From 3fd25abba9bbd16f5b1981894495837a4623aa38 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Tue, 5 Oct 2010 17:51:38 +0200
Subject: [PATCH 01/12] COMP: link liquids, thermophysicalFunctions libs when
 using liquidMixture

---
 src/thermophysicalModels/liquidMixture/Make/options | 4 ++++
 src/thermophysicalModels/liquids/Make/options       | 6 +++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/thermophysicalModels/liquidMixture/Make/options b/src/thermophysicalModels/liquidMixture/Make/options
index 506b8ac9a2..bfa6b569ba 100644
--- a/src/thermophysicalModels/liquidMixture/Make/options
+++ b/src/thermophysicalModels/liquidMixture/Make/options
@@ -5,3 +5,7 @@ EXE_INC = \
     -I$(LIB_SRC)/thermophysicalModels/combustion/lnInclude \
     -I$(LIB_SRC)/thermophysicalModels/thermophysicalFunctions/lnInclude
 
+LIB_LIBS = \
+    -lliquids \
+    -lthermophysicalFunctions
+
diff --git a/src/thermophysicalModels/liquids/Make/options b/src/thermophysicalModels/liquids/Make/options
index 8a129fda6c..b964b61294 100644
--- a/src/thermophysicalModels/liquids/Make/options
+++ b/src/thermophysicalModels/liquids/Make/options
@@ -1 +1,5 @@
-EXE_INC = -I$(LIB_SRC)/thermophysicalModels/thermophysicalFunctions/lnInclude
+EXE_INC = \
+    -I$(LIB_SRC)/thermophysicalModels/thermophysicalFunctions/lnInclude
+
+LIB_LIBS = \
+    -lthermophysicalFunctions

From e251b7b677a496ac19669ea7e3a98717323cb522 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Tue, 5 Oct 2010 17:53:30 +0200
Subject: [PATCH 02/12] STYLE: allow "solidProperties" dict entry for
 consistency with liquidMixture

- add size() method to liquidMixture and solidMixture
---
 .../liquidMixture/liquidMixture.C             | 35 ++++++++-----------
 .../liquidMixture/liquidMixture.H             | 10 +++++-
 .../solidMixture/solidMixture/solidMixture.C  | 25 +++++++++----
 .../solidMixture/solidMixture/solidMixture.H  | 22 ++++++++++--
 4 files changed, 62 insertions(+), 30 deletions(-)

diff --git a/src/thermophysicalModels/liquidMixture/liquidMixture/liquidMixture.C b/src/thermophysicalModels/liquidMixture/liquidMixture/liquidMixture.C
index 4941eab537..d46e3e110a 100644
--- a/src/thermophysicalModels/liquidMixture/liquidMixture/liquidMixture.C
+++ b/src/thermophysicalModels/liquidMixture/liquidMixture/liquidMixture.C
@@ -31,6 +31,7 @@ License
 
 const Foam::scalar Foam::liquidMixture::TrMax = 0.999;
 
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 Foam::liquidMixture::liquidMixture
@@ -41,32 +42,26 @@ Foam::liquidMixture::liquidMixture
     components_(thermophysicalProperties.lookup("liquidComponents")),
     properties_(components_.size())
 {
-    // use sub-dictionary "liquidProperties" if possible to avoid
+    // can use sub-dictionary "liquidProperties" to avoid
     // collisions with identically named gas-phase entries
     // (eg, H2O liquid vs. gas)
+    const dictionary* subDictPtr = thermophysicalProperties.subDictPtr
+    (
+        "liquidProperties"
+    );
+
+    const dictionary& props =
+    (
+        subDictPtr ? *subDictPtr : thermophysicalProperties
+    );
+
     forAll(components_, i)
     {
-        const dictionary* subDictPtr = thermophysicalProperties.subDictPtr
+        properties_.set
         (
-            "liquidProperties"
+            i,
+            liquid::New(props.lookup(components_[i]))
         );
-
-        if (subDictPtr)
-        {
-            properties_.set
-            (
-                i,
-                liquid::New(subDictPtr->lookup(components_[i]))
-            );
-        }
-        else
-        {
-            properties_.set
-            (
-                i,
-                liquid::New(thermophysicalProperties.lookup(components_[i]))
-            );
-        }
     }
 }
 
diff --git a/src/thermophysicalModels/liquidMixture/liquidMixture/liquidMixture.H b/src/thermophysicalModels/liquidMixture/liquidMixture/liquidMixture.H
index a5ae1c3fbb..8810256475 100644
--- a/src/thermophysicalModels/liquidMixture/liquidMixture/liquidMixture.H
+++ b/src/thermophysicalModels/liquidMixture/liquidMixture/liquidMixture.H
@@ -103,7 +103,7 @@ class liquidMixture
 {
     // Private data
 
-        // maximum reduced temperature
+        //- Maximum reduced temperature
         static const scalar TrMax;
 
         //- The names of the liquids
@@ -130,6 +130,7 @@ public:
 
     // Member Functions
 
+        //- Return the liquid names
         inline const List<word>& components() const
         {
             return components_;
@@ -141,6 +142,13 @@ public:
             return properties_;
         }
 
+        //- Return the number of liquids in the mixture
+        inline label size() const
+        {
+            return components_.size();
+        }
+
+
         //- Calculate the critical temperature of mixture
         scalar Tc(const scalarField& x) const;
 
diff --git a/src/thermophysicalModels/solidMixture/solidMixture/solidMixture.C b/src/thermophysicalModels/solidMixture/solidMixture/solidMixture.C
index 55ccd4057f..6cf5163397 100644
--- a/src/thermophysicalModels/solidMixture/solidMixture/solidMixture.C
+++ b/src/thermophysicalModels/solidMixture/solidMixture/solidMixture.C
@@ -35,13 +35,24 @@ Foam::solidMixture::solidMixture
     components_(thermophysicalProperties.lookup("solidComponents")),
     properties_(components_.size())
 {
+    // can use sub-dictionary "solidProperties" to avoid
+    // collisions with identically named gas-phase entries
+    const dictionary* subDictPtr = thermophysicalProperties.subDictPtr
+    (
+        "solidProperties"
+    );
+
+    const dictionary& props =
+    (
+        subDictPtr ? *subDictPtr : thermophysicalProperties
+    );
 
     forAll(components_, i)
     {
         properties_.set
         (
             i,
-            solid::New(thermophysicalProperties.lookup(components_[i]))
+            solid::New(props.lookup(components_[i]))
         );
     }
 }
@@ -82,12 +93,12 @@ Foam::scalar Foam::solidMixture::rho
     const scalarField& X
 ) const
 {
-    scalar tmp = 0.0;
+    scalar val = 0.0;
     forAll(properties_, i)
     {
-        tmp += properties_[i].rho()*X[i];
+        val += properties_[i].rho()*X[i];
     }
-    return tmp;
+    return val;
 }
 
 
@@ -96,12 +107,12 @@ Foam::scalar Foam::solidMixture::cp
     const scalarField& Y
 ) const
 {
-    scalar tmp = 0.0;
+    scalar val = 0.0;
     forAll(properties_, i)
     {
-        tmp += properties_[i].cp()*Y[i];
+        val += properties_[i].cp()*Y[i];
     }
-    return tmp;
+    return val;
 }
 
 
diff --git a/src/thermophysicalModels/solidMixture/solidMixture/solidMixture.H b/src/thermophysicalModels/solidMixture/solidMixture/solidMixture.H
index 50f8b54a6c..ba1d582ee5 100644
--- a/src/thermophysicalModels/solidMixture/solidMixture/solidMixture.H
+++ b/src/thermophysicalModels/solidMixture/solidMixture/solidMixture.H
@@ -25,7 +25,18 @@ Class
     Foam::solidMixture
 
 Description
-    Foam::solidMixture
+    A mixture of solids.
+
+Note
+    The dictionary constructor searches for the entry @c solidComponents,
+    which is a wordList. The solid properties of each component can either
+    be contained within a @c solidProperties sub-dictionary or (for legacy
+    purposes) can be found directly in the dictionary.
+    The @c solidProperties sub-dictionary entry should be used when possible
+    to avoid conflicts with identically named gas-phase entries.
+
+SeeAlso
+    Foam::liquidMixture
 
 \*---------------------------------------------------------------------------*/
 
@@ -74,7 +85,7 @@ public:
 
     // Member Functions
 
-        //- Return the sold names
+        //- Return the solid names
         inline const List<word>& components() const
         {
             return components_;
@@ -86,6 +97,13 @@ public:
             return properties_;
         }
 
+        //- Return the number of solids in the mixture
+        inline label size() const
+        {
+            return components_.size();
+        }
+
+
         //- Returns the mass fractions, given mole fractions
         scalarField Y(const scalarField& X) const;
 

From 9fd0959b88a06d2ea2ca4671462248e414b7b4ad Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Tue, 5 Oct 2010 18:19:17 +0200
Subject: [PATCH 03/12] ENH: generalize speciesTable as hashedWordList

BUG: incorrect speciesTable indices after assignment or reading from Istream
---
 src/OpenFOAM/Make/files                       |   1 +
 .../primitives/Lists/hashedWordList.C         | 159 ++++++++++++++++++
 .../primitives/Lists/hashedWordList.H         | 149 ++++++++++++++++
 .../primitives/Lists/hashedWordListI.H}       |  36 ++--
 .../chemkinReader/chemkinReader.C             |   4 +-
 src/thermophysicalModels/specie/Make/files    |   2 -
 .../specie/speciesTable/speciesTable.C        |  83 ---------
 .../specie/speciesTable/speciesTable.H        |  76 +--------
 8 files changed, 341 insertions(+), 169 deletions(-)
 create mode 100644 src/OpenFOAM/primitives/Lists/hashedWordList.C
 create mode 100644 src/OpenFOAM/primitives/Lists/hashedWordList.H
 rename src/{thermophysicalModels/specie/speciesTable/speciesTableI.H => OpenFOAM/primitives/Lists/hashedWordListI.H} (66%)
 delete mode 100644 src/thermophysicalModels/specie/speciesTable/speciesTable.C

diff --git a/src/OpenFOAM/Make/files b/src/OpenFOAM/Make/files
index d9548b67b1..78d9258543 100644
--- a/src/OpenFOAM/Make/files
+++ b/src/OpenFOAM/Make/files
@@ -85,6 +85,7 @@ $(primitiveLists)/vectorListIOList.C
 $(primitiveLists)/sphericalTensorList.C
 $(primitiveLists)/symmTensorList.C
 $(primitiveLists)/tensorList.C
+$(primitiveLists)/hashedWordList.C
 
 Streams = db/IOstreams
 $(Streams)/token/tokenIO.C
diff --git a/src/OpenFOAM/primitives/Lists/hashedWordList.C b/src/OpenFOAM/primitives/Lists/hashedWordList.C
new file mode 100644
index 0000000000..e9206bda8e
--- /dev/null
+++ b/src/OpenFOAM/primitives/Lists/hashedWordList.C
@@ -0,0 +1,159 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "hashedWordList.H"
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+void Foam::hashedWordList::rehash()
+{
+    indices_.clear();
+    forAll(*this, i)
+    {
+        indices_.insert(List<word>::operator[](i), i);
+    }
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::hashedWordList::hashedWordList()
+:
+    List<word>()
+{}
+
+
+Foam::hashedWordList::hashedWordList(const UList<word>& names)
+:
+    List<word>(names)
+{
+    rehash();
+}
+
+
+Foam::hashedWordList::hashedWordList(const hashedWordList& names)
+:
+    List<word>(static_cast<const UList<word>&>(names))
+{
+    rehash();
+}
+
+
+Foam::hashedWordList::hashedWordList(const Xfer< List<word> >& names)
+:
+    List<word>(names)
+{
+    rehash();
+}
+
+
+Foam::hashedWordList::hashedWordList
+(
+    const label nNames,
+    const char** names
+)
+:
+    List<word>(nNames)
+{
+    forAll(*this, i)
+    {
+        List<word>::operator[](i) = names[i];
+    }
+
+    rehash();
+}
+
+
+Foam::hashedWordList::hashedWordList
+(
+    const char** names
+)
+{
+    // count names
+    label nNames = 0;
+    for (unsigned i = 0; names[i] && *(names[i]); ++i)
+    {
+        ++nNames;
+    }
+
+    List<word>::setSize(nNames);
+    forAll(*this, i)
+    {
+        List<word>::operator[](i) = names[i];
+    }
+
+    rehash();
+}
+
+
+Foam::hashedWordList::hashedWordList(Istream& is)
+{
+    is  >> *this;
+}
+
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+void Foam::hashedWordList::clear()
+{
+    List<word>::clear();
+    indices_.clear();
+}
+
+
+void Foam::hashedWordList::append(const word& name)
+{
+    const label idx = size();
+    List<word>::append(name);
+    indices_.insert(name, idx);
+}
+
+
+void Foam::hashedWordList::transfer(List<word>& lst)
+{
+    List<word>::transfer(lst);
+    rehash();
+}
+
+
+// * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
+
+Foam::Istream& Foam::operator>>(Istream& is, hashedWordList& lst)
+{
+    is  >> static_cast<List<word>&>(lst);
+    lst.rehash();
+
+    return is;
+}
+
+
+Foam::Ostream& Foam::operator<<(Ostream& os, const hashedWordList& lst)
+{
+    os  << static_cast<const List<word>&>(lst);
+    return os;
+}
+
+
+// ************************************************************************* //
diff --git a/src/OpenFOAM/primitives/Lists/hashedWordList.H b/src/OpenFOAM/primitives/Lists/hashedWordList.H
new file mode 100644
index 0000000000..93a23d8db3
--- /dev/null
+++ b/src/OpenFOAM/primitives/Lists/hashedWordList.H
@@ -0,0 +1,149 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+Class
+    Foam::hashedWordList
+
+Description
+    A wordList with hashed indices for faster lookup by name.
+
+SourceFiles
+    hashedWordListI.H
+    hashedWordList.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef hashedWordList_H
+#define hashedWordList_H
+
+#include "wordList.H"
+#include "HashTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+class hashedWordList;
+
+// Forward declaration of friend functions and operators
+Istream& operator>>(Istream&, hashedWordList&);
+Ostream& operator<<(Ostream&, const hashedWordList&);
+
+
+/*---------------------------------------------------------------------------*\
+                       Class hashedWordList Declaration
+\*---------------------------------------------------------------------------*/
+
+class hashedWordList
+:
+    public List<word>
+{
+    // Private data
+
+        HashTable<label, word> indices_;
+
+
+    // Private Member Functions
+
+        //- rebuild the hash of indices
+        void rehash();
+
+public:
+
+    // Constructors
+
+        //- Construct null
+        hashedWordList();
+
+        //- Copy constructor.
+        hashedWordList(const hashedWordList&);
+
+        //- Construct from list of names
+        hashedWordList(const UList<word>& names);
+
+        //- Construct by transferring the parameter contents
+        hashedWordList(const Xfer< List<word> >& names);
+
+        //- Construct from number and list of names
+        hashedWordList(const label nNames, const char** names);
+
+        //- Construct from a NULL-terminated list of names
+        hashedWordList(const char** names);
+
+        //- Construct from Istream
+        hashedWordList(Istream&);
+
+
+    // Member Functions
+
+        //- Clear the list, i.e. set size to zero.
+        void clear();
+
+        //- Append an element at the end of the list
+        void append(const word&);
+
+        //- Does the list contain the specified name
+        inline bool contains(const word&) const;
+
+        //- Transfer the contents of the argument List into this list
+        //  and annul the argument list.
+        void transfer(List<word>&);
+
+
+    // Member Operators
+
+        //- Assignment operator from list of names
+        inline void operator=(const UList<word>& names);
+
+        //- Assignment operator.
+        inline void operator=(const hashedWordList&);
+
+        //- Allow readonly access to list of words
+        inline operator const Foam::UList<word>&() const;
+
+        //- Return name corresponding to specified index
+        inline const word& operator[](const label index) const;
+
+        //- Return index corresponding to specified name
+        inline label operator[](const word&) const;
+
+
+    // Istream operators
+
+        friend Istream& operator>>(Istream&, hashedWordList&);
+        friend Ostream& operator<<(Ostream&, const hashedWordList&);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "hashedWordListI.H"
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/thermophysicalModels/specie/speciesTable/speciesTableI.H b/src/OpenFOAM/primitives/Lists/hashedWordListI.H
similarity index 66%
rename from src/thermophysicalModels/specie/speciesTable/speciesTableI.H
rename to src/OpenFOAM/primitives/Lists/hashedWordListI.H
index 8a8c85694a..1e736aa6c5 100644
--- a/src/thermophysicalModels/specie/speciesTable/speciesTableI.H
+++ b/src/OpenFOAM/primitives/Lists/hashedWordListI.H
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -21,32 +21,44 @@ License
     You should have received a copy of the GNU General Public License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
-Description
-
 \*---------------------------------------------------------------------------*/
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-inline bool Foam::speciesTable::contains(const word& specieName) const
+inline bool Foam::hashedWordList::contains(const word& name) const
 {
-    return specieIndices_.found(specieName);
+    return indices_.found(name);
 }
 
 
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
-inline const Foam::word& Foam::speciesTable::operator[]
-(
-    const label specieIndex
-) const
+inline void Foam::hashedWordList::operator=(const UList<word>& lst)
 {
-    return wordList::operator[](specieIndex);
+    List<word>::operator=(lst);
+    rehash();
 }
 
 
-inline Foam::label Foam::speciesTable::operator[](const word& specieName) const
+inline void Foam::hashedWordList::operator=(const hashedWordList& lst)
 {
-    return specieIndices_[specieName];
+    operator=(static_cast<const UList<word>&>(lst));
+}
+
+
+inline const Foam::word& Foam::hashedWordList::operator[]
+(
+    const label index
+) const
+{
+    return List<word>::operator[](index);
+}
+
+
+// could return -1 instead of bombing out
+inline Foam::label Foam::hashedWordList::operator[](const word& name) const
+{
+    return indices_[name];
 }
 
 
diff --git a/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinReader.C b/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinReader.C
index 80418cbc83..b474c59451 100644
--- a/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinReader.C
+++ b/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinReader.C
@@ -859,7 +859,7 @@ Foam::chemkinReader::chemkinReader
 :
     lineNo_(1),
     specieNames_(10),
-    speciesTable_(static_cast<const wordList&>(wordList()))
+    speciesTable_()
 {
     read(CHEMKINFileName, thermoFileName);
 }
@@ -870,7 +870,7 @@ Foam::chemkinReader::chemkinReader(const dictionary& thermoDict)
 :
     lineNo_(1),
     specieNames_(10),
-    speciesTable_(static_cast<const wordList&>(wordList()))
+    speciesTable_()
 {
     fileName chemkinFile
     (
diff --git a/src/thermophysicalModels/specie/Make/files b/src/thermophysicalModels/specie/Make/files
index 428f6d8fc7..0e0eacae89 100644
--- a/src/thermophysicalModels/specie/Make/files
+++ b/src/thermophysicalModels/specie/Make/files
@@ -1,12 +1,10 @@
 atomicWeights = atomicWeights
 specie = specie
-speciesTable = speciesTable
 equationOfState = equationOfState
 reactions = reaction/reactions
 
 $(atomicWeights)/atomicWeights.C
 $(specie)/specie.C
-$(speciesTable)/speciesTable.C
 $(equationOfState)/perfectGas/perfectGas.C
 $(reactions)/makeChemkinReactions.C
 $(reactions)/makeReactionThermoReactions.C
diff --git a/src/thermophysicalModels/specie/speciesTable/speciesTable.C b/src/thermophysicalModels/specie/speciesTable/speciesTable.C
deleted file mode 100644
index 3c5b0cb176..0000000000
--- a/src/thermophysicalModels/specie/speciesTable/speciesTable.C
+++ /dev/null
@@ -1,83 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2010 OpenCFD Ltd.
-     \\/     M anipulation  |
--------------------------------------------------------------------------------
-License
-    This file is part of OpenFOAM.
-
-    OpenFOAM is free software: you can redistribute it and/or modify it
-    under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
-    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
-    for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
-
-\*---------------------------------------------------------------------------*/
-
-#include "speciesTable.H"
-
-// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
-
-void Foam::speciesTable::setIndices()
-{
-    forAll(*this, i)
-    {
-        specieIndices_.insert(wordList::operator[](i), i);
-    }
-}
-
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-// Construct from list of specie names
-Foam::speciesTable::speciesTable(const wordList& specieNames)
-:
-    wordList(specieNames)
-{
-    setIndices();
-}
-
-
-// Construct from number of species and list of specie names
-Foam::speciesTable::speciesTable(const label nSpecies, const char** specieNames)
-:
-    wordList(nSpecies)
-{
-    forAll(*this, i)
-    {
-        wordList::operator[](i) = specieNames[i];
-    }
-
-    setIndices();
-}
-
-
-// Construct from Istream
-Foam::speciesTable::speciesTable(Istream& is)
-:
-    wordList(is)
-{
-    setIndices();
-}
-
-
-// * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
-
-Foam::Istream& Foam::operator>>(Istream& is, speciesTable& st)
-{
-    is >> static_cast<wordList&>(st);
-    st.setIndices();
-
-    return is;
-}
-
-// ************************************************************************* //
diff --git a/src/thermophysicalModels/specie/speciesTable/speciesTable.H b/src/thermophysicalModels/specie/speciesTable/speciesTable.H
index 4e7013d015..72533ad0a6 100644
--- a/src/thermophysicalModels/specie/speciesTable/speciesTable.H
+++ b/src/thermophysicalModels/specie/speciesTable/speciesTable.H
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -21,89 +21,25 @@ License
     You should have received a copy of the GNU General Public License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
-Class
+Typedef
     Foam::speciesTable
 
 Description
-    A table of species
-
-SourceFiles
-    speciesTableI.H
-    speciesTable.C
+    A table of species as a hashedWordList
 
 \*---------------------------------------------------------------------------*/
 
 #ifndef speciesTable_H
 #define speciesTable_H
 
-#include "wordList.H"
-#include "HashTable.H"
+#include "hashedWordList.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 namespace Foam
 {
-
-/*---------------------------------------------------------------------------*\
-                           Class speciesTable Declaration
-\*---------------------------------------------------------------------------*/
-
-class speciesTable
-:
-    public wordList
-{
-    // Private data
-
-        HashTable<label> specieIndices_;
-
-
-    // Private Member Functions
-
-        void setIndices();
-
-
-public:
-
-    // Constructors
-
-        //- Construct from list of specie names
-        speciesTable(const wordList& specieNames);
-
-        //- Construct from number of species and list of specie names
-        speciesTable(const label nSpecies, const char** specieNames);
-
-        //- Construct from Istream
-        speciesTable(Istream&);
-
-
-    // Member Functions
-
-        //- Does the table contain the given specie
-        inline bool contains(const word& specieName) const;
-
-
-    // Member Operators
-
-        //- Return a specie's name
-        inline const word& operator[](const label) const;
-
-        //- Lookup a specie's name and return its index
-        inline label operator[](const word&) const;
-
-
-    // Istream operators
-
-        friend Istream& operator>>(Istream&, speciesTable&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "speciesTableI.H"
+    typedef hashedWordList speciesTable;
+}
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

From dcc00e2cc9033090620f55e57ba8e9236c35f119 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Tue, 5 Oct 2010 18:50:44 +0200
Subject: [PATCH 04/12] STYLE: added verbatim/endverbatim in doxygen docs

---
 .../greyMeanAbsorptionEmission.H              | 58 ++++++-------
 .../wideBandAbsorptionEmission.H              | 85 +++++++++----------
 .../thirdBodyEfficienciesI.H                  |  4 +-
 3 files changed, 73 insertions(+), 74 deletions(-)

diff --git a/src/thermophysicalModels/radiation/submodels/absorptionEmissionModel/greyMeanAbsorptionEmission/greyMeanAbsorptionEmission.H b/src/thermophysicalModels/radiation/submodels/absorptionEmissionModel/greyMeanAbsorptionEmission/greyMeanAbsorptionEmission.H
index deec87298d..0ac653c9c0 100644
--- a/src/thermophysicalModels/radiation/submodels/absorptionEmissionModel/greyMeanAbsorptionEmission/greyMeanAbsorptionEmission.H
+++ b/src/thermophysicalModels/radiation/submodels/absorptionEmissionModel/greyMeanAbsorptionEmission/greyMeanAbsorptionEmission.H
@@ -44,38 +44,38 @@ Description
     The look-up table ("speciesTable") file should be in constant
 
     i.e. dictionary
+    @verbatim
+        LookUpTableFileName     "speciesTable";
 
-    LookUpTableFileName     "speciesTable";
+        EhrrCoeff       0.0;
 
-    EhrrCoeff                0.0;
+        CO2
+        {
+            Tcommon     300.;   // Common Temp
+            invTemp     true;   // Is the polynomial using inverse temperature?
+            Tlow        300.;   // Low Temp
+            Thigh       2500.;  // High Temp
 
-    CO2
-    {
-        Tcommon         300.;   // Common Temp
-        invTemp         true;   // Is the polynomial using inverse temperature?
-        Tlow            300.;   // Low Temp
-        Thigh           2500.;  // High Temp
-
-        loTcoeffs       // coeffs for T < Tcommon
-        (
-            0           //  a0            +
-            0           //  a1*T          +
-            0           //  a2*T^(+/-)2   +
-            0           //  a3*T^(+/-)3   +
-            0           //  a4*T^(+/-)4   +
-            0           //  a5*T^(+/-)5   +
-        );
-        hiTcoeffs       // coeffs for T > Tcommon
-        (
-            18.741
-            -121.31e3
-            273.5e6
-            -194.05e9
-            56.31e12
-            -5.8169e15
-        );
-
-    }
+            loTcoeffs           // coeffs for T < Tcommon
+            (
+                0               //  a0            +
+                0               //  a1*T          +
+                0               //  a2*T^(+/-)2   +
+                0               //  a3*T^(+/-)3   +
+                0               //  a4*T^(+/-)4   +
+                0               //  a5*T^(+/-)5   +
+            );
+            hiTcoeffs           // coeffs for T > Tcommon
+            (
+                18.741
+                -121.31e3
+                273.5e6
+                -194.05e9
+                56.31e12
+                -5.8169e15
+            );
+        }
+    @endverbatim
 
 SourceFiles
     greyMeanAbsorptionEmission.C
diff --git a/src/thermophysicalModels/radiation/submodels/absorptionEmissionModel/wideBandAbsorptionEmission/wideBandAbsorptionEmission.H b/src/thermophysicalModels/radiation/submodels/absorptionEmissionModel/wideBandAbsorptionEmission/wideBandAbsorptionEmission.H
index f1194b3f0c..4b93da89de 100644
--- a/src/thermophysicalModels/radiation/submodels/absorptionEmissionModel/wideBandAbsorptionEmission/wideBandAbsorptionEmission.H
+++ b/src/thermophysicalModels/radiation/submodels/absorptionEmissionModel/wideBandAbsorptionEmission/wideBandAbsorptionEmission.H
@@ -46,53 +46,52 @@ Description
     The look Up table file should be in the constant directory.
 
     band dictionary:
-
-    band0
-    {
-        bandLimits (1.0e-6 2.63e-6);
-        EhrrCoeff       0.0;
-        species
+    @verbatim
+        band0
         {
-            CH4
+            bandLimits (1.0e-6 2.63e-6);
+            EhrrCoeff       0.0;
+            species
             {
-                Tcommon         300.;
-                Tlow            300.;
-                Thigh           2500.;
-                invTemp         false;
-                loTcoeffs (0 0 0 0 0 0) ;
-                hiTcoeffs (.1 0 0 0 0 0);
-            }
-            CO2
-            {
-                Tcommon         300.;
-                Tlow            300.;
-                Thigh           2500.;
-                invTemp         false;
-                loTcoeffs (0 0 0 0 0 0) ;
-                hiTcoeffs (.1 0 0 0 0 0);
-            }
-
-            H2O
-            {
-                Tcommon         300.;
-                Tlow            300.;
-                Thigh           2500.;
-                invTemp         false;
-                loTcoeffs (0 0 0 0 0 0) ;
-                hiTcoeffs (.1 0 0 0 0 0);
-            }
-
-            Ysoot
-            {
-                Tcommon         300.;
-                Tlow            300.;
-                Thigh           2500.;
-                invTemp         false;
-                loTcoeffs (0 0 0 0 0 0) ;
-                hiTcoeffs (.1 0 0 0 0 0);
+                CH4
+                {
+                    Tcommon         300.;
+                    Tlow            300.;
+                    Thigh           2500.;
+                    invTemp         false;
+                    loTcoeffs (0 0 0 0 0 0) ;
+                    hiTcoeffs (.1 0 0 0 0 0);
+                }
+                CO2
+                {
+                    Tcommon         300.;
+                    Tlow            300.;
+                    Thigh           2500.;
+                    invTemp         false;
+                    loTcoeffs (0 0 0 0 0 0) ;
+                    hiTcoeffs (.1 0 0 0 0 0);
+                }
+                H2O
+                {
+                    Tcommon         300.;
+                    Tlow            300.;
+                    Thigh           2500.;
+                    invTemp         false;
+                    loTcoeffs (0 0 0 0 0 0) ;
+                    hiTcoeffs (.1 0 0 0 0 0);
+                }
+                Ysoot
+                {
+                    Tcommon         300.;
+                    Tlow            300.;
+                    Thigh           2500.;
+                    invTemp         false;
+                    loTcoeffs (0 0 0 0 0 0) ;
+                    hiTcoeffs (.1 0 0 0 0 0);
+                }
             }
         }
-    }
+    @endverbatim
 
 
 SourceFiles
diff --git a/src/thermophysicalModels/specie/reaction/reactionRate/thirdBodyEfficiencies/thirdBodyEfficienciesI.H b/src/thermophysicalModels/specie/reaction/reactionRate/thirdBodyEfficiencies/thirdBodyEfficienciesI.H
index 8e8096fa71..dd6008f09e 100644
--- a/src/thermophysicalModels/specie/reaction/reactionRate/thirdBodyEfficiencies/thirdBodyEfficienciesI.H
+++ b/src/thermophysicalModels/specie/reaction/reactionRate/thirdBodyEfficiencies/thirdBodyEfficienciesI.H
@@ -42,7 +42,7 @@ inline Foam::thirdBodyEfficiencies::thirdBodyEfficiencies
             "thirdBodyEfficiencies::thirdBodyEfficiencies"
             "(const speciesTable& species, const scalarList& efficiencies)"
         )   << "number of efficiencies = " << size()
-            << " is not equat to the number of species " << species_.size()
+            << " is not equal to the number of species " << species_.size()
             << exit(FatalError);
     }
 }
@@ -105,7 +105,7 @@ inline Foam::thirdBodyEfficiencies::thirdBodyEfficiencies
             "(const speciesTable& species, Istream& is)",
             is
         )   << "number of efficiencies = " << size()
-            << " is not equat to the number of species " << species_.size()
+            << " is not equal to the number of species " << species_.size()
             << exit(FatalIOError);
     }
 }

From 9eb1ae73070118a72a5868be0a155737e98d1c64 Mon Sep 17 00:00:00 2001
From: graham <g.macpherson@opencfd.co.uk>
Date: Thu, 7 Oct 2010 17:48:32 +0100
Subject: [PATCH 05/12] STYLE:  Output spacing.

---
 src/lagrangian/basic/Cloud/CloudIO.C | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/lagrangian/basic/Cloud/CloudIO.C b/src/lagrangian/basic/Cloud/CloudIO.C
index 87b23e4538..c18174baec 100644
--- a/src/lagrangian/basic/Cloud/CloudIO.C
+++ b/src/lagrangian/basic/Cloud/CloudIO.C
@@ -121,9 +121,9 @@ void Foam::Cloud<ParticleType>::initCloud(const bool checkClass)
     }
     else
     {
-        Pout<< "Cannot read particle positions file " << nl
+        Pout<< "Cannot read particle positions file:" << nl
             << "    " << ioP.path() << nl
-            << "    assuming the initial cloud contains 0 particles." << endl;
+            << "Assuming the initial cloud contains 0 particles." << endl;
     }
 
     // Ask for the tetBasePtIs to trigger all processors to build

From dd5ed76a707f90f233620805177f6b41b748732c Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Fri, 8 Oct 2010 15:56:58 +0200
Subject: [PATCH 06/12] ENH: avoid costly pow() when evaluating Polynomial

    OLD timings:
    ~~~~~~~~~~~~~~~~~~
    evaluate:     -6.82572e+31 in 10.38 s
    hard-coded 0: -6.82572e+31 in 0.2 s
    hard-coded 1: -6.82572e+31 in 10.37 s
    hard-coded 2: -6.82572e+31 in 0.24 s

    New timings:
    ~~~~~~~~~~~~~~~~~~
    evaluate:     -6.82572e+31 in 0.11 s
---
 applications/test/Polynomial/Make/options     |  4 +-
 applications/test/Polynomial/PolynomialTest.C | 94 +++++++++++++++++++
 .../functions/Polynomial/Polynomial.C         |  7 +-
 3 files changed, 101 insertions(+), 4 deletions(-)

diff --git a/applications/test/Polynomial/Make/options b/applications/test/Polynomial/Make/options
index 1b98398577..4c3dd783cb 100644
--- a/applications/test/Polynomial/Make/options
+++ b/applications/test/Polynomial/Make/options
@@ -1,3 +1,3 @@
-EXE_INC = \
+EXE_INC =
 
-EXE_LIBS = \
+EXE_LIBS =
diff --git a/applications/test/Polynomial/PolynomialTest.C b/applications/test/Polynomial/PolynomialTest.C
index 4b7db7ef6f..d3fa03e595 100644
--- a/applications/test/Polynomial/PolynomialTest.C
+++ b/applications/test/Polynomial/PolynomialTest.C
@@ -32,9 +32,14 @@ Description
 #include "IFstream.H"
 #include "Polynomial.H"
 #include "Random.H"
+#include "cpuTime.H"
 
 using namespace Foam;
 
+const int nCoeffs = 8;
+const scalar coeff[] = { 0.11, 0.45, -0.94, 1.58, 2.58, 0.08, 3.15, -4.78 };
+
+
 scalar polyValue(const scalar x)
 {
     // Hard-coded polynomial 8 coeff (7th order)
@@ -65,10 +70,43 @@ scalar intPolyValue(const scalar x)
 }
 
 
+scalar polyValue1(const scalar x)
+{
+    // "normal" evaluation using pow()
+    scalar value = coeff[0];
+
+    for (int i=1; i < nCoeffs; ++i)
+    {
+        value += coeff[i]*pow(x, i);
+    }
+
+    return value;
+}
+
+
+// calculation avoiding pow()
+scalar polyValue2(const scalar x)
+{
+    scalar value = coeff[0];
+
+    scalar powX = x;
+    for (int i=1; i < nCoeffs; ++i, powX *= x)
+    {
+        value += coeff[i] * powX;
+    }
+
+    return value;
+}
+
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 int main(int argc, char *argv[])
 {
+    const label n = 10000;
+    const label nIters = 1000;
+    scalar sum = 0.0;
+
     IFstream is("polyTestInput");
 
     Polynomial<8> poly("testPoly", is);
@@ -118,6 +156,62 @@ int main(int argc, char *argv[])
         Info<< endl;
     }
 
+
+    //
+    // test speed of Polynomial:
+    //
+    Info<< "start timing loops" << nl
+        << "~~~~~~~~~~~~~~~~~~" << endl;
+
+    cpuTime timer;
+
+    for (int loop = 0; loop < n; ++loop)
+    {
+        sum = 0.0;
+        for (label iter = 0; iter < nIters; ++iter)
+        {
+            sum += poly.evaluate(loop+iter);
+        }
+    }
+    Info<< "evaluate:     " << sum
+        << " in " << timer.cpuTimeIncrement() << " s\n";
+
+
+    for (int loop = 0; loop < n; ++loop)
+    {
+        sum = 0.0;
+        for (label iter = 0; iter < nIters; ++iter)
+        {
+            sum += polyValue(loop+iter);
+        }
+    }
+    Info<< "hard-coded 0: " << sum
+        << " in " << timer.cpuTimeIncrement() << " s\n";
+
+
+    for (int loop = 0; loop < n; ++loop)
+    {
+        sum = 0.0;
+        for (label iter = 0; iter < nIters; ++iter)
+        {
+            sum += polyValue1(loop+iter);
+        }
+    }
+    Info<< "hard-coded 1: " << sum
+        << " in " << timer.cpuTimeIncrement() << " s\n";
+
+    for (int loop = 0; loop < n; ++loop)
+    {
+        sum = 0.0;
+        for (label iter = 0; iter < nIters; ++iter)
+        {
+            sum += polyValue2(loop+iter);
+        }
+    }
+    Info<< "hard-coded 2: " << sum
+        << " in " << timer.cpuTimeIncrement() << " s\n";
+
+
     Info<< nl << "Done." << endl;
 
     return 0;
diff --git a/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.C b/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.C
index 1e7b7aa618..903bdffe2b 100644
--- a/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.C
+++ b/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.C
@@ -101,9 +101,12 @@ Foam::scalar Foam::Polynomial<PolySize>::evaluate(const scalar x) const
 {
     scalar y = this->v_[0];
 
-    for (label i=1; i<PolySize; i++)
+    // avoid costly pow() in calculation
+    scalar powX = x;
+    for (label i=1; i<PolySize; ++i)
     {
-        y += this->v_[i]*pow(x, i);
+        y += this->v_[i]*powX;
+        powX *= x;
     }
 
     if (logActive_)

From 71b7e7cee158b53e509c11c1d9720be940a4a6b7 Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@Germany>
Date: Fri, 8 Oct 2010 17:54:13 +0200
Subject: [PATCH 07/12] ENH: add StaticAssert to Polynomial - positive number
 of terms only

ENH: allow construct from UList of coefficients, from C-arrays
     avoid uninitialized values for null constructor
---
 applications/test/Polynomial/PolynomialTest.C | 51 +++++++++---------
 applications/test/Polynomial/polyTestInput    | 11 ----
 .../functions/Polynomial/Polynomial.C         | 53 ++++++++++++++++---
 .../functions/Polynomial/Polynomial.H         | 14 ++++-
 4 files changed, 85 insertions(+), 44 deletions(-)
 delete mode 100644 applications/test/Polynomial/polyTestInput

diff --git a/applications/test/Polynomial/PolynomialTest.C b/applications/test/Polynomial/PolynomialTest.C
index d3fa03e595..fbfbcc2000 100644
--- a/applications/test/Polynomial/PolynomialTest.C
+++ b/applications/test/Polynomial/PolynomialTest.C
@@ -29,29 +29,30 @@ Description
 
 \*---------------------------------------------------------------------------*/
 
-#include "IFstream.H"
+#include "IStringStream.H"
 #include "Polynomial.H"
 #include "Random.H"
 #include "cpuTime.H"
 
 using namespace Foam;
 
-const int nCoeffs = 8;
-const scalar coeff[] = { 0.11, 0.45, -0.94, 1.58, 2.58, 0.08, 3.15, -4.78 };
+const int PolySize = 8;
+const scalar coeff[] = { 0.11, 0.45, -0.94, 1.58, -2.58, 0.08, 3.15, -4.78 };
+const char* polyDef = "testPoly (0.11 0.45 -0.94 1.58 -2.58 0.08 3.15 -4.78)";
 
 
 scalar polyValue(const scalar x)
 {
     // Hard-coded polynomial 8 coeff (7th order)
     return
-        0.11
-      + 0.45*x
-      - 0.94*sqr(x)
-      + 1.58*pow3(x)
-      - 2.58*pow4(x)
-      + 0.08*pow5(x)
-      + 3.15*pow6(x)
-      - 4.78*x*pow6(x);
+        coeff[0]
+      + coeff[1]*x
+      + coeff[2]*sqr(x)
+      + coeff[3]*pow3(x)
+      + coeff[4]*pow4(x)
+      + coeff[5]*pow5(x)
+      + coeff[6]*pow6(x)
+      + coeff[7]*x*pow6(x);
 }
 
 
@@ -59,14 +60,14 @@ scalar intPolyValue(const scalar x)
 {
     // Hard-coded integrated form of above polynomial
     return
-        0.11*x
-      + 0.45/2.0*sqr(x)
-      - 0.94/3.0*pow3(x)
-      + 1.58/4.0*pow4(x)
-      - 2.58/5.0*pow5(x)
-      + 0.08/6.0*pow6(x)
-      + 3.15/7.0*x*pow6(x)
-      - 4.78/8.0*x*x*pow6(x);
+        coeff[0]*x
+      + coeff[1]/2.0*sqr(x)
+      + coeff[2]/3.0*pow3(x)
+      + coeff[3]/4.0*pow4(x)
+      + coeff[4]/5.0*pow5(x)
+      + coeff[5]/6.0*pow6(x)
+      + coeff[6]/7.0*x*pow6(x)
+      + coeff[7]/8.0*x*x*pow6(x);
 }
 
 
@@ -75,7 +76,7 @@ scalar polyValue1(const scalar x)
     // "normal" evaluation using pow()
     scalar value = coeff[0];
 
-    for (int i=1; i < nCoeffs; ++i)
+    for (int i=1; i < PolySize; ++i)
     {
         value += coeff[i]*pow(x, i);
     }
@@ -84,15 +85,16 @@ scalar polyValue1(const scalar x)
 }
 
 
-// calculation avoiding pow()
 scalar polyValue2(const scalar x)
 {
+    // calculation avoiding pow()
     scalar value = coeff[0];
 
     scalar powX = x;
-    for (int i=1; i < nCoeffs; ++i, powX *= x)
+    for (int i=1; i < PolySize; ++i)
     {
         value += coeff[i] * powX;
+        powX *= x;
     }
 
     return value;
@@ -107,9 +109,10 @@ int main(int argc, char *argv[])
     const label nIters = 1000;
     scalar sum = 0.0;
 
-    IFstream is("polyTestInput");
+    Info<< "null poly = " << (Polynomial<8>()) << nl << endl;
 
-    Polynomial<8> poly("testPoly", is);
+    // Polynomial<8> poly("testPoly", IStringStream(polyDef)());
+    Polynomial<8> poly(coeff);
     Polynomial<9> intPoly(poly.integrate(0.0));
 
     Info<< "poly = " << poly << endl;
diff --git a/applications/test/Polynomial/polyTestInput b/applications/test/Polynomial/polyTestInput
deleted file mode 100644
index 4ba8f65e51..0000000000
--- a/applications/test/Polynomial/polyTestInput
+++ /dev/null
@@ -1,11 +0,0 @@
-    testPoly
-    (
-        0.11
-        0.45
-       -0.94
-        1.58
-       -2.58
-        0.08
-        3.15
-       -4.78
-    )
diff --git a/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.C b/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.C
index 903bdffe2b..cff3744644 100644
--- a/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.C
+++ b/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.C
@@ -33,7 +33,50 @@ Foam::Polynomial<PolySize>::Polynomial()
     VectorSpace<Polynomial<PolySize>, scalar, PolySize>(),
     logActive_(false),
     logCoeff_(0.0)
-{}
+{
+    for (int i = 0; i < PolySize; ++i)
+    {
+        this->v_[i] = 0.0;
+    }
+}
+
+
+template<int PolySize>
+Foam::Polynomial<PolySize>::Polynomial(const scalar coeffs[PolySize])
+:
+    VectorSpace<Polynomial<PolySize>, scalar, PolySize>(),
+    logActive_(false),
+    logCoeff_(0.0)
+{
+    for (int i=0; i<PolySize; i++)
+    {
+        this->v_[i] = coeffs[i];
+    }
+}
+
+
+template<int PolySize>
+Foam::Polynomial<PolySize>::Polynomial(const UList<scalar>& coeffs)
+:
+    VectorSpace<Polynomial<PolySize>, scalar, PolySize>(),
+    logActive_(false),
+    logCoeff_(0.0)
+{
+    if (coeffs.size() != PolySize)
+    {
+        FatalErrorIn
+        (
+            "Polynomial<PolySize>::Polynomial(const UList<scalar>&)"
+        )   << "Size mismatch: Needed " << PolySize
+            << " but got " << coeffs.size()
+            << nl << exit(FatalError);
+    }
+
+    for (int i = 0; i < PolySize; ++i)
+    {
+        this->v_[i] = coeffs[i];
+    }
+}
 
 
 template<int PolySize>
@@ -173,13 +216,9 @@ Foam::Polynomial<PolySize>::integrateMinus1(const scalar intConstant)
     }
 
     newCoeffs[0] = intConstant;
-
-    if (PolySize > 0)
+    for (label i=1; i<PolySize; ++i)
     {
-        for (label i=1; i<PolySize; i++)
-        {
-            newCoeffs[i] = this->v_[i]/i;
-        }
+        newCoeffs[i] = this->v_[i]/i;
     }
 
     return newCoeffs;
diff --git a/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.H b/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.H
index cbfe045803..f2449d1835 100644
--- a/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.H
+++ b/src/OpenFOAM/primitives/functions/Polynomial/Polynomial.H
@@ -29,7 +29,7 @@ Description
 
         poly = logCoeff*log(x) + sum(coeff_[i]*x^i)
 
-    where 0 <= i <= n
+    where 0 \<= i \<= n
 
     - integer powers, starting at zero
     - evaluate(x) to evaluate the poly for a given value
@@ -51,6 +51,7 @@ SourceFiles
 #include "scalar.H"
 #include "Ostream.H"
 #include "VectorSpace.H"
+#include "StaticAssert.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -79,6 +80,9 @@ class Polynomial
 :
     public VectorSpace<Polynomial<PolySize>, scalar, PolySize>
 {
+    //- Size must be positive (non-zero)
+    StaticAssert(PolySize > 0);
+
     // Private data
 
         //- Include the log term? - only activated using integrateMinus1()
@@ -97,9 +101,15 @@ public:
 
     // Constructors
 
-        //- Construct null
+        //- Construct null, with all coefficients = 0.0
         Polynomial();
 
+        //- Construct from C-array of coefficients
+        explicit Polynomial(const scalar coeffs[PolySize]);
+
+        //- Construct from a list of coefficients
+        explicit Polynomial(const UList<scalar>& coeffs);
+
         //- Construct from name and Istream
         Polynomial(const word& name, Istream& is);
 

From f2842e76b9ec4cadce0146f778aed2ae77c246f9 Mon Sep 17 00:00:00 2001
From: graham <g.macpherson@opencfd.co.uk>
Date: Fri, 8 Oct 2010 20:34:59 +0100
Subject: [PATCH 08/12] BUG:  discrete tut tweaks and fixes to make them run.

---
 .../meshes/primitiveMesh/primitiveMesh.H      | 10 ++-
 .../primitiveMesh/primitiveMeshFindCell.C     | 25 ++++++--
 src/lagrangian/basic/Particle/ParticleI.H     | 29 +++++----
 .../molecule/moleculeCloud/moleculeCloud.C    |  2 +-
 .../dsmcFoam/freeSpacePeriodic/Allclean       |  2 +-
 .../constant/polyMesh/blockMeshDict           | 61 +++++++++++++------
 .../dsmcFoam/freeSpaceStream/Allclean         |  2 +-
 .../dsmcFoam/supersonicCorner/Allclean        |  2 +-
 .../dsmcFoam/wedge15Ma5/Allclean              |  2 +-
 .../mdEquilibrationFoam/Allclean              |  4 +-
 .../mdEquilibrationFoam/periodicCubeArgon/0/U | 51 ++++++++++++++++
 .../constant/polyMesh/blockMeshDict           | 61 +++++++++++++------
 .../periodicCubeArgon/system/controlDict      |  2 +-
 .../mdEquilibrationFoam/periodicCubeWater/0/U | 51 ++++++++++++++++
 .../constant/polyMesh/blockMeshDict           | 61 +++++++++++++------
 .../mdFoam/nanoNozzle/system/controlDict      |  4 +-
 16 files changed, 280 insertions(+), 89 deletions(-)
 create mode 100644 tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/0/U
 create mode 100644 tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/0/U

diff --git a/src/OpenFOAM/meshes/primitiveMesh/primitiveMesh.H b/src/OpenFOAM/meshes/primitiveMesh/primitiveMesh.H
index 61c3da9bb9..a0b52f63d1 100644
--- a/src/OpenFOAM/meshes/primitiveMesh/primitiveMesh.H
+++ b/src/OpenFOAM/meshes/primitiveMesh/primitiveMesh.H
@@ -686,8 +686,14 @@ public:
 
         // Useful derived info
 
-            //- Is the point in the cell bounding box
-            bool pointInCellBB(const point& p, label celli) const;
+            //- Is the point in the cell bounding box, option relative
+            //  tolerance to increase the effective size of the boundBox
+            bool pointInCellBB
+            (
+                const point& p,
+                label celli,
+                scalar tol = 0
+            ) const;
 
             //- Is the point in the cell
             bool pointInCell(const point& p, label celli) const;
diff --git a/src/OpenFOAM/meshes/primitiveMesh/primitiveMeshFindCell.C b/src/OpenFOAM/meshes/primitiveMesh/primitiveMeshFindCell.C
index fecbc3c6fb..228097654c 100644
--- a/src/OpenFOAM/meshes/primitiveMesh/primitiveMeshFindCell.C
+++ b/src/OpenFOAM/meshes/primitiveMesh/primitiveMeshFindCell.C
@@ -30,16 +30,33 @@ License
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 // Is the point in the cell bounding box
-bool Foam::primitiveMesh::pointInCellBB(const point& p, label celli) const
+bool Foam::primitiveMesh::pointInCellBB
+(
+    const point& p,
+    label celli,
+    scalar tol
+) const
 {
-    return boundBox
+    boundBox bb
     (
         cells()[celli].points
         (
             faces(),
             points()
-        )
-    ).contains(p);
+        ),
+        false
+    );
+
+    if (tol > SMALL)
+    {
+        bb = boundBox
+        (
+            bb.min() - tol*bb.span(),
+            bb.max() + tol*bb.span()
+        );
+    }
+
+    return bb.contains(p);
 }
 
 
diff --git a/src/lagrangian/basic/Particle/ParticleI.H b/src/lagrangian/basic/Particle/ParticleI.H
index 35d658d115..50c727fe4a 100644
--- a/src/lagrangian/basic/Particle/ParticleI.H
+++ b/src/lagrangian/basic/Particle/ParticleI.H
@@ -970,11 +970,12 @@ inline void Foam::Particle<ParticleType>::initCellFacePt()
                 // number, but hasn't been able to find a cell to
                 // occupy.
 
-                if(!cloud_.polyMesh_.pointInCellBB(position_, oldCellI))
+                if(!cloud_.polyMesh_.pointInCellBB(position_, oldCellI, 0.1))
                 {
-                    // If the position is not inside the bound-box of
-                    // the cell that it thought it should be in, then
-                    // this is considered an error.
+                    // If the position is not inside the (slightly
+                    // extended) bound-box of the cell that it thought
+                    // it should be in, then this is considered an
+                    // error.
 
                     FatalErrorIn
                     (
@@ -985,18 +986,20 @@ inline void Foam::Particle<ParticleType>::initCellFacePt()
                         ")"
                     )   << "cell, tetFace and tetPt search failure at position "
                         << position_ << nl
+                        << "for requested cell " << oldCellI << nl
                         << abort(FatalError);
                 }
 
-                // The position is in the bound-box of the cell.  This
-                // situation may arise because the face decomposition
-                // of the cell is not the same as when the particle
-                // acquired the cell index.  For example, it has been
-                // read into a mesh that has made a different face
-                // base-point decision for a boundary face and now
-                // this particle is in a position that is not in the
-                // mesh.  Gradually move the particle towards the
-                // centre of the cell that it thought that it was in.
+                // The position is in the (slightly extended)
+                // bound-box of the cell.  This situation may arise
+                // because the face decomposition of the cell is not
+                // the same as when the particle acquired the cell
+                // index.  For example, it has been read into a mesh
+                // that has made a different face base-point decision
+                // for a boundary face and now this particle is in a
+                // position that is not in the mesh.  Gradually move
+                // the particle towards the centre of the cell that it
+                // thought that it was in.
 
                 cellI_ = oldCellI;
 
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
index ef50886ebf..da5f1ce1dd 100644
--- a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
@@ -1108,7 +1108,7 @@ Foam::moleculeCloud::moleculeCloud
     mesh_(mesh),
     pot_(pot),
     cellOccupancy_(mesh_.nCells()),
-    il_(mesh_, pot_.pairPotentials().rCutMax(), true),
+    il_(mesh_, pot_.pairPotentials().rCutMax(), false),
     constPropList_(),
     rndGen_(clock::getTime())
 {
diff --git a/tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/Allclean b/tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/Allclean
index 2bdc236211..38adb1cefa 100755
--- a/tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/Allclean
+++ b/tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/Allclean
@@ -5,6 +5,6 @@ cd ${0%/*} || exit 1    # run from this directory
 . $WM_PROJECT_DIR/bin/tools/CleanFunctions
 
 cleanCase
-rm -rf 0/lagrangian 0/dsmcSigmaTcRMax
+rm -rf 0/lagrangian 0/dsmcSigmaTcRMax 0/uniform > /dev/null 2>&1
 
 # ----------------------------------------------------------------- end-of-file
diff --git a/tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/constant/polyMesh/blockMeshDict
index 219238e7f9..9ecb2ad4ad 100644
--- a/tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/constant/polyMesh/blockMeshDict
+++ b/tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/constant/polyMesh/blockMeshDict
@@ -34,29 +34,50 @@ blocks
     hex (0 1 2 3 4 5 6 7) (20 16 16) simpleGrading (1 1 1)
 );
 
-patches
+boundary
 (
-    cyclic
-    xPeriodic
-    (
-        (1 2 6 5)
-        (0 4 7 3)
-    )
+    xPeriodic_half0
+    {
+        type cyclic;
+        faces ((1 2 6 5));
+        neighbourPatch xPeriodic_half1;
+    }
 
-    cyclic
-    yPeriodic
-    (
-        (2 3 7 6)
-        (0 1 5 4)
-    )
+    xPeriodic_half1
+    {
+        type cyclic;
+        faces ((0 4 7 3));
+        neighbourPatch xPeriodic_half0;
+    }
 
-    cyclic
-    zPeriodic
-    (
-        (4 5 6 7)
-        (0 3 2 1)
-    )
-)
+    yPeriodic_half0
+    {
+        type cyclic;
+        faces ((2 3 7 6));
+        neighbourPatch yPeriodic_half1;
+    }
+
+    yPeriodic_half1
+    {
+        type cyclic;
+        faces ((0 1 5 4));
+        neighbourPatch yPeriodic_half0;
+    }
+
+    zPeriodic_half0
+    {
+        type cyclic;
+        faces ((4 5 6 7));
+        neighbourPatch zPeriodic_half1;
+    }
+
+    zPeriodic_half1
+    {
+        type cyclic;
+        faces ((0 3 2 1));
+        neighbourPatch zPeriodic_half0;
+    }
+);
 
 mergePatchPairs
 (
diff --git a/tutorials/discreteMethods/dsmcFoam/freeSpaceStream/Allclean b/tutorials/discreteMethods/dsmcFoam/freeSpaceStream/Allclean
index 2bdc236211..38adb1cefa 100755
--- a/tutorials/discreteMethods/dsmcFoam/freeSpaceStream/Allclean
+++ b/tutorials/discreteMethods/dsmcFoam/freeSpaceStream/Allclean
@@ -5,6 +5,6 @@ cd ${0%/*} || exit 1    # run from this directory
 . $WM_PROJECT_DIR/bin/tools/CleanFunctions
 
 cleanCase
-rm -rf 0/lagrangian 0/dsmcSigmaTcRMax
+rm -rf 0/lagrangian 0/dsmcSigmaTcRMax 0/uniform > /dev/null 2>&1
 
 # ----------------------------------------------------------------- end-of-file
diff --git a/tutorials/discreteMethods/dsmcFoam/supersonicCorner/Allclean b/tutorials/discreteMethods/dsmcFoam/supersonicCorner/Allclean
index 2bdc236211..38adb1cefa 100755
--- a/tutorials/discreteMethods/dsmcFoam/supersonicCorner/Allclean
+++ b/tutorials/discreteMethods/dsmcFoam/supersonicCorner/Allclean
@@ -5,6 +5,6 @@ cd ${0%/*} || exit 1    # run from this directory
 . $WM_PROJECT_DIR/bin/tools/CleanFunctions
 
 cleanCase
-rm -rf 0/lagrangian 0/dsmcSigmaTcRMax
+rm -rf 0/lagrangian 0/dsmcSigmaTcRMax 0/uniform > /dev/null 2>&1
 
 # ----------------------------------------------------------------- end-of-file
diff --git a/tutorials/discreteMethods/dsmcFoam/wedge15Ma5/Allclean b/tutorials/discreteMethods/dsmcFoam/wedge15Ma5/Allclean
index 2bdc236211..38adb1cefa 100755
--- a/tutorials/discreteMethods/dsmcFoam/wedge15Ma5/Allclean
+++ b/tutorials/discreteMethods/dsmcFoam/wedge15Ma5/Allclean
@@ -5,6 +5,6 @@ cd ${0%/*} || exit 1    # run from this directory
 . $WM_PROJECT_DIR/bin/tools/CleanFunctions
 
 cleanCase
-rm -rf 0/lagrangian 0/dsmcSigmaTcRMax
+rm -rf 0/lagrangian 0/dsmcSigmaTcRMax 0/uniform > /dev/null 2>&1
 
 # ----------------------------------------------------------------- end-of-file
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
index 5af6a2bb22..5306205a8b 100755
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
@@ -7,7 +7,7 @@ cd ${0%/*} || exit 1    # run from this directory
 (
     cd periodicCubeArgon || exit
 
-    rm -rf 0/*
+    rm -rf 0/lagrangian 0/uniform
     rm -f Ar-Ar
     rm -f electrostatic
     rm -f constant/idList
@@ -19,7 +19,7 @@ cd ${0%/*} || exit 1    # run from this directory
 (
     cd periodicCubeWater || exit
 
-    rm -rf 0/*
+    rm -rf 0/lagrangian 0/uniform
     rm -f O-O
     rm -f electrostatic
     rm -f constant/idList
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/0/U b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/0/U
new file mode 100644
index 0000000000..c93ca94b21
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/0/U
@@ -0,0 +1,51 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volVectorField;
+    location    "0";
+    object      U;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [ 0 1 -1 0 0 0 0 ];
+
+internalField   uniform ( 0 0 0 );
+
+boundaryField
+{
+    periodicX_half0
+    {
+        type            cyclic;
+    }
+    periodicY_half0
+    {
+        type            cyclic;
+    }
+    periodicZ_half0
+    {
+        type            cyclic;
+    }
+    periodicY_half1
+    {
+        type            cyclic;
+    }
+    periodicZ_half1
+    {
+        type            cyclic;
+    }
+    periodicX_half1
+    {
+        type            cyclic;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict
index 0846dec79a..789934700a 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict
@@ -34,29 +34,50 @@ blocks
     hex (0 1 2 3 4 5 6 7) liquid (12 12 12) simpleGrading (1 1 1)
 );
 
-patches
+boundary
 (
-    cyclic
-    periodicX
-    (
-        (1 2 6 5)
-        (0 4 7 3)
-    )
+    periodicX_half0
+    {
+        type cyclic;
+        faces ((1 2 6 5));
+        neighbourPatch periodicX_half1;
+    }
 
-    cyclic
-    periodicY
-    (
-        (2 3 7 6)
-        (0 1 5 4)
-    )
+    periodicX_half1
+    {
+        type cyclic;
+        faces ((0 4 7 3));
+        neighbourPatch periodicX_half0;
+    }
 
-    cyclic
-    periodicZ
-    (
-        (0 3 2 1)
-        (4 5 6 7)
-    )
-)
+    periodicY_half0
+    {
+        type cyclic;
+        faces ((2 3 7 6));
+        neighbourPatch periodicY_half1;
+    }
+
+    periodicY_half1
+    {
+        type cyclic;
+        faces ((0 1 5 4));
+        neighbourPatch periodicY_half0;
+    }
+
+    periodicZ_half0
+    {
+        type cyclic;
+        faces ((4 5 6 7));
+        neighbourPatch periodicZ_half1;
+    }
+
+    periodicZ_half1
+    {
+        type cyclic;
+        faces ((0 3 2 1));
+        neighbourPatch periodicZ_half0;
+    }
+);
 
 mergePatchPairs
 (
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
index c2723fa60f..e2233c88c2 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
@@ -22,7 +22,7 @@ startTime       0;
 
 stopAt          endTime;
 
-endTime         1e-10;
+endTime         5e-11;
 
 deltaT          1e-14;
 
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/0/U b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/0/U
new file mode 100644
index 0000000000..c93ca94b21
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/0/U
@@ -0,0 +1,51 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volVectorField;
+    location    "0";
+    object      U;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [ 0 1 -1 0 0 0 0 ];
+
+internalField   uniform ( 0 0 0 );
+
+boundaryField
+{
+    periodicX_half0
+    {
+        type            cyclic;
+    }
+    periodicY_half0
+    {
+        type            cyclic;
+    }
+    periodicZ_half0
+    {
+        type            cyclic;
+    }
+    periodicY_half1
+    {
+        type            cyclic;
+    }
+    periodicZ_half1
+    {
+        type            cyclic;
+    }
+    periodicX_half1
+    {
+        type            cyclic;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict
index 790a0f4fe5..1d301a3638 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict
@@ -34,29 +34,50 @@ blocks
     hex (0 1 2 3 4 5 6 7) liquid (12 12 11) simpleGrading (1 1 1)
 );
 
-patches
+boundary
 (
-    cyclic
-    periodicX
-    (
-        (1 2 6 5)
-        (0 4 7 3)
-    )
+    periodicX_half0
+    {
+        type cyclic;
+        faces ((1 2 6 5));
+        neighbourPatch periodicX_half1;
+    }
 
-    cyclic
-    periodicY
-    (
-        (2 3 7 6)
-        (0 1 5 4)
-    )
+    periodicX_half1
+    {
+        type cyclic;
+        faces ((0 4 7 3));
+        neighbourPatch periodicX_half0;
+    }
 
-    cyclic
-    periodicZ
-    (
-        (0 3 2 1)
-        (4 5 6 7)
-    )
-)
+    periodicY_half0
+    {
+        type cyclic;
+        faces ((2 3 7 6));
+        neighbourPatch periodicY_half1;
+    }
+
+    periodicY_half1
+    {
+        type cyclic;
+        faces ((0 1 5 4));
+        neighbourPatch periodicY_half0;
+    }
+
+    periodicZ_half0
+    {
+        type cyclic;
+        faces ((4 5 6 7));
+        neighbourPatch periodicZ_half1;
+    }
+
+    periodicZ_half1
+    {
+        type cyclic;
+        faces ((0 3 2 1));
+        neighbourPatch periodicZ_half0;
+    }
+);
 
 mergePatchPairs
 (
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict
index abf063b4f2..a9a721bbce 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict
@@ -22,13 +22,13 @@ startTime       0;
 
 stopAt          endTime;
 
-endTime         5e-12;
+endTime         2e-13;
 
 deltaT          1e-15;
 
 writeControl    runTime;
 
-writeInterval   2e-13;
+writeInterval   5e-14;
 
 purgeWrite      0;
 

From 9ad02ff740bbe298233a5458166f632aed831bc6 Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Fri, 8 Oct 2010 22:50:58 +0100
Subject: [PATCH 09/12] fireFoam: Updated solver and tutorials from
 OpenFOAM-1.7.x

---
 .../solvers/combustion/fireFoam/UEqn.H        |   6 +-
 .../fireFoam/combustionModels/Make/files      |   2 +-
 ...bustionModelNew.C => newCombustionModel.C} |  19 +-
 .../infinitelyFastChemistry.H                 |   5 +-
 .../noCombustion/noCombustion.H               |   5 +-
 .../combustion/fireFoam/createFields.H        |  35 +-
 .../solvers/combustion/fireFoam/pEqn.H        |  60 +--
 .../fireFoam/les/smallPoolFire2D/0/IDefault   |   2 +-
 .../fireFoam/les/smallPoolFire2D/0/p          |  15 +-
 .../fireFoam/les/smallPoolFire2D/0/p_rgh      |  52 ++
 .../constant/polyMesh/boundary                |  16 +-
 .../les/smallPoolFire2D/system/controlDict    |   4 +-
 .../les/smallPoolFire2D/system/fvSchemes      |  13 +-
 .../les/smallPoolFire2D/system/fvSolution     |   6 +-
 .../fireFoam/les/smallPoolFire3D/0/G          |  32 ++
 .../fireFoam/les/smallPoolFire3D/0/IDefault   |  32 ++
 .../fireFoam/les/smallPoolFire3D/0/T          |  49 ++
 .../fireFoam/les/smallPoolFire3D/0/U          |  52 ++
 .../fireFoam/les/smallPoolFire3D/0/alphaSgs   |  44 ++
 .../fireFoam/les/smallPoolFire3D/0/b          |  44 ++
 .../fireFoam/les/smallPoolFire3D/0/ft         |  48 ++
 .../fireFoam/les/smallPoolFire3D/0/fu         |  49 ++
 .../fireFoam/les/smallPoolFire3D/0/k          |  49 ++
 .../fireFoam/les/smallPoolFire3D/0/muSgs      |  43 ++
 .../fireFoam/les/smallPoolFire3D/0/p          |  48 ++
 .../fireFoam/les/smallPoolFire3D/0/p_rgh      |  48 ++
 .../fireFoam/les/smallPoolFire3D/Allrun       |  17 +
 .../smallPoolFire3D/constant/LESProperties    |  84 +++
 .../les/smallPoolFire3D/constant/SpeciesTable | 491 ++++++++++++++++++
 .../constant/combustionProperties             |  31 ++
 .../fireFoam/les/smallPoolFire3D/constant/g   |  21 +
 .../constant/polyMesh/blockMeshDict           |  64 +++
 .../constant/polyMesh/boundary                |  46 ++
 .../constant/radiationProperties              | 150 ++++++
 .../constant/thermophysicalProperties         |  54 ++
 .../constant/turbulenceProperties             |  22 +
 .../les/smallPoolFire3D/makeFaceSet.setSet    |   1 +
 .../les/smallPoolFire3D/system/controlDict    |  56 ++
 .../smallPoolFire3D/system/createPatchDict    |  57 ++
 .../smallPoolFire3D/system/decomposeParDict   |  45 ++
 .../les/smallPoolFire3D/system/fvSchemes      |  67 +++
 .../les/smallPoolFire3D/system/fvSolution     | 103 ++++
 .../constant/polyMesh/blockMeshDict           |   5 +-
 .../constant/polyMesh/boundary                |   2 +-
 44 files changed, 1998 insertions(+), 96 deletions(-)
 rename applications/solvers/combustion/fireFoam/combustionModels/combustionModel/{combustionModelNew.C => newCombustionModel.C} (77%)
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire2D/0/p_rgh
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/G
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/IDefault
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/T
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/U
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/alphaSgs
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/b
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/ft
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/fu
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/k
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/muSgs
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/p
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/0/p_rgh
 create mode 100755 tutorials/combustion/fireFoam/les/smallPoolFire3D/Allrun
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/LESProperties
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/SpeciesTable
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/combustionProperties
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/g
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/polyMesh/blockMeshDict
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/polyMesh/boundary
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/radiationProperties
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/thermophysicalProperties
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/turbulenceProperties
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/makeFaceSet.setSet
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/system/controlDict
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/system/createPatchDict
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/system/decomposeParDict
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/system/fvSchemes
 create mode 100644 tutorials/combustion/fireFoam/les/smallPoolFire3D/system/fvSolution

diff --git a/applications/solvers/combustion/fireFoam/UEqn.H b/applications/solvers/combustion/fireFoam/UEqn.H
index 4a2d03490d..a77c262831 100644
--- a/applications/solvers/combustion/fireFoam/UEqn.H
+++ b/applications/solvers/combustion/fireFoam/UEqn.H
@@ -13,7 +13,9 @@ solve
   ==
     fvc::reconstruct
     (
-        fvc::interpolate(rho)*(g & mesh.Sf())
-      - fvc::snGrad(p)*mesh.magSf()
+        (
+          - ghf*fvc::snGrad(rho)
+          - fvc::snGrad(p_rgh)
+        )*mesh.magSf()
     )
 );
diff --git a/applications/solvers/combustion/fireFoam/combustionModels/Make/files b/applications/solvers/combustion/fireFoam/combustionModels/Make/files
index 86696b0709..5b1262b70d 100644
--- a/applications/solvers/combustion/fireFoam/combustionModels/Make/files
+++ b/applications/solvers/combustion/fireFoam/combustionModels/Make/files
@@ -1,5 +1,5 @@
 combustionModel/combustionModel.C
-combustionModel/combustionModelNew.C
+combustionModel/newCombustionModel.C
 
 infinitelyFastChemistry/infinitelyFastChemistry.C
 
diff --git a/applications/solvers/combustion/fireFoam/combustionModels/combustionModel/combustionModelNew.C b/applications/solvers/combustion/fireFoam/combustionModels/combustionModel/newCombustionModel.C
similarity index 77%
rename from applications/solvers/combustion/fireFoam/combustionModels/combustionModel/combustionModelNew.C
rename to applications/solvers/combustion/fireFoam/combustionModels/combustionModel/newCombustionModel.C
index e23386589c..62781b0fdb 100644
--- a/applications/solvers/combustion/fireFoam/combustionModels/combustionModel/combustionModelNew.C
+++ b/applications/solvers/combustion/fireFoam/combustionModels/combustionModel/newCombustionModel.C
@@ -29,19 +29,22 @@ License
 
 Foam::autoPtr<Foam::combustionModel> Foam::combustionModel::New
 (
-    const dictionary& propDict,
+    const dictionary& combustionProperties,
     const hsCombustionThermo& thermo,
     const compressible::turbulenceModel& turbulence,
     const surfaceScalarField& phi,
     const volScalarField& rho
 )
 {
-    const word modelType(propDict.lookup("combustionModel"));
+    word combustionModelTypeName = combustionProperties.lookup
+    (
+        "combustionModel"
+    );
 
-    Info<< "Selecting combustion model " << modelType << endl;
+    Info<< "Selecting combustion model " << combustionModelTypeName << endl;
 
     dictionaryConstructorTable::iterator cstrIter =
-        dictionaryConstructorTablePtr_->find(modelType);
+        dictionaryConstructorTablePtr_->find(combustionModelTypeName);
 
     if (cstrIter == dictionaryConstructorTablePtr_->end())
     {
@@ -49,14 +52,14 @@ Foam::autoPtr<Foam::combustionModel> Foam::combustionModel::New
         (
             "combustionModel::New"
         )   << "Unknown combustionModel type "
-            << modelType << nl << nl
-            << "Valid combustionModels are : " << endl
-            << dictionaryConstructorTablePtr_->toc()
+            << combustionModelTypeName << endl << endl
+            << "Valid  combustionModels are : " << endl
+            << dictionaryConstructorTablePtr_->sortedToc()
             << exit(FatalError);
     }
 
     return autoPtr<combustionModel>
-        (cstrIter()(propDict, thermo, turbulence, phi, rho));
+        (cstrIter()(combustionProperties, thermo, turbulence, phi, rho));
 }
 
 
diff --git a/applications/solvers/combustion/fireFoam/combustionModels/infinitelyFastChemistry/infinitelyFastChemistry.H b/applications/solvers/combustion/fireFoam/combustionModels/infinitelyFastChemistry/infinitelyFastChemistry.H
index 851f119feb..53832f21b9 100644
--- a/applications/solvers/combustion/fireFoam/combustionModels/infinitelyFastChemistry/infinitelyFastChemistry.H
+++ b/applications/solvers/combustion/fireFoam/combustionModels/infinitelyFastChemistry/infinitelyFastChemistry.H
@@ -88,8 +88,9 @@ public:
         );
 
 
-    //- Destructor
-    virtual ~infinitelyFastChemistry();
+    // Destructor
+
+        virtual ~infinitelyFastChemistry();
 
 
     // Member Functions
diff --git a/applications/solvers/combustion/fireFoam/combustionModels/noCombustion/noCombustion.H b/applications/solvers/combustion/fireFoam/combustionModels/noCombustion/noCombustion.H
index 9e15f0d300..b3f8bb225e 100644
--- a/applications/solvers/combustion/fireFoam/combustionModels/noCombustion/noCombustion.H
+++ b/applications/solvers/combustion/fireFoam/combustionModels/noCombustion/noCombustion.H
@@ -83,8 +83,9 @@ public:
         );
 
 
-    //- Destructor
-    virtual ~noCombustion();
+    // Destructor
+
+        virtual ~noCombustion();
 
     // Member Functions
 
diff --git a/applications/solvers/combustion/fireFoam/createFields.H b/applications/solvers/combustion/fireFoam/createFields.H
index 9a6274bb1a..6a1a40b777 100644
--- a/applications/solvers/combustion/fireFoam/createFields.H
+++ b/applications/solvers/combustion/fireFoam/createFields.H
@@ -35,6 +35,7 @@ const volScalarField& psi = thermo.psi();
 volScalarField& ft = composition.Y("ft");
 volScalarField& fu = composition.Y("fu");
 
+
 Info<< "Reading field U\n" << endl;
 
 volVectorField U
@@ -73,7 +74,7 @@ IOdictionary combustionProperties
 Info<< "Creating combustion model\n" << endl;
 autoPtr<combustionModel> combustion
 (
-    combustionModel::New
+    combustionModel::combustionModel::New
     (
         combustionProperties,
         thermo,
@@ -83,6 +84,29 @@ autoPtr<combustionModel> combustion
     )
 );
 
+
+Info<< "Calculating field g.h\n" << endl;
+volScalarField gh("gh", g & mesh.C());
+surfaceScalarField ghf("gh", g & mesh.Cf());
+
+Info<< "Reading field p_rgh\n" << endl;
+volScalarField p_rgh
+(
+    IOobject
+    (
+        "p_rgh",
+        runTime.timeName(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh
+);
+
+// Force p_rgh to be consistent with p
+p_rgh = p - rho*gh;
+
+
 volScalarField dQ
 (
     IOobject
@@ -103,15 +127,6 @@ volScalarField DpDt =
     fvc::DDt(surfaceScalarField("phiU", phi/fvc::interpolate(rho)), p);
 
 
-Info<< "Calculating field g.h\n" << endl;
-volScalarField gh("gh", g & mesh.C());
-
-surfaceScalarField ghf("gh", g & mesh.Cf());
-
-p += rho*gh;
-
-thermo.correct();
-
 dimensionedScalar initialMass = fvc::domainIntegrate(rho);
 
 
diff --git a/applications/solvers/combustion/fireFoam/pEqn.H b/applications/solvers/combustion/fireFoam/pEqn.H
index 8d1ed0d9f8..b31a7c6636 100644
--- a/applications/solvers/combustion/fireFoam/pEqn.H
+++ b/applications/solvers/combustion/fireFoam/pEqn.H
@@ -1,5 +1,3 @@
-bool closedVolume = false;
-
 rho = thermo.rho();
 
 volScalarField rUA = 1.0/UEqn.A();
@@ -15,43 +13,41 @@ surfaceScalarField phiU
     )
 );
 
-phi = phiU + rhorUAf*fvc::interpolate(rho)*(g & mesh.Sf());
+phi = phiU - rhorUAf*ghf*fvc::snGrad(rho)*mesh.magSf();
 
 for (int nonOrth=0; nonOrth<=nNonOrthCorr; nonOrth++)
 {
-       surfaceScalarField rhorUAf = fvc::interpolate(rho*rUA);
+    surfaceScalarField rhorUAf = fvc::interpolate(rho*rUA);
 
-        fvScalarMatrix pEqn
+    fvScalarMatrix p_rghEqn
+    (
+        fvm::ddt(psi, p_rgh) + fvc::ddt(psi, rho)*gh
+      + fvc::div(phi)
+      - fvm::laplacian(rhorUAf, p_rgh)
+    );
+
+    p_rghEqn.solve
+    (
+        mesh.solver
         (
-            fvm::ddt(psi,p)
-          + fvc::div(phi)
-          - fvm::laplacian(rhorUAf, p)
-        );
-
-        closedVolume = p.needReference();
-
-        pEqn.solve
-        (
-            mesh.solver
+            p_rgh.select
             (
-                p.select
                 (
-                    (
-                        finalIter
-                     && corr == nCorr-1
-                     && nonOrth == nNonOrthCorr
-                    )
+                    finalIter
+                 && corr == nCorr-1
+                 && nonOrth == nNonOrthCorr
                 )
             )
-        );
+        )
+    );
 
-        if (nonOrth == nNonOrthCorr)
-        {
-            phi += pEqn.flux();
-        }
+    if (nonOrth == nNonOrthCorr)
+    {
+        phi += p_rghEqn.flux();
+    }
 }
 
-DpDt = fvc::DDt(surfaceScalarField("phiU", phi/fvc::interpolate(rho)), p);
+p = p_rgh + rho*gh;
 
 #include "rhoEqn.H"
 #include "compressibleContinuityErrs.H"
@@ -59,12 +55,4 @@ DpDt = fvc::DDt(surfaceScalarField("phiU", phi/fvc::interpolate(rho)), p);
 U += rUA*fvc::reconstruct((phi - phiU)/rhorUAf);
 U.correctBoundaryConditions();
 
-// For closed-volume cases adjust the pressure and density levels
-// to obey overall mass continuity
-if (closedVolume)
-{
-    p +=
-        (initialMass - fvc::domainIntegrate(thermo.psi()*p))
-       /fvc::domainIntegrate(thermo.psi());
-    rho = thermo.rho();
-}
+DpDt = fvc::DDt(surfaceScalarField("phiU", phi/fvc::interpolate(rho)), p);
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/IDefault b/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/IDefault
index 8b93ee55fc..94f365296e 100644
--- a/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/IDefault
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/IDefault
@@ -24,7 +24,7 @@ boundaryField
     {
         type            greyDiffusiveRadiation;
         T               T;
-        emissivity      1.0
+        emissivity      1.0;
         value           uniform 0;
     }
 }
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/p b/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/p
index 58e445ea2d..a18b7d7bc5 100644
--- a/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/p
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/p
@@ -11,7 +11,7 @@ FoamFile
     format      ascii;
     class       volScalarField;
     location    "0";
-    object      p;
+    object      p_rgh;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -23,26 +23,23 @@ boundaryField
 {
     outlet
     {
-        type            buoyantPressure;
-        value           uniform 101325;
+        type            calculated;
+        value           $internalField;
     }
 
     sides
     {
-        type            uniformDensityHydrostaticPressure;
-        rho             1.2;
-        pRefValue       101325;
-        pRefPoint       (0 0 0);
+        type            calculated;
         value           $internalField;
     }
     base
     {
-        type            buoyantPressure;
+        type            calculated;
         value           $internalField;
     }
     inlet
     {
-        type            buoyantPressure;
+        type            calculated;
         value           $internalField;
     }
     frontBack
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/p_rgh b/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/p_rgh
new file mode 100644
index 0000000000..1e165b9bbf
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire2D/0/p_rgh
@@ -0,0 +1,52 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      p_rgh;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [1 -1 -2 0 0 0 0];
+
+internalField   uniform 101325;
+
+boundaryField
+{
+    outlet
+    {
+        type            buoyantPressure;
+        value           uniform 101325;
+    }
+
+    sides
+    {
+        type            fixedValue;
+        value           $internalField;
+    }
+    base
+    {
+        type            buoyantPressure;
+        value           $internalField;
+    }
+    inlet
+    {
+        type            buoyantPressure;
+        value           $internalField;
+    }
+    frontBack
+    {
+        type            empty;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire2D/constant/polyMesh/boundary b/tutorials/combustion/fireFoam/les/smallPoolFire2D/constant/polyMesh/boundary
index c056cb28ee..3adde43e11 100644
--- a/tutorials/combustion/fireFoam/les/smallPoolFire2D/constant/polyMesh/boundary
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire2D/constant/polyMesh/boundary
@@ -15,31 +15,37 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-4
+5
 (
     base
     {
         type            patch;
-        nFaces          150;
+        nFaces          134;
         startFace       44700;
     }
     outlet
     {
         type            patch;
         nFaces          150;
-        startFace       44850;
+        startFace       44834;
     }
     sides
     {
         type            patch;
         nFaces          300;
-        startFace       45000;
+        startFace       44984;
     }
     frontAndBack
     {
         type            empty;
         nFaces          45000;
-        startFace       45300;
+        startFace       45284;
+    }
+    inlet
+    {
+        type            patch;
+        nFaces          16;
+        startFace       90284;
     }
 )
 
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/controlDict b/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/controlDict
index 8f07c5184f..43eca8296c 100644
--- a/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/controlDict
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/controlDict
@@ -36,7 +36,7 @@ writeFormat     ascii;
 
 writePrecision  6;
 
-writeCompression off;
+writeCompression uncompressed;
 
 timeFormat      general;
 
@@ -44,7 +44,7 @@ timePrecision   6;
 
 graphFormat     raw;
 
-runTimeModifiable true;
+runTimeModifiable yes;
 
 adjustTimeStep  yes;
 
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/fvSchemes b/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/fvSchemes
index 870100d127..b52f49447a 100644
--- a/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/fvSchemes
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/fvSchemes
@@ -44,16 +44,7 @@ divSchemes
 
 laplacianSchemes
 {
-    default         none;
-    laplacian(muEff,U) Gauss linear corrected;
-    laplacian(DkEff,k) Gauss linear corrected;
-    laplacian(DBEff,B) Gauss linear corrected;
-    laplacian(alphaEff,hs) Gauss linear uncorrected;
-    laplacian(alphaEff,fu) Gauss linear uncorrected;
-    laplacian(alphaEff,ft) Gauss linear uncorrected;
-    laplacian((((rho*(1|A(U)))*rho)*gh)) Gauss linear uncorrected;
-    laplacian(interpolate((rho*(1|A(U)))),p) Gauss linear uncorrected;
-    laplacian(gammaRad,G) Gauss linear corrected;
+    default         Gauss linear uncorrected;
 }
 
 interpolationSchemes
@@ -69,7 +60,7 @@ snGradSchemes
 fluxRequired
 {
     default         no;
-    p;
+    p_rgh;
 }
 
 
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/fvSolution b/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/fvSolution
index e97f1de618..8c855503fc 100644
--- a/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/fvSolution
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire2D/system/fvSolution
@@ -33,7 +33,7 @@ solvers
         relTol              0;
     };
 
-    p
+    p_rgh
     {
         solver              GAMG;
         tolerance           1e-7;
@@ -45,9 +45,9 @@ solvers
         mergeLevels     1;
     };
 
-    pFinal
+    p_rghFinal
     {
-        $p;
+        $p_rgh;
         tolerance           1e-7;
         relTol              0;
     };
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/G b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/G
new file mode 100644
index 0000000000..c0b1c57ad9
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/G
@@ -0,0 +1,32 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    object      G;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [1 0 -3 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    ".*"
+    {
+        type            MarshakRadiation;
+        T               T;
+        emissivity      1;
+        value           uniform 0;
+    }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/IDefault b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/IDefault
new file mode 100644
index 0000000000..32b03c16d5
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/IDefault
@@ -0,0 +1,32 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    object      IDefault;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [1 0 -3 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    ".*"
+    {
+        type            greyDiffusiveRadiation;
+        T               T;
+        emissivity      1.0;
+        value           uniform 0;
+    }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/T b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/T
new file mode 100644
index 0000000000..7d8327178d
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/T
@@ -0,0 +1,49 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      T;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 1 0 0 0];
+
+internalField   uniform 300;
+
+boundaryField
+{
+    outlet
+    {
+        type            inletOutlet;
+        inletValue      uniform 300;
+        value           uniform 300;
+    }
+    sides
+    {
+        type            inletOutlet;
+        inletValue      uniform 300;
+        value           uniform 300;
+    }
+    base
+    {
+        type            zeroGradient;
+    }
+    inlet
+    {
+        type            fixedValue;
+        value           uniform 300;
+    }
+
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/U b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/U
new file mode 100644
index 0000000000..79d4bcf728
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/U
@@ -0,0 +1,52 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volVectorField;
+    location    "0";
+    object      U;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 1 -1 0 0 0 0];
+
+internalField   uniform (0 0 0);
+
+boundaryField
+{
+    outlet
+    {
+
+        type            inletOutlet;
+        inletValue      uniform (0 0 0);
+        value           uniform (0 0 0);
+
+    }
+    sides
+    {
+        type            pressureInletOutletVelocity;
+        outletValue     uniform (0 0 0);
+        value           uniform (0 0 0);
+    }
+    base
+    {
+        type            fixedValue;
+        value           uniform (0 0 0);
+    }
+    inlet
+    {
+        type            fixedValue;
+        value           uniform (0 0.05 0);
+    }
+
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/alphaSgs b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/alphaSgs
new file mode 100644
index 0000000000..ed7509d9f4
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/alphaSgs
@@ -0,0 +1,44 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      alphaSgs;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [1 -1 -1 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    outlet
+    {
+        type            zeroGradient;
+    }
+    sides
+    {
+        type            zeroGradient;
+    }
+    base
+    {
+        type            zeroGradient;
+    }
+    inlet
+    {
+        type            zeroGradient;
+    }
+
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/b b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/b
new file mode 100644
index 0000000000..57a6d5ab27
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/b
@@ -0,0 +1,44 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      b;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    outlet
+    {
+        type            zeroGradient;
+    }
+    sides
+    {
+        type            zeroGradient;
+    }
+    base
+    {
+        type            zeroGradient;
+    }
+    inlet
+    {
+        type            zeroGradient;
+    }
+
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/ft b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/ft
new file mode 100644
index 0000000000..1dc73a2624
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/ft
@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      ft;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    outlet
+    {
+        type            inletOutlet;
+        inletValue      uniform 0;
+        value           uniform 0;
+    }
+    sides
+    {
+        type            inletOutlet;
+        inletValue      uniform 0;
+        value           uniform 0;
+    }
+    base
+    {
+        type            zeroGradient;
+    }
+    inlet
+    {
+        type            fixedValue;
+        value           uniform 1.0;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/fu b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/fu
new file mode 100644
index 0000000000..0ca8b79198
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/fu
@@ -0,0 +1,49 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      fu;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 0 0 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    outlet
+    {
+        type            inletOutlet;
+        inletValue      uniform 0;
+        value           uniform 0;
+    }
+    sides
+    {
+        type            inletOutlet;
+        inletValue      uniform 0;
+        value           uniform 0;
+    }
+    base
+    {
+        type            zeroGradient;
+    }
+    inlet
+    {
+        type            fixedValue;
+        value           uniform 1.0;
+    }
+
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/k b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/k
new file mode 100644
index 0000000000..89387dba53
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/k
@@ -0,0 +1,49 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      k;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -2 0 0 0 0];
+
+internalField   uniform 1e-4;
+
+boundaryField
+{
+    outlet
+    {
+        type            inletOutlet;
+        inletValue      uniform 1e-4;
+        value           uniform 1e-4;
+    }
+    sides
+    {
+        type            inletOutlet;
+        inletValue      uniform 1e-4;
+        value           uniform 1e-4;
+    }
+    base
+    {
+        type            zeroGradient;
+    }
+    inlet
+    {
+        type            fixedValue;
+        value           uniform 1e-4;
+    }
+
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/muSgs b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/muSgs
new file mode 100644
index 0000000000..d94861f4ba
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/muSgs
@@ -0,0 +1,43 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      muSgs;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [1 -1 -1 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    outlet
+    {
+        type            zeroGradient;
+    }
+    sides
+    {
+        type            zeroGradient;
+    }
+    base
+    {
+        type            zeroGradient;
+    }
+    inlet
+    {
+        type            zeroGradient;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/p b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/p
new file mode 100644
index 0000000000..f403fa62a9
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/p
@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      p;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [1 -1 -2 0 0 0 0];
+
+internalField   uniform 101325;
+
+boundaryField
+{
+    outlet
+    {
+        type           calculated;
+        value          $internalField;
+    }
+
+    sides
+    {
+        type           calculated;
+        value          $internalField;
+    }
+    base
+    {
+        type           calculated;
+        value          $internalField;
+    }
+    inlet
+    {
+        type           calculated;
+        value          $internalField;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/p_rgh b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/p_rgh
new file mode 100644
index 0000000000..47b78e4c87
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/0/p_rgh
@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      p_rgh;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [1 -1 -2 0 0 0 0];
+
+internalField   uniform 101325;
+
+boundaryField
+{
+    outlet
+    {
+        type            buoyantPressure;
+        value           $internalField;
+    }
+
+    sides
+    {
+        type            fixedValue;
+        value           $internalField;
+    }
+    base
+    {
+        type            buoyantPressure;
+        value           $internalField;
+    }
+    inlet
+    {
+        type            buoyantPressure;
+        value           $internalField;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/Allrun b/tutorials/combustion/fireFoam/les/smallPoolFire3D/Allrun
new file mode 100755
index 0000000000..9ea9e89ae6
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/Allrun
@@ -0,0 +1,17 @@
+#!/bin/sh
+
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+# Set application name
+application="fireFoam"
+
+runApplication blockMesh
+runApplication setSet -batch makeFaceSet.setSet
+runApplication createPatch -overwrite
+runApplication decomposePar -force
+
+# Run
+runParallel $application 4
+
+# -----------------------------------------------------------------------------
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/LESProperties b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/LESProperties
new file mode 100644
index 0000000000..958b0085f8
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/LESProperties
@@ -0,0 +1,84 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+    version     2.0;
+    format      binary;
+    class       dictionary;
+    location    "constant";
+    object      LESProperties;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+LESModel       oneEqEddy;
+
+delta          cubeRootVol;
+
+turbulence      on;
+
+printCoeffs     on;
+
+
+cubeRootVolCoeffs
+{
+    deltaCoeff      1;
+}
+
+PrandtlCoeffs
+{
+    delta           cubeRootVol;
+    cubeRootVolCoeffs
+    {
+        deltaCoeff      1;
+    }
+    smoothCoeffs
+    {
+        delta           cubeRootVol;
+        cubeRootVolCoeffs
+        {
+            deltaCoeff      1;
+        }
+        maxDeltaRatio   1.1;
+    }
+    Cdelta           0.158;
+}
+
+vanDriestCoeffs
+{
+    delta           cubeRootVol;
+    cubeRootVolCoeffs
+    {
+        deltaCoeff      1;
+    }
+    smoothCoeffs
+    {
+        delta           cubeRootVol;
+        cubeRootVolCoeffs
+        {
+            deltaCoeff      1;
+        }
+        maxDeltaRatio   1.1;
+    }
+    Aplus            26;
+    Cdelta           0.158;
+}
+
+smoothCoeffs
+{
+    delta           cubeRootVol;
+    cubeRootVolCoeffs
+    {
+        deltaCoeff      1;
+    }
+    maxDeltaRatio   1.1;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/SpeciesTable b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/SpeciesTable
new file mode 100644
index 0000000000..b4b0eee712
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/SpeciesTable
@@ -0,0 +1,491 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      SpeciesTable;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+fields
+1
+(
+
+{
+    name            ft;
+    min             0;
+    max             1;
+    N               100;
+}
+
+)
+;
+output
+5
+(
+
+{
+    name            CH4;
+}
+
+
+{
+    name            CO2;
+}
+
+
+{
+    name            H2O;
+}
+
+
+{
+    name            CO;
+}
+
+
+{
+    name            soot;
+}
+
+)
+;
+values
+6
+(
+
+101
+(
+0.001
+0.011
+0.021
+0.031
+0.041
+0.051
+0.061
+0.071
+0.081
+0.091
+0.101
+0.111
+0.121
+0.131
+0.141
+0.151
+0.161
+0.171
+0.181
+0.191
+0.201
+0.211
+0.221
+0.231
+0.241
+0.251
+0.261
+0.271
+0.281
+0.291
+0.301
+0.311
+0.321
+0.331
+0.341
+0.351
+0.361
+0.371
+0.381
+0.391
+0.401
+0.411
+0.421
+0.431
+0.441
+0.451
+0.461
+0.471
+0.481
+0.491
+0.501
+0.511
+0.521
+0.531
+0.541
+0.551
+0.561
+0.571
+0.581
+0.591
+0.601
+0.611
+0.621
+0.631
+0.641
+0.651
+0.661
+0.671
+0.681
+0.691
+0.701
+0.711
+0.721
+0.731
+0.741
+0.751
+0.761
+0.771
+0.781
+0.791
+0.801
+0.811
+0.821
+0.831
+0.841
+0.851
+0.861
+0.871
+0.881
+0.891
+0.901
+0.911
+0.921
+0.931
+0.941
+0.951
+0.961
+0.971
+0.981
+0.991
+0.999
+)
+
+
+101
+(
+0
+0
+0
+0
+0
+0
+0.0105883
+0.0285208
+0.0461843
+0.0635849
+0.0807284
+0.0976204
+0.114266
+0.130672
+0.146842
+0.162782
+0.178496
+0.193989
+0.209266
+0.224332
+0.23919
+0.253845
+0.268301
+0.282563
+0.296633
+0.310517
+0.324216
+0.337736
+0.35108
+0.364251
+0.377252
+0.390087
+0.402759
+0.415271
+0.427625
+0.439826
+0.451876
+0.463777
+0.475532
+0.487144
+0.498616
+0.50995
+0.521148
+0.532214
+0.543149
+0.553955
+0.564635
+0.575191
+0.585626
+0.595941
+0.606138
+0.61622
+0.626187
+0.636044
+0.64579
+0.655428
+0.66496
+0.674387
+0.683712
+0.692935
+0.702059
+0.711085
+0.720014
+0.728849
+0.73759
+0.74624
+0.754799
+0.763269
+0.771652
+0.779948
+0.788159
+0.796287
+0.804332
+0.812297
+0.820181
+0.827987
+0.835715
+0.843367
+0.850943
+0.858445
+0.865875
+0.873232
+0.880518
+0.887735
+0.894882
+0.901961
+0.908974
+0.91592
+0.922802
+0.929619
+0.936373
+0.943064
+0.949694
+0.956263
+0.962772
+0.969222
+0.975614
+0.981948
+0.988226
+0.994448
+0.999385
+)
+
+
+101
+(
+0.00200328
+0.0213922
+0.0396804
+0.0569589
+0.0733092
+0.088804
+0.0940165
+0.0923125
+0.0906341
+0.0889806
+0.0873516
+0.0857465
+0.0841647
+0.0826058
+0.0810693
+0.0795547
+0.0780615
+0.0765893
+0.0751376
+0.073706
+0.0722942
+0.0709016
+0.0695279
+0.0681728
+0.0668357
+0.0655165
+0.0642147
+0.06293
+0.0616621
+0.0604105
+0.0591751
+0.0579555
+0.0567514
+0.0555625
+0.0543885
+0.0532292
+0.0520842
+0.0509534
+0.0498363
+0.0487329
+0.0476428
+0.0465658
+0.0455017
+0.0444503
+0.0434112
+0.0423844
+0.0413695
+0.0403664
+0.0393749
+0.0383948
+0.0374258
+0.0364678
+0.0355206
+0.0345841
+0.033658
+0.0327421
+0.0318364
+0.0309406
+0.0300546
+0.0291781
+0.0283112
+0.0274535
+0.026605
+0.0257655
+0.0249349
+0.024113
+0.0232997
+0.0224948
+0.0216983
+0.0209099
+0.0201297
+0.0193573
+0.0185928
+0.0178361
+0.0170869
+0.0163452
+0.0156108
+0.0148837
+0.0141638
+0.0134509
+0.0127449
+0.0120458
+0.0113535
+0.0106678
+0.00998859
+0.00931588
+0.00864953
+0.00798947
+0.00733558
+0.0066878
+0.00604604
+0.00541021
+0.00478022
+0.00415601
+0.00353749
+0.00292458
+0.00231721
+0.00171531
+0.00111879
+0.000527591
+5.8413e-05
+)
+
+
+101
+(
+0.00400655
+0.0427844
+0.0793607
+0.113918
+0.146618
+0.177608
+0.188033
+0.184625
+0.181268
+0.177961
+0.174703
+0.171493
+0.168329
+0.165212
+0.162139
+0.159109
+0.156123
+0.153179
+0.150275
+0.147412
+0.144588
+0.141803
+0.139056
+0.136346
+0.133671
+0.131033
+0.128429
+0.12586
+0.123324
+0.120821
+0.11835
+0.115911
+0.113503
+0.111125
+0.108777
+0.106458
+0.104168
+0.101907
+0.0996727
+0.0974658
+0.0952856
+0.0931317
+0.0910035
+0.0889006
+0.0868225
+0.0847688
+0.082739
+0.0807328
+0.0787498
+0.0767895
+0.0748516
+0.0729356
+0.0710413
+0.0691682
+0.067316
+0.0654843
+0.0636728
+0.0618812
+0.0601091
+0.0583563
+0.0566223
+0.054907
+0.05321
+0.051531
+0.0498697
+0.0482259
+0.0465993
+0.0449896
+0.0433965
+0.0418198
+0.0402593
+0.0387147
+0.0371857
+0.0356721
+0.0341737
+0.0326903
+0.0312216
+0.0297674
+0.0283276
+0.0269018
+0.0254899
+0.0240917
+0.022707
+0.0213355
+0.0199772
+0.0186318
+0.0172991
+0.0159789
+0.0146712
+0.0133756
+0.0120921
+0.0108204
+0.00956045
+0.00831202
+0.00707498
+0.00584917
+0.00463443
+0.00343062
+0.00223758
+0.00105518
+0.000116826
+)
+
+101{0}
+101{0}
+)
+;
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/combustionProperties b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/combustionProperties
new file mode 100644
index 0000000000..ba1c9a7919
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/combustionProperties
@@ -0,0 +1,31 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      combustionProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+combustionModel    infinitelyFastChemistry;
+
+infinitelyFastChemistryCoeffs
+{
+    C       10.0;
+}
+
+noCombustionCoeffs
+{
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/g b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/g
new file mode 100644
index 0000000000..81cfdb427d
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/g
@@ -0,0 +1,21 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       uniformDimensionedVectorField;
+    location    "constant";
+    object      g;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 1 -2 0 0 0 0];
+value           (0 -9.8 0);
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/polyMesh/blockMeshDict b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/polyMesh/blockMeshDict
new file mode 100644
index 0000000000..97cfc596c0
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/polyMesh/blockMeshDict
@@ -0,0 +1,64 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      blockMeshDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+convertToMeters 1;
+
+vertices
+(
+    (-0.3 0   -0.3)
+    ( 0.3 0   -0.3)
+    ( 0.3 1.0 -0.3)
+    (-0.3 1.0 -0.3)
+    (-0.3 0    0.3)
+    ( 0.3 0    0.3)
+    ( 0.3 1.0  0.3)
+    (-0.3 1.0  0.3)
+
+);
+
+blocks
+(
+    hex (0 1 2 3 4 5 6 7) (70 70 70) simpleGrading (1 1 1)
+);
+
+edges
+(
+);
+
+patches
+(
+    patch base
+    (
+        (0 1 5 4)
+    )
+    patch outlet
+    (
+        (3 2 6 7)
+    )
+    patch sides
+    (
+        (0 4 7 3)
+        (0 1 2 3)
+        (1 5 6 2)
+        (4 5 6 7)
+    )
+);
+
+mergePatchPairs
+(
+);
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/polyMesh/boundary b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/polyMesh/boundary
new file mode 100644
index 0000000000..a3059febad
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/polyMesh/boundary
@@ -0,0 +1,46 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       polyBoundaryMesh;
+    location    "constant/polyMesh";
+    object      boundary;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+4
+(
+    base
+    {
+        type            patch;
+        nFaces          4704;
+        startFace       1014300;
+    }
+    outlet
+    {
+        type            patch;
+        nFaces          4900;
+        startFace       1019004;
+    }
+    sides
+    {
+        type            patch;
+        nFaces          19600;
+        startFace       1023904;
+    }
+    inlet
+    {
+        type            patch;
+        nFaces          196;
+        startFace       1043504;
+    }
+)
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/radiationProperties b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/radiationProperties
new file mode 100644
index 0000000000..500834ae4a
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/radiationProperties
@@ -0,0 +1,150 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      radiationProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+radiation       on;
+
+radiationModel  fvDOM;
+
+noRadiation
+{
+}
+
+P1Coeffs
+{
+}
+
+fvDOMCoeffs
+{
+    nPhi    2;          // azimuthal angles in PI/2 on X-Y.(from Y to X)
+    nTheta  2;          // polar angles in PI (from Z to X-Y plane)
+    convergence 1e-3;   // convergence criteria for radiation iteration
+    maxIter 10;         // maximum number of iterations
+}
+
+// Number of flow iterations per radiation iteration
+solverFreq 10;
+
+absorptionEmissionModel constantAbsorptionEmission;
+
+constantAbsorptionEmissionCoeffs
+{
+    a               a [ 0 -1 0 0 0 0 0 ] 0.1;
+    e               e [ 0 -1 0 0 0 0 0 ] 0.1;
+    E               E [ 1 -1 -3 0 0 0 0 ] 0;
+}
+
+greyMeanAbsorptionEmissionCoeffs
+{
+    lookUpTableFileName     "SpeciesTable";
+
+    EhrrCoeff                0.0;
+
+    CO2
+    {
+        Tcommon         300;   //Common Temp
+        invTemp         true;   //Is the polynomio using inverse temperature.
+        Tlow            200;   //Low Temp
+        Thigh           2500;  //High Temp
+
+        loTcoeffs       //coefss for T < Tcommon
+        (
+            0           //  a0            +
+            0           //  a1*T          +
+            0           //  a2*T^(+/-)2   +
+            0           //  a3*T^(+/-)3   +
+            0           //  a4*T^(+/-)4   +
+            0           //  a5*T^(+/-)5   +
+        );
+        hiTcoeffs        //coefss for T > Tcommon
+        (
+            18.741
+            -121.31e3
+            273.5e6
+            -194.05e9
+            56.31e12
+            -5.8169e15
+        );
+
+    }
+
+    H2O
+    {
+        Tcommon         300;
+        invTemp         true;
+        Tlow            200;
+        Thigh           2500;
+
+        loTcoeffs
+        (
+            0
+            0
+            0
+            0
+            0
+            0
+        );
+        hiTcoeffs
+        (
+            -0.23093
+            -1.12390e3
+             9.4153e6
+            -2.99885e9
+             0.51382e12
+            -1.868e10
+        );
+    }
+
+    CH4
+    {
+        Tcommon         300;
+        Tlow            200;
+        Thigh           2500;
+        invTemp         false;
+
+        loTcoeffs
+        (
+            0
+            0
+            0
+            0
+            0
+            0
+        );
+        hiTcoeffs
+        (
+            6.6334
+            -0.0035686
+            1.6682e-8
+            2.5611e-10
+            -2.6558e-14
+            0
+        );
+    }
+
+}
+
+scatterModel    constantScatter;
+
+constantScatterCoeffs
+{
+    sigma           sigma [ 0 -1 0 0 0 0 0 ] 0;
+    C               C [ 0 0 0 0 0 0 0 ] 0;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/thermophysicalProperties b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/thermophysicalProperties
new file mode 100644
index 0000000000..090dd1c924
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/thermophysicalProperties
@@ -0,0 +1,54 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version         2.0;
+    format          ascii;
+    class           dictionary;
+    object          thermophysicalProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+thermoType hsPsiMixtureThermo<veryInhomogeneousMixture<sutherlandTransport<specieThermo<janafThermo<perfectGas>>>>>;
+
+stoichiometricAirFuelMassRatio stoichiometricAirFuelMassRatio [0 0 0 0 0 0 0] 17.1271;
+stoichiometricOxygenFuelMassRatio stoichiometricOxygenFuelMassRatio [0 0 0 0 0 0 0] 4.0;
+qFuel qFuel [0 2 -2 0 0 0 0] 5.00264e+07;
+
+fuel fuel   1   16.0428
+    200 6000    1000
+    1.63543 0.0100844 -3.36924e-06 5.34973e-10 -3.15528e-14 -10005.6 9.9937
+    5.14988 -0.013671 4.91801e-05 -4.84744e-08 1.66694e-11 -10246.6 -4.64132
+    1.67212e-06 170.672;
+
+oxidant  oxidant   1   28.8504
+    200 6000    1000
+    3.10131 0.00124137 -4.18816e-07 6.64158e-11 -3.91274e-15 -985.266 5.35597
+    3.58378 -0.000727005 1.67057e-06 -1.09203e-10 -4.31765e-13 -1050.53 3.11239
+    1.67212e-06 170.672;
+
+reactants reactants  1   27.6004
+    200 6000    1000
+    2.95825 0.00210441 -7.06762e-07 1.12145e-10 -6.61028e-15 -1865.61 5.80859
+    3.73662 -0.00199028 6.30727e-06 -4.82941e-09 1.23723e-12 -1948.03 2.35566
+    1.67212e-06 170.672;
+
+burntProducts burntProducts  1   27.6334
+    200 6000    1000
+    3.0602 0.00182422 -5.93878e-07 8.93807e-11 -4.97595e-15 -10998.7 5.32209
+    3.54628 0.000378279 2.02797e-07 9.31602e-10 -6.84016e-13 -11102.1 2.90098
+    1.67212e-06 170.672;
+
+products  products  1   27.6004
+    200 6000    1000
+    3.05615 0.0018477 -6.01767e-07 9.06474e-11 -5.05149e-15 -10995.9 5.33537
+    3.55084 0.000338343 3.42018e-07 7.91162e-10 -6.34688e-13 -11099.7 2.87954
+    1.67212e-06 170.672;
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/turbulenceProperties b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/turbulenceProperties
new file mode 100644
index 0000000000..a247de0973
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/constant/turbulenceProperties
@@ -0,0 +1,22 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      binary;
+    class       dictionary;
+    location    "constant";
+    object      turbulenceProperties;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+simulationType  LESModel;
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/makeFaceSet.setSet b/tutorials/combustion/fireFoam/les/smallPoolFire3D/makeFaceSet.setSet
new file mode 100644
index 0000000000..042be546b2
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/makeFaceSet.setSet
@@ -0,0 +1 @@
+faceSet f0 new boxToFace (-0.06 -0.001 -0.06)(0.06 0.005 0.06)
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/controlDict b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/controlDict
new file mode 100644
index 0000000000..94380a9e76
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/controlDict
@@ -0,0 +1,56 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version         2.0;
+    format          ascii;
+    class           dictionary;
+    object          controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+application     fireFoam;
+
+startFrom       latestTime;
+
+startTime       0.0;
+
+stopAt          endTime;
+
+endTime         10.0;
+
+deltaT          0.001;
+
+writeControl    adjustableRunTime;
+
+writeInterval   0.1;
+
+purgeWrite      0;
+
+writeFormat     ascii;
+
+writePrecision  6;
+
+writeCompression uncompressed;
+
+timeFormat      general;
+
+timePrecision   6;
+
+graphFormat     raw;
+
+runTimeModifiable yes;
+
+adjustTimeStep  yes;
+
+maxCo           0.25;
+
+maxDeltaT       0.1;
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/createPatchDict b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/createPatchDict
new file mode 100644
index 0000000000..0b0d58af95
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/createPatchDict
@@ -0,0 +1,57 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      createPatchDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// This application/dictionary controls:
+// - optional: create new patches from boundary faces (either given as
+//   a set of patches or as a faceSet)
+// - always: order faces on coupled patches such that they are opposite. This
+//   is done for all coupled faces, not just for any patches created.
+// - optional: synchronise points on coupled patches.
+
+// Tolerance used in matching faces. Absolute tolerance is span of
+// face times this factor. To load incorrectly matches meshes set this
+// to a higher value.
+matchTolerance 1E-3;
+
+// Do a synchronisation of coupled points after creation of any patches.
+pointSync true;
+
+// Patches to create.
+patches
+(
+    {
+        // Name of new patch
+        name inlet;
+
+        // Type of new patch
+        patchInfo
+        {
+            type patch;
+        }
+
+        // How to construct: either from 'patches' or 'set'
+        constructFrom set;
+
+        // If constructFrom = patches : names of patches. Wildcards allowed.
+        patches ("periodic.*");
+
+        // If constructFrom = set : name of faceSet
+        set f0;
+    }
+);
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/decomposeParDict b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/decomposeParDict
new file mode 100644
index 0000000000..535f85cc63
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/decomposeParDict
@@ -0,0 +1,45 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      decomposeParDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+numberOfSubdomains 4;
+
+method          hierarchical;
+
+simpleCoeffs
+{
+    n               ( 1 2 2 );
+    delta           0.001;
+}
+
+hierarchicalCoeffs
+{
+    n               ( 1 2 2 );
+    delta           0.001;
+    order           xyz;
+}
+
+manualCoeffs
+{
+    dataFile        "cellDecomposition";
+}
+
+metisCoeffs
+{
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/fvSchemes b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/fvSchemes
new file mode 100644
index 0000000000..da8d7f4f3a
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/fvSchemes
@@ -0,0 +1,67 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+ddtSchemes
+{
+    default         Euler;
+}
+
+gradSchemes
+{
+    default         Gauss linear;
+}
+
+divSchemes
+{
+    default         none;
+    div(phi,U)      Gauss limitedLinear 1;
+    div(phi,k)      Gauss limitedLinear 1;
+    flux(phi,ft)    Gauss limitedLinear01 1;
+    div(phi,ft_b_h) Gauss multivariateSelection
+    {
+        fu              limitedLinear01 1;
+        ft              limitedLinear01 1;
+        hs              limitedLinear 1;
+    };
+    div((muEff*dev2(grad(U).T()))) Gauss linear;
+    div(phiU,p)     Gauss linear;
+    div(Ji,Ii_h)    Gauss upwind;
+}
+
+laplacianSchemes
+{
+    default         Gauss linear corrected;
+}
+
+interpolationSchemes
+{
+    default         linear;
+}
+
+snGradSchemes
+{
+    default         corrected;
+}
+
+fluxRequired
+{
+    default         no;
+    p_rgh;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/fvSolution b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/fvSolution
new file mode 100644
index 0000000000..8c855503fc
--- /dev/null
+++ b/tutorials/combustion/fireFoam/les/smallPoolFire3D/system/fvSolution
@@ -0,0 +1,103 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSolution;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+solvers
+{
+    rho
+    {
+        solver              PCG;
+        preconditioner      DIC;
+        tolerance           1e-7;
+        relTol              0.1;
+    };
+
+    rhoFinal
+    {
+        $rho;
+        tolerance           1e-7;
+        relTol              0;
+    };
+
+    p_rgh
+    {
+        solver              GAMG;
+        tolerance           1e-7;
+        relTol              0.01;
+        smoother            GaussSeidel;
+        cacheAgglomeration  true;
+        nCellsInCoarsestLevel   10;
+        agglomerator    faceAreaPair;
+        mergeLevels     1;
+    };
+
+    p_rghFinal
+    {
+        $p_rgh;
+        tolerance           1e-7;
+        relTol              0;
+    };
+
+
+    "(U|ft|fu|k|hs)"
+    {
+        solver          smoothSolver;
+        smoother        GaussSeidel;
+        tolerance       1e-7;
+        relTol          0.1;
+        nSweeps         1;
+    };
+
+    "(U|ft|fu|k|hs)Final"
+    {
+        $U;
+        tolerance       1e-7;
+        relTol          0;
+    };
+
+
+    Ii
+    {
+        solver              GAMG;
+        tolerance           1e-4;
+        relTol              0;
+        smoother            DILU;
+        cacheAgglomeration  true;
+        nCellsInCoarsestLevel   10;
+        agglomerator    faceAreaPair;
+        mergeLevels     1;
+    }
+
+    G
+    {
+        solver          PCG;
+        preconditioner  DIC;
+        tolerance       1e-06;
+        relTol          0;
+    }
+
+}
+
+PISO
+{
+    momentumPredictor yes;
+    nOuterCorrectors  1;
+    nCorrectors       2;
+    nNonOrthogonalCorrectors 0;
+}
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/blockMeshDict b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/blockMeshDict
index fd92f75904..24c7aabc47 100644
--- a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/blockMeshDict
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/blockMeshDict
@@ -28,20 +28,19 @@ vertices
     ( 662300  4.7545e+06  2100)
     ( 662300  4.7545e+06  1028)
 );
+
 blocks
 (
     hex (0 1 2 3 4 5 6 7) (20 60 60) simpleGrading (10.0 1 1)
 );
 
-
-edges           
 edges
 (
 );
 
 patches
 (
-    patch maxX 
+    patch maxX
     (
         (3 7 6 2)
     )
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/boundary b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/boundary
index cbc211f5e8..60dad0ef57 100644
--- a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/boundary
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/boundary
@@ -8,7 +8,7 @@
 FoamFile
 {
     version     2.0;
-    format      ascii;
+    format      binary;
     class       polyBoundaryMesh;
     location    "constant/polyMesh";
     object      boundary;

From 5aaaf361d28cff6b81f0cf89f1fd7f6c8ce2972a Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Fri, 8 Oct 2010 22:51:35 +0100
Subject: [PATCH 10/12] activeBaffleVelocity: Corrected opening limiter logic

---
 .../activeBaffleVelocityFvPatchVectorField.C                    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/finiteVolume/fields/fvPatchFields/derived/activeBaffleVelocity/activeBaffleVelocityFvPatchVectorField.C b/src/finiteVolume/fields/fvPatchFields/derived/activeBaffleVelocity/activeBaffleVelocityFvPatchVectorField.C
index 2593c7ad1a..92309507c1 100644
--- a/src/finiteVolume/fields/fvPatchFields/derived/activeBaffleVelocity/activeBaffleVelocityFvPatchVectorField.C
+++ b/src/finiteVolume/fields/fvPatchFields/derived/activeBaffleVelocity/activeBaffleVelocityFvPatchVectorField.C
@@ -249,7 +249,7 @@ void Foam::activeBaffleVelocityFvPatchVectorField::updateCoeffs()
                 min
                 (
                     openFraction_
-                  + max
+                  + min
                     (
                         this->db().time().deltaTValue()/openingTime_,
                         maxOpenFractionDelta_

From 195510935deaab455c75957de30477dbe7f9fd97 Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Fri, 8 Oct 2010 22:52:18 +0100
Subject: [PATCH 11/12] Courant number: new formulation

Improves boundary handling
Corresponds better to FVM equations
---
 .../multiphase/interFoam/alphaCourantNo.H     |  17 +--
 .../postProcessing/velocityField/Co/Co.C      | 124 +++++-------------
 .../compressible/compressibleCourantNo.H      |  12 +-
 .../cfdTools/incompressible/CourantNo.H       |  11 +-
 4 files changed, 51 insertions(+), 113 deletions(-)

diff --git a/applications/solvers/multiphase/interFoam/alphaCourantNo.H b/applications/solvers/multiphase/interFoam/alphaCourantNo.H
index b970d4ce23..ffd039c77a 100644
--- a/applications/solvers/multiphase/interFoam/alphaCourantNo.H
+++ b/applications/solvers/multiphase/interFoam/alphaCourantNo.H
@@ -22,7 +22,7 @@ License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
 Global
-    CourantNo
+    alphaCourantNo
 
 Description
     Calculates and outputs the mean and maximum Courant Numbers.
@@ -39,17 +39,14 @@ scalar meanAlphaCoNum = 0.0;
 
 if (mesh.nInternalFaces())
 {
-    surfaceScalarField alphaf = fvc::interpolate(alpha1);
+    scalarField sumPhi =
+        pos(alpha1 - 0.01)*pos(0.99 - alpha1)
+       *fvc::surfaceSum(mag(phi))().internalField();
 
-    surfaceScalarField SfUfbyDelta =
-        pos(alphaf - 0.01)*pos(0.99 - alphaf)
-       *mesh.surfaceInterpolation::deltaCoeffs()*mag(phi);
+    alphaCoNum = 0.5*max(sumPhi/mesh.V().field())*runTime.deltaT().value();
 
-    alphaCoNum = max(SfUfbyDelta/mesh.magSf())
-        .value()*runTime.deltaT().value();
-
-    meanAlphaCoNum = (sum(SfUfbyDelta)/sum(mesh.magSf()))
-        .value()*runTime.deltaT().value();
+    meanAlphaCoNum =
+        0.5*(sum(sumPhi)/sum(mesh.V().field()))*runTime.deltaT().value();
 }
 
 Info<< "Interface Courant Number mean: " << meanAlphaCoNum
diff --git a/applications/utilities/postProcessing/velocityField/Co/Co.C b/applications/utilities/postProcessing/velocityField/Co/Co.C
index c64ca9e2b1..73653e3726 100644
--- a/applications/utilities/postProcessing/velocityField/Co/Co.C
+++ b/applications/utilities/postProcessing/velocityField/Co/Co.C
@@ -25,7 +25,7 @@ Application
     Co
 
 Description
-    Calculates and writes the Co number as a surfaceScalarField obtained
+    Calculates and writes the Co number as a volScalarField obtained
     from field phi.
 
     The -noWrite option just outputs the max values without writing the
@@ -38,52 +38,6 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-namespace Foam
-{
-    tmp<volScalarField> Co(const surfaceScalarField& Cof)
-    {
-        const fvMesh& mesh = Cof.mesh();
-
-        tmp<volScalarField> tCo
-        (
-            new volScalarField
-            (
-                IOobject
-                (
-                    "Co",
-                    mesh.time().timeName(),
-                    mesh
-                ),
-                mesh,
-                dimensionedScalar("0", Cof.dimensions(), 0)
-            )
-        );
-
-        volScalarField& Co = tCo();
-
-        // Set local references to mesh data
-        const unallocLabelList& owner = mesh.owner();
-        const unallocLabelList& neighbour = mesh.neighbour();
-
-        forAll(owner, facei)
-        {
-            label own = owner[facei];
-            label nei = neighbour[facei];
-
-            Co[own] = max(Co[own], Cof[facei]);
-            Co[nei] = max(Co[nei], Cof[facei]);
-        }
-
-        forAll(Co.boundaryField(), patchi)
-        {
-            Co.boundaryField()[patchi] = Cof.boundaryField()[patchi];
-        }
-
-        return tCo;
-    }
-}
-
-
 void Foam::calc(const argList& args, const Time& runTime, const fvMesh& mesh)
 {
     bool writeResults = !args.optionFound("noWrite");
@@ -98,15 +52,28 @@ void Foam::calc(const argList& args, const Time& runTime, const fvMesh& mesh)
 
     if (phiHeader.headerOk())
     {
-        autoPtr<surfaceScalarField> CoPtr;
+        volScalarField Co
+        (
+            IOobject
+            (
+                "Co",
+                runTime.timeName(),
+                mesh,
+                IOobject::NO_READ
+            ),
+            mesh,
+            dimensionedScalar("0", dimless, 0),
+            zeroGradientFvPatchScalarField::typeName
+        );
 
         Info<< "    Reading phi" << endl;
         surfaceScalarField phi(phiHeader, mesh);
-        Info<< "    Calculating Co" << endl;
 
         if (phi.dimensions() == dimensionSet(1, 0, -1, 0, 0))
         {
-            // compressible
+            Info<< "    Calculating compressible Co" << endl;
+
+            Info<< "    Reading rho" << endl;
             volScalarField rho
             (
                 IOobject
@@ -119,60 +86,34 @@ void Foam::calc(const argList& args, const Time& runTime, const fvMesh& mesh)
                 mesh
             );
 
-            CoPtr.set
-            (
-                new surfaceScalarField
-                (
-                    IOobject
-                    (
-                        "Cof",
-                        runTime.timeName(),
-                        mesh,
-                        IOobject::NO_READ
-                    ),
-                    (
-                        mesh.surfaceInterpolation::deltaCoeffs()
-                      * (mag(phi)/(fvc::interpolate(rho)*mesh.magSf()))
-                      * runTime.deltaT()
-                    )
-                )
-            );
+            Co.dimensionedInternalField() =
+                (0.5*runTime.deltaT())
+               *fvc::surfaceSum(mag(phi))().dimensionedInternalField()
+               /(rho*mesh.V());
+            Co.correctBoundaryConditions();
         }
         else if (phi.dimensions() == dimensionSet(0, 3, -1, 0, 0))
         {
-            // incompressible
-            CoPtr.set
-            (
-                new surfaceScalarField
-                (
-                    IOobject
-                    (
-                        "Cof",
-                        runTime.timeName(),
-                        mesh,
-                        IOobject::NO_READ
-                    ),
-                    (
-                        mesh.surfaceInterpolation::deltaCoeffs()
-                      * (mag(phi)/mesh.magSf())
-                      * runTime.deltaT()
-                    )
-                )
-            );
+            Info<< "    Calculating incompressible Co" << endl;
+
+            Co.dimensionedInternalField() =
+                (0.5*runTime.deltaT())
+               *fvc::surfaceSum(mag(phi))().dimensionedInternalField()
+               /mesh.V();
+            Co.correctBoundaryConditions();
         }
         else
         {
             FatalErrorIn(args.executable())
                 << "Incorrect dimensions of phi: " << phi.dimensions()
-                    << abort(FatalError);
+                << abort(FatalError);
         }
 
-        Info<< "Co max : " << max(CoPtr()).value() << endl;
+        Info<< "Co max : " << max(Co).value() << endl;
 
         if (writeResults)
         {
-            CoPtr().write();
-            Co(CoPtr())().write();
+            Co.write();
         }
     }
     else
@@ -183,4 +124,5 @@ void Foam::calc(const argList& args, const Time& runTime, const fvMesh& mesh)
     Info<< "\nEnd\n" << endl;
 }
 
+
 // ************************************************************************* //
diff --git a/src/finiteVolume/cfdTools/compressible/compressibleCourantNo.H b/src/finiteVolume/cfdTools/compressible/compressibleCourantNo.H
index b618efbd0d..d8f7a6cbc0 100644
--- a/src/finiteVolume/cfdTools/compressible/compressibleCourantNo.H
+++ b/src/finiteVolume/cfdTools/compressible/compressibleCourantNo.H
@@ -34,14 +34,14 @@ scalar meanCoNum = 0.0;
 
 if (mesh.nInternalFaces())
 {
-    surfaceScalarField SfUfbyDelta =
-        mesh.surfaceInterpolation::deltaCoeffs()*mag(phi)/fvc::interpolate(rho);
+    scalarField sumPhi =
+        fvc::surfaceSum(mag(phi))().internalField()
+       /rho.internalField();
 
-    CoNum = max(SfUfbyDelta/mesh.magSf())
-        .value()*runTime.deltaTValue();
+    CoNum = 0.5*max(sumPhi/mesh.V().field())*runTime.deltaT().value();
 
-    meanCoNum = (sum(SfUfbyDelta)/sum(mesh.magSf()))
-        .value()*runTime.deltaTValue();
+    meanCoNum =
+        0.5*(sum(sumPhi)/sum(mesh.V().field()))*runTime.deltaT().value();
 }
 
 Info<< "Courant Number mean: " << meanCoNum
diff --git a/src/finiteVolume/cfdTools/incompressible/CourantNo.H b/src/finiteVolume/cfdTools/incompressible/CourantNo.H
index 83bc8765ac..2d2e82ade1 100644
--- a/src/finiteVolume/cfdTools/incompressible/CourantNo.H
+++ b/src/finiteVolume/cfdTools/incompressible/CourantNo.H
@@ -34,14 +34,13 @@ scalar meanCoNum = 0.0;
 
 if (mesh.nInternalFaces())
 {
-    surfaceScalarField SfUfbyDelta =
-        mesh.surfaceInterpolation::deltaCoeffs()*mag(phi);
+    scalarField sumPhi =
+        fvc::surfaceSum(mag(phi))().internalField();
 
-    CoNum = max(SfUfbyDelta/mesh.magSf())
-        .value()*runTime.deltaTValue();
+    CoNum = 0.5*max(sumPhi/mesh.V().field())*runTime.deltaT().value();
 
-    meanCoNum = (sum(SfUfbyDelta)/sum(mesh.magSf()))
-        .value()*runTime.deltaTValue();
+    meanCoNum =
+        0.5*(sum(sumPhi)/sum(mesh.V().field()))*runTime.deltaT().value();
 }
 
 Info<< "Courant Number mean: " << meanCoNum

From ad3abe37386595e481566a41525ed5a33905f9f0 Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Sun, 10 Oct 2010 23:19:16 +0100
Subject: [PATCH 12/12] Courant Numbers: Corrected reductions for parallel
 running

---
 applications/solvers/multiphase/interFoam/alphaCourantNo.H    | 4 ++--
 .../cfdTools/compressible/compressibleCourantNo.H             | 4 ++--
 src/finiteVolume/cfdTools/incompressible/CourantNo.H          | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/applications/solvers/multiphase/interFoam/alphaCourantNo.H b/applications/solvers/multiphase/interFoam/alphaCourantNo.H
index ffd039c77a..12d1b933d4 100644
--- a/applications/solvers/multiphase/interFoam/alphaCourantNo.H
+++ b/applications/solvers/multiphase/interFoam/alphaCourantNo.H
@@ -43,10 +43,10 @@ if (mesh.nInternalFaces())
         pos(alpha1 - 0.01)*pos(0.99 - alpha1)
        *fvc::surfaceSum(mag(phi))().internalField();
 
-    alphaCoNum = 0.5*max(sumPhi/mesh.V().field())*runTime.deltaT().value();
+    alphaCoNum = 0.5*gMax(sumPhi/mesh.V().field())*runTime.deltaT().value();
 
     meanAlphaCoNum =
-        0.5*(sum(sumPhi)/sum(mesh.V().field()))*runTime.deltaT().value();
+        0.5*(gSum(sumPhi)/gSum(mesh.V().field()))*runTime.deltaT().value();
 }
 
 Info<< "Interface Courant Number mean: " << meanAlphaCoNum
diff --git a/src/finiteVolume/cfdTools/compressible/compressibleCourantNo.H b/src/finiteVolume/cfdTools/compressible/compressibleCourantNo.H
index d8f7a6cbc0..73da862406 100644
--- a/src/finiteVolume/cfdTools/compressible/compressibleCourantNo.H
+++ b/src/finiteVolume/cfdTools/compressible/compressibleCourantNo.H
@@ -38,10 +38,10 @@ if (mesh.nInternalFaces())
         fvc::surfaceSum(mag(phi))().internalField()
        /rho.internalField();
 
-    CoNum = 0.5*max(sumPhi/mesh.V().field())*runTime.deltaT().value();
+    CoNum = 0.5*gMax(sumPhi/mesh.V().field())*runTime.deltaT().value();
 
     meanCoNum =
-        0.5*(sum(sumPhi)/sum(mesh.V().field()))*runTime.deltaT().value();
+        0.5*(gSum(sumPhi)/sum(mesh.V().field()))*runTime.deltaT().value();
 }
 
 Info<< "Courant Number mean: " << meanCoNum
diff --git a/src/finiteVolume/cfdTools/incompressible/CourantNo.H b/src/finiteVolume/cfdTools/incompressible/CourantNo.H
index 2d2e82ade1..caef48a396 100644
--- a/src/finiteVolume/cfdTools/incompressible/CourantNo.H
+++ b/src/finiteVolume/cfdTools/incompressible/CourantNo.H
@@ -37,10 +37,10 @@ if (mesh.nInternalFaces())
     scalarField sumPhi =
         fvc::surfaceSum(mag(phi))().internalField();
 
-    CoNum = 0.5*max(sumPhi/mesh.V().field())*runTime.deltaT().value();
+    CoNum = 0.5*gMax(sumPhi/mesh.V().field())*runTime.deltaT().value();
 
     meanCoNum =
-        0.5*(sum(sumPhi)/sum(mesh.V().field()))*runTime.deltaT().value();
+        0.5*(gSum(sumPhi)/sum(mesh.V().field()))*runTime.deltaT().value();
 }
 
 Info<< "Courant Number mean: " << meanCoNum