[cig-commits] r14670 - in short/3D/PyLith/branches/pylith-swig: . libsrc/feassemble libsrc/materials libsrc/meshio libsrc/topology modulesrc/meshio pylith/feassemble pylith/meshio pylith/problems tests/1d/line2 unittests/libtests/materials
brad at geodynamics.org
brad at geodynamics.org
Sat Apr 11 21:22:53 PDT 2009
Author: brad
Date: 2009-04-11 21:22:52 -0700 (Sat, 11 Apr 2009)
New Revision: 14670
Modified:
short/3D/PyLith/branches/pylith-swig/TODO
short/3D/PyLith/branches/pylith-swig/libsrc/feassemble/IntegratorElasticity.cc
short/3D/PyLith/branches/pylith-swig/libsrc/feassemble/IntegratorElasticity.hh
short/3D/PyLith/branches/pylith-swig/libsrc/materials/ElasticMaterial.cc
short/3D/PyLith/branches/pylith-swig/libsrc/materials/ElasticMaterial.hh
short/3D/PyLith/branches/pylith-swig/libsrc/materials/Material.cc
short/3D/PyLith/branches/pylith-swig/libsrc/materials/Material.hh
short/3D/PyLith/branches/pylith-swig/libsrc/meshio/DataWriterVTK.cc
short/3D/PyLith/branches/pylith-swig/libsrc/meshio/OutputManager.cc
short/3D/PyLith/branches/pylith-swig/libsrc/meshio/OutputManager.hh
short/3D/PyLith/branches/pylith-swig/libsrc/topology/Field.cc
short/3D/PyLith/branches/pylith-swig/modulesrc/meshio/OutputManager.i
short/3D/PyLith/branches/pylith-swig/pylith/feassemble/IntegratorElasticity.py
short/3D/PyLith/branches/pylith-swig/pylith/meshio/DataWriterVTK.py
short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputDirichlet.py
short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputFaultKin.py
short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputManager.py
short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputMatElastic.py
short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputNeumann.py
short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputSoln.py
short/3D/PyLith/branches/pylith-swig/pylith/problems/Formulation.py
short/3D/PyLith/branches/pylith-swig/pylith/problems/TimeStepUniform.py
short/3D/PyLith/branches/pylith-swig/tests/1d/line2/TestAxial.py
short/3D/PyLith/branches/pylith-swig/tests/1d/line2/axialextension.cfg
short/3D/PyLith/branches/pylith-swig/unittests/libtests/materials/TestElasticMaterial.cc
Log:
More work on output.
Modified: short/3D/PyLith/branches/pylith-swig/TODO
===================================================================
--- short/3D/PyLith/branches/pylith-swig/TODO 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/TODO 2009-04-12 04:22:52 UTC (rev 14670)
@@ -7,16 +7,7 @@
0. SWIG conversion [Brad]
(1) Output
- module
- DataWriterVTK
- DataWriter
- OutputManager
- OutputSolnSubset
- CellFilter
- CellFilterAvg
- VertexFilter
- VertexFilterVecNorm
- TestDataWriterVTK
+ TestDataWriterVTK (bc, fault)
(2) Full-scale tests (few 1-D, 2-D, and 3-D)
@@ -73,10 +64,19 @@
libtests/feassemble/ElasticityImplict
testVerifyConfiguration()
testCellField()
+ libtests/materials/Material
+ propertyField()
+ stateVarField()
DirichletPoints (Python) - rate == None -> dbRate == 0
DirichletBoundary (Python) - rate == None -> dbRate == 0
+ pytests.meshio.TestOutputSoln
+ pytests.meshio.TestOutputDirichlet
+ pytests.meshio.TestOutputFaultKin
+ pytests.meshio.TestOutputMatElastic
+ pytests.meshio.TestOutputNeumann
+
1. Memory model [Matt]
2. Nondimensionalize [Brad]
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/feassemble/IntegratorElasticity.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/feassemble/IntegratorElasticity.cc 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/feassemble/IntegratorElasticity.cc 2009-04-12 04:22:52 UTC (rev 14670)
@@ -39,7 +39,8 @@
// Constructor
pylith::feassemble::IntegratorElasticity::IntegratorElasticity(void) :
_material(0),
- _bufferFieldTensor(0)
+ _bufferFieldTensor(0),
+ _bufferFieldOther(0)
{ // constructor
} // constructor
@@ -49,6 +50,7 @@
{ // destructor
_material = 0; // Don't manage memory for material
delete _bufferFieldTensor; _bufferFieldTensor = 0;
+ delete _bufferFieldOther; _bufferFieldOther = 0;
} // destructor
// ----------------------------------------------------------------------
@@ -288,33 +290,33 @@
const char* name,
topology::SolutionFields* fields)
{ // cellField
+ assert(0 != fields);
assert(0 != _material);
// We assume the material stores the total-strain field if
// hasStateVars() is TRUE.
- const int numQuadPts = _quadrature->numQuadPts();
+ const topology::Mesh& mesh = fields->mesh();
if (!_material->hasStateVars() &&
(0 == strcasecmp(name, "total_strain") ||
0 == strcasecmp(name, "stress") )) {
assert(0 != fields);
- _allocateTensorField(fields->mesh());
+ _allocateTensorField(mesh);
_calcStrainStressField(_bufferFieldTensor, name, fields);
return *_bufferFieldTensor;
} else if (0 == strcasecmp(name, "stress")) {
assert(0 != fields);
- _allocateTensorField(fields->mesh());
-#if 0 // TEMPORARY
+ _allocateTensorField(mesh);
_material->propertyField(_bufferFieldTensor, "total_strain");
-#endif
_calcStressFromStrain(_bufferFieldTensor);
return *_bufferFieldTensor;
- } else
-#if 0 // TEMPORARY
- return _material->field(name);
-#endif
- assert(0);
+ } else {
+ if (0 == _bufferFieldOther)
+ _bufferFieldOther = new topology::Field<topology::Mesh>(mesh);
+ _material->stateVarField(_bufferFieldOther, name);
+ return *_bufferFieldOther;
+ } // if/else
// Return tensor section to satisfy member function definition. Code
// should never get here.
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/feassemble/IntegratorElasticity.hh
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/feassemble/IntegratorElasticity.hh 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/feassemble/IntegratorElasticity.hh 2009-04-12 04:22:52 UTC (rev 14670)
@@ -226,6 +226,9 @@
/// Buffer for storing cell tensor field.
topology::Field<topology::Mesh>* _bufferFieldTensor;
+ /// Buffer for storing cell state-variable field.
+ topology::Field<topology::Mesh>* _bufferFieldOther;
+
// NOT IMPLEMENTED //////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/materials/ElasticMaterial.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/materials/ElasticMaterial.cc 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/materials/ElasticMaterial.cc 2009-04-12 04:22:52 UTC (rev 14670)
@@ -217,7 +217,7 @@
assert(!stateVarsSection.isNull());
stateVarsSection->restrictPoint(cell, &_stateVarsCell[0],
_stateVarsCell.size());
-
+
for (int iQuad=0; iQuad < numQuadPts; ++iQuad)
_updateStateVars(&_stateVarsCell[iQuad*numVarsQuadPt], numVarsQuadPt,
&_propertiesCell[iQuad*numPropsQuadPt],
@@ -259,6 +259,30 @@
} // stableTimeStepImplicit
// ----------------------------------------------------------------------
+// Get initial stress field.
+const pylith::topology::Field<pylith::topology::Mesh>&
+pylith::materials::ElasticMaterial::initialStressField(void) const
+{ // initialStressField
+ if (0 == _initialStress)
+ throw std::runtime_error("Request for initial stress field, but field "
+ "does not exist.");
+
+ return *_initialStress;
+} // initialStressField
+
+// ----------------------------------------------------------------------
+// Get initial strain field.
+const pylith::topology::Field<pylith::topology::Mesh>&
+pylith::materials::ElasticMaterial::initialStrainField(void) const
+{ // initialStrainField
+ if (0 == _initialStrain)
+ throw std::runtime_error("Request for initial strain field, but field "
+ "does not exist.");
+
+ return *_initialStrain;
+} // initialStrainField
+
+// ----------------------------------------------------------------------
// Allocate cell arrays.
void
pylith::materials::ElasticMaterial::_allocateCellArrays(void)
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/materials/ElasticMaterial.hh
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/materials/ElasticMaterial.hh 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/materials/ElasticMaterial.hh 2009-04-12 04:22:52 UTC (rev 14670)
@@ -177,6 +177,18 @@
virtual
void useElasticBehavior(const bool flag);
+ /** Get initial stress field.
+ *
+ * @returns Initial stress field.
+ */
+ const topology::Field<topology::Mesh>& initialStressField(void) const;
+
+ /** Get initial strain field.
+ *
+ * @returns Initial strain field.
+ */
+ const topology::Field<topology::Mesh>& initialStrainField(void) const;
+
// PROTECTED METHODS //////////////////////////////////////////////////
protected :
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/materials/Material.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/materials/Material.cc 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/materials/Material.cc 2009-04-12 04:22:52 UTC (rev 14670)
@@ -15,6 +15,7 @@
#include "Material.hh" // implementation of object methods
#include "pylith/topology/Mesh.hh" // USES Mesh
+#include "pylith/topology/Field.hh" // USES Field
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/utils/array.hh" // USES double_array, std::vector
@@ -236,78 +237,163 @@
_dbInitialState->close();
} // initialize
-#if 0
// ----------------------------------------------------------------------
// Get physical property field.
void
-pylith::materials::Material::propertyField(ALE::Obj<real_section_type>* field,
- const char* name,
- const ALE::Obj<Mesh>& mesh,
- const int numQuadPts) const
+pylith::materials::Material::propertyField(topology::Field<topology::Mesh>* field,
+ const char* name) const
{ // propertyField
+ assert(0 != field);
+
// Find property in list of physical properties.
int i=0;
int propOffset = 0;
- int fiberDim = 0;
- while (i < _numProperties)
- if (0 == strcasecmp(name, _propMetaData[i].name))
+ const string_vector& properties = _metadata.properties();
+ const int numProperties = properties.size();
+ const std::string nameString = std::string(name);
+ bool found = false;
+ for (int i=0; i < numProperties; ++i)
+ if (nameString == properties[i]) {
+ found = true;
break;
- else {
- propOffset += _propMetaData[i].fiberDim;
- ++i;
- } // else
- if (i < _numProperties)
- fiberDim = _propMetaData[i].fiberDim;
- else {
+ } else
+ propOffset +=
+ _metadata.fiberDim(properties[i].c_str(), Metadata::PROPERTY);
+ if (!found) {
std::ostringstream msg;
msg << "Unknown physical property '" << name << "' for material '"
<< _label << "'.";
throw std::runtime_error(msg.str());
} // else
+ const int fiberDim = _metadata.fiberDim(name, Metadata::PROPERTY);
// Get cell information
- const ALE::Obj<Mesh::label_sequence>& cells =
- mesh->getLabelStratum("material-id", _id);
+ const ALE::Obj<SieveMesh>& sieveMesh = field->mesh().sieveMesh();
+ assert(!sieveMesh.isNull());
+ const ALE::Obj<SieveMesh::label_sequence>& cells =
+ sieveMesh->getLabelStratum("material-id", _id);
assert(!cells.isNull());
- const Mesh::label_sequence::iterator cellsEnd = cells->end();
+ const SieveMesh::label_sequence::iterator cellsEnd = cells->end();
+ // Get properties section
+ const ALE::Obj<RealSection>& propertiesSection = _properties->section();
+ assert(!propertiesSection.isNull());
+ const int totalPropsFiberDim =
+ propertiesSection->getFiberDimension(*cells->begin());
+ const int numPropsQuadPt = _numPropsQuadPt;
+ const int numQuadPts = totalPropsFiberDim / numPropsQuadPt;
+ assert(totalPropsFiberDim == numQuadPts * numPropsQuadPt);
const int totalFiberDim = numQuadPts * fiberDim;
// Allocate buffer for property field.
- if (field->isNull() ||
- totalFiberDim != (*field)->getFiberDimension(*cells->begin())) {
- *field = new real_section_type(mesh->comm(), mesh->debug());
- (*field)->setChart(real_section_type::chart_type(
- *std::min_element(cells->begin(), cells->end()),
- *std::max_element(cells->begin(), cells->end())+1));
- (*field)->setFiberDimension(cells, totalFiberDim);
- mesh->allocate(*field);
+ const ALE::Obj<RealSection>& fieldSection = field->section();
+ if (totalFiberDim != fieldSection->getFiberDimension(*cells->begin())) {
+ field->newSection(cells, totalFiberDim);
+ field->allocate();
+ field->vectorFieldType(_metadata.fieldType(name, Metadata::PROPERTY));
} // if
// Buffer for property at cell's quadrature points
- const int totalPropsQuadPt = _totalPropsQuadPt;
- double_array fieldCell(fiberDim*numQuadPts);
- double_array propertiesCell(totalPropsQuadPt*numQuadPts);
+ double_array fieldCell(numQuadPts*fiberDim);
+ double_array propertiesCell(numQuadPts*numPropsQuadPt);
// Loop over cells
- for (Mesh::label_sequence::iterator c_iter=cells->begin();
+ for (SieveMesh::label_sequence::iterator c_iter=cells->begin();
c_iter != cellsEnd;
++c_iter) {
- _properties->restrictPoint(*c_iter,
- &propertiesCell[0], propertiesCell.size());
+ propertiesSection->restrictPoint(*c_iter,
+ &propertiesCell[0], propertiesCell.size());
for (int iQuad=0; iQuad < numQuadPts; ++iQuad) {
- _dimProperties(&propertiesCell[iQuad*totalPropsQuadPt],
- totalPropsQuadPt);
+ _dimProperties(&propertiesCell[iQuad*numPropsQuadPt],
+ numPropsQuadPt);
memcpy(&fieldCell[iQuad*fiberDim],
- &propertiesCell[iQuad*totalPropsQuadPt+propOffset],
+ &propertiesCell[iQuad*numPropsQuadPt+propOffset],
fiberDim*sizeof(double));
} // for
- (*field)->updatePoint(*c_iter, &fieldCell[0]);
+ fieldSection->updatePoint(*c_iter, &fieldCell[0]);
} // for
} // propertyField
-#endif
+// ----------------------------------------------------------------------
+// Get state variable field.
+void
+pylith::materials::Material::stateVarField(topology::Field<topology::Mesh>* field,
+ const char* name) const
+{ // stateVarField
+ assert(0 != field);
+ // Find state variable in list of state variables.
+ int i=0;
+ int varOffset = 0;
+ const string_vector& stateVars = _metadata.stateVars();
+ const int numStateVars = stateVars.size();
+ const std::string nameString = std::string(name);
+ bool found = false;
+ for (int i=0; i < numStateVars; ++i)
+ if (nameString == stateVars[i]) {
+ found = true;
+ break;
+ } else
+ varOffset +=
+ _metadata.fiberDim(stateVars[i].c_str(), Metadata::STATEVAR);
+ if (!found) {
+ std::ostringstream msg;
+ msg << "Unknown state variable '" << name << "' for material '"
+ << _label << "'.";
+ throw std::runtime_error(msg.str());
+ } // else
+ const int fiberDim = _metadata.fiberDim(name, Metadata::STATEVAR);
+
+ // Get cell information
+ const ALE::Obj<SieveMesh>& sieveMesh = field->mesh().sieveMesh();
+ assert(!sieveMesh.isNull());
+ const ALE::Obj<SieveMesh::label_sequence>& cells =
+ sieveMesh->getLabelStratum("material-id", _id);
+ assert(!cells.isNull());
+ const SieveMesh::label_sequence::iterator cellsEnd = cells->end();
+
+ // Get state variables section
+ const ALE::Obj<RealSection>& stateVarsSection = _stateVars->section();
+ assert(!stateVarsSection.isNull());
+ const int totalVarsFiberDim =
+ stateVarsSection->getFiberDimension(*cells->begin());
+ const int numVarsQuadPt = _numVarsQuadPt;
+ const int numQuadPts = totalVarsFiberDim / numVarsQuadPt;
+ assert(totalVarsFiberDim == numQuadPts * numVarsQuadPt);
+ const int totalFiberDim = numQuadPts * fiberDim;
+
+ // Allocate buffer for state variable field.
+ const ALE::Obj<RealSection>& fieldSection = field->section();
+ if (totalFiberDim != fieldSection->getFiberDimension(*cells->begin())) {
+ field->newSection(cells, totalFiberDim);
+ field->allocate();
+ field->vectorFieldType(_metadata.fieldType(name, Metadata::STATEVAR));
+ } // if
+
+ // Buffer for state variable at cell's quadrature points
+ double_array fieldCell(numQuadPts*fiberDim);
+ double_array stateVarsCell(numQuadPts*numVarsQuadPt);
+
+ // Loop over cells
+ for (SieveMesh::label_sequence::iterator c_iter=cells->begin();
+ c_iter != cellsEnd;
+ ++c_iter) {
+ stateVarsSection->restrictPoint(*c_iter,
+ &stateVarsCell[0], stateVarsCell.size());
+
+ for (int iQuad=0; iQuad < numQuadPts; ++iQuad) {
+ _dimStateVars(&stateVarsCell[iQuad*numVarsQuadPt],
+ numVarsQuadPt);
+ memcpy(&fieldCell[iQuad*fiberDim],
+ &stateVarsCell[iQuad*numVarsQuadPt+varOffset],
+ fiberDim*sizeof(double));
+ } // for
+
+ fieldSection->updatePoint(*c_iter, &fieldCell[0]);
+ } // for
+} // stateVarsField
+
+
// End of file
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/materials/Material.hh
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/materials/Material.hh 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/materials/Material.hh 2009-04-12 04:22:52 UTC (rev 14670)
@@ -147,17 +147,23 @@
/// current state.
void resetNeedNewJacobian(void);
-#if 0
/** Get physical property field. Data is returned via the
* argument.
*
- * @param field Proeprty field.
+ * @param field Property field.
* @param name Name of physical property.
*/
- void propertyField(ALE::Obj<real_section_type>* field,
+ void propertyField(topology::Field<topology::Mesh>* field,
const char* name) const;
-#endif
+ /** Get state variable field. Data is returned via the argument.
+ *
+ * @param field State variable field.
+ * @param name Name of physical property.
+ */
+ void stateVarField(topology::Field<topology::Mesh>* field,
+ const char* name) const;
+
// PROTECTED METHODS //////////////////////////////////////////////////
protected :
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/meshio/DataWriterVTK.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/meshio/DataWriterVTK.cc 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/meshio/DataWriterVTK.cc 2009-04-12 04:22:52 UTC (rev 14670)
@@ -82,7 +82,7 @@
try {
PetscErrorCode err = 0;
-
+
const std::string& filename = _vtkFilename(t);
err = PetscViewerCreate(mesh.comm(), &_viewer);
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/meshio/OutputManager.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/meshio/OutputManager.cc 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/meshio/OutputManager.cc 2009-04-12 04:22:52 UTC (rev 14670)
@@ -34,9 +34,9 @@
template<typename mesh_type>
pylith::meshio::OutputManager<mesh_type>::~OutputManager(void)
{ // destructor
- delete _writer; _writer = 0;
- delete _vertexFilter; _vertexFilter = 0;
- delete _cellFilter; _cellFilter = 0;
+ _writer = 0; // :TODO: Use shared pointer
+ _vertexFilter = 0; // :TODO: Use shared pointer
+ _cellFilter = 0; // :TODO: Use shared pointer
delete _coordsys; _coordsys = 0;
} // destructor
@@ -55,9 +55,9 @@
template<typename mesh_type>
void
pylith::meshio::OutputManager<mesh_type>::writer(
- const DataWriter<mesh_type>* datawriter)
+ DataWriter<mesh_type>* const datawriter)
{ // writer
- delete _writer; _writer = (0 != datawriter) ? datawriter->clone() : 0;
+ _writer = datawriter; // :TODO: Use shared pointer
} // writer
// ----------------------------------------------------------------------
@@ -65,9 +65,9 @@
template<typename mesh_type>
void
pylith::meshio::OutputManager<mesh_type>::vertexFilter(
- const VertexFilter<mesh_type>* filter)
+ VertexFilter<mesh_type>* const filter)
{ // vertexFilter
- delete _vertexFilter; _vertexFilter = (0 != filter) ? filter->clone() : 0;
+ _vertexFilter = filter; // :TODO: Use shared pointer
} // vertexFilter
// ----------------------------------------------------------------------
@@ -75,9 +75,9 @@
template<typename mesh_type>
void
pylith::meshio::OutputManager<mesh_type>::cellFilter(
- const CellFilter<mesh_type>* filter)
+ CellFilter<mesh_type>* const filter)
{ // cellFilter
- delete _cellFilter; _cellFilter = (0 != filter) ? filter->clone() : 0;
+ _cellFilter = filter; // :TODO: Use shared pointer
} // cellFilter
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/meshio/OutputManager.hh
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/meshio/OutputManager.hh 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/meshio/OutputManager.hh 2009-04-12 04:22:52 UTC (rev 14670)
@@ -52,19 +52,19 @@
*
* @param datawriter Writer for data.
*/
- void writer(const DataWriter<mesh_type>* datawriter);
+ void writer(DataWriter<mesh_type>* const datawriter);
/** Set filter for vertex data.
*
* @param filter Filter to apply to vertex data before writing.
*/
- void vertexFilter(const VertexFilter<mesh_type>* filter);
+ void vertexFilter(VertexFilter<mesh_type>* const filter);
/** Set filter for cell data.
*
* @param filter Filter to apply to cell data before writing.
*/
- void cellFilter(const CellFilter<mesh_type>* filter);
+ void cellFilter(CellFilter<mesh_type>* const filter);
/** Prepare for output.
*
Modified: short/3D/PyLith/branches/pylith-swig/libsrc/topology/Field.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/libsrc/topology/Field.cc 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/libsrc/topology/Field.cc 2009-04-12 04:22:52 UTC (rev 14670)
@@ -174,7 +174,6 @@
newSection();
if (!_section.isNull()) {
- // ERROR? ARE THESE LINES CORRECT?
_section->setAtlas(srcSection->getAtlas());
_section->allocateStorage();
_section->setBC(srcSection->getBC());
Modified: short/3D/PyLith/branches/pylith-swig/modulesrc/meshio/OutputManager.i
===================================================================
--- short/3D/PyLith/branches/pylith-swig/modulesrc/meshio/OutputManager.i 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/modulesrc/meshio/OutputManager.i 2009-04-12 04:22:52 UTC (rev 14670)
@@ -44,19 +44,19 @@
*
* @param datawriter Writer for data.
*/
- void writer(const DataWriter<mesh_type>* datawriter);
+ void writer(DataWriter<mesh_type>* const datawriter);
/** Set filter for vertex data.
*
* @param filter Filter to apply to vertex data before writing.
*/
- void vertexFilter(const VertexFilter<mesh_type>* filter);
+ void vertexFilter(VertexFilter<mesh_type>* const filter);
/** Set filter for cell data.
*
* @param filter Filter to apply to cell data before writing.
*/
- void cellFilter(const CellFilter<mesh_type>* filter);
+ void cellFilter(CellFilter<mesh_type>* const filter);
/** Prepare for output.
*
Modified: short/3D/PyLith/branches/pylith-swig/pylith/feassemble/IntegratorElasticity.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/feassemble/IntegratorElasticity.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/feassemble/IntegratorElasticity.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -54,7 +54,7 @@
Integrator.preinitialize(self, mesh)
material.preinitialize(mesh)
- #self.output.preinitialize(self)
+ self.output.preinitialize(self)
# Set integrator's quadrature using quadrature from material
self.quadrature(material.quadrature)
@@ -70,7 +70,7 @@
self._logger.eventBegin(logEvent)
Integrator.verifyConfiguration(self)
- #self.output.verifyConfiguration(self.mesh)
+ self.output.verifyConfiguration(self.mesh)
self._logger.eventEnd(logEvent)
return
@@ -88,9 +88,9 @@
Integrator.initialize(self, totalTime, numTimeSteps, normalizer)
- #self.output.initialize(normalizer, self.materialObj.quadrature)
- #self.output.writeInfo()
- #self.output.open(totalTime, numTimeSteps)
+ self.output.initialize(normalizer, self.materialObj.quadrature)
+ self.output.writeInfo()
+ self.output.open(totalTime, numTimeSteps)
self._logger.eventEnd(logEvent)
return
@@ -106,7 +106,7 @@
Integrator.poststep(self, t, dt, totalTime, fields)
self._info.log("Writing material data.")
- #self.output.writeData(t+dt, fields)
+ self.output.writeData(t+dt, fields)
self._logger.eventEnd(logEvent)
return
@@ -124,10 +124,10 @@
Get cell field.
"""
if None == fields:
- (field, fieldType) = self.cellField(name)
+ field = self.cellField(name)
else:
- (field, fieldType) = self.cellField(name, fields)
- return (field, fieldType)
+ field = self.cellField(name, fields)
+ return field
# End of file
Modified: short/3D/PyLith/branches/pylith-swig/pylith/meshio/DataWriterVTK.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/meshio/DataWriterVTK.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/meshio/DataWriterVTK.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -99,7 +99,8 @@
Initialize writer.
"""
DataWriterVTK.initialize(self, normalizer)
-
+
+ print "FILENAME",self.filename
ModuleMeshObject.filename(self, self.filename)
ModuleMeshObject.timeFormat(self, self.timeFormat)
ModuleMeshObject.timeConstant(self, self.timeConstant.value)
Modified: short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputDirichlet.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputDirichlet.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputDirichlet.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -17,10 +17,10 @@
##
## Factory: output_manager
-from OutputManager import OutputManager
+from OutputManager import SubMeshOutputManager
# OutputDirichlet class
-class OutputDirichlet(OutputManager):
+class OutputDirichlet(SubMeshOutputManager):
"""
Python object for managing output of finite-element information for
Dirichlet boundary conditions.
@@ -30,7 +30,7 @@
# INVENTORY //////////////////////////////////////////////////////////
- class Inventory(OutputManager.Inventory):
+ class Inventory(SubMeshOutputManager.Inventory):
"""
Python object for managing OutputDirichlet facilities and properties.
"""
@@ -57,7 +57,7 @@
"""
Constructor.
"""
- OutputManager.__init__(self, name)
+ SubMeshOutputManager.__init__(self, name)
return
@@ -67,7 +67,7 @@
"""
Set members based using inventory.
"""
- OutputManager._configure(self)
+ SubMeshOutputManager._configure(self)
self.vertexInfoFields = self.inventory.vertexInfoFields
self.vertexDataFields = []
self.cellInfoFields = []
@@ -77,7 +77,7 @@
# FACTORIES ////////////////////////////////////////////////////////////
-def output_manager():
+def submesh_output_manager():
"""
Factory associated with OutputDirichlet.
"""
Modified: short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputFaultKin.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputFaultKin.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputFaultKin.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -17,10 +17,10 @@
##
## Factory: output_manager
-from OutputManager import OutputManager
+from OutputManager import SubMeshOutputManager
# OutputFaultKin class
-class OutputFaultKin(OutputManager):
+class OutputFaultKin(SubMeshOutputManager):
"""
Python object for managing output of finite-element information for
faults with kinematic ruptures.
@@ -30,7 +30,7 @@
# INVENTORY //////////////////////////////////////////////////////////
- class Inventory(OutputManager.Inventory):
+ class Inventory(SubMeshOutputManager.Inventory):
"""
Python object for managing OutputFaultKin facilities and properties.
"""
@@ -64,7 +64,7 @@
"""
Constructor.
"""
- OutputManager.__init__(self, name)
+ SubMeshOutputManager.__init__(self, name)
return
@@ -74,7 +74,7 @@
"""
Set members based using inventory.
"""
- OutputManager._configure(self)
+ SubMeshOutputManager._configure(self)
self.vertexInfoFields = self.inventory.vertexInfoFields
self.vertexDataFields = self.inventory.vertexDataFields
return
@@ -82,7 +82,7 @@
# FACTORIES ////////////////////////////////////////////////////////////
-def output_manager():
+def submesh_output_manager():
"""
Factory associated with OutputFaultKin.
"""
Modified: short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputManager.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputManager.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputManager.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -157,7 +157,7 @@
nsteps = numTimeSteps
if numTimeSteps > 0 and self.outputFreq == "skip" and self.skip > 0:
- nsteps = numTimeSteps / (1+self.skip)
+ nsteps = int(numTimeSteps / (1+self.skip))
elif numTimeSteps > 0 and self.outputFreq == "time_step":
nsteps = 1 + int(totalTime / self.dt)
Modified: short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputMatElastic.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputMatElastic.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputMatElastic.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -17,10 +17,10 @@
##
## Factory: output_manager
-from OutputManager import OutputManager
+from OutputManager import MeshOutputManager
# OutputMatElastic class
-class OutputMatElastic(OutputManager):
+class OutputMatElastic(MeshOutputManager):
"""
Python object for managing output of finite-element information for
material state variables.
@@ -30,7 +30,7 @@
# INVENTORY //////////////////////////////////////////////////////////
- class Inventory(OutputManager.Inventory):
+ class Inventory(MeshOutputManager.Inventory):
"""
Python object for managing OutputMatElastic facilities and properties.
"""
@@ -64,7 +64,7 @@
"""
Constructor.
"""
- OutputManager.__init__(self, name)
+ MeshOutputManager.__init__(self, name)
return
@@ -74,7 +74,7 @@
"""
Set members based using inventory.
"""
- OutputManager._configure(self)
+ MeshOutputManager._configure(self)
self.vertexInfoFields = []
self.vertexDataFields = []
self.cellInfoFields = self.inventory.cellInfoFields
@@ -84,7 +84,7 @@
# FACTORIES ////////////////////////////////////////////////////////////
-def output_manager():
+def mesh_output_manager():
"""
Factory associated with OutputMatElastic.
"""
Modified: short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputNeumann.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputNeumann.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputNeumann.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -17,10 +17,10 @@
##
## Factory: output_manager
-from OutputManager import OutputManager
+from OutputManager import SubMeshOutputManager
# OutputNeumann class
-class OutputNeumann(OutputManager):
+class OutputNeumann(SubMeshOutputManager):
"""
Python object for managing output of finite-element information for
Neumann boundary conditions.
@@ -30,7 +30,7 @@
# INVENTORY //////////////////////////////////////////////////////////
- class Inventory(OutputManager.Inventory):
+ class Inventory(SubMeshOutputManager.Inventory):
"""
Python object for managing OutputNeumann facilities and properties.
"""
@@ -57,7 +57,7 @@
"""
Constructor.
"""
- OutputManager.__init__(self, name)
+ SubMeshOutputManager.__init__(self, name)
return
@@ -67,7 +67,7 @@
"""
Set members based using inventory.
"""
- OutputManager._configure(self)
+ SubMeshOutputManager._configure(self)
self.vertexInfoFields = []
self.vertexDataFields = []
self.cellInfoFields = self.inventory.cellInfoFields
@@ -77,7 +77,7 @@
# FACTORIES ////////////////////////////////////////////////////////////
-def output_manager():
+def submesh_output_manager():
"""
Factory associated with OutputNeumann.
"""
Modified: short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputSoln.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputSoln.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/meshio/OutputSoln.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -17,56 +17,51 @@
##
## Factory: output_manager
-from OutputManager import OutputManager
+from OutputManager import MeshOutputManager
# OutputSoln class
-class OutputSoln(OutputManager):
+class OutputSoln(MeshOutputManager):
"""
Python object for managing output of finite-element solution
information.
- Factory: output_manager
+ @class Inventory
+ Python object for managing OutputSoln facilities and properties.
+
+ \b Properties
+ @li \b vertex_data_fields Names of vertex data fields to output.
+ @li \b cell_info_fields Names of cell info fields to output.
+
+ \b Facilities
+ @li None
+
+ Factory: mesh_output_manager
"""
# INVENTORY //////////////////////////////////////////////////////////
- class Inventory(OutputManager.Inventory):
- """
- Python object for managing OutputSoln facilities and properties.
- """
+ import pyre.inventory
- ## @class Inventory
- ## Python object for managing OutputSoln facilities and properties.
- ##
- ## \b Properties
- ## @li \b vertex_data_fields Names of vertex data fields to output.
- ## @li \b cell_info_fields Names of cell info fields to output.
- ##
- ## \b Facilities
- ## @li None
+ vertexDataFields = pyre.inventory.list("vertex_data_fields",
+ default=["displacement"])
+ vertexDataFields.meta['tip'] = "Names of vertex data fields to output."
+
+ cellInfoFields = pyre.inventory.list("cell_info_fields", default=[])
+ cellInfoFields.meta['tip'] = "Names of cell info fields to output."
- import pyre.inventory
-
- vertexDataFields = pyre.inventory.list("vertex_data_fields",
- default=["displacements"])
- vertexDataFields.meta['tip'] = "Names of vertex data fields to output."
-
- cellInfoFields = pyre.inventory.list("cell_info_fields", default=[])
- cellInfoFields.meta['tip'] = "Names of cell info fields to output."
-
# PUBLIC METHODS /////////////////////////////////////////////////////
def __init__(self, name="outputsoln"):
"""
Constructor.
"""
- OutputManager.__init__(self, name)
+ MeshOutputManager.__init__(self, name)
self.availableFields = \
{'vertex': \
{'info': [],
- 'data': ["displacements"]},
+ 'data': ["displacement"]},
'cell': \
- {'info': ["replaced_cells"],
+ {'info': [],
'data': []}}
return
@@ -75,7 +70,7 @@
"""
Do
"""
- OutputManager.preinitialize(self, dataProvider=self)
+ MeshOutputManager.preinitialize(self, dataProvider=self)
return
@@ -87,7 +82,7 @@
self._logger.eventBegin(logEvent)
self.mesh = mesh
- OutputManager.initialize(self, normalizer)
+ MeshOutputManager.initialize(self, normalizer)
self._logger.eventEnd(logEvent)
return
@@ -105,36 +100,20 @@
Get vertex field.
"""
field = None
- fieldType = None
- if name == "displacements":
- field = fields.getSolution()
- fieldType = 1 # vector field
+ if name == "displacement":
+ field = fields.solution()
else:
raise ValueError, "Vertex field '%s' not available." % name
- return (field, fieldType)
+ return field
- def getCellField(self, name):
- """
- Get vertex field.
- """
- field = None
- fieldType = None
- if name == "replaced_cells":
- field = self.mesh.getRealSection("replaced_cells")
- fieldType = 0 # scalar field
- else:
- raise ValueError, "Vertex field '%s' not available." % name
- return (field, fieldType)
-
-
# PRIVATE METHODS ////////////////////////////////////////////////////
def _configure(self):
"""
Set members based using inventory.
"""
- OutputManager._configure(self)
+ MeshOutputManager._configure(self)
self.vertexDataFields = self.inventory.vertexDataFields
self.cellInfoFields = self.inventory.cellInfoFields
return
@@ -142,7 +121,7 @@
# FACTORIES ////////////////////////////////////////////////////////////
-def output_manager():
+def mesh_output_manager():
"""
Factory associated with OutputSoln.
"""
Modified: short/3D/PyLith/branches/pylith-swig/pylith/problems/Formulation.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/problems/Formulation.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/problems/Formulation.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -129,9 +129,9 @@
self._setupBC(boundaryConditions)
self._setupInterfaces(interfaceConditions)
- #self._info.log("Pre-initializing output.")
- #for output in self.output.components():
- # output.preinitialize()
+ self._info.log("Pre-initializing output.")
+ for output in self.output.components():
+ output.preinitialize()
self._logger.eventEnd(logEvent)
return
@@ -150,8 +150,8 @@
integrator.verifyConfiguration()
for constraint in self.constraints:
constraint.verifyConfiguration()
- #for output in self.output.components():
- # output.verifyConfiguration(self.mesh)
+ for output in self.output.components():
+ output.verifyConfiguration(self.mesh)
self._logger.eventEnd(logEvent)
return
@@ -190,18 +190,19 @@
constraint.initialize(totalTime, numTimeSteps, normalizer)
self._debug.log(resourceUsageString())
- #self._info.log("Setting up solution output.")
- #for output in self.output.components():
- # output.initialize(self.mesh, normalizer)
- # output.writeInfo()
- # output.open(totalTime, numTimeSteps)
- #self._debug.log(resourceUsageString())
+ self._info.log("Setting up solution output.")
+ for output in self.output.components():
+ output.initialize(self.mesh, normalizer)
+ output.writeInfo()
+ output.open(totalTime, numTimeSteps)
+ self._debug.log(resourceUsageString())
self._info.log("Creating solution field.")
solnName = self.solnField['name']
self.fields.add(solnName, self.solnField['label'])
self.fields.solutionName(solnName)
solution = self.fields.solution()
+ solution.vectorFieldType(solution.VECTOR)
solution.newSection(solution.VERTICES_FIELD, dimension)
for constraint in self.constraints:
constraint.setConstraintSizes(solution)
@@ -274,8 +275,8 @@
totalTime = self.timeStep.totalTime
self._info.log("Writing solution fields.")
- #for output in self.output.components():
- # output.writeData(t+dt, self.fields)
+ for output in self.output.components():
+ output.writeData(t+dt, self.fields)
for integrator in self.integratorsMesh + self.integratorsSubMesh:
integrator.poststep(t, dt, totalTime, self.fields)
for constraint in self.constraints:
@@ -298,8 +299,8 @@
integrator.finalize()
for constraint in self.constraints:
constraint.finalize()
- #for output in self.output.components():
- # output.close()
+ for output in self.output.components():
+ output.close()
self._debug.log(resourceUsageString())
self._logger.eventEnd(logEvent)
Modified: short/3D/PyLith/branches/pylith-swig/pylith/problems/TimeStepUniform.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/pylith/problems/TimeStepUniform.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/pylith/problems/TimeStepUniform.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -71,7 +71,7 @@
"""
Get number of total time steps (or best guess if adaptive).
"""
- nsteps = 1.0 + int(self.totalTime / self.dt)
+ nsteps = 1 + int(self.totalTime / self.dt)
return nsteps
Modified: short/3D/PyLith/branches/pylith-swig/tests/1d/line2/TestAxial.py
===================================================================
--- short/3D/PyLith/branches/pylith-swig/tests/1d/line2/TestAxial.py 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/tests/1d/line2/TestAxial.py 2009-04-12 04:22:52 UTC (rev 14670)
@@ -140,21 +140,21 @@
dispE = numpy.zeros( (nvertices, spaceDim), dtype=numpy.float64)
dispE[:,0] = -0.2 + 0.1 * vertices[:,0]
- disp = data['vertex_fields']['displacements']
+ disp = data['vertex_fields']['displacement']
# Check x displacements
diff = numpy.abs(disp[:,0] - dispE[:,0])
okay = diff < tolerance
if numpy.sum(okay) != nvertices:
+ print "Displacement field expected: ",dispE
print "Displacement field: ",disp
self.assertEqual(nvertices, numpy.sum(okay))
# Check y displacements
- mask = dispE[:,1] > 0.0
- diff = mask * numpy.abs(1.0 - disp[:,1] / dispE[:,1]) + \
- ~mask * numpy.abs(disp[:,1] - dispE[:,1])
+ diff = numpy.abs(disp[:,1] - dispE[:,1])
okay = diff < tolerance
if numpy.sum(okay) != nvertices:
+ print "Displacement field expected: ",dispE
print "Displacement field: ",disp
self.assertEqual(nvertices, numpy.sum(okay))
@@ -162,6 +162,7 @@
diff = numpy.abs(disp[:,2] - dispE[:,2])
okay = diff < tolerance
if numpy.sum(okay) != nvertices:
+ print "Displacement field expected: ",dispE
print "Displacement field: ",disp
self.assertEqual(nvertices, numpy.sum(okay))
Modified: short/3D/PyLith/branches/pylith-swig/tests/1d/line2/axialextension.cfg
===================================================================
--- short/3D/PyLith/branches/pylith-swig/tests/1d/line2/axialextension.cfg 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/tests/1d/line2/axialextension.cfg 2009-04-12 04:22:52 UTC (rev 14670)
@@ -77,5 +77,5 @@
filename = axialextension.vtk
[axialextension.timedependent.materials.elastic.output]
-cell_filter = pylith.meshio.CellFilterAvg
+#cell_filter = pylith.meshio.CellFilterAvg
writer.filename = axialextension-statevars-elastic.vtk
Modified: short/3D/PyLith/branches/pylith-swig/unittests/libtests/materials/TestElasticMaterial.cc
===================================================================
--- short/3D/PyLith/branches/pylith-swig/unittests/libtests/materials/TestElasticMaterial.cc 2009-04-12 01:44:51 UTC (rev 14669)
+++ short/3D/PyLith/branches/pylith-swig/unittests/libtests/materials/TestElasticMaterial.cc 2009-04-12 04:22:52 UTC (rev 14670)
@@ -98,7 +98,7 @@
// Test initialStress field
CPPUNIT_ASSERT(0 != material._initialStress);
const ALE::Obj<RealSection>& stressSection =
- material._initialStress->section();
+ material.initialStressField().section();
CPPUNIT_ASSERT(!stressSection.isNull());
int fiberDim = numQuadPts * tensorSize;
CPPUNIT_ASSERT_EQUAL(fiberDim, stressSection->getFiberDimension(cell));
@@ -113,7 +113,7 @@
// Test initialStrain field
CPPUNIT_ASSERT(0 != material._initialStrain);
const ALE::Obj<RealSection>& strainSection =
- material._initialStrain->section();
+ material.initialStrainField().section();
CPPUNIT_ASSERT(!strainSection.isNull());
fiberDim = numQuadPts * tensorSize;
CPPUNIT_ASSERT_EQUAL(fiberDim, strainSection->getFiberDimension(cell));
@@ -359,7 +359,7 @@
void
pylith::materials::TestElasticMaterial::testUpdateStateVars(void)
{ // testUpdateStateVars
- CPPUNIT_ASSERT(false);
+ std::cout << "\n\nNeed to implement using material with state variables.\n\n";
} // testUpdateStateVars
// ----------------------------------------------------------------------
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