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Merged
joewallwork merged 11 commits into from
Nov 10, 2025
Merged

XIOS: Handle DGSField #952

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b49cd2a
Handle DGStressFields
joewallwork Oct 14, 2025
86ee59d
Consider DGS in XIOS write test
joewallwork Oct 14, 2025
4da3042
Consider DGS in XIOS read test
joewallwork Oct 14, 2025
f59e367
Rework dimension logic
joewallwork Oct 14, 2025
e786e6f
Docs on DGSField in XIOS
joewallwork Oct 14, 2025
7ab746e
Post-rebase fixes
joewallwork Oct 21, 2025
d5f47bc
Define tice based on DGSTRESSCOMP, not DG
joewallwork Oct 21, 2025
a133b32
Merge branch 'issue917_xios-write-diag-time' into issue911_xios-dgs
joewallwork Nov 3, 2025
79f22c4
Use DGSField for consistency
joewallwork Nov 3, 2025
a15d40e
Merge branch 'issue917_xios-write-diag-time' into issue911_xios-dgs
joewallwork Nov 4, 2025
d38a858
Merge branch 'issue917_xios-write-diag-time' into issue911_xios-dgs
joewallwork Nov 4, 2025
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8 changes: 6 additions & 2 deletions core/src/ParaGridIO_Xios.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -70,9 +70,13 @@ ModelState ParaGridIO::getModelState(const std::string& filePath)
DGField field(ModelArray::Type::DG);
field.resize();
state.merge(ModelState { { { fieldId, field } }, {} });
} else if (type == ModelArray::Type::DGSTRESS) {
DGSField field(ModelArray::Type::DGSTRESS);
field.resize();
state.merge(ModelState { { { fieldId, field } }, {} });
} else {
throw std::runtime_error(
"ParaGridIO::getModelState: field type for field" + fieldId + " is not supported.");
throw std::runtime_error("ParaGridIO::getModelState: field type for field " + fieldId
+ " is not supported.");
}
}

Expand Down
45 changes: 34 additions & 11 deletions core/src/Xios.cpp
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Expand Up @@ -781,21 +781,27 @@ void Xios::affixModelMetadata()
size_t counter = 0;
for (ModelArray::Dimension dim : ModelArray::typeDimensions[type]) {
const std::string domainName = ModelArray::definedDimensions[dim].name;
// Add 1 in the case of vertex-based field types
ModelArray::Base base = ModelArray::baseTypes[type];
size_t extension = (base == ModelArray::Base::Vertex) ? 1 : 0;
if (counter == 0) {
cxios_set_domain_ni_glo(domain, (int)metadata.getGlobalExtentX() + extension);
if (dim == ModelArray::Dimension::X) {
cxios_set_domain_ni_glo(domain, metadata.getGlobalExtentX());
cxios_set_domain_ni(domain, metadata.getLocalExtentX());
} else if (dim == ModelArray::Dimension::XVERTEX) {
cxios_set_domain_ni_glo(domain, metadata.getGlobalExtentX() + 1);
cxios_set_domain_ni(domain, metadata.getLocalExtentX() + 1);
} else {
throw std::runtime_error(
"Xios: Could not set domain extents based on dimension '"
+ ModelArray::definedDimensions.at(dim).name + "'");
}
if (!cxios_is_defined_domain_ni_glo(domain)) {
throw std::runtime_error(
"Xios: Failed to set global x-size for domain '" + domainId + "'");
}
cxios_set_domain_ni(domain, (int)metadata.getLocalExtentX() + extension);
if (!cxios_is_defined_domain_ni(domain)) {
throw std::runtime_error(
"Xios: Failed to set local x-size for domain '" + domainId + "'");
}
cxios_set_domain_ibegin(domain, (int)metadata.getLocalCornerX());
cxios_set_domain_ibegin(domain, metadata.getLocalCornerX());
if (!cxios_is_defined_domain_ibegin(domain)) {
throw std::runtime_error(
"Xios: Failed to set local starting x-index for domain '" + domainId + "'");
Expand All @@ -811,17 +817,26 @@ void Xios::affixModelMetadata()
"Xios: Failed to set longitude name for domain '" + domainId + "'");
}
} else if (counter == 1) {
cxios_set_domain_nj_glo(domain, (int)metadata.getGlobalExtentY() + extension);
if (dim == ModelArray::Dimension::Y) {
cxios_set_domain_nj_glo(domain, metadata.getGlobalExtentY());
cxios_set_domain_nj(domain, metadata.getLocalExtentY());
} else if (dim == ModelArray::Dimension::YVERTEX) {
cxios_set_domain_nj_glo(domain, metadata.getGlobalExtentY() + 1);
cxios_set_domain_nj(domain, metadata.getLocalExtentY() + 1);
} else {
throw std::runtime_error(
"Xios: Could not set domain extents based on dimension '"
+ ModelArray::definedDimensions.at(dim).name + "'");
}
if (!cxios_is_defined_domain_nj_glo(domain)) {
throw std::runtime_error(
"Xios: Failed to set global y-size for domain '" + domainId + "'");
}
cxios_set_domain_nj(domain, (int)metadata.getLocalExtentY() + extension);
if (!cxios_is_defined_domain_nj(domain)) {
throw std::runtime_error(
"Xios: Failed to set local y-size for domain '" + domainId + "'");
}
cxios_set_domain_jbegin(domain, (int)metadata.getLocalCornerY());
cxios_set_domain_jbegin(domain, metadata.getLocalCornerY());
if (!cxios_is_defined_domain_jbegin(domain)) {
throw std::runtime_error(
"Xios: Failed to set local starting y-index for domain '" + domainId + "'");
Expand Down Expand Up @@ -1655,8 +1670,12 @@ void Xios::write(const std::string fieldId, ModelArray& modelarray)
} else if (type == ModelArray::Type::DG) {
cxios_write_data_k83(fieldId.c_str(), fieldId.length(), modelarray.getData(), dims[0],
dims[1], ModelArray::size(ModelArray::Dimension::DG), -1);
} else if (type == ModelArray::Type::DGSTRESS) {
cxios_write_data_k83(fieldId.c_str(), fieldId.length(), modelarray.getData(), dims[0],
dims[1], ModelArray::size(ModelArray::Dimension::DGSTRESS), -1);
} else {
throw std::invalid_argument("Only HFields, VertexFields, and DGFields are supported");
throw std::invalid_argument(
"Only HFields, VertexFields, DGFields, and DGSFields are supported");
}
}

Expand Down Expand Up @@ -1688,8 +1707,12 @@ void Xios::read(const std::string fieldId, ModelArray& modelarray)
} else if (type == ModelArray::Type::DG) {
cxios_read_data_k83(fieldId.c_str(), fieldId.length(), modelarray.getData(), dims[0],
dims[1], ModelArray::size(ModelArray::Dimension::DG));
} else if (type == ModelArray::Type::DGSTRESS) {
cxios_read_data_k83(fieldId.c_str(), fieldId.length(), modelarray.getData(), dims[0],
dims[1], ModelArray::size(ModelArray::Dimension::DGSTRESS));
} else {
throw std::invalid_argument("Only HFields, VertexFields, and DGFields are supported");
throw std::invalid_argument(
"Only HFields, VertexFields, DGFields, and DGSFields are supported");
}
}
}
Expand Down
2 changes: 1 addition & 1 deletion core/src/discontinuousgalerkin/ModelArrayDetails.cpp
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Expand Up @@ -84,7 +84,7 @@ const std::map<ModelArray::Type, std::string> ModelArray::typeNames = {
{ ModelArray::Type::U, "UField" },
{ ModelArray::Type::V, "VField" },
{ ModelArray::Type::DG, "DGField" },
{ ModelArray::Type::DGSTRESS, "DGStressField" },
{ ModelArray::Type::DGSTRESS, "DGSField" },
{ ModelArray::Type::CG, "CGField" },
};

Expand Down
4 changes: 4 additions & 0 deletions core/src/include/Xios.hpp
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Expand Up @@ -180,10 +180,12 @@ class Xios : public Configured<Xios> {
std::map<ModelArray::Type, std::string> axisIds = {
{ ModelArray::Type::VERTEX, "VertexAxis" },
{ ModelArray::Type::DG, "DGAxis" },
{ ModelArray::Type::DGSTRESS, "DGSAxis" },
};
std::map<std::string, std::string> axisNames = {
{ "VertexAxis", "ncoords" },
{ "DGAxis", "dg_comp" },
{ "DGSAxis", "dgstress_comp" },
};
xios::CAxisGroup* getAxisGroup();
xios::CAxis* getAxis(const std::string axisId);
Expand All @@ -193,6 +195,7 @@ class Xios : public Configured<Xios> {
{ ModelArray::Type::H, "HDomain" },
{ ModelArray::Type::VERTEX, "VertexDomain" },
{ ModelArray::Type::DG, "HDomain" },
{ ModelArray::Type::DGSTRESS, "HDomain" },
};
xios::CDomainGroup* getDomainGroup();
xios::CDomain* getDomain(std::string domainId);
Expand All @@ -217,6 +220,7 @@ class Xios : public Configured<Xios> {
{ ModelArray::Type::H, "HGrid" },
{ ModelArray::Type::VERTEX, "VertexGrid" },
{ ModelArray::Type::DG, "DGGrid" },
{ ModelArray::Type::DGSTRESS, "DGSGrid" },
};

/* File */
Expand Down
12 changes: 10 additions & 2 deletions core/test/XiosRead_test.cpp
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Expand Up @@ -24,6 +24,7 @@ const std::string restartFilename = testFilesDir + "/xios_test_input.nc";
const std::string forcingFilename = testFilesDir + "/xios_test_forcing.nc";

static const int DG = 3;
static const int DGSTRESSCOMP = 8;

namespace Nextsim {

Expand All @@ -46,7 +47,8 @@ MPI_TEST_CASE("TestXiosRead", 2)
config << "restart_period = P0-0T01:30:00" << std::endl;
config << "partition_file = xios_test_partition_metadata_2.nc" << std::endl;
config << "[XiosInput]" << std::endl;
config << "field_names = " << maskName << "," << coordsName << "," << hiceName << std::endl;
config << "field_names = " << maskName << "," << coordsName << "," << hiceName << ","
<< ticeName << std::endl;
config << "[XiosForcing]" << std::endl;
config << "filename = " << forcingFilename << std::endl;
config << "field_names = " << uName << std::endl;
Expand Down Expand Up @@ -76,8 +78,10 @@ MPI_TEST_CASE("TestXiosRead", 2)

// TODO: We could deduce this from the NetCDF file
ModelArray::setNComponents(ModelArray::Type::DG, DG);
ModelArray::setNComponents(ModelArray::Type::DGSTRESS, DGSTRESSCOMP);
ModelArray::setNComponents(ModelArray::Type::VERTEX, ModelArray::nCoords);
REQUIRE(ModelArray::nComponents(ModelArray::Type::DG) == DG);
REQUIRE(ModelArray::nComponents(ModelArray::Type::DGSTRESS) == DGSTRESSCOMP);
REQUIRE(ModelArray::nComponents(ModelArray::Type::VERTEX) == ModelArray::nCoords);

// Affix ModelMetadata to Xios handler
Expand Down Expand Up @@ -119,6 +123,11 @@ MPI_TEST_CASE("TestXiosRead", 2)
float expected = 1.0 * (d + DG * (i + nx * j));
REQUIRE(entry.second.components({ i, j })[d] == doctest::Approx(expected));
}
} else if (entry.first == ticeName) {
for (size_t d = 0; d < DGSTRESSCOMP; ++d) {
REQUIRE(entry.second.components({ i, j })[d]
== doctest::Approx(2.0 * (d + DGSTRESSCOMP * (i + nx * j))));
}
}
}
}
Expand Down Expand Up @@ -149,5 +158,4 @@ MPI_TEST_CASE("TestXiosRead", 2)
xiosHandler.context_finalize();
Finalizer::finalize();
}

}
17 changes: 16 additions & 1 deletion core/test/XiosWrite_test.cpp
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Expand Up @@ -24,6 +24,7 @@ const std::string restartFilename = testFilesDir + "/xios_test_output.nc";
const std::string diagnosticFilename = testFilesDir + "/xios_test_diagnostic.nc";

static const int DG = 3;
static const int DGSTRESSCOMP = 8;

namespace Nextsim {

Expand All @@ -46,7 +47,8 @@ MPI_TEST_CASE("TestXiosWrite", 2)
config << "partition_file = xios_test_partition_metadata_2.nc" << std::endl;
config << "restart_period = P0-0T01:30:00" << std::endl;
config << "[XiosOutput]" << std::endl;
config << "field_names = " << maskName << "," << coordsName << "," << hiceName << std::endl;
config << "field_names = " << maskName << "," << coordsName << "," << hiceName << ","
<< ticeName << std::endl;
config << "[XiosDiagnostic]" << std::endl;
config << "filename = " << diagnosticFilename << std::endl;
config << "field_names = " << uName << std::endl;
Expand Down Expand Up @@ -84,8 +86,10 @@ MPI_TEST_CASE("TestXiosWrite", 2)
ModelArray::setDimension(ModelArray::Dimension::XVERTEX, nx_glo + 1, nx + 1, 0);
ModelArray::setDimension(ModelArray::Dimension::YVERTEX, ny_glo + 1, ny + 1, 0);
ModelArray::setNComponents(ModelArray::Type::DG, DG);
ModelArray::setNComponents(ModelArray::Type::DGSTRESS, DGSTRESSCOMP);
ModelArray::setNComponents(ModelArray::Type::VERTEX, ModelArray::nCoords);
REQUIRE(ModelArray::nComponents(ModelArray::Type::DG) == DG);
REQUIRE(ModelArray::nComponents(ModelArray::Type::DGSTRESS) == DGSTRESSCOMP);
REQUIRE(ModelArray::nComponents(ModelArray::Type::VERTEX) == ModelArray::nCoords);

// Affix ModelMetadata to Xios handler
Expand All @@ -96,6 +100,7 @@ MPI_TEST_CASE("TestXiosWrite", 2)
xiosHandler.setFieldType(maskName, ModelArray::Type::H);
xiosHandler.setFieldType(coordsName, ModelArray::Type::VERTEX);
xiosHandler.setFieldType(hiceName, ModelArray::Type::DG);
xiosHandler.setFieldType(ticeName, ModelArray::Type::DGSTRESS);
xiosHandler.setFieldType(uName, ModelArray::Type::H);

// Set file split frequency for restarts (but not diagnostics)
Expand Down Expand Up @@ -130,6 +135,15 @@ MPI_TEST_CASE("TestXiosWrite", 2)
}
}
}
DGSField tice(ModelArray::Type::DGSTRESS);
tice.resize();
for (size_t j = 0; j < ny; ++j) {
for (size_t i = 0; i < nx; ++i) {
for (size_t d = 0; d < DGSTRESSCOMP; ++d) {
tice.components({ i, j })[d] = 2.0 * (d + DGSTRESSCOMP * (i + nx * j));
}
}
}
HField u(ModelArray::Type::H);
u.resize();

Expand Down Expand Up @@ -160,6 +174,7 @@ MPI_TEST_CASE("TestXiosWrite", 2)
{ maskName, mask },
{ coordsName, coordinates },
{ hiceName, hice },
{ ticeName, tice },
},
{} };
ModelState diagnostics = { {
Expand Down
18 changes: 18 additions & 0 deletions core/test/xios_test_input.cdl
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Expand Up @@ -36,6 +36,11 @@ variables:
DGAxis:standard_name = "DG DoFs" ;
DGAxis:long_name = "Discontinuous Galerkin number of degrees of freedom" ;
DGAxis:units = "-" ;
float DGSAxis(dgstress_comp) ;
DGSAxis:axis = "DGS" ;
DGSAxis:standard_name = "DGS DoFs" ;
DGSAxis:long_name = "Discontinuous Galerkin stress component number of degrees of freedom" ;
DGSAxis:units = "-" ;
float VertexAxis(ncoords) ;
VertexAxis:axis = "DIM" ;
VertexAxis:standard_name = "Dimension" ;
Expand All @@ -50,6 +55,9 @@ variables:
float mask(y, x) ;
mask:online_operation = "once" ;
mask:coordinates = "lat lon" ;
float tice(y, x, dgstress_comp) ;
tice:online_operation = "once" ;
tice:coordinates = "lat lon DGSAxis" ;

// global attributes:
:structure_name = "parametric_rectangular" ;
Expand Down Expand Up @@ -98,4 +106,14 @@ data:
mask =
0, 0, 0, 0,
1, 1, 1, 1 ;

tice =
0, 2, 4, 6, 8, 10, 12, 14,
16, 18, 20, 22, 24, 26, 28, 30,
0, 2, 4, 6, 8, 10, 12, 14,
16, 18, 20, 22, 24, 26, 28, 30,
32, 34, 36, 38, 40, 42, 44, 46,
48, 50, 52, 54, 56, 58, 60, 62,
32, 34, 36, 38, 40, 42, 44, 46,
48, 50, 52, 54, 56, 58, 60, 62 ;
}
5 changes: 5 additions & 0 deletions docs/xios.rst
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Expand Up @@ -78,6 +78,11 @@ As elsewhere in the model, these configuration values are parsed by calling the
building with MPI, you will need to pass the MPI communicator to this member
function when calling it.

The XIOS I/O implementation supports fields of ``HField``, ``VertexField``,
``DGField``, and ``DGSField``. When reading from file, the field type will
be deduced from its dimension. When writing to file, the field type should be
set using the ``setFieldType`` member function of the ``Xios`` handler class.

Developer notes
^^^^^^^^^^^^^^^

Expand Down
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