[cig-commits] r21309 - in short/3D/PyLith/branches/v1.8-mixedfault: libsrc/pylith/faults modulesrc/faults pylith/faults
rjolivet at geodynamics.org
rjolivet at geodynamics.org
Tue Jan 29 16:48:23 PST 2013
Author: rjolivet
Date: 2013-01-29 16:48:23 -0800 (Tue, 29 Jan 2013)
New Revision: 21309
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
short/3D/PyLith/branches/v1.8-mixedfault/modulesrc/faults/dkSelector.i
short/3D/PyLith/branches/v1.8-mixedfault/pylith/faults/dkSelector.py
Log:
Adding dkSelector in the faults
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 2013-01-30 00:48:23 UTC (rev 21309)
@@ -0,0 +1,183 @@
+// -*- 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;
+
+// ----------------------------------------------------------------------
+// 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");
+
+ // Create a 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);
+ assert(0 != _parameters);
+ _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
+void
+pylith::faults::dkSelector::dk(topology::Field<topology::SubMesh>* dk)
+{ // dk
+ assert(0 != dk);
+ assert(0 != _parameters);
+
+ // Get vertices in 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();
+
+ // Get sections
+ const topology::Field<topology::SubMesh>& DKSel =
+ _parameters->get("Dynamic Kinematic Selector");
+ const ALE::Obj<RealSection>& DKselSection = DKsel.section();
+ assert(!DKselSection.isNull());
+
+ for (label_sequence::iterator v_iter=verticesBegin;
+ v_iter != verticesEnd;
+ ++v_iter) {
+ DKselSection->restrictPoint(*v_iter, &_dkselVertex[0],
+ _dkselVertex.size());
+ // if dkselVertex is under 0.5, the vertex is kinematically controled
+ if ( _dkselVertex < 0.5 ){
+ _dkselVertex = 0.0;
+ else {
+ _dkselVertex = 1.0;
+ }
+ DKselSection->updateAddPoint(*v_iter, &_dkselVertex[0]);
+ } // for
+
+ PetscLogFlops(vertices->size());
+} // slip
+
+// 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 2013-01-30 00:48:23 UTC (rev 21309)
@@ -0,0 +1,97 @@
+// -*- 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 "pylith/topology/topologyfwd.hh" // USES Fields<Field<SubMesh> >
+
+#include "spatialdata/spatialdb/spatialdbfwd.hh" // USES SpatialDB
+
+#include "pylith/utils/array.hh" // HASA scalar_array
+
+// dkSelector -----------------------------------------------------------
+/** @brief Dynamic-Kinematic Selector
+ *
+ * If value is under .5 the fault vertex has its slip value controlled by EQsrc
+ *
+ */
+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)
+ *
+ * @param dk DK selector field over fault surface
+ *
+ * @returns dk for the time
+ */
+ void dk(topology::Field<topology::SubMesh>* const dkField);
+
+// NOT IMPLEMENTED //////////////////////////////////////////////////////
+private :
+
+ dkSelector(const dkSelector&); ///< Not implemented
+ const dkSelector& operator=(const dkSelector&); ///< Not implemented
+
+// PRIVATE MEMBERS //////////////////////////////////////////////////////
+private :
+
+ PylithScalar _dkselVertex; ///< Slip time at a vertex.
+
+ /// Spatial database for slip rate.
+ spatialdata::spatialdb::SpatialDB* _dbdksel;
+
+}; // class dkSelector
+
+#endif // pylith_faults_dkselector_hh
+
+
+// End of file
Added: short/3D/PyLith/branches/v1.8-mixedfault/modulesrc/faults/dkSelector.i
===================================================================
--- short/3D/PyLith/branches/v1.8-mixedfault/modulesrc/faults/dkSelector.i (rev 0)
+++ short/3D/PyLith/branches/v1.8-mixedfault/modulesrc/faults/dkSelector.i 2013-01-30 00:48:23 UTC (rev 21309)
@@ -0,0 +1,71 @@
+// -*- 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 modulesrc/faults/dkSelector.i
+ *
+ * @brief Python interface to C++ Fault object.
+ */
+
+namespace pylith {
+ namespace faults {
+
+ class 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 Spatial database
+ */
+ void dbdksel(spatialdata::spatialdb::SpatialDB* const db);
+
+ /** Initialize slip time function.
+ *
+ * @param faultMesh Finite-element mesh of fault.
+ * @param normalizer Nondimensionalization of scales.
+ */
+ void initialize(const pylith::topology::SubMesh& faultMesh,
+ const spatialdata::units::Nondimensional& normalizer);
+
+ /** Get dk on fault surface (time will be implemented through this guy)
+ *
+ * @param dk DK selector field over fault surface
+ *
+ * @returns dk for the time
+ */
+ void dk(pylith::topology::Field<pylith::topology::SubMesh>* const dkField);
+
+ }; // class dkSelector
+
+ } // faults
+} // pylith
+
+
+// End of file
Added: short/3D/PyLith/branches/v1.8-mixedfault/pylith/faults/dkSelector.py
===================================================================
--- short/3D/PyLith/branches/v1.8-mixedfault/pylith/faults/dkSelector.py (rev 0)
+++ short/3D/PyLith/branches/v1.8-mixedfault/pylith/faults/dkSelector.py 2013-01-30 00:48:23 UTC (rev 21309)
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+#
+# ----------------------------------------------------------------------
+#
+# 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.
+#
+# ----------------------------------------------------------------------
+#
+
+## @file pylith/faults/dkSelector.py
+##
+## @brief Python object for the dynamic-kinematic selector
+##
+
+from faults import dkSelector as ModuledkSelector
+
+# dkSelector class
+class dkSelector(ModuledkSelector):
+ """
+ Python object for a dynamic-kinematic selector
+
+ Inventory
+
+ \b Properties
+ @li None
+
+ \b Facilities
+ @li \b dynamic_kinematic_selector Spatial database of dk selector
+
+ """
+
+ # INVENTORY //////////////////////////////////////////////////////////
+
+ import pyre.inventory
+
+ from spatialdata.spatialdb.SimpleDB import SimpleDB
+
+ dbDKSel = pyre.inventory.facility("dynamic_kinematic_selector", family="spatial_database",
+ factory=SimpleDB)
+ dbDKSel.meta['tip'] = "Spatial database of dynamic-kinematic selector"
+
+
+ # PUBLIC METHODS /////////////////////////////////////////////////////
+
+ def __init__(self, name="dkselector"):
+ """
+ Constructor.
+ """
+ ModuledkSelector.__init__(self)
+ self._loggingPrefix = "DKsel "
+ return
+
+
+ # PRIVATE METHODS ////////////////////////////////////////////////////
+
+ def _configure(self):
+ """
+ Setup members using inventory.
+ """
+ ModuledkSelector.dbDKSel(self, self.inventory.dbDKSel)
+ return
+
+# End of file
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