some general information methods:
10991052

1053+
.. literalinclude:: ../../libs/blueprint/conduit_blueprint_mesh.hpp
1054+
:start-after: _matset_info_methods_start
1055+
:end-before: _matset_info_methods_end
1056+
:language: cpp
1057+
:dedent: 4
11001058

11011059

11021060
Material Set Accessors
@@ -1116,47 +1074,31 @@ We can ask questions about how the ``MatsetAccessor`` was created:
11161074
11171075
MatsetAccessor m_acc1 = MatsetAccessor(matset);
11181076
if (m_acc1.has_field())
1119-
{
11201077
std::cout << "matset accessor 1 has field" << std::endl;
1121-
}
11221078
if (m_acc1.has_specset())
1123-
{
11241079
std::cout << "matset accessor 1 has specset" << std::endl;
1125-
}
11261080
11271081
MatsetAccessor m_acc2 = MatsetAccessor(matset, field);
11281082
if (m_acc2.has_field())
1129-
{
11301083
std::cout << "matset accessor 2 has field" << std::endl;
1131-
}
11321084
if (m_acc2.has_specset())
1133-
{
11341085
std::cout << "matset accessor 2 has specset" << std::endl;
1135-
}
11361086
11371087
MatsetAccessor m_acc3 = MatsetAccessor(matset, specset);
11381088
if (m_acc3.has_field())
1139-
{
11401089
std::cout << "matset accessor 3 has field" << std::endl;
1141-
}
11421090
if (m_acc3.has_specset())
1143-
{
11441091
std::cout << "matset accessor 3 has specset" << std::endl;
1145-
}
11461092
11471093
MatsetAccessor m_acc4 = MatsetAccessor(matset, field, specset);
11481094
if (m_acc4.has_field())
1149-
{
11501095
std::cout << "matset accessor 4 has field" << std::endl;
1151-
}
11521096
if (m_acc4.has_specset())
1153-
{
11541097
std::cout << "matset accessor 4 has specset" << std::endl;
1155-
}
11561098
11571099
This produces the following:
11581100

1159-
.. code:: cpp
1101+
.. code:: text
11601102
11611103
matset accessor 2 has field
11621104
matset accessor 3 has specset
@@ -1171,8 +1113,8 @@ We can also ask about general matset information:
11711113
11721114
MatsetAccessor m_acc = MatsetAccessor(matset);
11731115
// buffer style
1174-
bool is_uni_buffer = m_acc.is_uni_buffer();
1175-
bool is_multi_buffer = m_acc.is_multi_buffer();
1116+
bool is_uni_buffer = m_acc.is_uni_buffer();
1117+
bool is_multi_buffer = m_acc.is_multi_buffer();
11761118
11771119
// dominance
11781120
bool is_element_dominant = m_acc.is_element_dominant();
@@ -1187,18 +1129,25 @@ Once we start writing loops over elements and materials, the indices of those lo
11871129
An element index means something different depending on what matset layout we are working with, as does a material index.
11881130

11891131
* For a **multi-buffer** **element-dominant** material set
1132+
11901133
* elements range from ``0`` to the number of elements
11911134
* materials range from ``0`` to the number of materials (these are material indices, not material identifiers)
11921135
* species range from ``0`` to the number of species for a given material
1136+
11931137
* For a **multi-buffer** **material-dominant** material set
1138+
11941139
* elements range from ``0`` to the number of elements for a given material
11951140
* materials range from ``0`` to the number of materials (these are material indices, not material identifiers)
11961141
* species range from ``0`` to the number of species for a given material
1142+
11971143
* For a **uni-buffer** **element-dominant** material set
1144+
11981145
* elements range from ``0`` to the number of elements
11991146
* materials range from ``0`` to the number of materials in a given element (these are material indices, not material identifiers)
12001147
* species range from ``0`` to the number of species for a given material in a given element
1148+
12011149
* For a **uni-buffer** **mateiral-dominant** material set
1150+
12021151
* indexing does not matter currently as this case is unsupported
12031152

12041153
**Element-dominant** material sets are easiest to walk by element, and **material-dominant** material sets are easiest to walk by material.
@@ -1219,16 +1168,21 @@ Here is an example of walking a material set and performing data retrieval using
12191168
const index_t num_mats = m_acc.num_mats();
12201169
for (index_t mat_idx = 0; mat_idx < num_mats; mat_idx ++)
12211170
{
1222-
const index_t mat_id = m_acc.get_mat_id(elem_idx, mat_idx);
1223-
const index_t mat_order_id = m_acc.get_mat_order_id(elem_idx, mat_idx);
1224-
const index_t elem_id = m_acc.get_elem_id(elem_idx, mat_idx);
1171+
// in a multi-buffer by element matset, these values
1172+
// only have meaning if vol_frac > 0
12251173
const float64 vol_frac = m_acc.get_vol_frac(elem_idx, mat_idx);
1226-
const float64 mset_val = m_acc.get_mset_val(elem_idx, mat_idx);
1227-
1228-
const index_t num_specs_for_mat = m_acc.num_spec_for_mat(elem_idx, mat_idx);
1229-
for (index_t spec_idx = 0; spec_idx < num_specs_for_mat; spec_idx ++)
1174+
if (vol_frac > 0.0)
12301175
{
1231-
const float64 mf_val = m_acc.get_mass_frac(elem_idx, mat_idx, spec_idx);
1176+
const index_t mat_id = m_acc.get_mat_id(elem_idx, mat_idx);
1177+
const index_t mat_order_id = m_acc.get_mat_order_id(elem_idx, mat_idx);
1178+
const index_t elem_id = m_acc.get_elem_id(elem_idx, mat_idx);
1179+
const float64 mset_val = m_acc.get_mset_val(elem_idx, mat_idx);
1180+
1181+
const index_t num_specs_for_mat = m_acc.num_spec_for_mat(elem_idx, mat_idx);
1182+
for (index_t spec_idx = 0; spec_idx < num_specs_for_mat; spec_idx ++)
1183+
{
1184+
const float64 mf_val = m_acc.get_mass_frac(elem_idx, mat_idx, spec_idx);
1185+
}
12321186
}
12331187
}
12341188
}
@@ -1240,6 +1194,7 @@ Here is an example of walking a material set and performing data retrieval using
12401194
for (index_t mat_idx = 0; mat_idx < num_mats; mat_idx ++)
12411195
{
12421196
// we ask for the number of elements for this material
1197+
// this method is only valid for material dominant matsets
12431198
const index_t num_elems_for_mat = m_acc.num_elems_for_mat(mat_idx);
12441199
for (index_t elem_idx = 0; elem_idx < num_elems_for_mat; elem_idx ++)
12451200
{
@@ -1264,6 +1219,7 @@ Here is an example of walking a material set and performing data retrieval using
12641219
for (index_t elem_idx = 0; elem_idx < num_elems; elem_idx ++)
12651220
{
12661221
// we ask for the number of materials in this element
1222+
// this method is only valid for sparse element dominant matsets
12671223
const index_t num_mats_for_elem = m_acc.num_mats_for_elem(elem_idx);
12681224
for (index_t mat_idx = 0; mat_idx < num_mats_for_elem; mat_idx ++)
12691225
{

‎src/libs/blueprint/conduit_blueprint_mesh.hpp‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -808,6 +808,7 @@ namespace matset
808808
bool CONDUIT_BLUEPRINT_API is_material_dominant(const conduit::Node &matset);
809809
// _matset_layout_determination_methods_end
810810

811+
// _matset_layout_conversions_start
811812
//-------------------------------------------------------------------------
812813
// creates a multi-buffer non-sparse case
813814
void CONDUIT_BLUEPRINT_API to_multi_buffer_by_element(const conduit::Node &src_matset,
@@ -829,7 +830,9 @@ namespace matset
829830
void CONDUIT_BLUEPRINT_API to_uni_buffer_by_material(const conduit::Node &src_matset,
830831
conduit::Node &dest_matset,
831832
const float64 epsilon = CONDUIT_EPSILON);
833+
// _matset_layout_conversions_end
832834

835+
// _matset_to_silo_start
833836
//-------------------------------------------------------------------------
834837
// Converts a blueprint matset to the silo style sparse mixed slot
835838
// representation.
@@ -840,7 +843,9 @@ namespace matset
840843
void CONDUIT_BLUEPRINT_API to_silo(const conduit::Node &matset,
841844
conduit::Node &dest,
842845
const float64 epsilon = CONDUIT_EPSILON);
846+
// _matset_to_silo_end
843847

848+
// _matset_create_matmap_methods_start
844849
//-------------------------------------------------------------------------
845850
// this will use set external if the matmap already exists
846851
void CONDUIT_BLUEPRINT_API create_or_reuse_material_map(const conduit::Node &matset,
@@ -849,6 +854,8 @@ namespace matset
849854
// this will use set if the matmap already exists
850855
void CONDUIT_BLUEPRINT_API create_or_copy_material_map(const conduit::Node &matset,
851856
conduit::Node &material_map);
857+
// _matset_create_matmap_methods_end
858+
// _matset_renumber_mat_ids_start
852859
//-------------------------------------------------------------------------
853860
// renumbers material ids to run between 0 and N-1 where N is the number of
854861
// materials.
@@ -858,6 +865,8 @@ namespace matset
858865
// renumbers material ids to run between 0 and N-1 where N is the number of
859866
// materials.
860867
void CONDUIT_BLUEPRINT_API renumber_material_ids(conduit::Node &matset);
868+
// _matset_renumber_mat_ids_end
869+
// _matset_info_methods_start
861870
//-------------------------------------------------------------------------
862871
index_t CONDUIT_BLUEPRINT_API count_elements_from_matset(const conduit::Node &matset);
863872
//-------------------------------------------------------------------------
@@ -867,6 +876,7 @@ namespace matset
867876
const std::string &matname,
868877
const index_t elem_id,
869878
const float64 epsilon = CONDUIT_EPSILON);
879+
// _matset_info_methods_end
870880
//-----------------------------------------------------------------------------
871881
std::map<int, std::string> CONDUIT_BLUEPRINT_API create_reverse_material_map(
872882
const conduit::Node &src_matset);

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