[cig-commits] r21357 - short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults
rjolivet at geodynamics.org
rjolivet at geodynamics.org
Mon Feb 11 13:51:54 PST 2013
Author: rjolivet
Date: 2013-02-11 13:51:53 -0800 (Mon, 11 Feb 2013)
New Revision: 21357
Added:
short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/DKSelector.cc
short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/DKSelector.hh
Removed:
short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/dkSelector.cc
short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/dkSelector.hh
Log:
dkSelector is now DKSelector
Added: short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/DKSelector.cc
===================================================================
--- short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/DKSelector.cc (rev 0)
+++ short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/DKSelector.cc 2013-02-11 21:51:53 UTC (rev 21357)
@@ -0,0 +1,185 @@
+// -*- C++ -*-
+//
+// ----------------------------------------------------------------------
+//
+// Brad T. Aagaard, U.S. Geological Survey
+// Charles A. Williams, GNS Science
+// Matthew G. Knepley, University of Chicago
+// Romain Jolivet, Caltech
+//
+// This code was developed as part of the Computational Infrastructure
+// for Geodynamics (http://geodynamics.org).
+//
+// Copyright (c) 2010-2012 University of California, Davis
+//
+// See COPYING for license information.
+//
+// ----------------------------------------------------------------------
+//
+
+#include <portinfo>
+
+#include "DKSelector.hh" // implementation of object methods
+
+#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Fields.hh" // USES Fields
+#include "pylith/topology/Field.hh" // USES Field
+
+#include "spatialdata/spatialdb/SpatialDB.hh" // USES SpatialDB
+#include "spatialdata/geocoords/CoordSys.hh" // USES CoordSys
+#include "spatialdata/units/Nondimensional.hh" // USES Nondimensional
+
+#include <cassert> // USES assert()
+#include <sstream> // USES std::ostringstream
+#include <stdexcept> // USES std::runtime_error
+
+// ----------------------------------------------------------------------
+typedef pylith::topology::SubMesh::SieveMesh SieveMesh;
+typedef pylith::topology::SubMesh::SieveMesh::label_sequence label_sequence;
+typedef pylith::topology::SubMesh::RealSection RealSection;
+typedef pylith::topology::SubMesh::RealUniformSection RealUniformSection;
+
+// ----------------------------------------------------------------------
+// Default constructor.
+pylith::faults::DKSelector::DKSelector(void) :
+ _dbdksel(0)
+{ // constructor
+} // constructor
+
+// ----------------------------------------------------------------------
+// Destructor.
+pylith::faults::DKSelector::~DKSelector(void)
+{ // destructor
+ deallocate();
+} // destructor
+
+// ----------------------------------------------------------------------
+// Deallocate PETSc and local data structures.
+void
+pylith::faults::DKSelector::deallocate(void)
+{ // deallocate
+ _dbdksel = 0;
+} // deallocate
+
+// ----------------------------------------------------------------------
+// Initialize dkselector
+void
+pylith::faults::DKSelector::initialize(
+ const topology::SubMesh& faultMesh,
+ const spatialdata::units::Nondimensional& normalizer)
+{ // initialize
+ assert(0 != _dbdksel);
+
+ // Get the spatial coordinate and the dimension of the problem
+ const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();
+ assert(0 != cs);
+ const int spaceDim = cs->spaceDim();
+
+ // Get the normalizing values
+ const PylithScalar lengthScale = normalizer.lengthScale();
+
+ // Get vertices in fault mesh
+ const ALE::Obj<SieveMesh>& sieveMesh = faultMesh.sieveMesh();
+ assert(!sieveMesh.isNull());
+ const ALE::Obj<label_sequence>& vertices = sieveMesh->depthStratum(0);
+ assert(!vertices.isNull());
+ const label_sequence::iterator verticesBegin = vertices->begin();
+ const label_sequence::iterator verticesEnd = vertices->end();
+
+ ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
+ logger.stagePush("Fault");
+
+ // Use parameter to go fetch into the spatial data (DKSel is a par array between 0 and 1; >0.5 is kinematic, <=0.5 is dynamic)
+ delete _parameters;
+ _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
+ _parameters->add("Dynamic Kinematic Selector","dynamic_kinematic_selector");
+ topology::Field<topology::SubMesh>& DKSel = _parameters->get("Dynamic Kinematic Selector");
+ DKSel.newSection(vertices, spaceDim);
+ DKSel.allocate();
+ DKSel.vectorFieldType(topology::FieldBase::VECTOR);
+ const ALE::Obj<RealSection>& DKSelSection = DKSel.section();
+ assert(!DKSelSection.isNull());
+
+ logger.stagePop();
+
+ // Open databases and set query values
+ _dbdksel->open();
+ const char* dkselValues[] = {"dynamic-kinematic"};
+ _dbdksel->queryVals(dkselValues, 1);
+
+ // Get coordinates of vertices
+ const ALE::Obj<RealSection>& coordinates =
+ sieveMesh->getRealSection("coordinates");
+ assert(!coordinates.isNull());
+
+ _dkselVertex.resize(spaceDim);
+ scalar_array vCoordsGlobal(spaceDim);
+ for (label_sequence::iterator v_iter=verticesBegin;
+ v_iter != verticesEnd;
+ ++v_iter) {
+ coordinates->restrictPoint(*v_iter,
+ &vCoordsGlobal[0], vCoordsGlobal.size());
+ normalizer.dimensionalize(&vCoordsGlobal[0], vCoordsGlobal.size(),
+ lengthScale);
+
+ int err = _dbdksel->query(&_dkselVertex[0], _dkselVertex.size(),
+ &vCoordsGlobal[0], vCoordsGlobal.size(), cs);
+ if (err) {
+ std::ostringstream msg;
+ msg << "Could not find DK Selector at (";
+ for (int i=0; i < spaceDim; ++i)
+ msg << " " << vCoordsGlobal[i];
+ msg << ") using spatial database " << _dbdksel->label() << ".";
+ throw std::runtime_error(msg.str());
+ } // if
+
+ DKSelSection->updatePoint(*v_iter, &_dkselVertex[0]);
+ } // for
+
+ // Close databases
+ _dbdksel->close();
+} // initialize
+
+// ----------------------------------------------------------------------
+// Get dynamic kinematic selector field on fault surface (time will be the argument in the future)
+void
+pylith::faults::DKSelector::dk(const topology::Field<topology::SubMesh>* dk)
+{ // dk
+ assert(0 != _parameters);
+
+ // Get fault mesh
+ const ALE::Obj<SieveMesh>& sieveMesh = dk->mesh().sieveMesh();
+ assert(!sieveMesh.isNull());
+ const ALE::Obj<label_sequence>& vertices = sieveMesh->depthStratum(0);
+ assert(!vertices.isNull());
+ const label_sequence::iterator verticesBegin = vertices->begin();
+ const label_sequence::iterator verticesEnd = vertices->end();
+
+ // Build the section
+ const topology::Field<topology::SubMesh>& DKSel = _parameters->get("Dynamic Kinematic Selector");
+ const ALE::Obj<RealSection>& DKSelSection = DKSel.section();
+ assert(!DKSelSection.isNull());
+ const ALE::Obj<RealSection>& dkSection = dk->section();
+
+ // Iterate over vertices
+ for (label_sequence::iterator v_iter=verticesBegin;
+ v_iter != verticesEnd;
+ ++v_iter) {
+
+ // take the good vertex in DKSelSection, put it in _dkselvv
+ DKSelSection->restrictPoint(*v_iter, &_dkselvv,1);
+ // if _dkselvv is under 0.5, the vertex is kinematically controled (put the time condition here)
+ if ( _dkselvv< 0.5 ){
+ _dkselvv = 0.0;
+ } else {
+ _dkselvv = 1.0;
+ }
+ // Put that thing in dkSection
+ dkSection->updatePoint(*v_iter, &_dkselvv);
+
+ } // for
+
+ PetscLogFlops(vertices->size());
+} // dk
+
+// End of file
Added: short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/DKSelector.hh
===================================================================
--- short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/DKSelector.hh (rev 0)
+++ short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/DKSelector.hh 2013-02-11 21:51:53 UTC (rev 21357)
@@ -0,0 +1,111 @@
+// -*- C++ -*-
+//
+// ----------------------------------------------------------------------
+//
+// Brad T. Aagaard, U.S. Geological Survey
+// Charles A. Williams, GNS Science
+// Matthew G. Knepley, University of Chicago
+//
+// This code was developed as part of the Computational Infrastructure
+// for Geodynamics (http://geodynamics.org).
+//
+// Copyright (c) 2010-2012 University of California, Davis
+//
+// See COPYING for license information.
+//
+// ----------------------------------------------------------------------
+//
+
+/** @file libsrc/faults/DKSelector.hh
+ *
+ * @brief C++ implementation of the dynamic kinematic selector
+ */
+
+#if !defined(pylith_faults_dkselector_hh)
+#define pylith_faults_dkselector_hh
+
+// Include directives ---------------------------------------------------
+#include "faultsfwd.hh" // forward declaration
+
+
+#include "pylith/topology/topologyfwd.hh" // USES Fields<Field<SubMesh> >
+#include "spatialdata/spatialdb/spatialdbfwd.hh" // USES SpatialDB
+#include "spatialdata/units/unitsfwd.hh" // USES Nondimensional
+
+#include "pylith/topology/SubMesh.hh" // USES Mesh
+
+#include "pylith/utils/array.hh" // HASA scalar_array
+
+// DKSelector -----------------------------------------------------------
+/** @brief Dynamic-Kinematic Selector
+ *
+ * If value is over .5 the fault vertex has its slip value controlled by EQsrc
+ *
+ */
+
+// ----------------------------------------------------------------------
+typedef pylith::topology::SubMesh::RealUniformSection RealUniformSection;
+
+// ----------------------------------------------------------------------
+class pylith::faults::DKSelector
+{ // class DKSelector
+
+// PUBLIC METHODS ///////////////////////////////////////////////////////
+public :
+
+ /// Default constructor.
+ DKSelector(void);
+
+ /// Destructor.
+ ~DKSelector(void);
+
+ /// Deallocate PETSc and local data structures.
+ virtual
+ void deallocate(void);
+
+ /** Set spatial database for dkselector
+ *
+ * @param db dksel
+ */
+ void dbdksel(spatialdata::spatialdb::SpatialDB* const db);
+
+ /** Initialize dkselector
+ *
+ * @param faultMesh Finite-element mesh of fault.
+ * @param normalizer Nondimensionalization of scales.
+ */
+ void initialize(const topology::SubMesh& faultMesh,
+ const spatialdata::units::Nondimensional& normalizer);
+
+ /** Get dk on fault surface (time will be implemented through this guy)
+ *
+ * @params faultMesh Finite-element mesh of fault.
+ *
+ * @returns a section for the given time (future)
+ */
+ void dk(const topology::Field<topology::SubMesh>* dk);
+
+// NOT IMPLEMENTED //////////////////////////////////////////////////////
+private :
+
+ DKSelector(const DKSelector&); ///< Not implemented
+ const DKSelector& operator=(const DKSelector&); ///< Not implemented
+
+// PRIVATE MEMBERS //////////////////////////////////////////////////////
+private :
+
+ scalar_array _dkselVertex; ///< dk sel at vertex.
+ PylithScalar _dkselvv; ///< used to check
+
+ /// Spatial database for dk selector.
+ spatialdata::spatialdb::SpatialDB* _dbdksel;
+
+ /// Parameters for perturbations.
+ topology::Fields<topology::Field<topology::SubMesh> >* _parameters;
+
+}; // class DKSelector
+
+#endif // pylith_faults_dkselector_hh
+
+
+// End of file
Deleted: short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/dkSelector.cc
===================================================================
--- short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/dkSelector.cc 2013-02-11 21:44:49 UTC (rev 21356)
+++ short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/dkSelector.cc 2013-02-11 21:51:53 UTC (rev 21357)
@@ -1,185 +0,0 @@
-// -*- C++ -*-
-//
-// ----------------------------------------------------------------------
-//
-// Brad T. Aagaard, U.S. Geological Survey
-// Charles A. Williams, GNS Science
-// Matthew G. Knepley, University of Chicago
-// Romain Jolivet, Caltech
-//
-// This code was developed as part of the Computational Infrastructure
-// for Geodynamics (http://geodynamics.org).
-//
-// Copyright (c) 2010-2012 University of California, Davis
-//
-// See COPYING for license information.
-//
-// ----------------------------------------------------------------------
-//
-
-#include <portinfo>
-
-#include "DKSelector.hh" // implementation of object methods
-
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
-#include "pylith/topology/Fields.hh" // USES Fields
-#include "pylith/topology/Field.hh" // USES Field
-
-#include "spatialdata/spatialdb/SpatialDB.hh" // USES SpatialDB
-#include "spatialdata/geocoords/CoordSys.hh" // USES CoordSys
-#include "spatialdata/units/Nondimensional.hh" // USES Nondimensional
-
-#include <cassert> // USES assert()
-#include <sstream> // USES std::ostringstream
-#include <stdexcept> // USES std::runtime_error
-
-// ----------------------------------------------------------------------
-typedef pylith::topology::SubMesh::SieveMesh SieveMesh;
-typedef pylith::topology::SubMesh::SieveMesh::label_sequence label_sequence;
-typedef pylith::topology::SubMesh::RealSection RealSection;
-typedef pylith::topology::SubMesh::RealUniformSection RealUniformSection;
-
-// ----------------------------------------------------------------------
-// Default constructor.
-pylith::faults::DKSelector::DKSelector(void) :
- _dbdksel(0)
-{ // constructor
-} // constructor
-
-// ----------------------------------------------------------------------
-// Destructor.
-pylith::faults::DKSelector::~DKSelector(void)
-{ // destructor
- deallocate();
-} // destructor
-
-// ----------------------------------------------------------------------
-// Deallocate PETSc and local data structures.
-void
-pylith::faults::DKSelector::deallocate(void)
-{ // deallocate
- _dbdksel = 0;
-} // deallocate
-
-// ----------------------------------------------------------------------
-// Initialize dkselector
-void
-pylith::faults::DKSelector::initialize(
- const topology::SubMesh& faultMesh,
- const spatialdata::units::Nondimensional& normalizer)
-{ // initialize
- assert(0 != _dbdksel);
-
- // Get the spatial coordinate and the dimension of the problem
- const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();
- assert(0 != cs);
- const int spaceDim = cs->spaceDim();
-
- // Get the normalizing values
- const PylithScalar lengthScale = normalizer.lengthScale();
-
- // Get vertices in fault mesh
- const ALE::Obj<SieveMesh>& sieveMesh = faultMesh.sieveMesh();
- assert(!sieveMesh.isNull());
- const ALE::Obj<label_sequence>& vertices = sieveMesh->depthStratum(0);
- assert(!vertices.isNull());
- const label_sequence::iterator verticesBegin = vertices->begin();
- const label_sequence::iterator verticesEnd = vertices->end();
-
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("Fault");
-
- // Use parameter to go fetch into the spatial data (DKSel is a par array between 0 and 1; >0.5 is kinematic, <=0.5 is dynamic)
- delete _parameters;
- _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
- _parameters->add("Dynamic Kinematic Selector","dynamic_kinematic_selector");
- topology::Field<topology::SubMesh>& DKSel = _parameters->get("Dynamic Kinematic Selector");
- DKSel.newSection(vertices, spaceDim);
- DKSel.allocate();
- DKSel.vectorFieldType(topology::FieldBase::VECTOR);
- const ALE::Obj<RealSection>& DKSelSection = DKSel.section();
- assert(!DKSelSection.isNull());
-
- logger.stagePop();
-
- // Open databases and set query values
- _dbdksel->open();
- const char* dkselValues[] = {"dynamic-kinematic"};
- _dbdksel->queryVals(dkselValues, 1);
-
- // Get coordinates of vertices
- const ALE::Obj<RealSection>& coordinates =
- sieveMesh->getRealSection("coordinates");
- assert(!coordinates.isNull());
-
- _dkselVertex.resize(spaceDim);
- scalar_array vCoordsGlobal(spaceDim);
- for (label_sequence::iterator v_iter=verticesBegin;
- v_iter != verticesEnd;
- ++v_iter) {
- coordinates->restrictPoint(*v_iter,
- &vCoordsGlobal[0], vCoordsGlobal.size());
- normalizer.dimensionalize(&vCoordsGlobal[0], vCoordsGlobal.size(),
- lengthScale);
-
- int err = _dbdksel->query(&_dkselVertex[0], _dkselVertex.size(),
- &vCoordsGlobal[0], vCoordsGlobal.size(), cs);
- if (err) {
- std::ostringstream msg;
- msg << "Could not find DK Selector at (";
- for (int i=0; i < spaceDim; ++i)
- msg << " " << vCoordsGlobal[i];
- msg << ") using spatial database " << _dbdksel->label() << ".";
- throw std::runtime_error(msg.str());
- } // if
-
- DKSelSection->updatePoint(*v_iter, &_dkselVertex[0]);
- } // for
-
- // Close databases
- _dbdksel->close();
-} // initialize
-
-// ----------------------------------------------------------------------
-// Get dynamic kinematic selector field on fault surface (time will be the argument in the future)
-void
-pylith::faults::DKSelector::dk(const topology::Field<topology::SubMesh>* dk)
-{ // dk
- assert(0 != _parameters);
-
- // Get fault mesh
- const ALE::Obj<SieveMesh>& sieveMesh = dk->mesh().sieveMesh();
- assert(!sieveMesh.isNull());
- const ALE::Obj<label_sequence>& vertices = sieveMesh->depthStratum(0);
- assert(!vertices.isNull());
- const label_sequence::iterator verticesBegin = vertices->begin();
- const label_sequence::iterator verticesEnd = vertices->end();
-
- // Build the section
- const topology::Field<topology::SubMesh>& DKSel = _parameters->get("Dynamic Kinematic Selector");
- const ALE::Obj<RealSection>& DKSelSection = DKSel.section();
- assert(!DKSelSection.isNull());
- const ALE::Obj<RealSection>& dkSection = dk->section();
-
- // Iterate over vertices
- for (label_sequence::iterator v_iter=verticesBegin;
- v_iter != verticesEnd;
- ++v_iter) {
-
- // take the good vertex in DKSelSection, put it in _dkselvv
- DKSelSection->restrictPoint(*v_iter, &_dkselvv,1);
- // if _dkselvv is under 0.5, the vertex is kinematically controled (put the time condition here)
- if ( _dkselvv< 0.5 ){
- _dkselvv = 0.0;
- } else {
- _dkselvv = 1.0;
- }
- // Put that thing in dkSection
- dkSection->updatePoint(*v_iter, &_dkselvv);
-
- } // for
-
- PetscLogFlops(vertices->size());
-} // dk
-
-// End of file
Deleted: short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/dkSelector.hh
===================================================================
--- short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/dkSelector.hh 2013-02-11 21:44:49 UTC (rev 21356)
+++ short/3D/PyLith/branches/v1.8-mixedfault/libsrc/pylith/faults/dkSelector.hh 2013-02-11 21:51:53 UTC (rev 21357)
@@ -1,111 +0,0 @@
-// -*- C++ -*-
-//
-// ----------------------------------------------------------------------
-//
-// Brad T. Aagaard, U.S. Geological Survey
-// Charles A. Williams, GNS Science
-// Matthew G. Knepley, University of Chicago
-//
-// This code was developed as part of the Computational Infrastructure
-// for Geodynamics (http://geodynamics.org).
-//
-// Copyright (c) 2010-2012 University of California, Davis
-//
-// See COPYING for license information.
-//
-// ----------------------------------------------------------------------
-//
-
-/** @file libsrc/faults/DKSelector.hh
- *
- * @brief C++ implementation of the dynamic kinematic selector
- */
-
-#if !defined(pylith_faults_dkselector_hh)
-#define pylith_faults_dkselector_hh
-
-// Include directives ---------------------------------------------------
-#include "faultsfwd.hh" // forward declaration
-
-
-#include "pylith/topology/topologyfwd.hh" // USES Fields<Field<SubMesh> >
-#include "spatialdata/spatialdb/spatialdbfwd.hh" // USES SpatialDB
-#include "spatialdata/units/unitsfwd.hh" // USES Nondimensional
-
-#include "pylith/topology/SubMesh.hh" // USES Mesh
-
-#include "pylith/utils/array.hh" // HASA scalar_array
-
-// DKSelector -----------------------------------------------------------
-/** @brief Dynamic-Kinematic Selector
- *
- * If value is over .5 the fault vertex has its slip value controlled by EQsrc
- *
- */
-
-// ----------------------------------------------------------------------
-typedef pylith::topology::SubMesh::RealUniformSection RealUniformSection;
-
-// ----------------------------------------------------------------------
-class pylith::faults::DKSelector
-{ // class DKSelector
-
-// PUBLIC METHODS ///////////////////////////////////////////////////////
-public :
-
- /// Default constructor.
- DKSelector(void);
-
- /// Destructor.
- ~DKSelector(void);
-
- /// Deallocate PETSc and local data structures.
- virtual
- void deallocate(void);
-
- /** Set spatial database for dkselector
- *
- * @param db dksel
- */
- void dbdksel(spatialdata::spatialdb::SpatialDB* const db);
-
- /** Initialize dkselector
- *
- * @param faultMesh Finite-element mesh of fault.
- * @param normalizer Nondimensionalization of scales.
- */
- void initialize(const topology::SubMesh& faultMesh,
- const spatialdata::units::Nondimensional& normalizer);
-
- /** Get dk on fault surface (time will be implemented through this guy)
- *
- * @params faultMesh Finite-element mesh of fault.
- *
- * @returns a section for the given time (future)
- */
- void dk(const topology::Field<topology::SubMesh>* dk);
-
-// NOT IMPLEMENTED //////////////////////////////////////////////////////
-private :
-
- DKSelector(const DKSelector&); ///< Not implemented
- const DKSelector& operator=(const DKSelector&); ///< Not implemented
-
-// PRIVATE MEMBERS //////////////////////////////////////////////////////
-private :
-
- scalar_array _dkselVertex; ///< dk sel at vertex.
- PylithScalar _dkselvv; ///< used to check
-
- /// Spatial database for dk selector.
- spatialdata::spatialdb::SpatialDB* _dbdksel;
-
- /// Parameters for perturbations.
- topology::Fields<topology::Field<topology::SubMesh> >* _parameters;
-
-}; // class DKSelector
-
-#endif // pylith_faults_dkselector_hh
-
-
-// End of file
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