Merge branch 'master' into subminimizationPerformance

Makefile

@@ -23,7 +23,8 @@
 AR          = ar
 FC          = gfortran
 CC          = g++
-FCFLAGS     = -Wall -O2 -fno-automatic -fbounds-check -ffpe-trap=zero -cpp -D"DATA_DIRECTORY='$(DATA_DIR)'"
+FFPE_TRAPS  ?= zero
+FCFLAGS     = -Wall -O2 -fno-automatic -fbounds-check -ffpe-trap=$(FFPE_TRAPS) -cpp -D"DATA_DIRECTORY='$(DATA_DIR)'"
 CCFLAGS     = -std=gnu++17
 
 UNAME_S := $(shell uname -s)
@@ -88,7 +89,7 @@ SHARED_LIB  = $(OBJ_DIR)/$(TC_LIB)
 ## C interface library:
 ## =================
 C_SRC       = Thermochimica-c.C Thermochimica-cxx.C
-C_OBJ       = $(C_SRC:.C=.o) 
+C_OBJ       = $(C_SRC:.C=.o)
 C_LNK       = $(addprefix $(OBJ_DIR)/,$(C_OBJ))
 TC-C_LIB    = libthermoc.a
 C_LIB  		= $(OBJ_DIR)/$(TC-C_LIB)
@@ -234,6 +235,6 @@ test: all dailytest
 ## DEBUG:
 ## ===========
 setdebug:
-	$(eval FCFLAGS = -Wall -O0 -g -fno-automatic -fbounds-check -ffpe-trap=zero -D"DATA_DIRECTORY='$(DATA_DIR)'")
+	$(eval FCFLAGS = -Wall -O0 -g -fno-automatic -fbounds-check -ffpe-trap=$(FFPE_TRAPS) -D"DATA_DIRECTORY='$(DATA_DIR)'")
 
 debug: setdebug all dailytest

src/Thermochimica-cxx.C

@@ -56,6 +56,11 @@ namespace Thermochimica
     TCAPI_setTemperaturePressure(&temperature, &pressure);
   }
 
+  void presetElementMass(int element, double mass)
+  {
+    TCAPI_presetElementMass(&element, &mass);
+  }
+
   void setElementMass(int element, double mass)
   {
     TCAPI_setElementMass(&element, &mass);
@@ -98,6 +103,80 @@ namespace Thermochimica
     TCAPI_resetThermoAll();
   }
 
+  // utilitiy functions for consistency check / database record
+  std::pair<std::size_t, std::size_t> getNumberPhasesDatabase()
+  {
+    int solution, condensed;
+    TCAPI_getNumberPhasesDatabase(&solution, &condensed);
+    return {(std::size_t)solution, (std::size_t)condensed};
+  }
+
+  std::vector<std::string> getPhaseNamesDatabase()
+  {
+    auto [n_soln_phases, n_cond_phases] = getNumberPhasesDatabase();
+    auto n_phases = n_soln_phases + n_cond_phases;
+
+    std::vector<std::string> phase_names(n_phases);
+
+    for (std::size_t i = 0; i < n_phases; ++i)
+      phase_names[i] = getPhaseNameAtIndex(i);
+
+    return phase_names;
+  }
+
+  std::vector<std::size_t> getNumberSpeciesDatabase()
+  {
+    auto [n_soln_phases, n_cond_phases] = getNumberPhasesDatabase();
+    (void)n_cond_phases;
+    std::vector<int> n_sp(n_soln_phases);
+    std::vector<std::size_t> n_species(n_soln_phases);
+    TCAPI_getNumberSpeciesDatabase(n_sp.data());
+    for (std::size_t i = 0; i < n_soln_phases; ++i)
+      n_species[i] = (std::size_t)n_sp[i];
+
+    return n_species;
+  }
+
+  std::string getPhaseNameAtIndex(int phase_index)
+  {
+    int length;
+    auto index = phase_index + 1; // Fortran indexing starts at 1 instead of 0
+
+    char *buffer = TCAPI_getPhaseNameAtIndex(&index, &length);
+
+    return std::string(buffer, buffer + length);
+  }
+
+  std::vector<std::vector<std::string>> getSpeciesDatabase()
+  {
+    auto [n_soln_phases, n_cond_phases] = getNumberPhasesDatabase();
+    (void)n_cond_phases;
+    std::vector<std::vector<std::string>> species(n_soln_phases);
+
+    for (std::size_t i = 0; i < n_soln_phases; ++i)
+      species[i] = getSpeciesInPhaseDatabase(i);
+
+    return species;
+  }
+
+  std::vector<std::string> getSpeciesInPhaseDatabase(int phase_index)
+  {
+    int length, index;
+    auto n_species = getNumberSpeciesDatabase();
+    auto n_species_phase = phase_index == 0 ? n_species[phase_index] : n_species[phase_index] - n_species[phase_index - 1];
+
+    std::vector<std::string> species(n_species_phase);
+
+    for (std::size_t i = 0; i < n_species_phase; ++i)
+    {
+      index = phase_index == 0 ? i + 1 : n_species[phase_index - 1] + i + 1;
+      char *buffer = TCAPI_getSpeciesAtIndex(&index, &length);
+      species[i] = std::string(buffer, buffer + length);
+    }
+
+    return species;
+  }
+
   // re-initialization-related functions
   void saveReinitData()
   {
@@ -113,15 +192,15 @@ namespace Thermochimica
 
   std::vector<double> getMolesPhase()
   {
-    auto [elements, species] = getReinitDataSizes();
+    auto elements = getReinitDataSizes().first;
     std::vector<double> molesPhase(elements);
     TCAPI_getMolesPhase(molesPhase.data());
     return molesPhase;
   }
 
   std::vector<int> getAssemblage()
   {
-    auto [elements, species] = getReinitDataSizes();
+    auto elements = getReinitDataSizes().first;
     std::vector<int> assemblage(elements);
     TCAPI_getAssemblage(assemblage.data());
     return assemblage;
@@ -140,7 +219,7 @@ namespace Thermochimica
 
   std::vector<double> getAllElementPotential()
   {
-    auto [elements, species] = getReinitDataSizes();
+    auto elements = getReinitDataSizes().first;
     std::vector<double> potential(elements);
     TCAPI_getAllElementPotential(potential.data());
     return potential;

src/Thermochimica-cxx.h

@@ -17,6 +17,7 @@ namespace Thermochimica
   void setStandardUnits();
   void setModelicaUnits();
   void setTemperaturePressure(double temperature, double pressure);
+  void presetElementMass(int element, double mass);
   void setElementMass(int element, double mass);
   int checkInfoThermo();
   void parseThermoFile();
@@ -26,6 +27,14 @@ namespace Thermochimica
   void resetThermo();
   void resetThermoAll();
 
+  // utilitiy functions for consistency check / database record
+  std::pair<std::size_t, std::size_t> getNumberPhasesDatabase();
+  std::vector<std::string> getPhaseNamesDatabase();
+  std::string getPhaseNameAtIndex(int phase_index);
+  std::vector<std::size_t> getNumberSpeciesDatabase();
+  std::vector<std::string> getSpeciesInPhaseDatabase(int phase_index);
+  std::vector<std::vector<std::string>> getSpeciesDatabase();
+
   // re-initialization-related functions
   void saveReinitData();
   std::pair<int, int> getReinitDataSizes();
@@ -69,7 +78,8 @@ namespace Thermochimica
   getMqmqaConstituentFraction(const std::string &phaseName, int sublattice, const std::string &constituent);
 
   // Reinitialization data
-  struct reinitData {
+  struct reinitData
+  {
     std::vector<int> assemblage;
     std::vector<double> molesPhase;
     std::vector<double> elementPotential;

src/Thermochimica.f90

@@ -467,7 +467,7 @@ subroutine Thermochimica
         ! Attempt a retry by re-initializing with first phase only
         call RetryCalculationFirstPhase
         ! Perform post-processing calculations of results:
-        if (INFOThermo == 0 .OR. INFOThermo == 12) call PostProcess
+        if (INFOThermo == 0 .OR. INFOThermo == 12) call PostProcessThermo
     end if
 
     if (lHeatCapacityEntropyEnthalpy .AND. .NOT. lHeatCapacityCurrent) call HeatCapacity

src/Thermochimica.h

@@ -46,6 +46,11 @@ extern "C"
   void TCAPI_printResults();
   void TCAPI_printState();
 
+  void TCAPI_getNumberPhasesDatabase(int *, int *);
+  char *TCAPI_getPhaseNameAtIndex(int *, int *);
+  void TCAPI_getNumberSpeciesDatabase(int *);
+  char *TCAPI_getSpeciesAtIndex(int *, int *);
+
   void TCAPI_resetInfoThermo();
   void TCAPI_resetThermo();
   void TCAPI_resetThermoAll();

src/api/CouplingUtilities.f90

@@ -202,6 +202,33 @@ subroutine SetElementMass(iAtom, dMass)
 
 end subroutine SetElementMass
 
+subroutine GetNumberPhasesDatabase(iNumSolnPhases, iNumConPhases)
+
+  USE ModuleParseCS, ONLY: nSpeciesCS, nSpeciesPhaseCS, nSolnPhasesSysCS
+
+  implicit none
+
+  integer, intent(out):: iNumSolnPhases, iNumConPhases
+
+  iNumConPhases = nSpeciesCS - MAXVAL(nSpeciesPhaseCS)
+  iNumSolnPhases = nSolnPhasesSysCS
+
+  return
+
+end subroutine GetNumberPhasesDatabase
+
+subroutine GetNumberSpeciesDatabase(nSpeciesDB)
+  USE ModuleParseCS, ONLY: nSolnPhasesSysCS, nSpeciesPhaseCS
+  implicit none
+
+  integer, intent(out), dimension(nSolnPhasesSysCS)     :: nSpeciesDB
+
+  nSpeciesDB = nSpeciesPhaseCS(1:size(nSpeciesDB))
+
+  return
+
+end subroutine GetNumberSpeciesDatabase
+
 subroutine GetElementMass(iAtom, dMass)
 
   USE ModuleThermoIO, ONLY: dElementMass