Merge pull request #48 from sdmytrievs/master

Calculating if the GEMS3k system is without an aqueous phase

Author: sdmytrievs

.github/workflows/ci-build.yml

@@ -21,15 +21,12 @@ jobs:
         os:
           - ubuntu-latest
           - windows-latest
-          - macos-13
           - macos-latest
         include:
           - os: ubuntu-latest
             conda_platform: linux-64
           - os: windows-latest
             conda_platform: win-64
-          - os: macos-13
-            conda_platform: osx-64
           - os: macos-latest
             conda_platform: osx-arm64
 
@@ -72,6 +69,13 @@ jobs:
           cmake --build build --target install --config Release || goto :eof
           python -c "import solmod4rkt" || goto :eof
 
+      - name: Run tests that read GEMS3K
+        shell: bash -l {0}
+        run: |
+          conda activate GEMS3K
+          python -c "import solmod4rkt"
+          conda list
+
       - name: Check conda
         run: |
           conda config --show

CMakeLists.txt

@@ -1,8 +1,8 @@
 # Require a certain version of cmake
-cmake_minimum_required(VERSION 3.16)
+cmake_minimum_required(VERSION 3.16..4.2)
 
 # Set the name of the project
-project(GEMS3K VERSION 4.4.3 LANGUAGES CXX C)
+project(GEMS3K VERSION 4.4.4 LANGUAGES CXX C)
 
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
@@ -150,10 +150,9 @@ configure_file(
   )
 
 # Set some necessary definitions
-add_definitions(-DNODEARRAYLEVEL)
-
-if(USE_THERMOFUN MATCHES ON)
-  add_definitions(-DUSE_THERMOFUN)
+if(USE_THERMOFUN MATCHES OFF)
+  add_definitions(-DNO_THERMOFUN)
+else()
   #add_definitions(-DUSE_THERMO_LOG)
 endif()
 

GEMS3K/databr.h

@@ -71,7 +71,7 @@ typedef struct  /// DATABR - template node data bridge structure
     Eh,     ///< Eh of aqueous solution (V)                                  -      -      +     +
     Tm,     ///< Actual total simulation time (s)                            +      +      -     -
     dt      ///< Actual time step (s) - needed for TKinMet, can change!      +      +     (+)   (+)
-#ifdef NODEARRAYLEVEL
+#ifndef NO_NODEARRAYLEVEL
       ,
 // \section  FMT variables (units or dimensionsless) - to be used for storing them
 //  at the nodearray level, normally not used in the single-node FMT-GEM coupling
@@ -189,7 +189,7 @@ f_IterDone, f_TK, f_P, f_Vs,f_Vi,
 f_Ms, f_Mi, f_Hs, f_Hi, f_Gs,
 f_IS, f_pH, f_pe, f_Eh,
 f_Tm, f_dt,
-//#ifdef NODEARRAYLEVEL
+//#ifndef NO_NODEARRAYLEVEL
 f_Dif,f_Vt, f_vp, f_eps,
 f_Km, f_Kf, f_S,  f_Tr, f_h,
 f_rho,f_al, f_at, f_av, f_hDl,

GEMS3K/datach_api.cpp

@@ -352,6 +352,12 @@ void datach_realloc(DATACH* CSD)
     CSD->denWg = new double[ 5*gridTP(CSD)];
     CSD->epsW = new double[ 5*gridTP(CSD)];
     CSD->epsWg = new double[ 5*gridTP(CSD)];
+    for(int  j=0; j<5*gridTP(CSD); j++ )  {
+        CSD->denW[j] = 0.;
+        CSD->denWg[j] = 0.;
+        CSD->epsW[j] = 0.;
+        CSD->epsWg[j] = 0.;
+    }
 
     CSD->G0 = new double[CSD->nDC*gridTP(CSD)];
     CSD->V0 = new double[CSD->nDC*gridTP(CSD)];
@@ -652,7 +658,7 @@ void databr_reset(DATABR *CnNde1, long int level)
     //  at the nodearray level = 0.; normally not used in the single-node FMT-GEM coupling
     CnNde1->Tm = 0.;
     CnNde1->dt = 0.;
-#ifdef NODEARRAYLEVEL
+#ifndef NO_NODEARRAYLEVEL
     CnNde1->Dif = 0.;
     CnNde1->Vt = 0.;
     CnNde1->vp = 0.;

GEMS3K/datach_formats.cpp

@@ -73,7 +73,7 @@ std::vector<io_formats::outField> DataBR_fields =  {  // [f_lga+1/*60*/]
   { "Eh",   0, 0, 1, "# Eh: Eh of aqueous solution, V (GEM output)" },
   { "Tm",   0, 0, 1, "# Tm: Actual total simulation time, s (kinetics, metastability, transport)" },
   { "dt",   0, 0, 1, "# dt: Actual time step, s (kinetics, metastability, transport)" },
-//#ifdef NODEARRAYLEVEL
+//#ifndef NO_NODEARRAYLEVEL
 // Scalar parameters below are only used at TNodeArray level
   { "Dif",  0, 0, 1, "# Dif: General diffusivity of disolved matter, m2/s (mass transport)" },
   { "Vt",   0, 0, 1, "# Vt: Total volume of the node, m3 (mass transport)" },
@@ -228,7 +228,7 @@ void databr_to_text_file(const DATACH* CSD, const DATABR* CNode, TIO& out_format
     prar.writeField(f_Tm, CNode->Tm, _comment, brief_mode  );
     prar.writeField(f_dt, CNode->dt, _comment, brief_mode  );
 
-#ifdef NODEARRAYLEVEL
+#ifndef NO_NODEARRAYLEVEL
     if( CNode->NodeStatusFMT != No_nodearray /*TNodeArray::na->nNodes() > 1*/ )
     {
         if( _comment )
@@ -308,7 +308,7 @@ void databr_to_text_file(const DATACH* CSD, const DATABR* CNode, TIO& out_format
 template<typename TIO>
 void databr_from_text_file(const DATACH* CSD, DATABR* CNode, TIO& in_format )
 {
-#ifndef NODEARRAYLEVEL
+#ifdef NO_NODEARRAYLEVEL
     double tmpVal;
 #endif
 
@@ -366,7 +366,7 @@ void databr_from_text_file(const DATACH* CSD, DATABR* CNode, TIO& in_format )
             break;
         case f_dt: rdar.readArray( "dt",  &CNode->dt, 1);
             break;
-#ifdef NODEARRAYLEVEL
+#ifndef NO_NODEARRAYLEVEL
         case f_Dif: rdar.readArray( "Dif",  &CNode->Dif, 1);
             break;
         case f_Vt: rdar.readArray( "Vt",  &CNode->Vt, 1);
@@ -848,7 +848,8 @@ void datach_to_file(const DATACH* CSD, GemDataStream& ff)
     ff.writeArray( CSD->ccPH, CSD->nPH );
 
     if( CSD->ccPH[0] == PH_AQUEL )
-    { ff.writeArray( CSD->denW,  5*gridTP(CSD) );
+    {
+        ff.writeArray( CSD->denW,  5*gridTP(CSD) );
         ff.writeArray( CSD->denWg,  5*gridTP(CSD) );
         ff.writeArray( CSD->epsW, 5*gridTP(CSD) );
         ff.writeArray( CSD->epsWg, 5*gridTP(CSD) );
@@ -924,7 +925,7 @@ void databr_to_file(const DATACH* CSD, const DATABR* CNode, GemDataStream& ff)
     // const data
     ff.writeArray( &CNode->NodeHandle, 6 );
 
-#ifdef NODEARRAYLEVEL
+#ifndef NO_NODEARRAYLEVEL
     if( CNode->NodeStatusFMT != No_nodearray )
         ff.writeArray( &CNode->TK, 32 );
     else
@@ -967,7 +968,7 @@ void databr_from_file(const DATACH* CSD, DATABR* CNode, GemDataStream& ff)
     // const data
     ff.readArray( &CNode->NodeHandle, 6 );
 
-#ifdef NODEARRAYLEVEL
+#ifndef NO_NODEARRAYLEVEL
     if( CNode->NodeStatusFMT != No_nodearray )
         ff.readArray( &CNode->TK, 32 );
     else

GEMS3K/gems3k_impex.cpp

@@ -27,7 +27,7 @@ std::string GEMS3KGenerator::gen_dbr_name(const std::string the_name, int time_p
 GEMS3KGenerator::GEMS3KGenerator(const std::string &filepath, long anIV, IOModes file_mode):
     ipmfiles_lst_name(filepath), nIV(anIV), io_mode(file_mode)
 {
-#ifndef USE_THERMOFUN
+#ifdef NO_THERMOFUN
     ErrorIf( io_mode>=f_thermofun, ipmfiles_lst_name, " ThermoFun as an option is hidden");
 #endif
     set_internal_data();
@@ -88,7 +88,7 @@ void GEMS3KGenerator::load_dat_lst_file()
 
     if( files_mode() >= f_thermofun )
     {
-#ifdef USE_THERMOFUN
+#ifndef NO_THERMOFUN
         f_getline( f_lst, thermofun_file_name, ' ');
         trim(thermofun_file_name, "\"");
 #else

GEMS3K/gems3k_version.h

@@ -1,7 +1,7 @@
 #pragma once
 
-#define GEMS3K_VERSION "4.4.3"
-#define GEMS3K_VERSION_HASH "33622fe"
+#define GEMS3K_VERSION "4.4.4"
+#define GEMS3K_VERSION_HASH "0995d4c"
 #define GEMS3K_GIT_BRANCH "master"
-#define GEMS3K_ChemicalFun "0.1.12"
-#define GEMS3K_ThermoFun "0.5.2"
+#define GEMS3K_ChemicalFun "0.1.13"
+#define GEMS3K_ThermoFun "0.5.4"

GEMS3K/jsonconfig.cpp

@@ -287,9 +287,9 @@ std::string GemsSettings::logger_section_name = "log";
 
 std::set<std::string> GemsSettings::default_gems3k_loggers = {
     "gems3k", "ipm", "tnode", "kinmet", "solmod",
-    #ifdef USE_THERMOFUN
+#ifndef NO_THERMOFUN
     "chemicalfun", "thermofun"
-    #endif
+#endif
 };
 
 std::string GemsSettings::gems3k_logger_pattern("[%n] [%^%l%$] %v");

GEMS3K/ms_multi_diff.cpp

@@ -390,11 +390,21 @@ void TMultiBase::load_all_thermodynamic_from_grid(TNode* aNa, double TK, double
             {
                 Go = dCH->G0[ jj+xTP];
                 Vv = dCH->V0[ jj+xTP]*1e5;
-                if( dCH->S0 ) S0 = dCH->S0[ jj+xTP];
-                if( dCH->H0 ) h0 = dCH->H0[ jj+xTP];
-                if( dCH->Cp0 ) Cp0 = dCH->Cp0[ jj+xTP];
-                if( dCH->A0 ) a0 = dCH->A0[ jj+xTP];
-                if( dCH->U0 ) h0 = dCH->U0[ jj+xTP];
+                if( dCH->S0 ) {
+                    S0 = dCH->S0[ jj+xTP];
+                }
+                if( dCH->H0 ) {
+                    h0 = dCH->H0[ jj+xTP];
+                }
+                if( dCH->Cp0 ) {
+                    Cp0 = dCH->Cp0[ jj+xTP];
+                }
+                if(dCH->A0) {
+                    a0 = dCH->A0[ jj+xTP];
+                }
+                if(dCH->U0) {
+                    u0 = dCH->U0[ jj+xTP];
+                }
             }
             else
             {

GEMS3K/ms_multi_format.cpp

@@ -688,6 +688,11 @@ void TMultiBase::from_text_file_gemipm( TIO& in_format,  DATACH  *dCH )
         Error( "Error", ret);
     }
 
+    // Try fix error 09.12.2025 lost pm.E after reading gems3k files
+    if( pm.E && dCH->ccIC[dCH->nICb-1] != IC_CHARGE) {
+        pm.E = 0;
+    }
+
     PAalp_ = PAalp;
     PSigm_ = PSigm;
     multi_realloc( PAalp, PSigm );
@@ -832,6 +837,7 @@ void TMultiBase::from_text_file_gemipm( TIO& in_format,  DATACH  *dCH )
                 alloc_SitFr(LsSitSum);
                 fillValue( pm.SitFr, 0., LsSitSum );
                 rddar.readArray( "MoiSN", pm.MoiSN,  LsMsnSum);
+                // ??? rddar.readArray( "SitFr", pm.SitFr,  LsSitSum);
             }
             break;
         }