Merged with release-2.5

Author: SteveMaas1978

Documentation/FEBioStudioReleaseNotes.txt

@@ -4,6 +4,60 @@
 
 *****************************************************************
 
+===========================================================================
+
+ R E L E A S E   2.5   1/16/2024
+
+===========================================================================
+
+New Features:
+* Added "physics" color mode option, which colors each surface depending on how it is used in the model's loads and boundary conditions.
+* Added support for file extension dyn (will read lsdyna input file).
+* Added support for exporting 3D image data to several formats.
+* Added support for reading and writing quadratic beam elements to febio4 format.
+
+Improvements:
+* Inverted faces but not elements in NetGen mesher, to produce correct mesh output upon conversion to editable mesh.
+* Added ability to merge multiple STEP objects into single STEP object upon import, allowing conforming meshing with Netgen
+* Added Fluent mesh exporting capability
+* Added a log message when attempting to export wrong Mesh type to Fluent. Made export distinguish mixed face types versus uniform face types
+* Updated copyright statement on splash and about box.
+* Added febio format 4.0 export for post docs.
+* Added nodal fluid flux plot variable to FSI analyses
+* Deletion of multiple parts will now process much faster.
+* All new documents are now added to the recent files list.
+* Added icons to model search panel, and a column for the type. Filter now also searches type strings.
+* Implemented more efficient way of tracking output when running febio in a thread.
+* Modified mesh building algorithm in post lsdyna importer to speed it up.
+* In the Project panel, added support to load fs2 files via folder import, and fixed bug when moving files to a folder.
+* Added options to set caps when rendering smooth paths and cylinders. Beam ends are now rendered as flat. Fixed issue with rendering colormaps on solid beams.
+
+Bug Fixes:
+* Fixed issue with FSModel::GetEnumValues for getting dof_list.
+* Fixed some issues with reading feb3 files.
+* Added checks when rendering objects to make sure a valid render mesh exists.
+* Timeline panel is now updated when states are deleted.
+* Fixed issue with saving the correct model file name when saving fsps files.
+* Fixed issue with reading surfaces of febio files that uses node numbering that does not start at one.
+* Fixed issue with rendering images with correct orientation in slice view. Also fixed bug in rendering z-slice.
+* Updated ImageMap tool and WarpImageFilter to work with rotated images. Fixed bug caused by missing cases in 3DImage::Value
+* Fixed bug in loading models with DICOM images
+* Fixed issue with volume rendering images with orientation.
+* Image models are now rendered with correct orientation.
+* Fixed issue in kinemat build tool.
+* Fixed problem with input of numbers in a property form.
+* Fixed issue where shell IDs were not copied from lsdyna file.
+* Fixed issue with rare case where elements have duplicate IDs.
+* Fixed string overflow in FEBio import.
+* Fixed issue with importing nodesets from old feb files.
+* Fixed issue with volume rendering of signed int image data.
+* Made some fixes to old febio and nike3d file readers.
+* Fixed bug in rendering of general springs.
+* Fixed problem with reading discrete element sets from LSDYNA file.
+* Fixed bug in curve-projection tool that did not take transform of curves into account.
+* Fixed issue with rendering half-spheres in special case.
+
+
 ===========================================================================
 
  R E L E A S E   2.4   11/15/2023

Documentation/FEBioStudio_User_Manual.lyx

@@ -124,13 +124,13 @@ status open
 User's Manual
 \series default
 \emph on
-Version 2.4
+Version 2.5
 \end_layout
 
 \begin_layout Date
 
 \series bold
-Last Updated: November 15, 2023
+Last Updated: January 16, 2024
 \end_layout
 
 \begin_layout Standard

Documentation/FEBioStudio_User_Manual.pdf

@@ -25,9 +25,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.*/
 
 #pragma once
-#include <string>
 #include <FSCore/FSObject.h>
-
 #include <string>
 
 using std::string;

Documentation/Figures/graph.png

@@ -2634,6 +2634,7 @@ const char* ElementTypeString(int ntype)
 	case FE_PENTA15: sztype = "penta15"; break;
     case FE_PYRA13 : sztype = "pyra13"; break;
 	case FE_BEAM2  : sztype = "line2"; break;
+	case FE_BEAM3  : sztype = "line3"; break;
 	default:
 		assert(false);
 	}

FEBio/FEBioException.h

@@ -522,6 +522,13 @@ bool FEBioFormat::ParseControlSection(XMLTag& tag)
 	FEBioInputModel& febio = GetFEBioModel();
 	FSModel& fem = GetFSModel();
 
+	if (m_nAnalysis == -1)
+	{
+		int moduleId = FEBio::GetModuleId("solid");
+		if (moduleId < 0) { throw XMLReader::InvalidAttributeValue(tag, "type", "solid"); }
+		FileReader()->GetProject().SetModule(moduleId, false);
+	}
+
 	// create a new analysis step from these control settings
 	if (m_pstep == 0) m_pstep = NewStep(fem, m_nAnalysis);
 	FSAnalysisStep* pstep = dynamic_cast<FSAnalysisStep*>(m_pstep);
@@ -1118,6 +1125,9 @@ FSMaterial* FEBioFormat::ParseMaterial(XMLTag& tag, const char* szmat, int propT
 		// HACK: a little hack to read in the "EFD neo-Hookean2" materials of the old datamap plugin. 
 		if (strcmp(szmat, "EFD neo-Hookean2") == 0) pm = FEMaterialFactory::Create(fem, "EFD neo-Hookean");
 
+		// HACK: "St.Venant-Kirchhoff" was renamed to "isotropic elastic"
+		if (strcmp(szmat, "St.Venant-Kirchhoff") == 0) pm = FEMaterialFactory::Create(fem, "isotropic elastic", propType);
+
 		// FBS1 never supported these materials, so we'll just use the FEBio classes.
 		if ((strcmp(szmat, "remodeling solid"      ) == 0) ||
 			(strcmp(szmat, "hyperelastic"          ) == 0) ||

FEBio/FEBioExport25.cpp

@@ -27,7 +27,6 @@ SOFTWARE.*/
 #include "stdafx.h"
 #include "FEBioFormat3.h"
 #include <FEMLib/FERigidConstraint.h>
-#include <GeomLib/FSGroup.h>
 #include <GeomLib/GMeshObject.h>
 #include <FEMLib/FEInitialCondition.h>
 #include <FEMLib/FEBodyLoad.h>
@@ -1010,7 +1009,7 @@ void FEBioFormat3::ParseGeometrySurface(FEBioInputModel::Part* part, XMLTag& tag
 
 			// make zero-based
 			vector<int> node(N);
-			for (int j = 0; j < N; ++j) node[j] = nf[j] - 1;
+			for (int j = 0; j < N; ++j) node[j] = nf[j];// -1;
 			s.m_face.push_back(node);
 
 			++tag;
@@ -1312,6 +1311,13 @@ bool FEBioFormat3::ParseSurfaceDataSection(XMLTag& tag)
 	}
 	else dataType = FEMeshData::DATA_TYPE::DATA_SCALAR;
 
+	const char* szgen = tag.AttributeValue("generator", true);
+	if (szgen)
+	{
+		tag.skip();
+		return true;
+	}
+
 	FSSurface* feSurf = feb.FindNamedSurface(surf->cvalue());
 	FSMesh* feMesh = feSurf->GetMesh();
 

FEBio/FEBioFormat.cpp

@@ -26,7 +26,6 @@ SOFTWARE.*/
 
 #include "stdafx.h"
 #include "FEBioFormat4.h"
-#include <GeomLib/FSGroup.h>
 #include <GeomLib/GMeshObject.h>
 #include <FEMLib/FEInitialCondition.h>
 #include <FEMLib/FEBodyLoad.h>
@@ -671,6 +670,7 @@ void FEBioFormat4::ParseGeometryElements(FEBioInputModel::Part* part, XMLTag& ta
 	else if (strcmp(sztype, "TRI6G14"     ) == 0) ntype = FE_TRI6;
 	else if (strcmp(sztype, "TRI6G21"     ) == 0) ntype = FE_TRI6;
 	else if (strcmp(sztype, "line2"       ) == 0) ntype = FE_BEAM2;
+	else if (strcmp(sztype, "line3"       ) == 0) ntype = FE_BEAM3;
 	else throw XMLReader::InvalidTag(tag);
 
 	// get the optional material attribute
@@ -902,9 +902,9 @@ void FEBioFormat4::ParseGeometrySurface(FEBioInputModel::Part* part, XMLTag& tag
 			// read the node numbers
 			tag.value(nf, N);
 
-			// make zero-based
+			// copy to vector
 			vector<int> node(N);
-			for (int j = 0; j < N; ++j) node[j] = nf[j] - 1;
+			for (int j = 0; j < N; ++j) node[j] = nf[j];
 			s.m_face.push_back(node);
 
 			++tag;

FEBio/FEBioFormat3.cpp

@@ -103,6 +103,12 @@ bool FEBioFormatOld::ParseModuleSection(XMLTag &tag)
 		assert(false);
 	}
 */
+
+	const char* sztype = atype.cvalue();
+	int moduleId = FEBio::GetModuleId(sztype);
+	if (moduleId < 0) { throw XMLReader::InvalidAttributeValue(tag, "type", sztype); }
+	FileReader()->GetProject().SetModule(moduleId, false);
+
 	return (m_nAnalysis != -1);}
 
 //=============================================================================
@@ -484,6 +490,7 @@ void FEBioFormatOld::ParseBCFixed(FSStep* pstep, XMLTag &tag)
 
 			// create a nodeset of this BC
 			FSNodeSet* pg = new FSNodeSet(po);
+			po->AddFENodeSet(pg);
 
 			// assign the nodes to this group
 			for (int i = 0; i<N; ++i) if (BC[i] & ntype) { pg->add(i); BC[i] &= (~ntype); }
@@ -494,6 +501,7 @@ void FEBioFormatOld::ParseBCFixed(FSStep* pstep, XMLTag &tag)
 				FSFixedDisplacement* pbc = new FSFixedDisplacement(&fem, pg, ntype, pstep->GetID());
 				sprintf(szname, "FixedDisplacement%02d", CountBCs<FSFixedDisplacement>(fem)+1);
 				pbc->SetName(szname);
+				pg->SetName(szname);
 				pstep->AddComponent(pbc);
 			}
 			else if (ntype < 64)
@@ -502,20 +510,23 @@ void FEBioFormatOld::ParseBCFixed(FSStep* pstep, XMLTag &tag)
 				FSFixedRotation* pbc = new FSFixedRotation(&fem, pg, ntype, pstep->GetID());
 				sprintf(szname, "FixedRotation%02d", CountBCs<FSFixedRotation>(fem)+1);
 				pbc->SetName(szname);
+				pg->SetName(szname);
 				pstep->AddComponent(pbc);
 			}
 			else if (ntype == 64)
 			{
 				FSFixedTemperature* pbc = new FSFixedTemperature(&fem, pg, 1, pstep->GetID());
 				sprintf(szname, "FixedTemperature%02d", CountBCs<FSFixedTemperature>(fem)+1);
 				pbc->SetName(szname);
+				pg->SetName(szname);
 				pstep->AddComponent(pbc);
 			}
 			else if (ntype == 128)
 			{
 				FSFixedFluidPressure* pbc = new FSFixedFluidPressure(&fem, pg, 1, pstep->GetID());
 				sprintf(szname, "FixedFluidPressure%02d", CountBCs<FSFixedFluidPressure>(fem)+1);
 				pbc->SetName(szname);
+				pg->SetName(szname);
 				pstep->AddComponent(pbc);
 			}
 			else
@@ -526,6 +537,7 @@ void FEBioFormatOld::ParseBCFixed(FSStep* pstep, XMLTag &tag)
 					FSFixedConcentration* pbc = new FSFixedConcentration(&fem, pg, ntype, pstep->GetID());
 					sprintf(szname, "FixedConcentration%02d", CountBCs<FSFixedConcentration>(fem)+1);
 					pbc->SetName(szname);
+					pg->SetName(szname);
 					pstep->AddComponent(pbc);
 				}
 			}
@@ -612,6 +624,7 @@ void FEBioFormatOld::ParseBCPrescribed(FSStep* pstep, XMLTag& tag)
 	}
 
 	// create the prescribed BC
+	FEBioInputModel& feb = GetFEBioModel();
 	FSModel& fem = GetFSModel();
 	char szname[256];
 	vector<FSPrescribedDOF*> pBC(nns);
@@ -628,6 +641,7 @@ void FEBioFormatOld::ParseBCPrescribed(FSStep* pstep, XMLTag& tag)
 			FSNodeSet* pg = new FSNodeSet(po);
 			sprintf(szname, "Nodeset%02d", i + 1);
 			pg->SetName(szname);
+			po->AddFENodeSet(pg);
 
 			// make a new boundary condition
 			FSPrescribedDOF* pbc = 0;
@@ -706,12 +720,17 @@ void FEBioFormatOld::ParseBCPrescribed(FSStep* pstep, XMLTag& tag)
 		FSPrescribedDOF* pbc = pBC[ng];
 //		pbc->GetLoadCurve()->SetID(lc);
 		pbc->SetScaleFactor(DC[i].s);
+		if (DC[i].lc >= 0)
+		{
+			feb.AddParamCurve(pbc->GetParam("scale"), DC[i].lc);
+		}
 	}
 }
 
 //-----------------------------------------------------------------------------
 void FEBioFormatOld::ParseForceLoad(FSStep *pstep, XMLTag &tag)
 {
+	FEBioInputModel& feb = GetFEBioModel();
 	FSModel& fem = GetFSModel();
 
 	// count how many prescibed nodes there are
@@ -790,6 +809,7 @@ void FEBioFormatOld::ParseForceLoad(FSStep *pstep, XMLTag &tag)
 		if (cc[j][i] >= 0)
 		{
 			FSNodeSet* pg = new FSNodeSet(po);
+			po->AddFENodeSet(pg);
 			sprintf(szname, "ForceNodeset%02d", i + 1);
 			pg->SetName(szname);
 
@@ -799,6 +819,11 @@ void FEBioFormatOld::ParseForceLoad(FSStep *pstep, XMLTag &tag)
 			pFC[cc[j][i]] = pbc;
 			pNS[cc[j][i]] = pg;
 			pstep->AddComponent(pbc);
+
+			if (FC[i].lc >= 0)
+			{
+				feb.AddParamCurve(pbc->GetParam("scale"), FC[i].lc);
+			}
 		}
 	}
 
@@ -1532,6 +1557,7 @@ bool FEBioFormatOld::ParseInitialSection(XMLTag& tag)
 			FSNodalVelocities* pbc = new FSNodalVelocities(&fem, pg, v, m_pBCStep->GetID());
 			char szname[64] = { 0 };
 			sprintf(szname, "InitialVelocity%02d", CountBCs<FSNodalVelocities>(fem) + 1);
+			if (pg) { pg->SetName(szname); po->AddFENodeSet(pg); }
 			pbc->SetName(szname);
 			m_pBCStep->AddComponent(pbc);
 		}
@@ -1571,6 +1597,7 @@ bool FEBioFormatOld::ParseInitialSection(XMLTag& tag)
 			FSInitConcentration* pbc = new FSInitConcentration(&fem, pg, bc, c, m_pBCStep->GetID());
 			char szname[64] = { 0 };
 			sprintf(szname, "InitialConcentration%02d", CountBCs<FSInitConcentration>(fem) + 1);
+			if (pg) { pg->SetName(szname); po->AddFENodeSet(pg); }
 			pbc->SetName(szname);
 			m_pBCStep->AddComponent(pbc);
 		}
@@ -1603,6 +1630,7 @@ bool FEBioFormatOld::ParseInitialSection(XMLTag& tag)
 			char szname[64] = { 0 };
 			sprintf(szname, "InitialFluidPressure%02d", CountBCs<FSInitFluidPressure>(fem) + 1);
 			pbc->SetName(szname);
+			if (pg) { pg->SetName(szname); po->AddFENodeSet(pg); }
 			m_pBCStep->AddComponent(pbc);
 		}
 		else if (tag == "temperature")	// initial temperature
@@ -1634,6 +1662,7 @@ bool FEBioFormatOld::ParseInitialSection(XMLTag& tag)
 			char szname[64] = { 0 };
 			sprintf(szname, "InitialTemperature%02d", CountBCs<FSInitTemperature>(fem) + 1);
 			pbc->SetName(szname);
+			if (pg) { pg->SetName(szname); po->AddFENodeSet(pg); }
 			m_pBCStep->AddComponent(pbc);
 		}
 		else ParseUnknownTag(tag);
@@ -1764,16 +1793,25 @@ void FEBioFormatOld::ParseContactSliding(FSStep* pstep, XMLTag& tag)
 
 				// create a new surface
 				FSSurface* ps = new FSSurface(po);
+				po->AddFESurface(ps);
 				if (ntype == 1)
 				{
 					pms = ps;
 					if (szn) ps->SetName(szn);
+					else {
+						sprintf(szbuf, "SecondarySurface%02d", CountInterfaces<FSSlidingWithGapsInterface>(fem) + 1);
+						ps->SetName(szbuf);
+					}
 					pi->SetSecondarySurface(ps);
 				}
 				else
 				{
 					pss = ps;
 					if (szn) ps->SetName(szn);
+					else {
+						sprintf(szbuf, "PrimarySurface%02d", CountInterfaces<FSSlidingWithGapsInterface>(fem) + 1);
+						ps->SetName(szbuf);
+					}
 					pi->SetPrimarySurface(ps);
 				}
 
@@ -2381,6 +2419,7 @@ void FEBioFormatOld::ParseRigidWall(FSStep* pstep, XMLTag& tag)
 			FSSurface* ps = new FSSurface(po);
 			pci->SetItemList(ps);
 			if (szn) ps->SetName(szn);
+			po->AddFESurface(ps);
 
 			// read the surface
 			ParseContactSurface(ps, tag);
@@ -2455,6 +2494,8 @@ void FEBioFormatOld::ParseContactRigid(FSStep *pstep, XMLTag &tag)
 			if (sz) sprintf(szbuf, "%s", szname);
 			else sprintf(szbuf, "RigidInterface%02d", i + 1);
 			pi->SetName(szbuf);
+			pn->SetName(szbuf);
+			po->AddFENodeSet(pn);
 			pstep->AddComponent(pi);
 		}
 	}