Merge branch 'develop' of https://github.com/febiosoftware/FEBio into develop

Author: gateshian

FEAMR/FEHexRefine.cpp

@@ -36,6 +36,7 @@ SOFTWARE.*/
 #include <FECore/FEMeshAdaptorCriterion.h>
 #include <FECore/log.h>
 #include <FECore/FEModel.h>
+#include <stdexcept>
 
 BEGIN_FECORE_CLASS(FEHexRefine, FERefineMesh)
 	ADD_PARAMETER(m_elemRefine, "max_elem_refine");

FEAMR/FEHexRefine2D.cpp

@@ -35,6 +35,7 @@ SOFTWARE.*/
 #include <FECore/FEMeshAdaptorCriterion.h>
 #include <FECore/FESurface.h>
 #include <FECore/log.h>
+#include <stdexcept>
 
 BEGIN_FECORE_CLASS(FEHexRefine2D, FERefineMesh)
 	ADD_PARAMETER(m_elemRefine, "max_elem_refine");

FEAMR/FEMMGRemesh.cpp

@@ -40,6 +40,7 @@ SOFTWARE.*/
 #include "FEDomainShapeInterpolator.h"
 #include <FECore/FECoreKernel.h>
 #include <FECore/FEMaterial.h>
+#include <stdexcept>
 #ifdef HAS_MMG
 #include "mmg/mmg3d/libmmg3d.h"
 

FEAMR/FERefineMesh.cpp

@@ -44,6 +44,7 @@ SOFTWARE.*/
 #include "FELeastSquaresInterpolator.h"
 #include "FEMeshShapeInterpolator.h"
 #include "FEDomainShapeInterpolator.h"
+#include <stdexcept>
 
 BEGIN_FECORE_CLASS(FERefineMesh, FEMeshAdaptor)
 	ADD_PARAMETER(m_maxiter, "max_iters");

FEAMR/FETestRefine.cpp

@@ -31,6 +31,7 @@ SOFTWARE.*/
 #include <FECore/FESurface.h>
 #include <FECore/FEModel.h>
 #include <FECore/log.h>
+#include <stdexcept>
 
 BEGIN_FECORE_CLASS(FETestRefine, FERefineMesh)
 END_FECORE_CLASS();

FEAMR/FETetRefine.cpp

@@ -31,6 +31,7 @@ SOFTWARE.*/
 #include <FECore/FESurface.h>
 #include <FECore/FEModel.h>
 #include <FECore/log.h>
+#include <stdexcept>
 
 BEGIN_FECORE_CLASS(FETetRefine, FERefineMesh)
 END_FECORE_CLASS();

FEBioMech/FEUncoupledViscoElasticDamage.cpp

@@ -28,7 +28,7 @@
 #include "FEUncoupledViscoElasticDamage.h"
 #include <FECore/log.h>
 #include <FECore/FEModel.h>
-
+#include <stdexcept>
 
 //-----------------------------------------------------------------------------
 BEGIN_FECORE_CLASS(FEUncoupledViscoElasticDamage, FEUncoupledMaterial)

FEBioMech/FEViscoElasticDamage.cpp

@@ -28,6 +28,7 @@
 #include "FEViscoElasticDamage.h"
 #include <FECore/log.h>
 #include <FECore/FEModel.h>
+#include <stdexcept>
 
 
 //-----------------------------------------------------------------------------

FEBioMech/ObjectDataRecord.cpp

@@ -41,19 +41,21 @@ ObjectDataRecord::ObjectDataRecord(FEModel* pfem) : DataRecord(pfem, FE_DATA_RB)
 //-----------------------------------------------------------------------------
 void ObjectDataRecord::SetData(const char* szexpr)
 {
-	std::vector<DataRecordItem> data = ProcessDataString(szexpr);
-	if (data.empty()) throw UnknownDataField(szexpr);
+	std::vector<std::string> strings = SplitDataString(szexpr);
+	if (strings.empty()) throw UnknownDataField(szexpr);
 
 	m_Data.clear();
 	m_data = szexpr;
-	for (int i=0; i<data.size(); ++i)
+	for (int i=0; i<strings.size(); ++i)
 	{
-		FELogObjectData* pdata = fecore_new<FELogObjectData>(data[i].name.c_str(), GetFEModel());
-		if (pdata == nullptr) throw UnknownDataField(data[i].name);
+		DataRecordItem it = ProcessDataString(strings[i].c_str());
+		if (!it.isValid()) throw UnknownDataField(strings[i]);
+		FELogObjectData* pdata = fecore_new<FELogObjectData>(it.name.c_str(), GetFEModel());
+		if (pdata == nullptr) throw UnknownDataField(it.name);
 		m_Data.push_back(pdata);
 
-		if (!ApplyDataRecordItem(*pdata, data[i]))
-			throw UnknownDataField(data[i].name);
+		if (!ApplyDataRecordItem(*pdata, it))
+			throw UnknownDataField(strings[i]);
 	}
 }
 

FEBioMix/FEBiphasicSolidDomain.cpp

@@ -41,7 +41,7 @@ BEGIN_FECORE_CLASS(FEBiphasicSolidDomain, FESolidDomain)
     ADD_PARAMETER(m_secant_stress, "secant_stress");
     ADD_PARAMETER(m_secant_tangent, "secant_tangent");
     ADD_PARAMETER(m_secant_perm_tangent, "secant_permeability_tangent");
-	ADD_PARAMETER(m_auto_pressure_stab, "auto_pressure_stabilization");
+	ADD_PARAMETER(m_auto_pressure_stab, "auto_pressure_stabilization")->setEnums("off\0on\0adaptive\0");
 END_FECORE_CLASS();
 
 //-----------------------------------------------------------------------------
@@ -51,7 +51,7 @@ FEBiphasicSolidDomain::FEBiphasicSolidDomain(FEModel* pfem) : FESolidDomain(pfem
     m_secant_stress = false;
     m_secant_tangent = false;
     m_secant_perm_tangent = false;
-	m_auto_pressure_stab = false;
+	m_auto_pressure_stab = 0;
 
 	if (pfem)
 	{
@@ -138,6 +138,16 @@ void FEBiphasicSolidDomain::PreSolveUpdate(const FETimeInfo& timeInfo)
             mp.Update(timeInfo);
 		}
 	}
+
+	// see if we update the stabilization factor
+	if (m_auto_pressure_stab > 1)
+	{
+		if (!CalcAutoPressureStabilization())
+		{
+			feLogError("Failed to calculate automatic pressure stabilization factor.");
+			return;
+		}
+	}
 }
 
 //-----------------------------------------------------------------------------
@@ -158,7 +168,7 @@ bool FEBiphasicSolidDomain::Init()
 	// allocate nodal pressures
 	m_nodePressure.resize(Nodes(), 0.0);
 
-	if (m_auto_pressure_stab)
+	if (m_auto_pressure_stab > 0)
 	{
 		if (!CalcAutoPressureStabilization())
 		{
@@ -1267,6 +1277,8 @@ void FEBiphasicSolidDomain::GetNodalPressures(vector<double>& data)
 
 bool FEBiphasicSolidDomain::CalcAutoPressureStabilization()
 {
+	feLog("Updating stabilization factor for biphasic solid domain '%s'\n", GetName().c_str());
+
 	// make sure that the biphasic tau parameter is not zero
 	if (m_pMat->m_tau == 0.0)
 	{
@@ -1282,7 +1294,9 @@ bool FEBiphasicSolidDomain::CalcAutoPressureStabilization()
 
 	FEMesh& mesh = *GetMesh();
 
-	for (int i = 0; i < Elements(); ++i)
+	int NE = Elements();
+#pragma omp parallel for shared(EL, EEL, mesh)
+	for (int i = 0; i < NE; ++i)
 	{
 		FESolidElement& el = Element(i);
 
@@ -1304,7 +1318,6 @@ bool FEBiphasicSolidDomain::CalcAutoPressureStabilization()
 		{
 			FEMaterialPoint& mp = *el.GetMaterialPoint(n);
 			FEBiphasicMaterialPoint* bpt = (mp.ExtractData<FEBiphasicMaterialPoint>());
-			if (bpt == nullptr) return false;
 
 			// get the tangent stiffness
 			tens4dmm C = m_pMat->Tangent(mp);