[cig-commits] [commit] knepley/fix-parallel-mult-faults, knepley/upgrade-petsc-interface, master, next: Fixed bug in setting up fields for output of stable time step. (e5caf46)

[cig_noreply at geodynamics.org]

Repository : ssh://geoshell/pylith

On branches: knepley/fix-parallel-mult-faults,knepley/upgrade-petsc-interface,master,next
Link       : https://github.com/geodynamics/pylith/compare/a213c3005450d915f40c7137ff7d8dbbb439d334...1b3d6d3bc246edc4235d0051142d675d91e9be41

>---------------------------------------------------------------

commit e5caf46cc8abc00af300b37262268ee7510dd8c0
Author: Brad Aagaard <baagaard at usgs.gov>
Date:   Thu Mar 27 21:40:59 2014 -0700

    Fixed bug in setting up fields for output of stable time step.
    
    Visitor requires that the section be setup. Reorganize to prevent segfault or assertion.


>---------------------------------------------------------------

e5caf46cc8abc00af300b37262268ee7510dd8c0
 examples/bar_shearwave/tri3/pylithapp.cfg  |  2 +-
 libsrc/pylith/materials/ElasticMaterial.cc | 25 ++++++++++++++-----------
 tests_auto/2d/tri3/axialdisp.cfg           |  1 +
 tests_auto/2d/tri3/sheardisp.cfg           |  1 +
 4 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/examples/bar_shearwave/tri3/pylithapp.cfg b/examples/bar_shearwave/tri3/pylithapp.cfg
index 38e3c61..1287128 100644
--- a/examples/bar_shearwave/tri3/pylithapp.cfg
+++ b/examples/bar_shearwave/tri3/pylithapp.cfg
@@ -224,7 +224,7 @@ writer.time_format = %05.2f
 
 # Give basename for VTK output of state variables.
 [pylithapp.timedependent.materials.elastic.output]
-cell_info_fields = [mu,lambda,density,stable_dt_explicit]
+cell_info_fields = [stable_dt_explicit,mu,lambda,density]
 skip = 29
 writer.filename = output/shearwave-statevars.vtk
 writer.time_format = %05.2f
diff --git a/libsrc/pylith/materials/ElasticMaterial.cc b/libsrc/pylith/materials/ElasticMaterial.cc
index cfe08f1..b25f7af 100644
--- a/libsrc/pylith/materials/ElasticMaterial.cc
+++ b/libsrc/pylith/materials/ElasticMaterial.cc
@@ -292,18 +292,18 @@ pylith::materials::ElasticMaterial::stableTimeStepImplicit(const topology::Mesh&
   const PetscInt numCells = _materialIS->size();
  
   // Setup field if necessary.
-  topology::VecVisitorMesh* fieldVisitor = (field) ? new topology::VecVisitorMesh(*field) : 0;
+  topology::VecVisitorMesh* fieldVisitor = NULL;
   PetscScalar* fieldArray = NULL;
   if (field) {
-    assert(fieldVisitor);
     const int fiberDim = 1*numQuadPts;
     bool useCurrentField = false;
-    if (fieldVisitor->petscSection()) {
+    if (field->hasSection()) {
       // check fiber dimension
       int fiberDimCurrentLocal = 0;
       int fiberDimCurrent = 0;
       if (numCells > 0) {
-	fiberDimCurrentLocal = fieldVisitor->sectionDof(cells[0]);
+	topology::VecVisitorMesh fieldVisitor(*field);
+	fiberDimCurrentLocal = fieldVisitor.sectionDof(cells[0]);
       } // if
       MPI_Allreduce((void *) &fiberDimCurrentLocal, 
 		    (void *) &fiberDimCurrent, 1, 
@@ -320,6 +320,7 @@ pylith::materials::ElasticMaterial::stableTimeStepImplicit(const topology::Mesh&
     assert(_normalizer);
     field->scale(_normalizer->timeScale());
     field->vectorFieldType(topology::FieldBase::MULTI_SCALAR);
+    fieldVisitor = new topology::VecVisitorMesh(*field);assert(fieldVisitor);
     fieldArray = fieldVisitor->localArray();
   } // if
 
@@ -383,17 +384,17 @@ pylith::materials::ElasticMaterial::stableTimeStepExplicit(const topology::Mesh&
   const PetscInt numCells = _materialIS->size();
 
   // Setup field if necessary.
-  topology::VecVisitorMesh* fieldVisitor = (field) ? new topology::VecVisitorMesh(*field) : 0;
+  topology::VecVisitorMesh* fieldVisitor = NULL;
   PetscScalar *fieldArray = NULL;
   if (field) {
-    assert(fieldVisitor);
     const int fiberDim = 1*numQuadPts;
     bool useCurrentField = false;
-    if (fieldVisitor->petscSection()) {
+    if (field->hasSection()) {
       // check fiber dimension
       PetscInt fiberDimCurrentLocal = 0;
       if (numCells > 0) {
-	fiberDimCurrentLocal = fieldVisitor->sectionDof(cells[0]);
+	topology::VecVisitorMesh fieldVisitor(*field);
+	fiberDimCurrentLocal = fieldVisitor.sectionDof(cells[0]);
       } // if
       PetscInt fiberDimCurrent = 0;
       MPI_Allreduce(&fiberDimCurrentLocal, &fiberDimCurrent, 1, MPIU_INT, MPI_MAX, field->mesh().comm());
@@ -408,6 +409,7 @@ pylith::materials::ElasticMaterial::stableTimeStepExplicit(const topology::Mesh&
     assert(_normalizer);
     field->scale(_normalizer->timeScale());
     field->vectorFieldType(topology::FieldBase::MULTI_SCALAR);
+    fieldVisitor = new topology::VecVisitorMesh(*field);assert(fieldVisitor);
     fieldArray = fieldVisitor->localArray();
   } // if
 
@@ -474,17 +476,17 @@ pylith::materials::ElasticMaterial::_stableTimeStepImplicitMax(const topology::M
     PetscDM dmMesh = mesh.dmMesh();assert(dmMesh);
 
     assert(_materialIS);
-    const PetscInt *cells = _materialIS->points();
+    const PetscInt* cells = _materialIS->points();
     const PetscInt numCells = _materialIS->size();
     
     // Setup field if necessary.
-    topology::VecVisitorMesh fieldVisitor(*field);
     const int fiberDim = 1*numQuadPts;
     bool useCurrentField = false;
-    if (fieldVisitor.petscSection()) {
+    if (field->hasSection()) {
       // check fiber dimension
       PetscInt fiberDimCurrentLocal = 0;
       if (numCells > 0) {
+	topology::VecVisitorMesh fieldVisitor(*field);
 	fiberDimCurrentLocal = fieldVisitor.sectionDof(cells[0]);
       } // if
       PetscInt fiberDimCurrent = 0;
@@ -500,6 +502,7 @@ pylith::materials::ElasticMaterial::_stableTimeStepImplicitMax(const topology::M
     assert(_normalizer);
     field->scale(_normalizer->timeScale());
     field->vectorFieldType(topology::FieldBase::MULTI_SCALAR);
+    topology::VecVisitorMesh fieldVisitor(*field);
     PetscScalar* fieldArray = fieldVisitor.localArray();
 
     scalar_array dtStableCell(numQuadPts);
diff --git a/tests_auto/2d/tri3/axialdisp.cfg b/tests_auto/2d/tri3/axialdisp.cfg
index c9fcb93..9e57435 100644
--- a/tests_auto/2d/tri3/axialdisp.cfg
+++ b/tests_auto/2d/tri3/axialdisp.cfg
@@ -106,6 +106,7 @@ writer = pylith.meshio.DataWriterHDF5
 writer.filename = axialdisp.h5
 
 [axialdisp.timedependent.materials.elastic.output]
+cell_info_fields = [stable_dt_implicit,mu,lambda,density]
 cell_filter = pylith.meshio.CellFilterAvg
 writer = pylith.meshio.DataWriterHDF5
 writer.filename = axialdisp-elastic.h5
diff --git a/tests_auto/2d/tri3/sheardisp.cfg b/tests_auto/2d/tri3/sheardisp.cfg
index 68310ea..b3bf3b7 100644
--- a/tests_auto/2d/tri3/sheardisp.cfg
+++ b/tests_auto/2d/tri3/sheardisp.cfg
@@ -116,6 +116,7 @@ writer = pylith.meshio.DataWriterHDF5
 writer.filename = sheardisp.h5
 
 [sheardisp.timedependent.materials.elastic.output]
+cell_info_fields = [stable_dt_explicit,mu,lambda,density]
 cell_filter = pylith.meshio.CellFilterAvg
 writer = pylith.meshio.DataWriterHDF5
 writer.filename = sheardisp-elastic.h5