From 8547ae173fa1452df6b44210e51455366a92aeb4 Mon Sep 17 00:00:00 2001
From: Will Bainbridge <http://cfd.direct>
Date: Tue, 20 Apr 2021 17:14:30 +0100
Subject: [PATCH] chemistryReductionMethods: Change dictionaries to lists

The "initialSet" and "fuelSpecies" settings for chemistry reduction
methods now have to be formatted as lists, rather than dictionaries.
This is so that the settings in the TDAC configuration files can be
overridden in a case without the dictionaries being merged.
---
 .../chemistry/TDAC/chemistryProperties.cfg    | 16 ++---
 .../TDAC/chemistryPropertiesFlame.cfg         | 16 ++---
 .../TDACChemistryModel/reduction/DAC/DAC.C    | 71 +++++--------------
 .../TDACChemistryModel/reduction/DRG/DRG.C    | 20 ++----
 .../reduction/DRGEP/DRGEP.C                   | 20 ++----
 .../TDACChemistryModel/reduction/PFA/PFA.C    | 23 ++----
 .../ic8h18_TDAC/constant/chemistryProperties  | 10 +--
 .../DLR_A_LTS/constant/chemistryProperties    | 16 ++---
 8 files changed, 59 insertions(+), 133 deletions(-)

diff --git a/etc/caseDicts/solvers/chemistry/TDAC/chemistryProperties.cfg b/etc/caseDicts/solvers/chemistry/TDAC/chemistryProperties.cfg
index a781416695..9478f00aa3 100644
--- a/etc/caseDicts/solvers/chemistry/TDAC/chemistryProperties.cfg
+++ b/etc/caseDicts/solvers/chemistry/TDAC/chemistryProperties.cfg
@@ -22,11 +22,11 @@ reduction
 
     // Search initiating set (SIS) of species, needed for most methods
     initialSet
-    {
-        CO;
-        CH4;
-        HO2;
-    }
+    (
+        CO
+        CH4
+        HO2
+    );
 
     // For DAC, option to automatically change the SIS switch from HO2 to H2O
     // and CO to CO2, + disable fuel
@@ -34,9 +34,9 @@ reduction
 
     // When automaticSIS, the method needs to know the fuel
     fuelSpecies
-    {
-        CH4 1;
-    }
+    (
+        (CH4 1)
+    );
 }
 
 tabulation
diff --git a/etc/caseDicts/solvers/chemistry/TDAC/chemistryPropertiesFlame.cfg b/etc/caseDicts/solvers/chemistry/TDAC/chemistryPropertiesFlame.cfg
index fffab2c068..597f33031d 100644
--- a/etc/caseDicts/solvers/chemistry/TDAC/chemistryPropertiesFlame.cfg
+++ b/etc/caseDicts/solvers/chemistry/TDAC/chemistryPropertiesFlame.cfg
@@ -22,11 +22,11 @@ reduction
 
     // Search initiating set (SIS) of species, needed for most methods
     initialSet
-    {
-        CO;
-        CH4;
-        HO2;
-    }
+    (
+        CO
+        CH4
+        HO2
+    );
 
     // For DAC, option to automatically change the SIS switch from HO2 to H2O
     // and CO to CO2, + disable fuel
@@ -34,9 +34,9 @@ reduction
 
     // When automaticSIS, the method needs to know the fuel
     fuelSpecies
-    {
-        CH4 1;
-    }
+    (
+        (CH4 1)
+    );
 }
 
 tabulation
diff --git a/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DAC/DAC.C b/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DAC/DAC.C
index d20d9f3805..68f179e2c3 100644
--- a/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DAC/DAC.C
+++ b/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DAC/DAC.C
@@ -35,7 +35,7 @@ Foam::chemistryReductionMethods::DAC<ThermoType>::DAC
 )
 :
     chemistryReductionMethod<ThermoType>(dict, chemistry),
-    searchInitSet_(this->coeffsDict_.subDict("initialSet").size()),
+    searchInitSet_(),
     zprime_(0),
     nbCLarge_(3),
     sC_(this->nSpecie_,0),
@@ -87,22 +87,10 @@ Foam::chemistryReductionMethods::DAC<ThermoType>::DAC
     ),
     forceFuelInclusion_(false)
 {
-    label j=0;
-    dictionary initSet = this->coeffsDict_.subDict("initialSet");
-    for (label i=0; i<chemistry.nSpecie(); i++)
+    const wordHashSet initSet(this->coeffsDict_.lookup("initialSet"));
+    forAllConstIter(wordHashSet, initSet, iter)
     {
-        if (initSet.found(chemistry.Y()[i].member()))
-        {
-            searchInitSet_[j++] = i;
-        }
-    }
-    if (j<searchInitSet_.size())
-    {
-        FatalErrorInFunction
-            << searchInitSet_.size()-j
-            << " species in the initial set is not in the mechanism "
-            << initSet
-            << exit(FatalError);
+        searchInitSet_.append(chemistry.mixture().species()[iter.key()]);
     }
 
     if (this->coeffsDict_.found("automaticSIS"))
@@ -195,52 +183,29 @@ Foam::chemistryReductionMethods::DAC<ThermoType>::DAC
     // According to the given mass fraction, an equivalent O/C ratio is computed
     if (automaticSIS_)
     {
-        dictionary fuelDict;
-        if (this->coeffsDict_.found("fuelSpecies"))
-        {
-            fuelDict = this->coeffsDict_.subDict("fuelSpecies");
-            fuelSpecies_ = fuelDict.toc();
-            if (fuelSpecies_.size() == 0)
-            {
-                FatalErrorInFunction
-                    << "With automatic SIS, the fuel species should be "
-                    << "specified in the fuelSpecies subDict"
-                    << exit(FatalError);
-            }
-        }
-        else
-        {
-            FatalErrorInFunction
-                << "With automatic SIS, the fuel species should be "
-                << "specified in the fuelSpecies subDict"
-                << exit(FatalError);
-        }
+        List<Tuple2<word, scalar>> fuelSpeciesEntry
+        (
+            this->coeffsDict_.lookup("fuelSpecies")
+        );
 
-        if (this->coeffsDict_.found("nbCLarge"))
-        {
-            nbCLarge_ = fuelDict.lookup<label>("nbCLarge");
-        }
-
-        fuelSpeciesID_.setSize(fuelSpecies_.size());
-        fuelSpeciesProp_.setSize(fuelSpecies_.size());
+        fuelSpecies_.setSize(fuelSpeciesEntry.size());
+        fuelSpeciesID_.setSize(fuelSpeciesEntry.size());
+        fuelSpeciesProp_.setSize(fuelSpeciesEntry.size());
         scalar Mmtot(0.0);
 
-        forAll(fuelSpecies_, i)
+        forAll(fuelSpeciesEntry, i)
         {
-            fuelSpeciesProp_[i] = fuelDict.lookup<scalar>(fuelSpecies_[i]);
-            for (label j=0; j<this->nSpecie_; j++)
-            {
-                if (this->chemistry_.Y()[j].member() == fuelSpecies_[i])
-                {
-                    fuelSpeciesID_[i] = j;
-                    break;
-                }
-            }
+            fuelSpecies_[i] = fuelSpeciesEntry[i].first();
+            fuelSpeciesProp_[i] = fuelSpeciesEntry[i].second();
+            fuelSpeciesID_[i] =
+                this->chemistry_.mixture().species()[fuelSpecies_[i]];
             scalar curMm =
                 this->chemistry_.specieThermos()[fuelSpeciesID_[i]].W();
             Mmtot += fuelSpeciesProp_[i]/curMm;
         }
 
+        this->coeffsDict_.readIfPresent("nbCLarge", nbCLarge_);
+
         Mmtot = 1.0/Mmtot;
         scalar nbC(0.0);
         scalar nbO(0.0);
diff --git a/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRG/DRG.C b/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRG/DRG.C
index 0f8337bdc9..a807df2ca2 100644
--- a/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRG/DRG.C
+++ b/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRG/DRG.C
@@ -35,24 +35,12 @@ Foam::chemistryReductionMethods::DRG<ThermoType>::DRG
 )
 :
     chemistryReductionMethod<ThermoType>(dict, chemistry),
-    searchInitSet_(this->coeffsDict_.subDict("initialSet").size())
+    searchInitSet_()
 {
-    label j=0;
-    dictionary initSet = this->coeffsDict_.subDict("initialSet");
-    for (label i=0; i<chemistry.nSpecie(); i++)
+    const wordHashSet initSet(this->coeffsDict_.lookup("initialSet"));
+    forAllConstIter(wordHashSet, initSet, iter)
     {
-        if (initSet.found(chemistry.Y()[i].member()))
-        {
-            searchInitSet_[j++] = i;
-        }
-    }
-    if (j<searchInitSet_.size())
-    {
-        FatalErrorInFunction
-            << searchInitSet_.size()-j
-            << " species in the initial set is not in the mechanism "
-            << initSet
-            << exit(FatalError);
+        searchInitSet_.append(chemistry.mixture().species()[iter.key()]);
     }
 }
 
diff --git a/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRGEP/DRGEP.C b/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRGEP/DRGEP.C
index 13a413bb49..ce765a8e48 100644
--- a/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRGEP/DRGEP.C
+++ b/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRGEP/DRGEP.C
@@ -36,29 +36,17 @@ Foam::chemistryReductionMethods::DRGEP<ThermoType>::DRGEP
 )
 :
     chemistryReductionMethod<ThermoType>(dict, chemistry),
-    searchInitSet_(this->coeffsDict_.subDict("initialSet").size()),
+    searchInitSet_(),
     sC_(this->nSpecie_,0),
     sH_(this->nSpecie_,0),
     sO_(this->nSpecie_,0),
     sN_(this->nSpecie_,0),
     NGroupBased_(50)
 {
-    label j=0;
-    dictionary initSet = this->coeffsDict_.subDict("initialSet");
-    for (label i=0; i<chemistry.nSpecie(); i++)
+    const wordHashSet initSet(this->coeffsDict_.lookup("initialSet"));
+    forAllConstIter(wordHashSet, initSet, iter)
     {
-        if (initSet.found(chemistry.Y()[i].member()))
-        {
-            searchInitSet_[j++]=i;
-        }
-    }
-    if (j<searchInitSet_.size())
-    {
-        FatalErrorInFunction
-            << searchInitSet_.size()-j
-            << " species in the initial set is not in the mechanism "
-            << initSet
-            << exit(FatalError);
+        searchInitSet_.append(chemistry.mixture().species()[iter.key()]);
     }
 
     if (this->coeffsDict_.found("NGroupBased"))
diff --git a/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/PFA/PFA.C b/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/PFA/PFA.C
index 6c0228c2c9..7375d0edbb 100644
--- a/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/PFA/PFA.C
+++ b/src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/PFA/PFA.C
@@ -35,27 +35,12 @@ Foam::chemistryReductionMethods::PFA<ThermoType>::PFA
 )
 :
     chemistryReductionMethod<ThermoType>(dict, chemistry),
-    searchInitSet_(this->coeffsDict_.subDict("initialSet").size())
+    searchInitSet_()
 {
-    label j=0;
-
-    dictionary initSet = this->coeffsDict_.subDict("initialSet");
-
-    for (label i=0; i<chemistry.nSpecie(); i++)
+    const wordHashSet initSet(this->coeffsDict_.lookup("initialSet"));
+    forAllConstIter(wordHashSet, initSet, iter)
     {
-        if (initSet.found(chemistry.Y()[i].member()))
-        {
-            searchInitSet_[j++] = i;
-        }
-    }
-
-    if (j<searchInitSet_.size())
-    {
-        FatalErrorInFunction
-            << searchInitSet_.size()-j
-            << " species in the initial set is not in the mechanism "
-            << initSet
-            << abort(FatalError);
+        searchInitSet_.append(chemistry.mixture().species()[iter.key()]);
     }
 }
 
diff --git a/tutorials/combustion/chemFoam/ic8h18_TDAC/constant/chemistryProperties b/tutorials/combustion/chemFoam/ic8h18_TDAC/constant/chemistryProperties
index ac61548863..fba67e6bec 100644
--- a/tutorials/combustion/chemFoam/ic8h18_TDAC/constant/chemistryProperties
+++ b/tutorials/combustion/chemFoam/ic8h18_TDAC/constant/chemistryProperties
@@ -40,11 +40,11 @@ reduction
 
     // Search initiating set (SIS) of species, needed for most methods
     initialSet
-    {
-        CO;
-        IC8H18;
-        HO2;
-    }
+    (
+        CO
+        IC8H18
+        HO2
+    );
 }
 
 // Tabulation is not effective for single-cell ignition calculations
diff --git a/tutorials/combustion/reactingFoam/RAS/DLR_A_LTS/constant/chemistryProperties b/tutorials/combustion/reactingFoam/RAS/DLR_A_LTS/constant/chemistryProperties
index 332408ad4a..848fb70d2b 100644
--- a/tutorials/combustion/reactingFoam/RAS/DLR_A_LTS/constant/chemistryProperties
+++ b/tutorials/combustion/reactingFoam/RAS/DLR_A_LTS/constant/chemistryProperties
@@ -48,11 +48,11 @@ reduction
 
     // Search initiating set (SIS) of species, needed for most methods
     initialSet
-    {
-        CO;
-        CH4;
-        HO2;
-    }
+    (
+        CO
+        CH4
+        HO2
+    );
 
     // For DAC, option to automatically change the SIS switch from HO2 to H2O
     // and CO to CO2, + disable fuel
@@ -60,9 +60,9 @@ reduction
 
     // When automaticSIS, the method needs to know the fuel
     fuelSpecies
-    {
-        CH4 1;
-    }
+    (
+        (CH4 1)
+    );
 }
 
 tabulation