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Catalyst API 2
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Added support for IOSS StrucuturedBlock zone connectivity
and boundary conditions.
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@tjotaha
tjotaha committed Nov 27, 2023
1 parent bce616a commit a41f1d3
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Showing 2 changed files with 158 additions and 26 deletions.
131 changes: 131 additions & 0 deletions packages/seacas/libraries/ioss/src/catalyst/Iocatalyst_DatabaseIO.C
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@
#include <Ioss_StructuredBlock.h> // for StructuredBlock

#include <Ioss_Utils.h> // for Utils, IOSS_ERROR, etc
#include <algorithm>
#include <climits>
#include <cstdlib>
#include <fmt/ostream.h>
Expand Down Expand Up @@ -162,6 +163,10 @@ namespace Iocatalyst {
return true;
}

void readZoneConnectivity(conduit_cpp::Node &&parent, Ioss::StructuredBlock *sb);
void readBoundaryConditions(conduit_cpp::Node &&parent, Ioss::StructuredBlock *sb);
Ioss::IJK_t readIJK(conduit_cpp::Node &&parent);

bool readModel(Ioss::Region *region);

bool readTime(Ioss::Region *region)
Expand Down Expand Up @@ -393,6 +398,7 @@ namespace Iocatalyst {
else if (retVal.empty()) {
retVal = entityGroup->generic_name();
}
std::replace(retVal.begin(), retVal.end(), '/', '-');
return retVal;
}

Expand Down Expand Up @@ -442,6 +448,75 @@ namespace Iocatalyst {
return true;
}

bool defineEntityGroup(conduit_cpp::Node parent,
const Ioss::StructuredBlockContainer &container)
{
for (auto group : container) {
this->addProperties(parent[getName(group)], group);
conduit_cpp::Node n;
for (auto zc : group->m_zoneConnectivity) {
defineZoneConnectivity(n, zc);
}
parent[getName(group) + "/zoneconnectivity"].set(n);

n.set_node(conduit_cpp::Node());
for (auto bc : group->m_boundaryConditions) {
defineBoundaryCondition(n, bc);
}
parent[getName(group) + "/boundaryconditions"].set(n);

parent[getName(group) + "/blocklocalnodeindex"].set(group->m_blockLocalNodeIndex);

n.set_node(conduit_cpp::Node());
for (auto gm : group->m_globalIdMap) {
conduit_cpp::Node m;
m["key"] = gm.first;
m["value"] = gm.second;
m.append().set(n);
}
parent[getName(group) + "/globalidmap"].set(n);
}
return true;
}

void defineZoneConnectivity(conduit_cpp::Node parent, Ioss::ZoneConnectivity &zc)
{
conduit_cpp::Node n;
n["m_connectionName"] = zc.m_connectionName;
n["m_donorName"] = zc.m_donorName;
n["m_transform"] = defineIJK(zc.m_transform);
n["m_ownerRangeBeg"] = defineIJK(zc.m_ownerRangeBeg);
n["m_ownerRangeEnd"] = defineIJK(zc.m_ownerRangeEnd);
n["m_ownerOffset"] = defineIJK(zc.m_ownerOffset);
n["m_donorRangeBeg"] = defineIJK(zc.m_donorRangeBeg);
n["m_donorRangeEnd"] = defineIJK(zc.m_donorRangeEnd);
n["m_donorOffset"] = defineIJK(zc.m_donorOffset);
n["m_ownerZone"] = zc.m_ownerZone;
n["m_donorZone"] = zc.m_donorZone;
n["m_fromDecomp"] = zc.m_fromDecomp;
parent.append().set(n);
}

void defineBoundaryCondition(conduit_cpp::Node parent, Ioss::BoundaryCondition &bc)
{
conduit_cpp::Node n;
n["m_bcName"] = bc.m_bcName;
n["m_famName"] = bc.m_famName;
n["m_rangeBeg"] = defineIJK(bc.m_rangeBeg);
n["m_rangeEnd"] = defineIJK(bc.m_rangeEnd);
n["m_face"] = bc.m_face;
parent.append().set(n);
}

conduit_cpp::Node defineIJK(Ioss::IJK_t &a)
{
conduit_cpp::Node n;
for (auto v : a) {
n.append().set(v);
}
return n;
}

template <typename GroupingEntityT>
bool addProperties(conduit_cpp::Node parent, GroupingEntityT *entityGroup)
{
Expand Down Expand Up @@ -641,10 +716,66 @@ namespace Iocatalyst {
this->readFields(child["fields"], block);
this->readFields(child[getName(&block->get_node_block()) + "/fields"],
&block->get_node_block());

readZoneConnectivity(child["zoneconnectivity"], block);
readBoundaryConditions(child["boundaryconditions"], block);

conduit_uint64 *my_vals = child["blocklocalnodeindex"].as_uint64_ptr();
block->m_blockLocalNodeIndex.clear();
for (int i = 0; i < child["blocklocalnodeindex"].number_of_elements(); i++) {
block->m_blockLocalNodeIndex.push_back(my_vals[i]);
}

conduit_cpp::Node &&n = child["globalidmap"];
block->m_globalIdMap.clear();
for (conduit_index_t i = 0, m = n.number_of_children(); i < m; ++i) {
auto &&c = n[i];
block->m_globalIdMap.push_back(
std::pair<size_t, size_t>(c["key"].as_int(), c["value"].as_int()));
}
}
return true;
}

void DatabaseIO::ImplementationT::readZoneConnectivity(conduit_cpp::Node &&parent,
Ioss::StructuredBlock *sb)
{
for (conduit_index_t idx = 0, max = parent.number_of_children(); idx < max; ++idx) {
auto &&child = parent[idx];
Ioss::ZoneConnectivity zc(child["m_connectionName"].as_string(),
child["m_ownerZone"].as_int(), child["m_donorName"].as_string(),
child["m_donorZone"].as_int(), readIJK(child["p_transform"]),
readIJK(child["m_ownerRangeBeg"]),
readIJK(child["m_ownerRangeEnd"]), readIJK(child["m_ownerOffset"]),
readIJK(child["m_donorRangeBeg"]),
readIJK(child["m_donorRangeEnd"]), readIJK(child["m_donorOffset"]));
zc.m_fromDecomp = child["m_fromDecomp"].as_int();
sb->m_zoneConnectivity.push_back(zc);
}
}

void DatabaseIO::ImplementationT::readBoundaryConditions(conduit_cpp::Node &&parent,
Ioss::StructuredBlock *sb)
{
for (conduit_index_t idx = 0, max = parent.number_of_children(); idx < max; ++idx) {

auto &&child = parent[idx];
Ioss::BoundaryCondition bc(child["m_bcName"].as_string(), child["m_famName"].as_string(),
readIJK(child["m_rangeBeg"]), readIJK(child["m_rangeEnd"]));
bc.m_face = child["m_face"].as_int();
sb->m_boundaryConditions.push_back(bc);
}
}

Ioss::IJK_t DatabaseIO::ImplementationT::readIJK(conduit_cpp::Node &&parent)
{
Ioss::IJK_t a{{0, 0, 0}};
for (auto i = 0; i < parent.number_of_children(); i++) {
a[i] = parent[i].as_int();
}
return a;
}

bool DatabaseIO::ImplementationT::readModel(Ioss::Region *region)
{
auto &node = this->DBNode;
Expand Down
53 changes: 27 additions & 26 deletions packages/seacas/libraries/ioss/src/catalyst_tests/CMakeLists.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -90,22 +90,21 @@ function(catalyst_test_ioshell_generated test_name
ioshell_gen_args
ioshell_output_file_name
test_time
diff_command
diff_args)
test_time_step)

set(CATALYST_FNAME catalyst_time_${test_time}_${ioshell_output_file_name})
set(IOSHELL_FNAME ioshell_time_${test_time}_${ioshell_output_file_name})
set(CATALYST_FNAME catalyst_time_${test_time_step}_${ioshell_output_file_name})
set(IOSHELL_FNAME ioshell_time_${test_time_step}_${ioshell_output_file_name})

TRIBITS_ADD_ADVANCED_TEST(${test_name}
TEST_0 EXEC io_shell ARGS --in_type generated ${ioshell_gen_args} ${ioshell_output_file_name}
DIRECTORY ../main
NOEXEPREFIX NOEXESUFFIX
NUM_MPI_PROCS 1
TEST_1 EXEC io_shell ARGS -out_type catalyst ${ioshell_output_file_name} ${test_time}
TEST_1 EXEC io_shell ARGS -out_type catalyst ${ioshell_output_file_name} ${test_time_step}
DIRECTORY ../main
NOEXEPREFIX NOEXESUFFIX
NUM_MPI_PROCS 1
TEST_2 EXEC io_shell ARGS -in_type catalyst ${test_time} ${CATALYST_FNAME}
TEST_2 EXEC io_shell ARGS -in_type catalyst ${test_time_step} ${CATALYST_FNAME}
DIRECTORY ../main
NOEXEPREFIX NOEXESUFFIX
NUM_MPI_PROCS 1
Expand All @@ -114,7 +113,7 @@ TRIBITS_ADD_ADVANCED_TEST(${test_name}
DIRECTORY ../main
NOEXEPREFIX NOEXESUFFIX
NUM_MPI_PROCS 1
TEST_4 EXEC ${diff_command} ARGS ${diff_args} ${IOSHELL_FNAME} ${CATALYST_FNAME}
TEST_4 EXEC exodiff ARGS -pedantic ${IOSHELL_FNAME} ${CATALYST_FNAME}
DIRECTORY ../../../../applications/exodiff
NOEXEPREFIX NOEXESUFFIX
NUM_MPI_PROCS 1
Expand All @@ -124,42 +123,43 @@ endfunction()

catalyst_test_ioshell_generated("catalyst_ioshell_10x10x10"
"10x10x10+times:4+variables:element,2,nodal,3"
"ioshell_10x10x10.g" "3" "exodiff" "-pedantic")
"ioshell_10x10x10.g" "3" "3")

catalyst_test_ioshell_generated("catalyst_ioshell_10x10x10_tets"
"10x10x10+tets:+times:2+variables:element,2,nodal,3"
"ioshell_10x10x10_tets.g" "1" "exodiff" "-pedantic")
"ioshell_10x10x10_tets.g" "1" "1")

catalyst_test_ioshell_generated("catalyst_ioshell_10x10x10_pyramids"
"10x10x10+pyramids:+times:2+variables:element,2,nodal,3"
"ioshell_10x10x10_pyramids.g" "1" "exodiff" "-pedantic")
"ioshell_10x10x10_pyramids.g" "1" "1")

catalyst_test_ioshell_generated("catalyst_ioshell_10x10x10_shell"
"10x10x10+shell:xX:+times:2+variables:element,2,nodal,3"
"ioshell_10x10x10_shell.g" "1" "exodiff" "-pedantic")
"ioshell_10x10x10_shell.g" "1" "1")

catalyst_test_ioshell_generated("catalyst_ioshell_10x10x10_nodeset"
"10x10x10+nodeset:xX:+times:2+variables:element,2,nodal,3,nodeset,4"
"ioshell_10x10x10_nodeset.g" "1" "exodiff" "-pedantic")
"ioshell_10x10x10_nodeset.g" "1" "1")

catalyst_test_ioshell_generated("catalyst_ioshell_10x10x10_sideset"
"10x10x10+sideset:xX:+times:2+variables:element,2,nodal,3,sideset,4"
"ioshell_10x10x10_sideset.g" "1" "exodiff" "-pedantic")
"ioshell_10x10x10_sideset.g" "1" "1")

function(catalyst_test_ioshell_exodus_file test_name
input_file
test_time)
test_time
test_time_step)

set(CATALYST_FNAME catalyst_time_${test_time}_${input_file})
set(IOSHELL_FNAME ioshell_time_${test_time}_${input_file})
set(CATALYST_FNAME catalyst_time_${test_time_step}_${input_file})
set(IOSHELL_FNAME ioshell_time_${test_time_step}_${input_file})
set(INPUT_FILE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../main/test/${input_file})

TRIBITS_ADD_ADVANCED_TEST(${test_name}
TEST_0 EXEC io_shell ARGS -out_type catalyst ${INPUT_FILE_PATH} ${test_time}
TEST_0 EXEC io_shell ARGS -out_type catalyst ${INPUT_FILE_PATH} ${test_time_step}
DIRECTORY ../main
NOEXEPREFIX NOEXESUFFIX
NUM_MPI_PROCS 1
TEST_1 EXEC io_shell ARGS -in_type catalyst ${test_time} ${CATALYST_FNAME}
TEST_1 EXEC io_shell ARGS -in_type catalyst ${test_time_step} ${CATALYST_FNAME}
DIRECTORY ../main
NOEXEPREFIX NOEXESUFFIX
NUM_MPI_PROCS 1
Expand All @@ -175,8 +175,8 @@ TRIBITS_ADD_ADVANCED_TEST(${test_name}
)
endfunction()

catalyst_test_ioshell_exodus_file("catalyst_ioshell_cube_g" "cube.g" "1")
catalyst_test_ioshell_exodus_file("catalyst_ioshell_two_block_g" "two-block.g" "1")
catalyst_test_ioshell_exodus_file("catalyst_ioshell_cube_g" "cube.g" "1" "1")
catalyst_test_ioshell_exodus_file("catalyst_ioshell_two_block_g" "two-block.g" "1" "1")

IF (TPL_ENABLE_CGNS)

Expand All @@ -200,18 +200,19 @@ if ( CGNS_CGNSDIFF_BINARY )

function(catalyst_test_ioshell_cgns_file test_name
input_file
test_time)
test_time
test_time_step)

set(CATALYST_FNAME catalyst_time_${test_time}_${input_file})
set(IOSHELL_FNAME ioshell_time_${test_time}_${input_file})
set(CATALYST_FNAME catalyst_time_${test_time_step}_${input_file})
set(IOSHELL_FNAME ioshell_time_${test_time_step}_${input_file})
set(INPUT_FILE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../main/test/${input_file})

TRIBITS_ADD_ADVANCED_TEST(${test_name}
TEST_0 EXEC io_shell ARGS -out_type catalyst ${INPUT_FILE_PATH} ${test_time}
TEST_0 EXEC io_shell ARGS -debug -out_type catalyst ${INPUT_FILE_PATH} ${test_time_step}
DIRECTORY ../main
NOEXEPREFIX NOEXESUFFIX
NUM_MPI_PROCS 1
TEST_1 EXEC io_shell ARGS -in_type catalyst ${test_time} ${CATALYST_FNAME}
TEST_1 EXEC io_shell ARGS -in_type catalyst ${test_time_step} ${CATALYST_FNAME}
DIRECTORY ../main
NOEXEPREFIX NOEXESUFFIX
NUM_MPI_PROCS 1
Expand All @@ -226,7 +227,7 @@ TRIBITS_ADD_ADVANCED_TEST(${test_name}
)
endfunction()

catalyst_test_ioshell_cgns_file("catalyst_ioshell_sparc1_cgns" "sparc1.cgns" "1")
catalyst_test_ioshell_cgns_file("catalyst_ioshell_sparc1_cgns" "sparc1.cgns" "15.992" "1")

endif()
endif()

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