[cig-commits] r21605 - short/3D/PyLith/trunk/libsrc/pylith/faults
brad at geodynamics.org
brad at geodynamics.org
Thu Mar 21 13:10:59 PDT 2013
Author: brad
Date: 2013-03-21 13:10:58 -0700 (Thu, 21 Mar 2013)
New Revision: 21605
Modified:
short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/StaticPerturbation.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc
Log:
Code cleanup. Remove ALE memory logger stuff.
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc 2013-03-21 20:04:45 UTC (rev 21604)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc 2013-03-21 20:10:58 UTC (rev 21605)
@@ -87,9 +87,6 @@
PetscErrorCode err;
err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("Fault");
-
delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
assert(_parameters);
_parameters->add("final slip", "final_slip");
@@ -122,8 +119,6 @@
PetscVec riseTimeVec = riseTime.localVector();assert(riseTimeVec);
PetscScalar *riseTimeArray = NULL;
- logger.stagePop();
-
// Open databases and set query values
_dbFinalSlip->open();
switch (spaceDim)
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc 2013-03-21 20:04:45 UTC (rev 21604)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc 2013-03-21 20:10:58 UTC (rev 21605)
@@ -85,9 +85,6 @@
PetscErrorCode err;
err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("Fault");
-
delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
assert(_parameters);
_parameters->add("slip rate", "slip_rate");
@@ -110,8 +107,6 @@
PetscVec slipTimeVec = slipTime.localVector();assert(slipTimeVec);
PetscScalar *slipTimeArray = NULL;
- logger.stagePop();
-
// Open databases and set query values
_dbSlipRate->open();
switch (spaceDim)
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc 2013-03-21 20:04:45 UTC (rev 21604)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc 2013-03-21 20:10:58 UTC (rev 21605)
@@ -151,9 +151,6 @@
const spatialdata::geocoords::CoordSys* cs = mesh.coordsys();
assert(cs);
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("FaultFields");
-
// Create field for relative velocity associated with Lagrange vertex k
_fields->add("relative velocity", "relative_velocity");
topology::Field<topology::SubMesh>& velRel = _fields->get("relative velocity");
@@ -162,7 +159,6 @@
velRel.vectorFieldType(topology::FieldBase::VECTOR);
velRel.scale(_normalizer->lengthScale() / _normalizer->timeScale());
- logger.stagePop();
} // initialize
// ----------------------------------------------------------------------
@@ -1665,13 +1661,8 @@
// Allocate buffer for tractions field (if necessary).
PetscSection tractionsSection = tractions->petscSection();
if (!tractionsSection) {
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("FaultFields");
-
const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
tractions->cloneSection(dispRel);
-
- logger.stagePop();
} // if
const PylithScalar pressureScale = _normalizer->pressureScale();
tractions->label("traction");
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc 2013-03-21 20:04:45 UTC (rev 21604)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc 2013-03-21 20:10:58 UTC (rev 21605)
@@ -101,9 +101,6 @@
_fields = new topology::Fields<topology::Field<topology::SubMesh> >(
*_faultMesh);
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("FaultFields");
-
// Allocate dispRel field
_fields->add("relative disp", "relative_disp");
topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
@@ -112,8 +109,6 @@
dispRel.vectorFieldType(topology::FieldBase::VECTOR);
dispRel.scale(_normalizer->lengthScale());
- logger.stagePop();
-
_quadrature->initializeGeometry();
#if defined(PRECOMPUTE_GEOMETRY)
@@ -1370,9 +1365,6 @@
PylithScalar jacobianDet = 0;
scalar_array refCoordsVertex(cohesiveDim);
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("FaultFields");
-
// Allocate orientation field.
scalar_array orientationVertex(orientationSize);
_fields->add("orientation", "orientation");
@@ -1393,8 +1385,6 @@
PetscVec orientationVec = orientation.localVector();
PetscScalar *orientationArray;
- logger.stagePop();
-
// Compute orientation of fault at constraint vertices
// Get section containing coordinates of vertices
@@ -1658,9 +1648,6 @@
err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
err = DMPlexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("FaultFields");
-
// Allocate area field.
_fields->add("area", "area");
topology::Field<topology::SubMesh>& area = _fields->get("area");
@@ -1676,8 +1663,6 @@
PetscScalar *areaArray;
assert(areaSection);assert(areaVec);
- logger.stagePop();
-
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
PetscVec coordVec;
@@ -1759,13 +1744,9 @@
// Allocate buffer for tractions field (if necessary).
PetscSection tractionsSection = tractions->petscSection();
if (!tractionsSection) {
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("FaultFields");
-
const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
tractions->cloneSection(dispRel);
tractionsSection = tractions->petscSection();
- logger.stagePop();
} // if
PetscVec tractionsVec = tractions->localVector();
PetscScalar *tractionsArray;
@@ -1819,9 +1800,6 @@
if (_fields->hasField("buffer (vector)"))
return;
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("OutputFields");
-
// Create vector field; use same shape/chart as relative
// displacement field.
assert(_faultMesh);
@@ -1832,8 +1810,6 @@
buffer.cloneSection(dispRel);
buffer.zero();
assert(buffer.vectorFieldType() == topology::FieldBase::VECTOR);
-
- logger.stagePop();
} // _allocateBufferVectorField
// ----------------------------------------------------------------------
@@ -1845,9 +1821,6 @@
if (_fields->hasField("buffer (scalar)"))
return;
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("OutputFields");
-
// Create vector field; use same shape/chart as area field.
assert(_faultMesh);
_fields->add("buffer (scalar)", "buffer");
@@ -1858,8 +1831,6 @@
buffer.scale(1.0);
buffer.zero();
assert(buffer.vectorFieldType() == topology::FieldBase::SCALAR);
-
- logger.stagePop();
} // _allocateBufferScalarField
// ----------------------------------------------------------------------
@@ -1971,9 +1942,6 @@
assert(faultDMMesh);
err = DMPlexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("OutputFields");
-
const int fiberDim = 1;
_fields->add("partition", "partition", pylith::topology::FieldBase::CELLS_FIELD, fiberDim);
topology::Field<topology::SubMesh>& partition = _fields->get("partition");
@@ -1999,8 +1967,6 @@
} // for
err = VecRestoreArray(partitionVec, &partitionArray);CHECK_PETSC_ERROR(err);
- logger.stagePop();
-
return partition;
} // if
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc 2013-03-21 20:04:45 UTC (rev 21604)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc 2013-03-21 20:10:58 UTC (rev 21605)
@@ -94,9 +94,6 @@
assert(dmMesh);
err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("Fault");
-
delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
assert(0 != _parameters);
_parameters->add("final slip", "final_slip");
@@ -132,8 +129,6 @@
PetscScalar *riseTimeArray;
assert(riseTimeSection);assert(riseTimeVec);
- logger.stagePop();
-
// Open databases and set query values
_dbFinalSlip->open();
switch (spaceDim)
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/StaticPerturbation.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/StaticPerturbation.cc 2013-03-21 20:04:45 UTC (rev 21604)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/StaticPerturbation.cc 2013-03-21 20:10:58 UTC (rev 21605)
@@ -85,10 +85,6 @@
const PylithScalar timeScale = normalizer.timeScale();
const PylithScalar pressureScale = normalizer.pressureScale();
- // Memory logging
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("Fault");
-
// Get vertices in fault mesh
const ALE::Obj<SieveMesh>& sieveMesh = faultMesh.sieveMesh();
assert(!sieveMesh.isNull());
@@ -109,8 +105,6 @@
const ALE::Obj<RealSection>& amplitudeSection = amplitude.section();
assert(!amplitudeSection.isNull());
- logger.stagePop();
-
// Open databases and set query values
_dbAmplitude->open();
switch (spaceDim)
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc 2013-03-21 20:04:45 UTC (rev 21604)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc 2013-03-21 20:10:58 UTC (rev 21605)
@@ -82,10 +82,6 @@
const PylithScalar lengthScale = normalizer.lengthScale();
const PylithScalar timeScale = normalizer.timeScale();
- // Memory logging
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("Fault");
-
// Get vertices in fault mesh
DM dmMesh = faultMesh.dmMesh();
PetscInt vStart, vEnd;
@@ -119,8 +115,6 @@
PetscScalar *slipTimeArray;
assert(slipTimeSection);assert(slipTimeVec);
- logger.stagePop();
-
// Open databases and set query values
_dbFinalSlip->open();
switch (spaceDim)
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc 2013-03-21 20:04:45 UTC (rev 21604)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc 2013-03-21 20:10:58 UTC (rev 21605)
@@ -88,10 +88,6 @@
const PylithScalar lengthScale = normalizer.lengthScale();
const PylithScalar timeScale = normalizer.timeScale();
- // Memory logging
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("Fault");
-
// Get vertices in fault mesh
DM dmMesh = faultMesh.dmMesh();
PetscInt vStart, vEnd;
@@ -125,8 +121,6 @@
PetscScalar *slipTimeArray;
assert(slipTimeSection);assert(slipTimeVec);
- logger.stagePop();
-
// Open databases and set query values
_dbAmplitude->open();
switch (spaceDim)
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc 2013-03-21 20:04:45 UTC (rev 21604)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc 2013-03-21 20:10:58 UTC (rev 21605)
@@ -84,16 +84,12 @@
const topology::Field<topology::SubMesh>& faultOrientation,
const spatialdata::units::Nondimensional& normalizer)
{ // initialize
- ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
- logger.stagePush("Fault");
-
const PylithScalar pressureScale = normalizer.pressureScale();
const PylithScalar timeScale = normalizer.timeScale();
const PylithScalar rateScale = pressureScale / timeScale;
_timeScale = timeScale;
- const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();
- assert(cs);
+ const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();assert(cs);
const int spaceDim = cs->spaceDim();
delete _parameters;
@@ -101,34 +97,40 @@
// Create section to hold time dependent values
_parameters->add("value", "traction", topology::FieldBase::VERTICES_FIELD, spaceDim);
- _parameters->get("value").vectorFieldType(topology::FieldBase::VECTOR);
- _parameters->get("value").scale(pressureScale);
- _parameters->get("value").allocate();
+ topology::Field<topology::SubMesh>& value = _parameters->get("value");
+ value.vectorFieldType(topology::FieldBase::VECTOR);
+ value.scale(pressureScale);
+ value.allocate();
if (_dbInitial) {
_parameters->add("initial", "traction_initial", topology::FieldBase::VERTICES_FIELD, spaceDim);
- _parameters->get("initial").vectorFieldType(topology::FieldBase::VECTOR);
- _parameters->get("initial").scale(pressureScale);
- _parameters->get("initial").allocate();
+ topology::Field<topology::SubMesh>& initial = _parameters->get("initial");
+ initial.vectorFieldType(topology::FieldBase::VECTOR);
+ initial.scale(pressureScale);
+ initial.allocate();
}
if (_dbRate) {
_parameters->add("rate", "traction_rate", topology::FieldBase::VERTICES_FIELD, spaceDim);
- _parameters->get("rate").vectorFieldType(topology::FieldBase::VECTOR);
- _parameters->get("rate").scale(rateScale);
- _parameters->get("rate").allocate();
+ topology::Field<topology::SubMesh>& rate = _parameters->get("rate");
+ rate.vectorFieldType(topology::FieldBase::VECTOR);
+ rate.scale(rateScale);
+ rate.allocate();
_parameters->add("rate time", "rate_start_time", topology::FieldBase::VERTICES_FIELD, 1);
- _parameters->get("rate time").vectorFieldType(topology::FieldBase::SCALAR);
- _parameters->get("rate time").scale(timeScale);
- _parameters->get("rate time").allocate();
+ topology::Field<topology::SubMesh>& rateTime = _parameters->get("rate time");
+ rateTime.vectorFieldType(topology::FieldBase::SCALAR);
+ rateTime.scale(timeScale);
+ rateTime.allocate();
} // if
if (_dbChange) {
_parameters->add("change", "traction_change", topology::FieldBase::VERTICES_FIELD, spaceDim);
- _parameters->get("change").vectorFieldType(topology::FieldBase::VECTOR);
- _parameters->get("change").scale(pressureScale);
- _parameters->get("change").allocate();
+ topology::Field<topology::SubMesh>& change = _parameters->get("change");
+ change.vectorFieldType(topology::FieldBase::VECTOR);
+ change.scale(pressureScale);
+ change.allocate();
_parameters->add("change time", "change_start_time", topology::FieldBase::VERTICES_FIELD, 1);
- _parameters->get("change time").vectorFieldType(topology::FieldBase::SCALAR);
- _parameters->get("change time").scale(timeScale);
- _parameters->get("change time").allocate();
+ topology::Field<topology::SubMesh>& changeTime = _parameters->get("change time");
+ changeTime.vectorFieldType(topology::FieldBase::SCALAR);
+ changeTime.scale(timeScale);
+ changeTime.allocate();
} // if
if (_dbInitial) { // Setup initial values, if provided.
@@ -238,8 +240,6 @@
if (_dbTimeHistory)
_dbTimeHistory->open();
} // if
-
- logger.stagePop();
} // initialize
// ----------------------------------------------------------------------
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