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Create zero vector on the fly in Xdmf files instead of in HDF5 file.
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For 2-D vector fields, create the zero z-component on the fly in the Xdmf file rather than creating a zero vector in the HDF5 file.
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@baagaard-usgs
baagaard-usgs committed May 23, 2017
1 parent fee9ed1 commit 862d200
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Showing 14 changed files with 44 additions and 122 deletions.
37 changes: 0 additions & 37 deletions libsrc/pylith/meshio/DataWriterHDF5.cc
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Expand Up @@ -239,43 +239,6 @@ pylith::meshio::DataWriterHDF5::open(const topology::Mesh& mesh,
const int cellDim = mesh.dimension();
HDF5::writeAttribute(h5, "/topology/cells", "cell_dim", (void*)&cellDim, H5T_NATIVE_INT);

// If 2-D, write zero vector for z components
if (2 == cs->spaceDim()) {
err = PetscViewerHDF5PushGroup(_viewer, "/zero"); PYLITH_CHECK_ERROR(err);

const char* vlabel = "vertex_zero";
topology::Field vzeroField(mesh);
vzeroField.newSection(coordinatesField, 1);
vzeroField.allocate();
vzeroField.zeroAll();
vzeroField.label(vlabel);
vzeroField.vectorFieldType(topology::FieldBase::SCALAR);
vzeroField.createScatterWithBC(mesh, "", 0, vlabel);
vzeroField.scatterLocalToGlobal(vlabel);

PetscVec vzeroVector = vzeroField.vector(vlabel); assert(vzeroVector);
err = PetscObjectTypeCompare((PetscObject) vzeroVector, VECSEQ, &isseq); PYLITH_CHECK_ERROR(err);
if (isseq) {err = VecView_Seq(vzeroVector, _viewer); PYLITH_CHECK_ERROR(err); }
else {err = VecView_MPI(vzeroVector, _viewer); PYLITH_CHECK_ERROR(err); }

const char* clabel = "cell_zero";
topology::Field czeroField(mesh);
czeroField.newSection(cStart, cEnd, 1);
czeroField.allocate();
czeroField.zeroAll();
czeroField.label(clabel);
czeroField.vectorFieldType(topology::FieldBase::SCALAR);
czeroField.createScatterWithBC(mesh, "", 0, clabel);
czeroField.scatterLocalToGlobal(clabel);

PetscVec czeroVector = czeroField.vector(clabel); assert(czeroVector);
err = PetscObjectTypeCompare((PetscObject) czeroVector, VECSEQ, &isseq); PYLITH_CHECK_ERROR(err);
if (isseq) {err = VecView_Seq(czeroVector, _viewer); PYLITH_CHECK_ERROR(err); }
else {err = VecView_MPI(czeroVector, _viewer); PYLITH_CHECK_ERROR(err); }

err = PetscViewerHDF5PopGroup(_viewer); PYLITH_CHECK_ERROR(err);
} // if

} catch (const std::exception& err) {
std::ostringstream msg;
msg << "Error while opening HDF5 file " << _hdf5Filename() << ".\n" << err.what();
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62 changes: 0 additions & 62 deletions libsrc/pylith/meshio/DataWriterHDF5Ext.cc
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Expand Up @@ -288,68 +288,6 @@ pylith::meshio::DataWriterHDF5Ext::open(const topology::Mesh& mesh,
_h5->writeAttribute("/topology/cells", "cell_dim", (void*)&cellDim, H5T_NATIVE_INT);
} // if

// If 2-D, write zero vector for z coordinate and z component in vectors
if (2 == cs->spaceDim()) {
if (!commRank) _h5->createGroup("/zero");
const char* vlabel = "vertex_zero";
const std::string& vfilenameZero = _datasetFilename(vlabel);
err = PetscViewerBinaryOpen(comm, vfilenameZero.c_str(), FILE_MODE_WRITE, &binaryViewer); PYLITH_CHECK_ERROR(err);
err = PetscViewerBinarySetSkipHeader(binaryViewer, PETSC_TRUE); PYLITH_CHECK_ERROR(err);
topology::Field vzeroField(mesh);
vzeroField.newSection(coordinatesField, 1);
vzeroField.allocate();
vzeroField.zeroAll();
vzeroField.label(vlabel);
vzeroField.vectorFieldType(topology::FieldBase::SCALAR);
vzeroField.createScatterWithBC(mesh, "", 0, vlabel);
vzeroField.scatterLocalToGlobal(vlabel);

PetscVec vzeroVector = vzeroField.vector(vlabel); assert(vzeroVector);
err = PetscObjectTypeCompare((PetscObject) vzeroVector, VECSEQ, &isseq); PYLITH_CHECK_ERROR(err);
if (isseq) {err = VecView_Seq(vzeroVector, binaryViewer); PYLITH_CHECK_ERROR(err); }
else {err = VecView_MPI(vzeroVector, binaryViewer); PYLITH_CHECK_ERROR(err); }

err = PetscViewerDestroy(&binaryViewer); PYLITH_CHECK_ERROR(err);

// Create external dataset for vertex_zero field
if (!commRank) {
const hsize_t ndims = 2;
hsize_t dims[ndims];
dims[0] = numVertices;
dims[1] = 1;
_h5->createDatasetRawExternal("/zero", vlabel, vfilenameZero.c_str(), dims, ndims, scalartype);
} // if

const char* clabel = "cell_zero";
const std::string& cfilenameZero = _datasetFilename(clabel);
err = PetscViewerBinaryOpen(comm, cfilenameZero.c_str(), FILE_MODE_WRITE, &binaryViewer); PYLITH_CHECK_ERROR(err);
err = PetscViewerBinarySetSkipHeader(binaryViewer, PETSC_TRUE); PYLITH_CHECK_ERROR(err);
topology::Field czeroField(mesh);
czeroField.newSection(cStart, cEnd, 1);
czeroField.allocate();
czeroField.zeroAll();
czeroField.label(clabel);
czeroField.vectorFieldType(topology::FieldBase::SCALAR);
czeroField.createScatterWithBC(mesh, "", 0, clabel);
czeroField.scatterLocalToGlobal(clabel);

PetscVec czeroVector = czeroField.vector(clabel); assert(czeroVector);
err = PetscObjectTypeCompare((PetscObject) czeroVector, VECSEQ, &isseq); PYLITH_CHECK_ERROR(err);
if (isseq) {err = VecView_Seq(czeroVector, binaryViewer); PYLITH_CHECK_ERROR(err); }
else {err = VecView_MPI(czeroVector, binaryViewer); PYLITH_CHECK_ERROR(err); }

err = PetscViewerDestroy(&binaryViewer); PYLITH_CHECK_ERROR(err);

// Create external dataset for vertex_zero field
if (!commRank) {
const hsize_t ndims = 2;
hsize_t dims[ndims];
dims[0] = numCells;
dims[1] = 1;
_h5->createDatasetRawExternal("/zero", clabel, cfilenameZero.c_str(), dims, ndims, scalartype);
} // if
} // if

} catch (const std::exception& err) {
std::ostringstream msg;
msg << "Error while opening HDF5 file " << _filename << ".\n" << err.what();
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13 changes: 9 additions & 4 deletions libsrc/pylith/meshio/Xdmf.cc
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Expand Up @@ -424,8 +424,10 @@ pylith::meshio::Xdmf::_writeDomainVertices(const int numVertices,
<< " &HeavyData;:/geometry/vertices\n"
<< " </DataItem>\n"
<< " </DataItem>\n"
<< " <DataItem Name=\"verticesZ\" ItemType=\"Uniform\" Dimensions=\"" << numVertices << " 1\" Format=\"HDF\">\n"
<< " &HeavyData;:/zero/vertex_zero\n"
<< " <DataItem Name=\"verticesZ\" ItemType=\"Function\" Dimensions=\"" << numVertices << " 1\" Function=\"0*$0\">\n"
<< " <DataItem Reference=\"XML\">\n"
<< " /Xdmf/Domain/DataItem[@Name=\"vertices\"]/DataItem[@Name=\"verticesX\"]\n"
<< " </DataItem>\n"
<< " </DataItem>\n"
<< " </DataItem>\n";
} else {
Expand Down Expand Up @@ -563,9 +565,12 @@ pylith::meshio::Xdmf::_writeGridAttribute(const FieldMetadata& metadata,
<< " </DataItem>\n"
<< " </DataItem>\n"
// z component
<< " <DataItem ItemType=\"Uniform\" Dimensions=\"" << metadata.numPoints << " 1\" Format=\"HDF\">\n"
<< " &HeavyData;:" << h5ZeroName << "\n"
<< " <DataItem ItemType=\"Function\" Dimensions=\"" << metadata.numPoints << " 1\" Function=\"0*$0\">\n"
<< " <DataItem Reference=\"XML\">\n"
<< " /Xdmf/Domain/Grid/Attribute[@Name=\"" << metadata.name << "\"]/DataItem[1]/DataItem[1]\n"
<< " </DataItem>\n"
<< " </DataItem>\n"
// close
<< " </DataItem>\n"
<< " </Attribute>\n";
} else {
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2 changes: 1 addition & 1 deletion m4
Submodule m4 updated 1 files
+0 −1 ax_lib_netcdf4.m4
2 changes: 1 addition & 1 deletion templates/friction/m4
Submodule m4 updated 8 files
+16 −47 ac_pkg_swig.m4
+0 −279 ax_lib_netcdf4.m4
+0 −34 cig_pkg_git.m4
+1 −2 cit_cppunit.m4
+0 −1 cit_hdf5.m4
+2 −2 cit_mpi.m4
+0 −1 cit_netcdf.m4
+4 −24 cit_petsc.m4
2 changes: 1 addition & 1 deletion templates/materials/m4
Submodule m4 updated 8 files
+16 −47 ac_pkg_swig.m4
+0 −279 ax_lib_netcdf4.m4
+0 −34 cig_pkg_git.m4
+1 −2 cit_cppunit.m4
+0 −1 cit_hdf5.m4
+2 −2 cit_mpi.m4
+0 −1 cit_netcdf.m4
+4 −24 cit_petsc.m4
12 changes: 8 additions & 4 deletions unittests/libtests/meshio/data/quad4_cell.xmf
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Expand Up @@ -25,8 +25,10 @@
&HeavyData;:/geometry/vertices
</DataItem>
</DataItem>
<DataItem Name="verticesZ" ItemType="Uniform" Dimensions="6 1" Format="HDF">
&HeavyData;:/zero/vertex_zero
<DataItem Name="verticesZ" ItemType="Function" Dimensions="6 1" Function="0*$0">
<DataItem Reference="XML">
/Xdmf/Domain/DataItem[@Name="vertices"]/DataItem[@Name="verticesX"]
</DataItem>
</DataItem>
</DataItem>
<!-- ============================================================ -->
Expand Down Expand Up @@ -119,8 +121,10 @@
&HeavyData;:/cell_fields/traction
</DataItem>
</DataItem>
<DataItem ItemType="Uniform" Dimensions="2 1" Format="HDF">
&HeavyData;:/zero/cell_zero
<DataItem ItemType="Function" Dimensions="2 1" Function="0*$0">
<DataItem Reference="XML">
/Xdmf/Domain/Grid/Attribute[@Name="traction"]/DataItem[1]/DataItem[1]
</DataItem>
</DataItem>
</DataItem>
</Attribute>
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Binary file modified unittests/libtests/meshio/data/quad4_points.h5
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Binary file modified unittests/libtests/meshio/data/quad4_points_vertex.h5
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12 changes: 8 additions & 4 deletions unittests/libtests/meshio/data/quad4_vertex.xmf
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Expand Up @@ -25,8 +25,10 @@
&HeavyData;:/geometry/vertices
</DataItem>
</DataItem>
<DataItem Name="verticesZ" ItemType="Uniform" Dimensions="6 1" Format="HDF">
&HeavyData;:/zero/vertex_zero
<DataItem Name="verticesZ" ItemType="Function" Dimensions="6 1" Function="0*$0">
<DataItem Reference="XML">
/Xdmf/Domain/DataItem[@Name="vertices"]/DataItem[@Name="verticesX"]
</DataItem>
</DataItem>
</DataItem>
<!-- ============================================================ -->
Expand Down Expand Up @@ -59,8 +61,10 @@
&HeavyData;:/vertex_fields/displacement
</DataItem>
</DataItem>
<DataItem ItemType="Uniform" Dimensions="6 1" Format="HDF">
&HeavyData;:/zero/vertex_zero
<DataItem ItemType="Function" Dimensions="6 1" Function="0*$0">
<DataItem Reference="XML">
/Xdmf/Domain/Grid/Attribute[@Name="displacement"]/DataItem[1]/DataItem[1]
</DataItem>
</DataItem>
</DataItem>
</Attribute>
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12 changes: 8 additions & 4 deletions unittests/libtests/meshio/data/tri3_cell.xmf
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Expand Up @@ -25,8 +25,10 @@
&HeavyData;:/geometry/vertices
</DataItem>
</DataItem>
<DataItem Name="verticesZ" ItemType="Uniform" Dimensions="6 1" Format="HDF">
&HeavyData;:/zero/vertex_zero
<DataItem Name="verticesZ" ItemType="Function" Dimensions="6 1" Function="0*$0">
<DataItem Reference="XML">
/Xdmf/Domain/DataItem[@Name="vertices"]/DataItem[@Name="verticesX"]
</DataItem>
</DataItem>
</DataItem>
<!-- ============================================================ -->
Expand Down Expand Up @@ -119,8 +121,10 @@
&HeavyData;:/cell_fields/traction
</DataItem>
</DataItem>
<DataItem ItemType="Uniform" Dimensions="2 1" Format="HDF">
&HeavyData;:/zero/cell_zero
<DataItem ItemType="Function" Dimensions="2 1" Function="0*$0">
<DataItem Reference="XML">
/Xdmf/Domain/Grid/Attribute[@Name="traction"]/DataItem[1]/DataItem[1]
</DataItem>
</DataItem>
</DataItem>
</Attribute>
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12 changes: 8 additions & 4 deletions unittests/libtests/meshio/data/tri3_vertex.xmf
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Expand Up @@ -25,8 +25,10 @@
&HeavyData;:/geometry/vertices
</DataItem>
</DataItem>
<DataItem Name="verticesZ" ItemType="Uniform" Dimensions="6 1" Format="HDF">
&HeavyData;:/zero/vertex_zero
<DataItem Name="verticesZ" ItemType="Function" Dimensions="6 1" Function="0*$0">
<DataItem Reference="XML">
/Xdmf/Domain/DataItem[@Name="vertices"]/DataItem[@Name="verticesX"]
</DataItem>
</DataItem>
</DataItem>
<!-- ============================================================ -->
Expand Down Expand Up @@ -59,8 +61,10 @@
&HeavyData;:/vertex_fields/displacement
</DataItem>
</DataItem>
<DataItem ItemType="Uniform" Dimensions="6 1" Format="HDF">
&HeavyData;:/zero/vertex_zero
<DataItem ItemType="Function" Dimensions="6 1" Function="0*$0">
<DataItem Reference="XML">
/Xdmf/Domain/Grid/Attribute[@Name="displacement"]/DataItem[1]/DataItem[1]
</DataItem>
</DataItem>
</DataItem>
</Attribute>
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