Improved performance managing the active parameter set.

CMakeLists.txt

@@ -938,6 +938,7 @@ message(STATUS "-----------------------------------------------------------
    Vendor               = ${BLA_VENDOR}
    LAPACK Libs          = ${CLAPACK_LIBRARIES}
    LAPACK LDFLAGS       = ${CLAPACK_LINKER_FLAGS}
+   LAPACK include       = ${CLAPACK_INCLUDE_DIR}
 
    crossguid Libs       = ${CROSSGUID_LIBRARY}
    cross include        = ${CROSSGUID_INCLUDE_DIR}

CMakeModules/FindCLAPACK.cmake

@@ -326,7 +326,7 @@ if (NOT CLAPACK_INCLUDE_DIR)
 endif (NOT CLAPACK_INCLUDE_DIR)
 
 if (NOT CLAPACK_INCLUDE_DIR)
-  set(CLAPACK_INCLUDE_DIR "${COPASI_SOURCE_DIR}")
+  set(CLAPACK_INCLUDE_DIR "${COPASI_SOURCE_DIR}/copasi/lapack")
 endif (NOT CLAPACK_INCLUDE_DIR)
 
 

copasi/CopasiDataModel/CDataModel.cpp

@@ -922,7 +922,7 @@ bool CDataModel::saveModel(const std::string & fileName, CProcessReport * pProce
       mData.pModel->compileIfNecessary(pProcessReport);
 
       // Assure that the parameter set reflects all changes made to the model.
-      mData.pModel->getActiveModelParameterSet().refreshFromModel(false);
+      mData.pModel->refreshActiveParameterSet();
     }
 
   catch (...)
@@ -1012,7 +1012,7 @@ std::string CDataModel::saveModelToString(CProcessReport * pProcessReport)
       mData.pModel->compileIfNecessary(pProcessReport);
 
       // Assure that the parameter set reflects all changes made to the model.
-      mData.pModel->getActiveModelParameterSet().refreshFromModel(false);
+      mData.pModel->refreshActiveParameterSet();
     }
 
   catch (...)
@@ -1203,7 +1203,6 @@ bool CDataModel::importSBML(const std::string & fileName,
   importer.setImportHandler(pProcessReport);
   importer.setImportInitialValueAnnotation(importInitialValues);
 
-
   CModel * pModel = NULL;
 
   SBMLDocument * pSBMLDocument = NULL;
@@ -2391,7 +2390,7 @@ bool CDataModel::importSEDML(const std::string & fileName,
   // Later this will be settable by the user in the preferences dialog
   // Later this will be settable by the user in the preferences dialog
   //   importer.setImportCOPASIMIRIAM(true);
-  importer.setImportHandler(pProcessReport);  
+  importer.setImportHandler(pProcessReport);
 
   CModel * pModel = NULL;
 
@@ -3419,7 +3418,7 @@ void CDataModel::commonAfterLoad(CProcessReport * pProcessReport,
           CCopasiMessage(CCopasiMessage::WARNING, validity.getIssueMessages().c_str());
         }
 
-      mData.pModel->updateInitialValues(CCore::Framework::ParticleNumbers);
+      mData.pModel->updateInitialValues(CCore::Framework::ParticleNumbers, false);
     }
 
   changed(false);
@@ -3466,12 +3465,12 @@ bool CDataModel::changeModelParameter(CDataObject * element, double value)
           bool isInitialConcentration = pRef->getObjectName() == "InitialConcentration" && pRef->getObjectDataModel() != NULL && pRef->getObjectDataModel()->getModel() != NULL;
 
           if (isInitialConcentration)
-            pRef->getObjectDataModel()->getModel()->updateInitialValues(pRef);
+            pRef->getObjectDataModel()->getModel()->updateInitialValues(pRef, false);
 
           *static_cast< double * >(pRef->getValuePointer()) = value;
 
           if (isInitialConcentration)
-            pRef->getObjectDataModel()->getModel()->updateInitialValues(pRef);
+            pRef->getObjectDataModel()->getModel()->updateInitialValues(pRef, false);
 
           return true;
         }
@@ -3537,6 +3536,7 @@ void CDataModel::reparameterizeFromIniFile(const std::string & fileName)
     }
 
   getModel()->compileIfNecessary(NULL); // compile if needed
+  getModel()->refreshActiveParameterSet();
 }
 
 const CDataObject * CDataModel::findObjectByDisplayName(const std::string & displayString) const
@@ -3692,7 +3692,6 @@ const CDataObject * CDataModel::findObjectByDisplayName(const std::string & disp
   return NULL;
 }
 
-
 #include <sbml/SBMLDocument.h>
 #include <sbml/conversion/ConversionProperties.h>
 
@@ -3703,12 +3702,13 @@ bool
 CDataModel::convertODEsToReactions()
 {
   std::string sbml = exportSBMLToString(NULL, 3, 1);
-  
+
   auto *doc = readSBMLFromString(sbml.c_str());
 
   ConversionProperties props;
   props.addOption("inferReactions", true,
                   "Infer reactions from rateRules in the model");
+
   if (doc->convert(props) != LIBSBML_OPERATION_SUCCESS)
     {
       CCopasiMessage(CCopasiMessage::ERROR, "Couldn't infer reactions: %s", doc->getErrorLog()->toString().c_str());
@@ -3723,16 +3723,17 @@ CDataModel::convertODEsToReactions()
 /*
  * Converts Reactions in this model to ODEs
  */
-bool 
+bool
 CDataModel::convertReactionsToODEs()
 {
   std::string sbml = exportSBMLToString(NULL, 3, 1);
-  
+
   auto *doc = readSBMLFromString(sbml.c_str());
 
   ConversionProperties props;
   props.addOption("replaceReactions", true,
-                 "Replace reactions with rateRules" );      
+                  "Replace reactions with rateRules");
+
   if (doc->convert(props) != LIBSBML_OPERATION_SUCCESS)
     {
       CCopasiMessage(CCopasiMessage::ERROR, "Couldn't convert reactions to ODEs: %s", doc->getErrorLog()->toString().c_str());
@@ -3744,8 +3745,7 @@ CDataModel::convertReactionsToODEs()
   return importSBMLFromString(newSBML.c_str());
 }
 
-
-bool 
+bool
 CDataModel::convertParametersToGlobal()
 {
   std::string sbml = exportSBMLToString(NULL, 3, 1);
@@ -3755,6 +3755,7 @@ CDataModel::convertParametersToGlobal()
   ConversionProperties props;
   props.addOption("promoteLocalParameters", true,
                   "Promotes all Local Parameters to Global ones");
+
   if (doc->convert(props) != LIBSBML_OPERATION_SUCCESS)
     {
       CCopasiMessage(CCopasiMessage::ERROR, "Couldn't promote local parameters: %s", doc->getErrorLog()->toString().c_str());

copasi/CopasiSE/CopasiSE.cpp

@@ -214,7 +214,8 @@ int main(int argc, char *argv[])
   COptions::getValue("License", License);
 
   COptions::getValue("ReportFile", ReportFileName);
-  // should a report filename be given, ensure that 
+
+  // should a report filename be given, ensure that
   // it is an absolute path
   if (!ReportFileName.empty())
     CDirEntry::makePathAbsolute(ReportFileName, COptions::getPWD());
@@ -625,8 +626,8 @@ int exportParametersToIniFile()
 
   if (!pDataModel || !pDataModel->getModel()) return -2;
 
-  pDataModel->getModel()->getActiveModelParameterSet().
-  saveToStream(fs, CCore::Framework::Concentration, "ini", "");
+  pDataModel->getModel()->refreshActiveParameterSet();
+  pDataModel->getModel()->getActiveModelParameterSet().saveToStream(fs, CCore::Framework::Concentration, "ini", "");
 
   fs.close();
 

copasi/UI/CQParameterOverviewWidget.cpp

@@ -399,10 +399,11 @@ void CQParameterOverviewWidget::slotBtnNew()
   if (answer == QMessageBox::Save)
     {
       // Save the parameter set to a new or existing set
+      pModel->refreshActiveParameterSet();
       saveParameterSet(&pModel->getActiveModelParameterSet());
     }
 
-  // TODO CRITICAL We need to record all changes to the model
+  // We need to record all changes to the model
   pSetToApply->updateModel();
 
   // Notify the GUI that the model state has changed.

copasi/UI/CQParameterSetsDM.cpp

@@ -1,4 +1,4 @@
-// Copyright (C) 2019 - 2021 by Pedro Mendes, Rector and Visitors of the
+// Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the
 // University of Virginia, University of Heidelberg, and University
 // of Connecticut School of Medicine.
 // All rights reserved.
@@ -189,7 +189,7 @@ bool CQParameterSetsDM::insertRows(int position, int rows, const QModelIndex & p
       while (pModel->getModelParameterSets().getIndex(TO_UTF8(Name)) != C_INVALID_INDEX)
         Name = QString("Parameter Set %1").arg(LocalTimeStamp().c_str());
 
-      CModelParameterSet * pNew = new CModelParameterSet(pModel->getActiveModelParameterSet(), NULL, false);
+      CModelParameterSet * pNew = new CModelParameterSet(pModel, NULL);
       pNew->setObjectName(TO_UTF8(Name));
       mpListOfParameterSets->add(pNew, true);
       ++mFetched;

copasi/model/CCompartment.cpp

@@ -74,7 +74,7 @@ bool CCompartment::applyData(const CData & data, CUndoData::CChangeSet & changes
     {
       const CData & Data = data.getProperty(CData::INITIAL_VALUE).toData();
       mIValue = Data.getProperty(CData::VALUE).toDouble();
-      mpModel->updateInitialValues(CCore::FrameworkNames.toEnum(Data.getProperty(CData::FRAMEWORK).toString(), CCore::Framework::ParticleNumbers));
+      mpModel->updateInitialValues(CCore::FrameworkNames.toEnum(Data.getProperty(CData::FRAMEWORK).toString(), CCore::Framework::ParticleNumbers), false);
       changes.add({CUndoData::Type::CHANGE, "State", mpModel->getStringCN(), mpModel->getStringCN()});
     }
 

copasi/model/CModel.cpp

@@ -1307,32 +1307,9 @@ CModelParameterSet & CModel::getActiveModelParameterSet()
   return mParameterSet;
 }
 
-void CModel::applyActiveParameterSet()
-{
-  CModelParameterSet * pParameterSet =
-    dynamic_cast< CModelParameterSet * >(CRootContainer::getKeyFactory()->get(mActiveParameterSetKey));
-
-  if (pParameterSet != NULL)
-    {
-      pParameterSet->updateModel();
-    }
-  else
-    {
-      /*
-      CModelParameterSet * pParameterSet = new CModelParameterSet(UTCTimeStamp());
-      mParameterSets.add(pParameterSet, true);
-      mActiveParameterSetKey = pParameterSet->getKey();
-      pParameterSet->createFromModel();
-      */
-    }
-
-  mParameterSet.createFromModel();
-  mActiveParameterSetKey = mParameterSet.getKey();
-}
-
 void CModel::refreshActiveParameterSet()
 {
-  mParameterSet.refreshFromModel(false);
+  mParameterSet.createFromModel();
 }
 
 CDataVectorN < CEvent > & CModel::getEvents()
@@ -1780,7 +1757,7 @@ bool CModel::setQuantityUnit(const std::string & name,
 
   mNumber2QuantityFactor = 1.0 / mQuantity2NumberFactor;
 
-  updateInitialValues(framework);
+  updateInitialValues(framework, false);
 
   return true;
 }

copasi/model/CModel.h

@@ -325,11 +325,6 @@ class CModel : public CModelEntity
   const CModelParameterSet & getActiveModelParameterSet() const;
   CModelParameterSet & getActiveModelParameterSet();
 
-  /**
-   * Update the model initial values from the active parameter set.
-   */
-  void applyActiveParameterSet();
-
   /**
    * refresh the active parameter set from the model initial values
    */
@@ -511,7 +506,7 @@ class CModel : public CModelEntity
    * @param refreshParameterSet (default: true) if true the active parameter set is refreshed
    * @return bool success
    */
-  bool updateInitialValues(const CCore::Framework & framework, bool refreshParameterSet=true);
+  bool updateInitialValues(const CCore::Framework & framework, bool refreshParameterSet = true);
 
   /**
    * Copy the current state value to the initial state
@@ -1036,7 +1031,7 @@ class CModel : public CModelEntity
    *
    * @see buildInitialRefreshSequence(std::set< const CDataObject * > & changedObjects)
    */
-  void updateInitialValues(std::set< const CDataObject * > & changedObjects, bool refreshParameterSet=true);
+  void updateInitialValues(std::set< const CDataObject * > & changedObjects, bool refreshParameterSet = true);
 
   /**
    * Builds and executes the the update sequence used to calculate all initial
@@ -1049,7 +1044,7 @@ class CModel : public CModelEntity
    *
    * @see updateInitialValues(std::set< const CDataObject * > & changedObjects)
    */
-  void updateInitialValues(const CDataObject * changedObject, bool refreshParameterSet=true);
+  void updateInitialValues(const CDataObject * changedObject, bool refreshParameterSet = true);
 
   /**
    * Initialize a vector of individual absolute tolerances

copasi/model/CModelParameterSet.cpp

@@ -203,6 +203,41 @@ CModelParameterSet::CModelParameterSet(const CModelParameterSet & src,
   compile();
 }
 
+CModelParameterSet::CModelParameterSet(CModel * pModel,
+                                       const CDataContainer * pParent):
+  CDataContainer("No Name", pParent, "ModelParameterSet"),
+  CAnnotation(),
+  CModelParameterGroup(NULL, CModelParameter::Type::Set),
+  mKey(CRootContainer::getKeyFactory()->add("ModelParameterSet", this)),
+  mpModel(pModel),
+  mpTimes(NULL),
+  mpCompartments(NULL),
+  mpSpecies(NULL),
+  mpModelValues(NULL),
+  mpReactions(NULL)
+{
+  initMiriamAnnotation(mKey);
+
+  // Create the proper structure that fits the parameter overview in the GUI
+  mpTimes = static_cast< CModelParameterGroup * >(CModelParameterGroup::add(Type::Group));
+  mpTimes->setCN(CDataString("Initial Time").getCN());
+
+  mpCompartments = static_cast< CModelParameterGroup * >(CModelParameterGroup::add(Type::Group));
+  mpCompartments->setCN(CDataString("Initial Compartment Sizes").getCN());
+
+  mpSpecies = static_cast< CModelParameterGroup * >(CModelParameterGroup::add(Type::Group));
+  mpSpecies->setCN(CDataString("Initial Species Values").getCN());
+
+  mpModelValues = static_cast< CModelParameterGroup * >(CModelParameterGroup::add(Type::Group));
+  mpModelValues->setCN(CDataString("Initial Global Quantities").getCN());
+
+  mpReactions = static_cast< CModelParameterGroup * >(CModelParameterGroup::add(Type::Group));
+  mpReactions->setCN(CDataString("Kinetic Parameters").getCN());
+  setObjectParent(pParent);
+
+  createFromModel();
+}
+
 // virtual
 CModelParameterSet::~CModelParameterSet()
 {
@@ -299,7 +334,8 @@ bool CModelParameterSet::setObjectParent(const CDataContainer * pParent)
 {
   bool success = CDataObject::setObjectParent(pParent);
 
-  mpModel = dynamic_cast< CModel * >(getObjectAncestor("Model"));
+  if (mpModel == nullptr)
+    mpModel = dynamic_cast< CModel * >(getObjectAncestor("Model"));
 
   return success;
 }
@@ -464,7 +500,7 @@ bool CModelParameterSet::updateModel()
 
   bool success = CModelParameterGroup::updateModel();
 
-  mpModel->updateInitialValues(CCore::Framework::ParticleNumbers);
+  mpModel->updateInitialValues(CCore::Framework::ParticleNumbers, true);
 
   return success;
 }

copasi/model/CModelParameterSet.h

@@ -100,6 +100,14 @@ class CModelParameterSet: public CDataContainer, public CModelParameterGroup, pu
                      const CDataContainer * pParent,
                      const bool & createMissing = false);
 
+  /**
+   * Specific constructor
+   * @param CModel * pModel
+   * @param const CDataContainer * pParent
+   */
+  CModelParameterSet(CModel * pModel,
+                     const CDataContainer * pParent);
+
   /**
    * Destructor
    */