Merge branch 'master' into dsmc

.gitignore

@@ -4,9 +4,13 @@
 # editor and misc backup files - anywhere
 *~
 .*~
-*.orig
 *.bak
+*.bak[0-9][0-9]
+*.orig
+*.orig[0-9][0-9]
 \#*\#
+
+# file-browser settings - anywhere
 .directory
 
 # CVS recovered versions - anywhere
@@ -18,7 +22,7 @@
 *.so
 *.jar
 
-# ignore derived files
+# derived files
 lex.yy.c
 
 # Corefiles
@@ -30,7 +34,7 @@ core
 # lnInclude (symlink) folders - anywhere
 lnInclude
 
-# build folder(s) - anywhere
+# build folders - anywhere
 linux*Gcc*/
 linux*Icc*/
 linuxming*/
@@ -41,15 +45,14 @@ SunOS*Gcc*/
 # reinstate wmake/rules that might look like build folders
 !wmake/rules/*/
 
-# but do continue to ignore the derived wmake files
-wmake/rules/*/dirToString
-wmake/rules/*/wmkdep
-
 # doxygen generated documentation
 doc/[Dd]oxygen/html
 doc/[Dd]oxygen/latex
 doc/[Dd]oxygen/man
 
+# Other HTML files e.g. ReleaseNotes-?.?.html
+*.html
+
 # source packages - anywhere
 *.tar.bz2
 *.tar.gz

Allwmake

@@ -1,13 +1,21 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # run from this directory
-set -x
+
+if [ "$PWD" != "$WM_PROJECT_DIR" ]
+then
+    echo "Error: Current directory in not \$WM_PROJECT_DIR"
+    echo "    The environment variable are not consistent with the installation."
+    echo "    Check the OpenFOAM entries in your dot-files and source them."
+    exit 1
+fi
 
 # wmake is required for subsequent targets
 ( cd wmake/src && make )
 
 # build ThirdParty sources
-( cd $WM_THIRD_PARTY_DIR && ./Allwmake )
+$WM_THIRD_PARTY_DIR/Allwmake
 
+# build OpenFOAM libraries and applications
 src/Allwmake
 applications/Allwmake
 

README

@@ -1,8 +1,8 @@
 #                            -*- mode: org; -*-
 #
-#+TITLE:             *OpenFOAM README for version 1.5*
+#+TITLE:             OpenFOAM README for version 1.6
 #+AUTHOR:                      OpenCFD Ltd.
-#+DATE:                       26 August 2008
+#+DATE:                         July 2009
 #+LINK:                  http://www.opencfd.co.uk
 #+OPTIONS: author:nil ^:{}
 
@@ -23,17 +23,15 @@
   section "Running OpenFOAM in 32-bit mode".
 
 *** Qt (from http://trolltech.com/products/qt)
-    The ParaView 3.3 visualisation package requires that Qt version 4.3.x MUST
+    The ParaView 3.6.1 visualisation package requires Qt to be installed on the
-    be installed on the system.  Earlier or more recent versions (4.2.x or
+    system.  ParaView's producers state that ParaView is only officially
-    4.4.x) will NOT work.  To check whether Qt4 is installed, and the version,
+    supported on Qt version 4.3.x.  However, we have found in limited tests that
-    type:
+    ParaView works satisfactorily with newer versions of Qt than 4.3.x.  To
+    check whether Qt4 is installed, and the version, type:
     + qmake --version
 
-    The ParaView binary executables in the ThirdParty distribution will only
+    Both 32-bit and 64-bit version of ParaView were compiled with Qt-4.4.3 (with
-    work with PRECISELY the same version of Qt with which it was compiled.  The
+    openSUSE-11.1).  If the user finds that a ParaView binary fails to run, then
-    64-bit version of ParaView was compiled with Qt-4.3.1 (with openSuSE-10.3)
-    and the 32-bit version of ParaView was compiled with Qt-4.3.2 (with
-    ubuntu-7.10).  If the user finds that a ParaView binary fails to run, then
     it is almost certainly due to a conflict in compiled and installed Qt
     versions and they will need to consult the section below on "Compiling
     ParaView and the PV3FoamReader module."
@@ -41,9 +39,11 @@
     The default versions of Qt used by some GNU/Linux releases are as follows.
     + ubuntu-7.10:   Version 4.3.2
     + ubuntu-8.04:   Version 4.3.4
-    + openSuSE-10.2: Version 4.2.1 - too old
+    + ubuntu-9.04:   Version 4.5.0
-    + openSuSE-10.3: Version 4.3.1
+    + openSUSE-10.2: Version 4.2.1 - too old
-    + openSuSE-11.0: Version 4.4.0 - too new
+    + openSUSE-10.3: Version 4.3.1
+    + openSUSE-11.0: Version 4.4.0
+    + openSUSE-11.1: Version 4.4.3
 
     Compilation and running of ParaView has been successful using the libraries
     downloaded in the "libqt4-dev" package on ubuntu.
@@ -51,7 +51,7 @@
     If you don't have an appropriate version of Qt installed you can download
     the sources from TrollTech e.g.:
     ftp://ftp.trolltech.com/qt/source/qt-x11-opensource-src-4.3.5.tar.bz2
-    and compile and install in /usr/local or some other location that does to
+    and compile and install in /usr/local or some other location that does not
     conflict with the pre-installed version.
 
 * Installation
@@ -61,14 +61,13 @@
   The environment variable settings are contained in files in an etc/ directory
   in the OpenFOAM release. e.g. in
 
-  + $HOME/OpenFOAM/OpenFOAM-<VERSION>/etc/
+  + $HOME/OpenFOAM/OpenFOAM-1.6/etc/
-  + where <VERSION> corresponds to the version 1.4, 1.5, ...
 
   1) EITHER, if running bash or ksh (if in doubt type 'echo $SHELL'), source the
     etc/bashrc file by adding the following line to the end of your
     $HOME/.bashrc file:
 
-    + . $HOME/OpenFOAM/OpenFOAM-<VERSION>/etc/bashrc
+    + . $HOME/OpenFOAM/OpenFOAM-1.6/etc/bashrc
 
     Then update the environment variables by sourcing the $HOME/.bashrc file by
     typing in the terminal:
@@ -78,7 +77,7 @@
   2) OR, if running tcsh or csh, source the etc/cshrc file by adding the
     following line to the end of your $HOME/.cshrc file:
 
-    + source $HOME/OpenFOAM/OpenFOAM-<VERSION>/etc/cshrc
+    + source $HOME/OpenFOAM/OpenFOAM-1.6/etc/cshrc
 
     Then update the environment variables by sourcing the $HOME/.cshrc file by
     typing in the terminal:
@@ -94,13 +93,13 @@
     appropriate resource file. Here is a bash/ksh/sh example:
 
     + export FOAM_INST_DIR=/data/app/OpenFOAM
-    + foamDotFile=$FOAM_INST_DIR/OpenFOAM-<VERSION>/etc/bashrc
+    + foamDotFile=$FOAM_INST_DIR/OpenFOAM-1.6/etc/bashrc
     + [ -f $foamDotFile ] && . $foamDotFile
 
     and a csh/tcsh example:
 
     + setenv FOAM_INST_DIR /data/app/OpenFOAM
-    + foamDotFile=$FOAM_INST_DIR/OpenFOAM-<VERSION>/etc/bashrc
+    + foamDotFile=$FOAM_INST_DIR/OpenFOAM-1.6/etc/bashrc
     + if ( -f $foamDotFile ) source $foamDotFile
 
     The value set in '$FOAM_INST_DIR' will be used to locate the remaining parts
@@ -113,7 +112,7 @@
   which may be obtained from http://gcc.gnu.org/.
 
   Install the compiler in
-  $WM_PROJECT_INST_DIR/ThirdParty/gcc-<GCC_VERSION>/platforms/$WM_ARCH$WM_COMPILER_ARCH/
+  $WM_THIRD_PARTY_DIR/gcc-<GCC_VERSION>/platforms/$WM_ARCH$WM_COMPILER_ARCH/
   and change the gcc version number in $WM_PROJECT_DIR/etc/settings.sh and
   $WM_PROJECT_DIR/etc/settings.csh appropriately and finally update the
   environment variables as in section 3.
@@ -121,10 +120,12 @@
   Now go to the top-level source directory $WM_PROJECT_DIR and execute the
   top-level build script './Allwmake'.  In principle this will build everything,
   but if problems occur with the build order it may be necessary to update the
-  environment variables and re-execute 'Allwmake'. If you experience
+  environment variables and re-execute './Allwmake'.
-  difficulties with building the source-pack, or your platform is not currently
+
-  supported, please contact <enquiries@OpenCFD.co.uk> to negotiate a support
+  If you experience difficulties with building the source-pack, or your platform
-  contract and we will do the port and maintain it for future releases.
+  is not currently supported, please contact <enquiries@OpenCFD.co.uk> to
+  negotiate a support contract and we will do the port and maintain it for
+  future releases.
 
 * Testing the installation
   To check your installation setup, execute the 'foamInstallationTest' script
@@ -135,33 +136,37 @@
 
 * Getting Started
   Create a project directory within the $HOME/OpenFOAM directory named
-  <USER>-<VERSION> (e.g. 'chris-1.5' for user chris and OpenFOAM version 1.5)
+  <USER>-1.6 (e.g. 'chris-1.6' for user chris and OpenFOAM version 1.6)
   and create a directory named 'run' within it, e.g. by typing:
 
-  + mkdir -p $HOME/OpenFOAM/${USER}-${WM_PROJECT_VERSION}/run
+  + mkdir -p $FOAM_RUN/run
 
   Copy the 'tutorial' examples directory in the OpenFOAM distribution to the
   'run' directory.  If the OpenFOAM environment variables are set correctly,
   then the following command will be correct:
 
-  + cp -r $WM_PROJECT_DIR/tutorials
+  + cp -r $WM_PROJECT_DIR/tutorials $FOAM_RUN
-    $HOME/OpenFOAM/${USER}-${WM_PROJECT_VERSION}/run
 
   Run the first example case of incompressible laminar flow in a cavity:
 
-  + cd $HOME/OpenFOAM/${USER}-${WM_PROJECT_VERSION}/run/tutorials/icoFoam/cavity
+  + cd $FOAM_RUN/tutorials/incompressible/icoFoam/cavity
   + blockMesh
   + icoFoam
   + paraFoam
 
-* Compiling Paraview 3.3 and the PV3FoamReader module
+  Refer to the OpenFOAM User Guide at http://www.OpenFOAM.org/doc/user.html for
-  A version of Qt 4.3.x must be installed to compile ParaView.  The compilation
+  more information.
-  is a fairly simple process using the supplied buildParaView3.3-cvs script that
+
-  has worked is our tests with other packages supplied in the ThirdParty
+* Compiling Paraview 3.6.1 and the PV3FoamReader module
-  directory, namely cmake-2.4.6 and gcc-4.3.1.  Execute the following:
+  If there are problems encountered with ParaView, then it may be necessary to
-  + cd $FOAM_INST_DIR/ThirdParty
+  compile ParaView from sources.  The compilation
-  + rm -rf ParaView3.3-cvs/platforms
+  is a fairly simple process using the makeParaView script
-  + buildParaView3.3-cvs
+  (found in ThirdParty directory), which has worked in our tests with other
+  packages supplied in the ThirdParty directory, namely cmake-2.6.4 and
+  gcc-4.3.3.  Execute the following:
+  + cd $WM_THIRD_PARTY_DIR
+  + rm -rf paraview-3.6.1/platforms
+  + ./makeParaView
 
   The PV3FoamReader module is an OpenFOAM utility that can be compiled in the
   usual manner as follows:
@@ -169,6 +174,21 @@
   + ./Allwclean
   + ./Allwmake
 
+*** Compiling Paraview with a local version of Qt
+    If the user still encounters problems with ParaView, it may relate to the
+    version of Qt, in which case, it is recommended that the user first
+    downloads a supported version of Qt /e.g./ 4.3.5 as described in the section
+    on "Qt".  The user should unpack the source pack in the $WM_THIRD_PARTY_DIR.
+    Then the user can build Qt by executing from within $WM_THIRD_PARTY_DIR:
+    + makeQt
+
+    The user should then compile ParaView using the local version of Qt by
+    executing makeParaView with the -qmake option, giving the full path of the
+    newly built qmake as an argument:
+    + makeParaView -qmake <path_to_qmake>
+
+    The user must then recompile the PV3FoamReader module as normal (see above).
+
 * Documentation
   http://www.OpenFOAM.org/doc
 

ReleaseNotes-1.5

@@ -1,176 +0,0 @@
-#                            -*- mode: org; -*-
-#
-#+TITLE:          *OpenFOAM release notes for version 1.5*
-#+AUTHOR:                      OpenCFD Ltd.
-#+DATE:                       07 October 2008
-#+LINK:                  http://www.opencfd.co.uk
-#+OPTIONS: author:nil ^:{}
-
-* Overview
-  OpenFOAM-1.5 is is a significant upgrade to version 1.4 in ways which are
-  outlined below.  This release passes all our standard tests and the tutorials
-  have been broadly checked.  If there are any bugs, please report them using
-  the instructions set out in: http://www.OpenFOAM.org/bugs.html.
-
-  Most of the developments for this release are in: new applications, e.g. for
-  multiphase flow and cavitation, buoyancy-flow and heat transfer, high speed
-  flows and even molecular dynamics; new utilities, e.g. for meshing and case
-  monitoring; and, new modelling, e.g. in Lagrangian particle tracking,
-  radiation and rotating frames of reference.  With these new applications come
-  numerous new example cases.
-
-* GNU/Linux version
-  The 64bit binary packs of the OpenFOAM release were compiled on a machine
-  running SuSE GNU/Linux version 10.3 and the 32bit on a machine running Ubuntu
-  GNU/Linux version 7.1 and also tested on Ubuntu 8.04.  We recommend that
-  users run OpenFOAM on one of these or a similar recent version of GNU/Linux.
-  This release has also been successfully compiled and tested on older GNU/Linux
-  releases but this requires the installation of Qt 4.3.? for ParaView-3 to run.
-
-* C++ Compiler version
-  + Released compiled with GCC 4.3.1, the latest version.
-  + Built in support for the Intel C++ 10.? compiler (untested).
-  + The choice of the compiler is controlled by the setting of the $WM_COMPILER
-    and $WM_COMPILER_ARCH environment variables in the OpenFOAM-1.5/etc/bashrc
-    (or cshrc) file.
-  + The location of the installation of the compiler is controlled by the
-    $compilerInstall environment variable in the OpenFOAM-1.5/etc/settings.sh
-    (or settings.csh) file.
-
-* Developments to solvers (applications)
-  + New rhoCentralFoam solver for high-speed, viscous, compressible flows using
-    non-oscillatory, central-upwind schemes.
-  + New interDyMFoam solver for 2 incompressible, isothermal, immiscible fluids
-    using a VoF phase-fraction based interface capturing approach, with optional
-    mesh motion and mesh topology changes including adaptive mesh
-    (un)refinement.  Useful for simulations such as tank filling, sloshing ---
-    using solid body motion e.g. SDA or SKA (6DoF) --- and slamming (using the
-    mesh motion solver) and other large-scale applications that benefit from the
-    efficiency gain of adaptive mesh (un)refinement of the interface.
-  + New compressibleInterFoam solver for 2 compressible, isothermal, immiscible
-    fluids using a volume of fluid (VoF) phase-fraction approach for
-    interface-capturing.  The momentum and other fluid properties are of the
-    "mixture" and a single momentum equation is solved.  Turbulence is modelled
-    using a run-time selectable incompressible LES model.
-  + New interPhaseChangeFoam solver for 2 incompressible, isothermal, immiscible
-    fluids with phase-change, e.g. cavitation.  Uses VoF interface capturing,
-    with momentum and other fluid properties described for the ``mixture'' and a
-    single momentum equation is solved.  The set of phase-change models provided
-    are designed to simulate cavitation but other mechanisms of phase-change are
-    supported within this solver framework.
-  + New rasCavitatingFoam solver for transient cavitation using a barotropic
-    compressibility model, with RAS turbulence.
-  + New lesCavitatingFoam solver for transient cavitation using a barotropic
-    compressibility model, with LES turbulence.
-  + New chtMultiRegionFoam solver that couples conjugate heat transfer in a
-    solid to a buoyancy-driven flow simulation.
-  + New PDRFoam solver for compressible premixed/partially-premixed turbulent
-    combustion that includes porosity/distributed resistance (PDR) modelling to
-    handle regions containing solid blockages which cannot be resolved by the
-    mesh.  Requires the PDR fields.
-  + New lesBuoyantFoam solver for transient, buoyant, turbulent flow of
-    compressible fluids for ventilation and heat-transfer. Turbulence is
-    modelled using a run-time selectable compressible LES model.
-  + New rhoPimpleFoam solver for transient, turbulent flow of compressible
-    fluids for ventilation and heat-transfer. Uses the flexible PIMPLE
-    (PISO-SIMPLE) solution for time-resolved and pseudo-transient simulations.
-  + New buoyantSimpleRadiationFoam solver for steady-state, buoyant, turbulent
-    flow of compressible fluids with radiation, for ventilation and
-    heat-transfer.
-  + New rhoTurbTwinParcelFoam solver for transient for compressible, turbulent
-    flow with two thermo-clouds.
-  + New gnemdFOAM solver for general purpose molecular dynamics that simulates
-    atoms in arbitrary shaped domains and average atomic/molecular quantities to
-    the mesh to create field data.
-  + New mdEqulibrationFoam solver to equilibrates and/or preconditions molecular
-    dynamics systems.
-  + Demonstration SRFSimpleFoam solver based on simpleFoam that incorporates the
-    SRF extensions (see below) for rotating flows.
-
-* Automatic mesher
-  New snappyHexMesh utility that generates split-hex meshes automatically from
-  triangulated (STL) surface geometries.  The mesh approximately conforms to
-  the surface by iteratively refining a starting mesh and morphing the
-  resulting split-hex mesh to the surface.  An optional phase will shrink back
-  the resulting mesh and insert cell layers.  It has a flexible specification
-  of mesh refinement level and robust surface handling with a pre-specified
-  final mesh quality.  It runs in parallel with a load balancing step every
-  iteration.
-
-* Developments to utilities
-  + New extrude2DMesh utility that extrudes 2D meshes into a 3D mesh.  2D meshes
-    are described by faces with 2 points, so can be used in combination with 2D
-    meshes converted with ccm26ToFoam.
-  + New couplePatches functionality integrated into createPatch, which
-    optionally synchronises ("couples") points and faces of coupled (cyclic,
-    processor) patches.
-  + New applyBoundaryLayer pre-processing utility to apply 1/7th power-law
-    boundary layers at walls, starting from uniform or potential flow solutions.
-  + New execFlowFunctionObjects utility executes functionObjects as a
-    post-processing activity, e.g. probes, sampling, force calculation.
-  + New changeDictionary utility makes batch changes to OpenFOAM input files,
-    e.g. to change boundary conditions of field files.
-  + New foamCalc utility, a generic post-processing field calculator tool
-  + New molConfig pre-processing utility for molecular dynamics cases.  Fills
-    zones of a mesh with single crystal lattices of specified structure,
-    density, orientation, alignment and temperature.
-  + Extended splitMeshRegions utility to split multi-zone meshes, e.g. defined
-    through cellZones, into separate meshes.
-  + Extended the foamToVTK, decomposePar, reconstructPar and mapFields utilities
-    to include support for multiple particle clouds in parallel processing.
-
-* Migration from ParaView 2.4 to ParaView 3.x
-  + Rewritten OpenFOAM Reader Module for version 3, a major redesign of
-    ParaView.
-  + New features include viewing patch names, reading of Lagrangian data,
-    handling of cell, face and point sets, multiple views.
-
-* Model development
-  + Overhauled the lagrangian library to support multiple clouds.
-  + New lagrangianIntermediate library incorporating a hierarchy of parcel and
-    cloud types, accommodating kinematic, thermodynamic and reacting
-    applications, including coupling to the new radiation library. Sub-models
-    are added at the relevant level of physics, e.g.:
-    - kinematic: injection, wall interaction, drag, dispersion;
-    - thermo: heat transfer;
-    - reacting: reacting composition, mass transfer, surface reactions.
-  + New single rotating frame of reference (SRF) library for rotating flow
-    applications, e.g. turbo-machinery.
-  + New radiation library including the P1 model and associated Marshak boundary
-    conditions for incident radiation.
-  + New displacementInterpolation motion solver for flexible mesh scaling.
-  + New molecularDynamics Lagrangian library to calculate intermolecular forces
-    between spherically symmetrical monatomic species in arbitrary geometries.
-
-* New functionObjects
-  To aid common monitoring and post-processing activities.
-  + forces: calculate the force and moment on a patch or set of patches, e.g. to
-    calculate the lift, drag and moment of an object in the flow.
-  + forceCoeffs: calculate the normalised force and moment on a patch or set of
-    patches, e.g. to calculate the lift, drag and moment coefficients of an
-    object in the flow.
-  + fieldAverage: calculate field arithmetic mean and prime-squared averages for
-    a list of fields.
-  + foamCalcFunctions: calculate field components, div, mag, magGrad or magSqr.
-
-* Improvements to boundary conditions
-  + Generalised jumpCyclic type: cyclic condition with an additional prescribed
-    jump in value.
-  + fan type: specialisation of jumpCyclic, applying a prescribed jump in
-    pressure to simulate a fan within a mesh.
-  + Generalised advective outflow boundary condition based on solving D/Dt(psi,
-    U) = 0 at the boundary.
-  + Additional turbulent flow inlet to specify mixing length and frequency.
-  + Generalisation of time varying set of boundary conditions.
-
-* Other
-  + New argument-free command execution, e.g typing "icoFoam" without root and
-    case directory arguments.
-  + Extended time command line options.
-  + Many enhancements to dictionary including macro substitution, optional
-    merging and default/overwrite behaviour, enhanced "#include" file handling
-    and the framework to support function evaluation.
-  + Cross-links between applications and Doxygen documentation with the "-doc"
-    argument.
-  + Non-blocking, non-buffered, parallel transfers with potential scaling
-    benefits for larger number of processors.

ReleaseNotes-1.6

@@ -0,0 +1,374 @@
+#                            -*- mode: org; -*-
+#
+#+TITLE:           OpenFOAM release notes for version 1.6
+#+AUTHOR:                      OpenCFD Ltd.
+#+DATE:                         July 2009
+#+LINK:                  http://www.opencfd.co.uk
+#+OPTIONS: author:nil ^:{}
+
+* Overview
+  OpenFOAM-1.6 is a significant upgrade to version 1.5 in ways that are
+  outlined below.  This release passes all our standard tests and the
+  tutorials have been broadly checked.  If there are any bugs, please report
+  them using the instructions set out here:
+  http://www.OpenFOAM.org/bugs.html.
+
+* GNU/Linux version
+  The 32bit and 64bit binary packs of the OpenFOAM release were compiled on
+  a machine running openSUSE GNU/Linux version 11.1 and also tested on
+  Ubuntu 9.  We recommend that users run OpenFOAM on one of these, or on a
+  similarly recent version of GNU/Linux.  This release has also been
+  successfully compiled and tested on older GNU/Linux releases, but this
+  requires the installation of Qt 4.3.? (the sources for which are supplied
+  with OpenFOAM-1.6, see README) for ParaView-3 to run.
+
+* C++ Compiler version
+  + Release compiled with GCC 4.3.3.
+  + Built-in support for the Intel C++ 10.? compiler (untested).
+  + The choice of the compiler is controlled by the setting of the
+    ~$WM_COMPILER~ and ~$WM_COMPILER_ARCH~ environment variables in the
+    /OpenFOAM-1.6/etc/bashrc/ (or /cshrc/) file.
+  + The location of the compiler installation is controlled by the
+    ~$compilerInstall~ environment variable in the
+    /OpenFOAM-1.6/etc/settings.sh/ (or /settings.csh/) file.
+
+* Library developments
+
+*** Core library
+
+***** Dictionary improvements/changes
+      + Dictionaries can use words (unquoted) or regular expressions (quoted)
+        for their keywords. When searching, an exact match has priority over a
+        regular expression match.  Multiple regular expressions are matched in
+        reverse order.
+      + The *new* =#includeIfPresent= directive is similar to the =#include=
+        directive, but does not generate an error if the file does not exist.
+      + The default =#inputMode= is now '=merge=', which corresponds to the most
+        general usage. The =#inputMode warn= corresponds to the previous default
+        behaviour.
+      + The *new* =#inputMode protect= can be used to conditionally merge
+        default values into existing dictionaries.
+      + *New* =digest()= method to calculate and return the SHA1 message digest.
+
+***** Regular Expressions
+      The addition of regular expressions marks a major improvement in
+      usability.
+      + *New* =regExp= class provides support for accessing POSIX extended
+        regular expresssions from within OpenFOAM.
+      + *New* =wordRe= class can contain a =word= or a =regExp= .
+      + *New* =stringListOps= to search string lists based on regular
+        expressions, =wordRe= or =wordReList=.
+      + =Istream= and =Ostream= now retain backslashes when reading/writing
+        strings.
+
+***** Convenience changes
+      + =IOobject= has a *new* constructor for creating an =IOobject= from a
+        single-path specification (eg, see =blockMesh -dict= option).
+      + =argList= has *new* convenience methods for accessing options more
+        directly: =option()=, =optionFound()=, =optionLookup()=, =optionRead()=,
+        =optionReadIfPresent()=.
+      + The *new* =readList(Istream&)= can read a bracket-delimited list or
+        handle a single value as a list of size 1. This can be a useful
+        convenience when processing command-line options.
+      + Export *new* environment variable =FOAM_CASENAME= that contains the
+        name part of the =FOAM_CASE= environment variable.
+
+*** Turbulence modelling
+    + Major development of turbulence model libraries to give extra flexibility
+      at the solver level.  For solvers that can support either RAS/LES
+      computations, the selection is made in the
+      /constant/turbulenceProperties/, by setting the =simulationType= keyword
+      to:
+      - =laminar=,
+      - =RASModel=,
+      - =LESModel=.
+    + Depending on the selection, the model is the instantiated from /constant//
+      - /RASProperties/,
+      - /LESProperties/.
+
+***** RAS wall functions
+      Wall functions are now run-time selectable per patch for RAS.
+      + Velocity:
+        - Apply to turbulent viscosities =nut= or =mut=,
+        - Apply to =k=, =Q=, =R=,
+        - Apply to =epsilon=, =omega=.
+      + Temperature:
+        - Apply to turbulent thermal diffusivity, =alphat= (compressible only).
+      + To apply wall functions:
+        - To recapture the functionality of previous OpenFOAM versions (v1.5 and
+          earlier) assign:
+          - for velocity:
+            - =nut=: =nutWallFunction=,
+            - =mut=: =muWallFunction=,
+            - =epsilon=: =epsilonWallFunction=,
+            - =omega=: =omegaWallFunction=,
+            - =k=, =q=, =R=: =kqRWallFunction=.
+          - for temperature:
+            - =alphat=: =alphatWallFunction=.
+        - New =alphaSgsJayatillekeWallFunction= thermal wall function for
+          compressible LES.
+
+***** *New* LES turbulence models
+      + Spalart-Allmaras DDES.
+      + Spalart-Allmaras IDDES.
+
+***** Upgrading:
+      + *New* utility - =applyWallFunctionBoundaryConditions=.
+      + Solvers will automatically update existing cases.
+        - New fields created based on the presence of the =nut/mut= field.
+        - Boundary conditions include scoping, i.e compressibility:: for
+          compressible solvers.
+        - Modified fields will be backed-up to /<field>.old/.
+      + NOTE:
+        - Fields are only updated for those fields associated with the current
+          turbulence model selection, i.e. if fields exist for use with other
+          models, they will not be updated.
+        - The new specification is not backwards compatible.
+
+*** Thermo-physical Models
+    + Old compressibility-based thermo package renamed
+      =basicThermo= \rightarrow =basicPsiThermo=.
+    + *New* =basicRhoThermo= thermo package.
+      - Additional density field stored.
+      - General form - can be used for other types of media, e.g. liquids.
+      - Additional polynomial-based thermodynamics:
+        - Equation of state: =icoPolynomial=,
+        - Transport: =polynomialTransport=,
+        - Thermo: =hPolynomialThermo=.
+    + Removed earlier hard-coding of gas thermophysics for chemistry modelling:
+      - =reactingMixture= now templated on thermo package,
+      - =chemistryModel= now templated on thermo package,
+      - =chemistrySolver= now templated on thermo package.
+    + *New* =fvDOM= radition model
+      - finite volume, discrete ordinates method.
+    + *New* (reinstated) =eThermo= thermodynamics package
+      - internal energy-based thermodynamics.
+
+*** Lagrangian
+
+***** Intermediate
+      + Overhaul of the underlying framework.
+      + Reacting now split into reacting and reacting multiphase.
+      + New structure for variable composition.
+      + Many new sub-models, including:
+        - Injection
+          - =PatchInjection= - injection local to patch face cells,
+          - =FieldActivatedInjection= - injection based on satisfying external
+            criterion,
+          - LookupTableInjection - explicity define injection locations and all
+            parcel properties.
+        - Post-processing
+          - patch post-processing - collect data for parcels impacting user,
+            defined patches.
+        - Patch interaction
+          - generalised behaviour for parcel interaction with patch.
+        - Phase change
+          - liquid evaporation.
+
+***** Coal combustion
+      + *New* library - extension of reacting-multiphase functionality.
+        - Surface reaction/combustion models.
+
+*** Discrete methods
+    + *New* library offering DSMC simulation functionality - see =dsmcFoam=
+      below.
+    + Significant development of the libraries offering molecular dynamics
+      simulation functionality - see =mdFoam= and =mdEquilibrationFoam= below.
+
+*** Numerics
+    + *new* polynomial-fit higher-order interpolation schemes:
+      - =biLinearFit=
+      - =linearFit=
+      - =quadraticLinearFit=
+      - =quadraticFit=
+      - =linearPureUpwindFit=
+      - =quadraticLinearPureUpwindFit=
+      - =quadraticLinearUpwindFit=
+      - =quadraticUpwindFit=
+      - =cubicUpwindFit=
+    + *new* polynomial-fit higher-order Sn-Grad: =quadraticFitSnGrad=.
+
+*** *New* surfMesh library
+    Provides a more efficient storage mechanism than possible with =triSurface=
+    without restrictions on the shape of the face (templated parameter).
+    + =MeshedSurface= class - with zero or more contiguous =surfZones= .
+    + =UnsortedMeshedSurface= class - unordered surface zones (as per
+      =triSurface=).
+    + =surfMesh= class - for reading/writing in native OpenFOAM format.
+
+* Solvers
+*** Solver restructuring
+    The upgrade to the turbulence models means that the simulation type, i.e.
+    laminar, RAS or LES can be selected at run time. This has allowed a reduction
+    in the number of solvers, simplifying the overall code structure
+    + Solvers which support laminar, RAS and LES:
+      - =turbFoam=, =oodles= \rightarrow =pisoFoam=.
+      - =turbDyMFoam= \rightarrow =pimpleDyMFoam=.
+      - =rhoTurbFoam=, =coodles= \rightarrow =rhoPisoFoam=.
+      - =xoodles= \rightarrow absorbed into =XiFoam=.
+      - =buoyantFoam=, =lesBuoyantFoam= \rightarrow =buoyantPisoFoam=.
+      - =interFoam=, =rasInterFoam=, =lesInterFoam= \rightarrow =interFoam=.
+      - =lesCavitatingFoam=, =rasCavitatingFoam= \rightarrow =cavitatingFoam=.
+    + Solvers which support LES only:
+      - =channelOodles= \rightarrow =channelFoam= (LES).
+    + =pd= replaced by static pressure =p=.  All solvers in which buoyancy affects
+      might be strong have been converted from using =pd= to =p= with improved
+      numerics to give equally good accuracy and stability.  This change is
+      prompted by the need to remove the confusion surrounding the meaning and
+      purpose of =pd=.
+    + =g= (acceleration due to gravity) is now a *new*
+      =uniformDimensionedVectorField= which has the behaviour of a field, is
+      registered to an =objectRegistry=, but stores only a single value.  Thus
+      =g= and other =UniformDimensionedFields= can be created and looked-up
+      elsewhere in the code, /e.g./ in =fvPatchFields=.
+
+*** Solver control improvements
+    Now uses consistent dictionary entries for the solver controls.
+    + This Allows dictionary substitutions and regular expressions in
+      /system/fvSolution/.
+    + The old solver control syntax is still supported (warning emitted), but
+      the *new* =foamUpgradeFvSolution= utility can be used to convert
+      /system/fvSolution/ to the new format.
+
+*** *New* Solvers
+    + =buoyantBoussinesqSimpleFoam= Steady state heat transfer solver using a
+      Boussinesq approximation for buoyancy, with laminar, RAS or LES turbulence
+      modelling.
+    + =buoyantBoussinesqPisoFoam= Transient heat transfer solver using a
+      Boussinesq approximation for buoyancy, with laminar, RAS or LES turbulence
+      modelling.
+    + =coalChemistryFoam= Transient, reacting lagrangian solver, employing a coal
+      cloud and a thermo cloud, with chemistry, and laminar, RAS or LES turbulence
+      modelling.
+    + =porousExplicitSourceReactingParcelFoam= Transient, reacting lagrangian
+      solver, employing a single phase reacting cloud, with porous media, explicit
+      mass sources, and laminar, RAS or LES turbulence modelling.
+    + =rhoReactingFoam= Density-based thermodynamics variant of the reactingFoam
+      solver, i.e. now applicable to liquid systems.
+    + =dsmcFoam= DSMC (Direct Simulation Monte-Carlo) solver for rarefied gas
+      dynamics simulations, able to simulate mixtures of an arbitrary number of
+      gas species.  The variable hard sphere collision model with Larsen-Borgnakke
+      internal energy redistribution (see "Molecular Gas Dynamics and the Direct
+      Simulation of Gas Flows" G.A. Bird, 1994) is available; other run-time
+      selectable collision models can be easily added.
+
+*** Updated solvers
+    + =mdFoam= Molecular Dynamics (MD) solver able to simulate a mixture of an
+      arbitrary number of mono-atomic and small, rigid polyatomic (i.e. H2O, N2)
+      molecular species, with 6 degree of freedom motion, in complex geometries. A
+      molecule of any species can be built by specifying its sites of mass and
+      charge. All molecules interact with short-range dispersion forces and
+      pairwise electrostatic interactions using methods described in: Fennell and
+      Gezelter, J. Chem. Phys. 124, 234104 (2006).
+    + =mdEquilibrationFoam= Similar to mdFoam, but employs velocity scaling to
+      adjust the simulation temperature to a target value. Useful to equilibrate a
+      case before simulation.
+    + =chtMultiRegionFoam= New boundary condition allows independent decomposition
+      of coupled regions without any constraint on the decomposition.
+
+* Boundary conditions
+  + Improved set of direct mapped boundary conditions.
+  + =buoyantPressureFvPatchScalarField=, the *new* buoyancy pressure boundary
+    condition now supports =p= and =pd= for backward compatibility.
+  + =uniformDensityHydrostaticPressure= is an additional pressure boundary
+    condition to aid the transition from =pd= to =p= as it behaves similarly to
+    specifying a uniform =pd= at an outlet for example.
+  + =activeBaffleVelocity= dynamically combines cyclic and wall patches so that
+    the flow through the patch can be controlled /e.g./ by pressure drop.
+  + =rotatingWallVelocity= specifies a rotating velocity, given the rotational
+    speed, origin and axis.
+
+* Utilities
+
+*** Improvements
+   + =blockMesh= has a *new* =-dict= option for specifying an alternative
+     dictionary for the block mesh description. The '=convertToMeters=' entry
+     is now optional, and the alternative '=scale=' entry can be used for
+     less typing.
+   + =foamToEnsight= has a *new* =-noPatches= option to suppress generation
+     of patches.
+   + =foamToEnsightParts= has *new* =-noMesh= and =-index= options that can
+     be useful when post-processing results incrementally.
+   + =snappyHexMesh= has lower memory footprint. New distributed triangulated
+     surface type for meshing surfaces with extremely large triangle count.
+     Now supports multi-region meshing of arbitrarily complex regions.
+
+*** *New* utilities
+   + =particleTracks= - generate particle tracks for lagrangian calculations.
+   + =dsmcInitialise= - preprocessing utility to create initial configurations
+     of DSMC particles in a geometry.
+   + =surfaceRedistributePar= - preprocessing utility to create distributed
+     triangulated surface.
+
+*** *New* foamCalc functions
+    + =interpolate= performs fvc::interpolate(<field>).
+    + =randomise= randomises a <field> by a given perturbation.
+    + =addSubtract= provides simple add/subtract field functionality.
+
+*** Usage
+   + =timeSelector= can now combine =-time ranges= and =-latestTime= options.
+     For example, -time '0.01:0.09' -latestTime vs. -time '0.01:'.
+     More reliable behaviour for cases missing /constant// or /0// directories.
+     When the =-noZero= option is enabled, =-latestTime= will not select the
+     =0/= directory unless the =-zeroTime= option is given.
+     This helps avoid ill effects caused by accidentally using the
+     /0// directory in certain utilities (eg, =reconstructPar=).
+   + =-region= option added to more utilities.
+
+*** Improvements to Paraview reader module
+   + =PV3FoamReader= added mesh region handling. The region name is parsed
+     from the filename. Eg, /case{region}.OpenFOAM/.
+   + =paraFoam= with a *new* =-region= option for specifying an alternative
+     region. A *new* =-touch= option to generate the /.OpenFOAM/ file only.
+     Only creates (and removes) /.OpenFOAM/ files if they didn't already
+     exist, which is useful in connection with the =-touch= option.
+
+* Post-processing
+  + Sampling on iso-surfaces, interpolated or non-interpolated.
+  + Sampling on surface defined by distance to surface (=distanceSurface=).
+  + Cutting planes for arbitrary meshes.
+  + Output to any surface geometry format supported by the =surfMesh= library.
+
+*** Function objects
+
+***** Improvements for function objects and time-looping
+      + The =functionObjectList= retains the order of the =functionObject=
+        order, which allows a chaining of operations. It is thus internally more
+        efficient when /system/controlDict/ uses =functions {..}= instead of
+        =functions (..)=, but both forms are supported.
+      + The =functionObject= now has an additional =end()= method that is called
+        when =Time::loop()= or =Time::run()= determine that the time-loop exits.
+        Accordingly, one of these two idioms should be used in solver code:
+        1. =while (runTime.loop() { ... }=,
+        2. =while (runTime.run()) { runTime++; ... }=.
+      + *New* =functionObjectList= now tracks the SHA1 message digest of the
+        sub-directories. This avoids reloading a =functionObject= when
+        something unrelated in /system/controlDict/ changed.
+
+***** *New* function objects:
+       + =systemCall= - executes a list of system instructions.
+       + =fieldMinMax= - computes the min/max of a <field>.
+       + =staticPressure= - converts kinematic pressure to static pressure.
+       + =dsmcFields= - calculates intensive fields (velocity and temperature)
+         from averaged extensive fields (i.e. momentum and energy).
+
+***** Usage
+       + Improved output control: =timeStep= or =outputTime=.
+
+* Tutorial restructuring
+  to reflect solver application structure.
+
+* Third-party Software
+  + =gcc= upgraded to version 4.3.3.
+  + =OpenMPI= upgraded to version 1.3.3.
+  + =ParaView= upgraded to version 3.6.1.
+  + =Scotch= *new* decomposition method: \\
+    Scotch (http://gforge.inria.fr/projects/scotch/) is a general multi-level
+    decomposition method originating from the ScAlApplix project (Inria). It is
+    a framework for general recursive partitioning methods and a such comparable
+    to Metis but with a permissive licence.
+
+    The corresponding decomposition method (in =decomposeParDict=) is
+    =scotch=.  An optional =strategy= string can be supplied to change the
+    decomposition methods; initial testing shows the default strategy producing
+    decompositions comparable in quality to Metis.

applications/Allwmake

@@ -1,5 +1,14 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # run from this directory
+
+if [ "$PWD" != "$WM_PROJECT_DIR/applications" ]
+then
+    echo "Error: Current directory in not \$WM_PROJECT_DIR/applications"
+    echo "    The environment variable are not consistent with the installation."
+    echo "    Check the OpenFOAM entries in your dot-files and source them."
+    exit 1
+fi
+
 set -x
 
 wmake all solvers

applications/solvers/combustion/PDRFoam/PDRFoam.C

@@ -26,8 +26,8 @@ Application
     PDRFoam
 
 Description
-    Compressible premixed/partially-premixed combustion solver with turbulence
+    Solver for compressible premixed/partially-premixed combustion with
-    modelling.
+    turbulence modelling.
 
     Combusting RANS code using the b-Xi two-equation model.
     Xi may be obtained by either the solution of the Xi transport

applications/solvers/combustion/PDRFoam/PDRModels/turbulence/PDRkEpsilon/PDRkEpsilon.C

@@ -25,10 +25,11 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "PDRkEpsilon.H"
-#include "wallFvPatch.H"
 #include "PDRDragModel.H"
 #include "addToRunTimeSelectionTable.H"
 
+#include "backwardsCompatibilityWallFunctions.H"
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 namespace Foam
@@ -82,29 +83,29 @@ PDRkEpsilon::PDRkEpsilon
             1.92
         )
     ),
-    alphak_
+    sigmak_
     (
         dimensioned<scalar>::lookupOrAddToDict
         (
-            "alphak",
+            "sigmak",
             coeffDict_,
             1.0
         )
     ),
-    alphaEps_
+    sigmaEps_
     (
         dimensioned<scalar>::lookupOrAddToDict
         (
-            "alphaEps",
+            "sigmaEps",
             coeffDict_,
-            0.76923
+            1.3
         )
     ),
-    alphah_
+    Prt_
     (
         dimensioned<scalar>::lookupOrAddToDict
         (
-            "alphah",
+            "Prt",
             coeffDict_,
             1.0
         )
@@ -147,9 +148,26 @@ PDRkEpsilon::PDRkEpsilon
             IOobject::NO_WRITE
         ),
         Cmu_*rho_*sqr(k_)/(epsilon_ + epsilonSmall_)
+    ),
+
+    alphat_
+    (
+        IOobject
+        (
+            "alphat",
+            runTime_.timeName(),
+            mesh_,
+            IOobject::NO_READ,
+            IOobject::AUTO_WRITE
+        ),
+        autoCreateAlphat("alphat", mesh_)
     )
 {
-#   include "wallViscosityI.H"
+    mut_ = Cmu_*rho_*sqr(k_)/(epsilon_ + epsilonSmall_);
+    mut_.correctBoundaryConditions();
+
+    alphat_ = mut_/Prt_;
+    alphat_.correctBoundaryConditions();
 
     printCoeffs();
 }
@@ -214,9 +232,9 @@ bool PDRkEpsilon::read()
         Cmu_.readIfPresent(coeffDict_);
         C1_.readIfPresent(coeffDict_);
         C2_.readIfPresent(coeffDict_);
-        alphak_.readIfPresent(coeffDict_);
+        sigmak_.readIfPresent(coeffDict());
-        alphaEps_.readIfPresent(coeffDict_);
+        sigmaEps_.readIfPresent(coeffDict());
-        alphah_.readIfPresent(coeffDict_);
+        Prt_.readIfPresent(coeffDict());
 
         return true;
     }
@@ -233,7 +251,12 @@ void PDRkEpsilon::correct()
     {
         // Re-calculate viscosity
         mut_ = rho_*Cmu_*sqr(k_)/(epsilon_ + epsilonSmall_);
-#       include "wallViscosityI.H"
+        mut_.correctBoundaryConditions();
+
+        // Re-calculate thermal diffusivity
+        alphat_ = mut_/Prt_;
+        alphat_.correctBoundaryConditions();
+
         return;
     }
 
@@ -250,6 +273,9 @@ void PDRkEpsilon::correct()
     volScalarField G = 2*mut_*(tgradU() && dev(symm(tgradU())));
     tgradU.clear();
 
+    // Update espsilon and G at the wall
+    epsilon_.boundaryField().updateCoeffs();
+
     // Add the blockage generation term so that it is included consistently
     // in both the k and epsilon equations
     const volScalarField& betav = U_.db().lookupObject<volScalarField>("betav");
@@ -259,8 +285,6 @@ void PDRkEpsilon::correct()
 
     volScalarField GR = drag.Gk();
 
-#   include "wallFunctionsI.H"
-
     // Dissipation equation
     tmp<fvScalarMatrix> epsEqn
     (
@@ -273,10 +297,10 @@ void PDRkEpsilon::correct()
       - fvm::Sp(C2_*betav*rho_*epsilon_/k_, epsilon_)
     );
 
-#   include "wallDissipationI.H"
-
     epsEqn().relax();
 
+    epsEqn().boundaryManipulate(epsilon_.boundaryField());
+
     solve(epsEqn);
     bound(epsilon_, epsilon0_);
 
@@ -298,12 +322,13 @@ void PDRkEpsilon::correct()
     solve(kEqn);
     bound(k_, k0_);
 
-
     // Re-calculate viscosity
     mut_ = rho_*Cmu_*sqr(k_)/epsilon_;
+    mut_.correctBoundaryConditions();
 
-#   include "wallViscosityI.H"
+    // Re-calculate thermal diffusivity
-
+    alphat_ = mut_/Prt_;
+    alphat_.correctBoundaryConditions();
 }
 
 

applications/solvers/combustion/PDRFoam/PDRModels/turbulence/PDRkEpsilon/PDRkEpsilon.H

@@ -29,6 +29,20 @@ Description
     Standard k-epsilon turbulence model with additional source terms
     corresponding to PDR basic drag model (\link basic.H \endlink)
 
+    The default model coefficients correspond to the following:
+    @verbatim
+        kEpsilonCoeffs
+        {
+            Cmu         0.09;
+            C1          1.44;
+            C2          1.92;
+            C3          -0.33;  // only for compressible
+            sigmak      1.0;    // only for compressible
+            sigmaEps    1.3;
+            Prt         1.0;    // only for compressible
+        }
+    @endverbatim
+
     The turbulence source term \f$ G_{R} \f$ appears in the
     \f$ \kappa-\epsilon \f$ equation for the generation of turbulence due to
     interaction with unresolved obstacles.
@@ -68,16 +82,21 @@ class PDRkEpsilon
 {
     // Private data
 
+    // Model coefficients
+
         dimensionedScalar Cmu_;
         dimensionedScalar C1_;
         dimensionedScalar C2_;
-        dimensionedScalar alphak_;
+        dimensionedScalar sigmak_;
-        dimensionedScalar alphaEps_;
+        dimensionedScalar sigmaEps_;
-        dimensionedScalar alphah_;
+        dimensionedScalar Prt_;
+
+    // Fields
 
         volScalarField k_;
         volScalarField epsilon_;
         volScalarField mut_;
+        volScalarField alphat_;
 
 
 public:
@@ -85,6 +104,7 @@ public:
     //- Runtime type information
     TypeName("PDRkEpsilon");
 
+
     // Constructors
 
         //- Construct from components
@@ -97,7 +117,7 @@ public:
         );
 
 
-    // Destructor
+    //- Destructor
     virtual ~PDRkEpsilon()
     {}
 
@@ -114,7 +134,7 @@ public:
         {
             return tmp<volScalarField>
             (
-                new volScalarField("DkEff", alphak_*mut_ + mu())
+                new volScalarField("DkEff", mut_/sigmak_ + mu())
             );
         }
 
@@ -123,7 +143,7 @@ public:
         {
             return tmp<volScalarField>
             (
-                new volScalarField("DepsilonEff", alphaEps_*mut_ + mu())
+                new volScalarField("DepsilonEff", mut_/sigmaEps_ + mu())
             );
         }
 
@@ -132,7 +152,7 @@ public:
         {
             return tmp<volScalarField>
             (
-                new volScalarField("alphaEff", alphah_*mut_ + alpha())
+                new volScalarField("alphaEff", alphat_ + alpha())
             );
         }
 

applications/solvers/combustion/XiFoam/UEqn.H

@@ -7,6 +7,8 @@
         rho*g
     );
 
+    UEqn.relax();
+
     if (momentumPredictor)
     {
         solve(UEqn == -fvc::grad(p));

applications/solvers/combustion/XiFoam/XiFoam.C

@@ -26,8 +26,8 @@ Application
     XiFoam
 
 Description
-    Compressible premixed/partially-premixed combustion solver with turbulence
+    Solver for compressible premixed/partially-premixed combustion with
-    modelling.
+    turbulence modelling.
 
     Combusting RANS code using the b-Xi two-equation model.
     Xi may be obtained by either the solution of the Xi transport
@@ -87,12 +87,12 @@ int main(int argc, char *argv[])
         runTime++;
         Info<< "Time = " << runTime.timeName() << nl << endl;
 
-        #include "rhoEqn.H"
+        // --- Pressure-velocity PIMPLE corrector loop
-        #include "UEqn.H"
+        for (int oCorr=0; oCorr<nOuterCorr; oCorr++)
-
-        // --- PISO loop
-        for (int corr=1; corr<=nCorr; corr++)
         {
+            #include "rhoEqn.H"
+            #include "UEqn.H"
+
             #include "ftEqn.H"
             #include "bEqn.H"
             #include "huEqn.H"
@@ -103,10 +103,14 @@ int main(int argc, char *argv[])
                 hu == h;
             }
 
-            #include "pEqn.H"
+            // --- PISO loop
-        }
+            for (int corr=1; corr<=nCorr; corr++)
+            {
+                #include "pEqn.H"
+            }
 
-        turbulence->correct();
+            turbulence->correct();
+        }
 
         rho = thermo.rho();
 

applications/solvers/combustion/XiFoam/bEqn.H

@@ -52,7 +52,7 @@ if (ign.ignited())
       + mvConvection->fvmDiv(phi, b)
       + fvm::div(phiSt, b, "div(phiSt,b)")
       - fvm::Sp(fvc::div(phiSt), b)
-      - fvm::laplacian(turbulence->muEff(), b)
+      - fvm::laplacian(turbulence->alphaEff(), b)
     );
 
 
@@ -90,7 +90,7 @@ if (ign.ignited())
     // ~~~~~~~~~~~~~~~~~
     surfaceScalarField phiXi =
         phiSt
-      - fvc::interpolate(fvc::laplacian(turbulence->muEff(), b)/mgb)*nf
+      - fvc::interpolate(fvc::laplacian(turbulence->alphaEff(), b)/mgb)*nf
       + fvc::interpolate(rho)*fvc::interpolate(Su*(1.0/Xi - Xi))*nf;
 
 

applications/solvers/combustion/XiFoam/ftEqn.H

@@ -1,7 +1,7 @@
 tmp<fv::convectionScheme<scalar> > mvConvection
 (
     fv::convectionScheme<scalar>::New
-    (    
+    (
         mesh,
         fields,
         phi,
@@ -17,6 +17,6 @@ if (composition.contains("ft"))
     (
         fvm::ddt(rho, ft)
       + mvConvection->fvmDiv(phi, ft)
-      - fvm::laplacian(turbulence->muEff(), ft)
+      - fvm::laplacian(turbulence->alphaEff(), ft)
     );
 }

applications/solvers/combustion/XiFoam/hEqn.H

@@ -1,5 +1,5 @@
 {
-    solve
+    fvScalarMatrix hEqn
     (
         fvm::ddt(rho, h)
       + mvConvection->fvmDiv(phi, h)
@@ -8,5 +8,8 @@
         DpDt
     );
 
+    hEqn.relax();
+    hEqn.solve();
+
     thermo.correct();
 }

applications/solvers/combustion/dieselEngineFoam/dieselEngineFoam.C

@@ -26,7 +26,7 @@ Application
     dieselFoam
 
 Description
-    Diesel engine spray and combustion code.
+    Solver for diesel engine spray and combustion.
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/combustion/dieselFoam/dieselFoam.C

@@ -26,7 +26,7 @@ Application
     dieselFoam
 
 Description
-    Diesel spray and combustion code.
+    Solver for diesel spray and combustion.
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/combustion/reactingFoam/reactingFoam.C

@@ -26,7 +26,7 @@ Application
     reactingFoam
 
 Description
-    Chemical reaction code.
+    Solver for combustion with chemical reactions.
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/combustion/rhoReactingFoam/rhoReactingFoam.C

@@ -26,7 +26,8 @@ Application
     rhoReactingFoam
 
 Description
-    Chemical reaction code using density based thermodynamics package.
+    Solver for combustion with chemical reactions using density based
+    thermodynamics package.
 
 \*---------------------------------------------------------------------------*/
 
@@ -68,10 +69,10 @@ int main(int argc, char *argv[])
 
         #include "chemistry.H"
         #include "rhoEqn.H"
-        #include "UEqn.H"
 
         for (label ocorr=1; ocorr <= nOuterCorr; ocorr++)
         {
+            #include "UEqn.H"
             #include "YEqn.H"
             #include "hEqn.H"
 

applications/solvers/compressible/rhoCentralFoam/Allwclean

@@ -1,5 +1,8 @@
 #!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
+set -x
 
 wclean libso BCs
 wclean
 
+# ----------------------------------------------------------------- end-of-file

applications/solvers/compressible/rhoCentralFoam/createFields.H

@@ -7,7 +7,7 @@ autoPtr<basicPsiThermo> pThermo
 basicPsiThermo& thermo = pThermo();
 
 volScalarField& p = thermo.p();
-volScalarField& h = thermo.h();
+volScalarField& e = thermo.e();
 const volScalarField& T = thermo.T();
 const volScalarField& psi = thermo.psi();
 const volScalarField& mu = thermo.mu();
@@ -70,7 +70,7 @@ volScalarField rhoE
         IOobject::NO_READ,
         IOobject::NO_WRITE
     ),
-    rho*(h + 0.5*magSqr(U)) - p
+    rho*(e + 0.5*magSqr(U))
 );
 
 surfaceScalarField pos

applications/solvers/compressible/rhoCentralFoam/rhoCentralFoam.C

@@ -76,10 +76,10 @@ int main(int argc, char *argv[])
         surfaceScalarField rPsi_neg =
             fvc::interpolate(rPsi, neg, "reconstruct(T)");
 
-        surfaceScalarField h_pos =
+        surfaceScalarField e_pos =
-            fvc::interpolate(h, pos, "reconstruct(T)");
+            fvc::interpolate(e, pos, "reconstruct(T)");
-        surfaceScalarField h_neg =
+        surfaceScalarField e_neg =
-            fvc::interpolate(h, neg, "reconstruct(T)");
+            fvc::interpolate(e, neg, "reconstruct(T)");
 
         surfaceVectorField U_pos = rhoU_pos/rho_pos;
         surfaceVectorField U_neg = rhoU_neg/rho_neg;
@@ -132,8 +132,8 @@ int main(int argc, char *argv[])
           + (a_pos*p_pos + a_neg*p_neg)*mesh.Sf();
 
         surfaceScalarField phiEp =
-            aphiv_pos*rho_pos*(h_pos + 0.5*magSqr(U_pos))
+            aphiv_pos*(rho_pos*(e_pos + 0.5*magSqr(U_pos)) + p_pos)
-          + aphiv_neg*rho_neg*(h_neg + 0.5*magSqr(U_neg))
+          + aphiv_neg*(rho_neg*(e_neg + 0.5*magSqr(U_neg)) + p_neg)
           + aSf*p_pos - aSf*p_neg;
 
         volTensorField tauMC("tauMC", mu*dev2(fvc::grad(U)().T()));
@@ -156,7 +156,7 @@ int main(int argc, char *argv[])
         {
             solve
             (
-                fvm::ddt(rho, U) - fvc::ddt(rho,U)
+                fvm::ddt(rho, U) - fvc::ddt(rho, U)
               - fvm::laplacian(mu, U)
               - fvc::div(tauMC)
             );
@@ -180,28 +180,27 @@ int main(int argc, char *argv[])
           - fvc::div(sigmaDotU)
         );
 
-        h = (rhoE + p)/rho - 0.5*magSqr(U);
+        e = rhoE/rho - 0.5*magSqr(U);
-        h.correctBoundaryConditions();
+        e.correctBoundaryConditions();
         thermo.correct();
         rhoE.boundaryField() =
             rho.boundaryField()*
             (
-                h.boundaryField() + 0.5*magSqr(U.boundaryField())
+                e.boundaryField() + 0.5*magSqr(U.boundaryField())
-            )
+            );
-          - p.boundaryField();
 
         if (!inviscid)
         {
             volScalarField k("k", thermo.Cp()*mu/Pr);
             solve
             (
-                fvm::ddt(rho, h) - fvc::ddt(rho, h)
+                fvm::ddt(rho, e) - fvc::ddt(rho, e)
-              - fvm::laplacian(thermo.alpha(), h)
+              - fvm::laplacian(thermo.alpha(), e)
-              + fvc::laplacian(thermo.alpha(), h)
+              + fvc::laplacian(thermo.alpha(), e)
               - fvc::laplacian(k, T)
             );
             thermo.correct();
-            rhoE = rho*(h + 0.5*magSqr(U)) - p;
+            rhoE = rho*(e + 0.5*magSqr(U));
         }
 
         p.dimensionedInternalField() =

applications/solvers/discreteMethods/dsmc/dsmcFoam/dsmcFoam.C

@@ -26,7 +26,8 @@ Application
     dsmcFoam
 
 Description
-    Direct Simulation Monte Carlo Solver for 3D, transient, multi-species flows
+    Direct simulation Monte Carlo (DSMC) solver for 3D, transient, multi-
+    species flows
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C

@@ -26,7 +26,7 @@ Application
     mdEquilibrationFoam
 
 Description
-    Equilibrates and/or preconditions MD systems
+    Equilibrates and/or preconditions molecular dynamics systems
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/discreteMethods/molecularDynamics/mdFoam/mdFoam.C

@@ -26,7 +26,7 @@ Application
     mdFoam
 
 Description
-    molecular dynamics solver for fluid dynamics
+    Molecular dynamics solver for fluid dynamics
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/heatTransfer/buoyantPisoFoam/buoyantPisoFoam.C

@@ -26,9 +26,11 @@ Application
     buoyantPisoFoam
 
 Description
-    Transient Solver for buoyant, turbulent flow of compressible fluids for
+    Transient solver for buoyant, turbulent flow of compressible fluids for
-    ventilation and heat-transfer. Turbulence is modelled using a run-time
+    ventilation and heat-transfer.
-    selectable compressible RAS or LES model.
+
+    Turbulence is modelled using a run-time selectable compressible RAS or
+    LES model.
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/incompressible/shallowWaterFoam/shallowWaterFoam.C

@@ -27,6 +27,7 @@ Application
 
 Description
     Transient solver for inviscid shallow-water equations with rotation.
+
     If the geometry is 3D then it is assumed to be one layers of cells and the
     component of the velocity normal to gravity is removed.
 

applications/solvers/lagrangian/porousExplicitSourceReactingParcelFoam/porousExplicitSourceReactingParcelFoam.C

@@ -26,13 +26,17 @@ Application
     porousExplicitSourceReactingParcelFoam
 
 Description
+    Transient PISO solver for compressible, laminar or turbulent flow with
+    reacting Lagrangian parcels for porous media, including explicit sources
+
+    The solver includes:
     - reacting parcel cloud
     - porous media
     - point mass sources
     - polynomial based, incompressible thermodynamics (f(T))
 
     Note: ddtPhiCorr not used here when porous zones are active
-    - not well defined for porous calcs
+    - not well defined for porous calculations
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/lagrangian/uncoupledKinematicParcelFoam/uncoupledKinematicParcelFoam.C

@@ -23,11 +23,13 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    kinematicParcelFoam
+    uncoupledKinematicParcelFoam
 
 Description
-    Transient solver for a single kinematicCloud. Uses pre-calculated velocity
+    Transient solver for the passive transport of a single kinematic
-    field to evolve a cloud.
+    particle could.
+
+    Uses a pre- calculated velocity field to evolve the cloud.
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/multiphase/bubbleFoam/createRASTurbulence.H

@@ -16,52 +16,93 @@
         RASProperties.lookup("turbulence")
     );
 
-    dictionary kEpsilonCoeffs
+    dictionary kEpsilonDict
     (
-        RASProperties.subDict("kEpsilonCoeffs")
+        RASProperties.subDictPtr("kEpsilonCoeffs")
     );
 
-
+    dimensionedScalar Cmu
-    scalar Cmu
     (
-        readScalar(kEpsilonCoeffs.lookup("Cmu"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "Cmu",
+            kEpsilonDict,
+            0.09
+        )
     );
 
-    scalar C1
+    dimensionedScalar C1
     (
-        readScalar(kEpsilonCoeffs.lookup("C1"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "C1",
+            kEpsilonDict,
+            1.44
+        )
     );
 
-    scalar C2
+    dimensionedScalar C2
     (
-        readScalar(kEpsilonCoeffs.lookup("C2"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "C2",
+            kEpsilonDict,
+            1.92
+        )
     );
 
-    scalar alphak
+    dimensionedScalar alphak
     (
-        readScalar(kEpsilonCoeffs.lookup("alphak"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "alphaEps",
+            kEpsilonDict,
+            1.0
+        )
     );
 
-    scalar alphaEps
+    dimensionedScalar alphaEps
     (
-        readScalar(kEpsilonCoeffs.lookup("alphaEps"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "alphaEps",
+            kEpsilonDict,
+            0.76923
+        )
     );
 
-    dictionary wallFunctionCoeffs
+    dictionary wallFunctionDict
     (
-        RASProperties.subDict("wallFunctionCoeffs")
+        RASProperties.subDictPtr("wallFunctionCoeffs")
     );
 
-    scalar kappa
+    dimensionedScalar kappa
     (
-        readScalar(wallFunctionCoeffs.lookup("kappa"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "kappa",
+            wallFunctionDict,
+            0.4187
+        )
     );
 
-    scalar E
+    dimensionedScalar E
     (
-        readScalar(wallFunctionCoeffs.lookup("E"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "E",
+            wallFunctionDict,
+            9.0
+        )
     );
 
+    if (RASProperties.lookupOrDefault<Switch>("printCoeffs", false))
+    {
+        Info<< "kEpsilonCoeffs" << kEpsilonDict << nl
+            << "wallFunctionCoeffs" << wallFunctionDict << endl;
+    }
+
+
     nearWallDist y(mesh);
 
 

applications/solvers/multiphase/bubbleFoam/kEpsilon.H

@@ -16,7 +16,11 @@ if(turbulence)
     (
         fvm::ddt(beta, epsilon)
       + fvm::div(phib, epsilon)
-      - fvm::laplacian(alphaEps*nuEffb, epsilon)
+      - fvm::laplacian
+        (
+            alphaEps*nuEffb, epsilon,
+            "laplacian(DepsilonEff,epsilon)"
+        )
       ==
          C1*beta*G*epsilon/k
        - fvm::Sp(C2*beta*epsilon/k, epsilon)
@@ -35,7 +39,11 @@ if(turbulence)
     (
         fvm::ddt(beta, k)
       + fvm::div(phib, k)
-      - fvm::laplacian(alphak*nuEffb, k)
+      - fvm::laplacian
+        (
+            alphak*nuEffb, k,
+            "laplacian(DkEff,k)"
+        )
       ==
         beta*G
       - fvm::Sp(beta*epsilon/k, k)

applications/solvers/multiphase/bubbleFoam/wallFunctions.H

@@ -1,8 +1,9 @@
 {
     labelList cellBoundaryFaceCount(epsilon.size(), 0);
 
-    scalar Cmu25 = ::pow(Cmu, 0.25);
+    scalar Cmu25 = ::pow(Cmu.value(), 0.25);
-    scalar Cmu75 = ::pow(Cmu, 0.75);
+    scalar Cmu75 = ::pow(Cmu.value(), 0.75);
+    scalar kappa_ = kappa.value();
 
     const fvPatchList& patches = mesh.boundary();
 
@@ -53,14 +54,14 @@
 
                 epsilon[faceCelli] +=
                      Cmu75*::pow(k[faceCelli], 1.5)
-                    /(kappa*y[patchi][facei]);
+                    /(kappa_*y[patchi][facei]);
 
                 if (yPlus > 11.6)
                 {
                     G[faceCelli] +=
                         nuw[facei]*magFaceGradU[facei]
                         *Cmu25*::sqrt(k[faceCelli])
-                        /(kappa*y[patchi][facei]);
+                        /(kappa_*y[patchi][facei]);
                 }
             }
         }

applications/solvers/multiphase/bubbleFoam/wallViscosity.H

@@ -1,5 +1,8 @@
 {
-    scalar Cmu25 = ::pow(Cmu, 0.25);
+    scalar Cmu25 = ::pow(Cmu.value(), 0.25);
+    scalar kappa_ = kappa.value();
+    scalar E_ = E.value();
+    scalar nub_ = nub.value();
 
     const fvPatchList& patches = mesh.boundary();
 
@@ -19,14 +22,14 @@
                 scalar yPlus =
                     Cmu25*y[patchi][facei]
                    *::sqrt(k[faceCelli])
-                   /nub.value();
+                   /nub_;
 
                 if (yPlus > 11.6)
                 {
                     nutw[facei] =
-                        yPlus*nub.value()*kappa
+                        yPlus*nub_*kappa_
-                       /::log(E*yPlus)
+                       /::log(E_*yPlus)
-                      - nub.value();
+                      - nub_;
                 }
                 else
                 {

applications/solvers/multiphase/compressibleInterDyMFoam/compressibleInterDyMFoam.C

@@ -27,11 +27,13 @@ Application
 
 Description
     Solver for 2 compressible, isothermal immiscible fluids using a VOF
-    (volume of fluid) phase-fraction based interface capturing approach.
+    (volume of fluid) phase-fraction based interface capturing approach,
-    The momentum and other fluid properties are of the "mixture" and a single
+    with optional mesh motion and mesh topology changes including adaptive
-    momentum equation is solved.
+    re-meshing.
 
-    Turbulence modelling is generic, i.e. laminar, RAS or LES may be selected.
+    The momentum and other fluid properties are of the "mixture" and a
+    single momentum equation is solved.  Turbulence modelling is generic,
+    i.e. laminar, RAS or LES may be selected.
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/multiphase/compressibleInterFoam/compressibleInterFoam.C

@@ -28,10 +28,11 @@ Application
 Description
     Solver for 2 compressible, isothermal immiscible fluids using a VOF
     (volume of fluid) phase-fraction based interface capturing approach.
+
     The momentum and other fluid properties are of the "mixture" and a single
     momentum equation is solved.
 
-    Turbulence modelling is generic, i.e. laminar, RAS or LES may be selected.
+    Turbulence modelling is generic, i.e.  laminar, RAS or LES may be selected.
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/multiphase/interFoam/interFoam.C

@@ -28,10 +28,11 @@ Application
 Description
     Solver for 2 incompressible, isothermal immiscible fluids using a VOF
     (volume of fluid) phase-fraction based interface capturing approach.
+
     The momentum and other fluid properties are of the "mixture" and a single
     momentum equation is solved.
 
-    Turbulence modelling is generic, i.e. laminar, RAS or LES may be selected.
+    Turbulence modelling is generic, i.e.  laminar, RAS or LES may be selected.
 
     For a two-fluid approach see twoPhaseEulerFoam.
 

applications/solvers/multiphase/interPhaseChangeFoam/interPhaseChangeFoam.C

@@ -28,8 +28,10 @@ Application
 Description
     Solver for 2 incompressible, isothermal immiscible fluids with phase-change
     (e.g. cavitation).  Uses a VOF (volume of fluid) phase-fraction based
-    interface capturing approach.  The momentum and other fluid properties are
+    interface capturing approach.
-    of the "mixture" and a single momentum equation is solved.
+
+    The momentum and other fluid properties are of the "mixture" and a
+    single momentum equation is solved.
 
     The set of phase-change models provided are designed to simulate cavitation
     but other mechanisms of phase-change are supported within this solver

applications/solvers/multiphase/multiphaseInterFoam/multiphaseInterFoam.C

@@ -27,7 +27,7 @@ Application
 
 Description
     Solver for n incompressible fluids which captures the interfaces and
-    includes surface-tension and contact-angle effects for each.
+    includes surface-tension and contact-angle effects for each phase.
 
     Turbulence modelling is generic, i.e. laminar, RAS or LES may be selected.
 

applications/solvers/multiphase/settlingFoam/createFields.H

@@ -228,57 +228,103 @@
         RASProperties.lookup("turbulence")
     );
 
-    const dictionary& kEpsilonCoeffs
+    dictionary kEpsilonDict
     (
-        RASProperties.subDict("kEpsilonCoeffs")
+        RASProperties.subDictPtr("kEpsilonCoeffs")
     );
 
-
+    dimensionedScalar Cmu
-    scalar Cmu
     (
-        readScalar(kEpsilonCoeffs.lookup("Cmu"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "Cmu",
+            kEpsilonDict,
+            0.09
+        )
     );
 
-    scalar C1
+    dimensionedScalar C1
     (
-        readScalar(kEpsilonCoeffs.lookup("C1"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "C1",
+            kEpsilonDict,
+            1.44
+        )
     );
 
-    scalar C2
+    dimensionedScalar C2
     (
-        readScalar(kEpsilonCoeffs.lookup("C2"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "C2",
+            kEpsilonDict,
+            1.92
+        )
     );
 
-    scalar C3
+    dimensionedScalar C3
     (
-        readScalar(kEpsilonCoeffs.lookup("C3"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "C3",
+            kEpsilonDict,
+            0.85
+        )
     );
 
-    scalar alphak
+    dimensionedScalar alphak
     (
-        readScalar(kEpsilonCoeffs.lookup("alphak"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "alphaEps",
+            kEpsilonDict,
+            1.0
+        )
     );
 
-    scalar alphaEps
+    dimensionedScalar alphaEps
     (
-        readScalar(kEpsilonCoeffs.lookup("alphaEps"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "alphaEps",
+            kEpsilonDict,
+            0.76923
+        )
     );
 
-    const dictionary& wallFunctionCoeffs
+    dictionary wallFunctionDict
     (
-        RASProperties.subDict("wallFunctionCoeffs")
+        RASProperties.subDictPtr("wallFunctionCoeffs")
     );
 
-    scalar kappa
+    dimensionedScalar kappa
     (
-        readScalar(wallFunctionCoeffs.lookup("kappa"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "kappa",
+            wallFunctionDict,
+            0.4187
+        )
     );
 
-    scalar E
+    dimensionedScalar E
     (
-        readScalar(wallFunctionCoeffs.lookup("E"))
+        dimensionedScalar::lookupOrAddToDict
+        (
+            "E",
+            wallFunctionDict,
+            9.0
+        )
     );
 
+    if (RASProperties.lookupOrDefault<Switch>("printCoeffs", false))
+    {
+        Info<< "kEpsilonCoeffs" << kEpsilonDict << nl
+            << "wallFunctionCoeffs" << wallFunctionDict << endl;
+    }
+
+
     nearWallDist y(mesh);
 
     Info<< "Reading field k\n" << endl;

applications/solvers/multiphase/settlingFoam/kEpsilon.H

@@ -26,7 +26,7 @@ if(turbulence)
       + fvm::div(phi, epsilon)
       - fvm::laplacian
         (
-            alphaEps*mut + mul, epsilon, 
+            alphaEps*mut + mul, epsilon,
             "laplacian(DepsilonEff,epsilon)"
         )
      ==
@@ -49,7 +49,11 @@ if(turbulence)
     (
         fvm::ddt(rho, k)
       + fvm::div(phi, k)
-      - fvm::laplacian(alphak*mut + mul, k, "laplacian(DkEff,k)")
+      - fvm::laplacian
+        (
+            alphak*mut + mul, k,
+            "laplacian(DkEff,k)"
+        )
      ==
         G
       - fvm::SuSp(Gcoef + 2.0/3.0*rho*divU, k)

applications/solvers/multiphase/settlingFoam/wallFunctions.H

@@ -1,8 +1,9 @@
 {
     labelList cellBoundaryFaceCount(epsilon.size(), 0);
 
-    scalar Cmu25 = ::pow(Cmu, 0.25);
+    scalar Cmu25 = ::pow(Cmu.value(), 0.25);
-    scalar Cmu75 = ::pow(Cmu, 0.75);
+    scalar Cmu75 = ::pow(Cmu.value(), 0.75);
+    scalar kappa_ = kappa.value();
 
     const fvPatchList& patches = mesh.boundary();
 
@@ -55,14 +56,14 @@
 
                 epsilon[faceCelli] +=
                     Cmu75*rho[faceCelli]*::pow(k[faceCelli], 1.5)
-                   /(kappa*y[patchi][facei]);
+                   /(kappa_*y[patchi][facei]);
 
                 if (yPlus > 11.6)
                 {
                     G[faceCelli] +=
                         mutw[facei]*magFaceGradU[facei]
                        *Cmu25*::sqrt(k[faceCelli])
-                       /(kappa*y[patchi][facei]);
+                       /(kappa_*y[patchi][facei]);
                 }
             }
         }

applications/solvers/multiphase/settlingFoam/wallViscosity.H

@@ -1,5 +1,7 @@
 {
-    scalar Cmu25 = ::pow(Cmu, 0.25);
+    scalar Cmu25 = ::pow(Cmu.value(), 0.25);
+    scalar kappa_ = kappa.value();
+    scalar E_ = E.value();
 
     const fvPatchList& patches = mesh.boundary();
 
@@ -26,7 +28,7 @@
                 {
                     mutw[facei] =
                         muw[facei]
-                       *(yPlus*kappa/::log(E*yPlus) - 1);
+                       *(yPlus*kappa_/::log(E_*yPlus) - 1);
                 }
                 else
                 {

applications/solvers/multiphase/twoPhaseEulerFoam/Allwclean

@@ -1,4 +1,10 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
+set -x
+
 wclean libso phaseModel
 wclean libso interfacialModels
 wclean libso kineticTheoryModels
 wclean
+
+# ----------------------------------------------------------------- end-of-file

applications/solvers/multiphase/twoPhaseEulerFoam/Make/options

@@ -1,4 +1,5 @@
 EXE_INC = \
+    -I../bubbleFoam \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/transportModels/incompressible/lnInclude \
     -IturbulenceModel \
@@ -6,7 +7,7 @@ EXE_INC = \
     -IinterfacialModels/lnInclude \
     -IphaseModel/lnInclude \
     -Iaveraging
-        
+
 EXE_LIBS = \
     -lEulerianInterfacialModels \
     -lfiniteVolume \

applications/solvers/multiphase/twoPhaseEulerFoam/createFields.H

@@ -91,34 +91,6 @@
         alpha*Ua + beta*Ub
     );
 
-    Info<< "Reading field k\n" << endl;
-    volScalarField k
-    (
-        IOobject
-        (
-            "k",
-            runTime.timeName(),
-            mesh,
-            IOobject::MUST_READ,
-            IOobject::AUTO_WRITE
-        ),
-        mesh
-    );
-
-    Info<< "Reading field epsilon\n" << endl;
-    volScalarField epsilon
-    (
-        IOobject
-        (
-            "epsilon",
-            runTime.timeName(),
-            mesh,
-            IOobject::MUST_READ,
-            IOobject::AUTO_WRITE
-        ),
-        mesh
-    );
-
     dimensionedScalar Cvm
     (
         transportProperties.lookup("Cvm")
@@ -156,114 +128,7 @@
         alpha*rhoa + beta*rhob
     );
 
-    IOdictionary RASProperties
+    #include "createRASTurbulence.H"
-    (
-        IOobject
-        (
-            "RASProperties",
-            runTime.constant(),
-            mesh,
-            IOobject::MUST_READ,
-            IOobject::NO_WRITE
-        )
-    );
-
-
-    Switch turbulence
-    (
-        RASProperties.lookup("turbulence")
-    );
-
-    dictionary kEpsilonCoeffs
-    (
-        RASProperties.subDict("kEpsilonCoeffs")
-    );
-
-
-    scalar Cmu
-    (
-        readScalar(kEpsilonCoeffs.lookup("Cmu"))
-    );
-
-    scalar C1
-    (
-        readScalar(kEpsilonCoeffs.lookup("C1"))
-    );
-
-    scalar C2
-    (
-        readScalar(kEpsilonCoeffs.lookup("C2"))
-    );
-
-    scalar alphak
-    (
-        readScalar(kEpsilonCoeffs.lookup("alphak"))
-    );
-
-    scalar alphaEps
-    (
-        readScalar(kEpsilonCoeffs.lookup("alphaEps"))
-    );
-
-    dictionary wallFunctionCoeffs
-    (
-        RASProperties.subDict("wallFunctionCoeffs")
-    );
-
-    scalar kappa
-    (
-        readScalar(wallFunctionCoeffs.lookup("kappa"))
-    );
-
-    scalar E
-    (
-        readScalar(wallFunctionCoeffs.lookup("E"))
-    );
-
-    nearWallDist y(mesh);
-
-    Info<< "Calculating field nutb\n" << endl;
-    volScalarField nutb
-    (
-        IOobject
-        (
-            "nutb",
-            runTime.timeName(),
-            mesh,
-            IOobject::NO_READ,
-            IOobject::AUTO_WRITE
-        ),
-        Cmu*sqr(k)/epsilon
-    );
-
-    Info<< "Calculating field nuEffa\n" << endl;
-    volScalarField nuEffa
-    (
-        IOobject
-        (
-            "nuEffa",
-            runTime.timeName(),
-            mesh,
-            IOobject::NO_READ,
-            IOobject::NO_WRITE
-        ),
-        sqr(Ct)*nutb + nua
-    );
-
-    Info<< "Calculating field nuEffb\n" << endl;
-    volScalarField nuEffb
-    (
-        IOobject
-        (
-            "nuEffb",
-            runTime.timeName(),
-            mesh,
-            IOobject::NO_READ,
-            IOobject::NO_WRITE
-        ),
-        nutb + nub
-    );
-
 
     Info<< "Calculating field DDtUa and DDtUb\n" << endl;
 

applications/solvers/multiphase/twoPhaseEulerFoam/turbulenceModel/kEpsilon.H

@@ -1,61 +0,0 @@
-if(turbulence)
-{
-    if (mesh.changing())
-    {
-        y.correct();
-    }
-
-    tmp<volTensorField> tgradUb = fvc::grad(Ub);
-    volScalarField G = 2*nutb*(tgradUb() && dev(symm(tgradUb())));
-    tgradUb.clear();
-
-#   include "wallFunctions.H"
-
-    // Dissipation equation
-    fvScalarMatrix epsEqn
-    (
-        fvm::ddt(beta, epsilon)
-      + fvm::div(phib, epsilon)
-      - fvm::laplacian
-        (
-            alphaEps*nuEffb,
-            epsilon,
-            "laplacian((alphaEps*nuEffb),epsilon)"
-        )
-      ==
-         C1*beta*G*epsilon/k
-       - fvm::Sp(C2*beta*epsilon/k, epsilon)
-    );
-
-#   include "wallDissipation.H"
-
-    epsEqn.relax();
-    epsEqn.solve();
-
-    epsilon.max(dimensionedScalar("zero", epsilon.dimensions(), 1.0e-15));
-
-
-    // Turbulent kinetic energy equation
-    fvScalarMatrix kEqn
-    (
-        fvm::ddt(beta, k)
-      + fvm::div(phib, k)
-      - fvm::laplacian(alphak*nuEffb, k, "laplacian((alphak*nuEffb),k)")
-      ==
-        beta*G
-      - fvm::Sp(beta*epsilon/k, k)
-    );
-    kEqn.relax();
-    kEqn.solve();
-
-    k.max(dimensionedScalar("zero", k.dimensions(), 1.0e-8));
-
-    //- Re-calculate turbulence viscosity
-    nutb = Cmu*sqr(k)/epsilon;
-
-#   include "wallViscosity.H"
-
-}
-
-nuEffa = sqr(Ct)*nutb + nua;
-nuEffb = nutb + nub;

applications/solvers/multiphase/twoPhaseEulerFoam/turbulenceModel/wallDissipation.H

@@ -1,51 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2009 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 2 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, write to the Free Software Foundation,
-    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-Global
-    wallDissipation
-
-Description
-    Set wall dissipation in the epsilon matrix
-
-\*---------------------------------------------------------------------------*/
-
-{
-    const fvPatchList& patches = mesh.boundary();
-
-    forAll(patches, patchi)
-    {
-        const fvPatch& p = patches[patchi];
-
-        if (isType<wallFvPatch>(p))
-        {
-            epsEqn.setValues
-            (
-                p.faceCells(),
-                epsilon.boundaryField()[patchi].patchInternalField()
-            );
-        }
-    }
-}
-
-// ************************************************************************* //

applications/solvers/multiphase/twoPhaseEulerFoam/turbulenceModel/wallFunctions.H

@@ -1,86 +0,0 @@
-{
-    labelList cellBoundaryFaceCount(epsilon.size(), 0);
-
-    scalar Cmu25 = ::pow(Cmu, 0.25);
-    scalar Cmu75 = ::pow(Cmu, 0.75);
-
-    const fvPatchList& patches = mesh.boundary();
-
-    //- Initialise the near-wall P field to zero
-    forAll(patches, patchi)
-    {
-        const fvPatch& currPatch = patches[patchi];
-
-        if (isType<wallFvPatch>(currPatch))
-        {
-            forAll(currPatch, facei)
-            {
-                label faceCelli = currPatch.faceCells()[facei];
-
-                epsilon[faceCelli] = 0.0;
-                G[faceCelli] = 0.0;
-            }
-        }
-    }
-
-    //- Accumulate the wall face contributions to epsilon and G
-    //  Increment cellBoundaryFaceCount for each face for averaging
-    forAll(patches, patchi)
-    {
-        const fvPatch& currPatch = patches[patchi];
-
-        if (isType<wallFvPatch>(currPatch))
-        {
-            const scalarField& nuw = nutb.boundaryField()[patchi];
-
-            scalarField magFaceGradU = mag(U.boundaryField()[patchi].snGrad());
-
-            forAll(currPatch, facei)
-            {
-                label faceCelli = currPatch.faceCells()[facei];
-
-                scalar yPlus =
-                    Cmu25*y[patchi][facei]
-                    *::sqrt(k[faceCelli])
-                    /nub.value();
-
-                // For corner cells (with two boundary or more faces),
-                // epsilon and G in the near-wall cell are calculated
-                // as an average
-
-                cellBoundaryFaceCount[faceCelli]++;
-
-                epsilon[faceCelli] +=
-                     Cmu75*::pow(k[faceCelli], 1.5)
-                    /(kappa*y[patchi][facei]);
-
-                if (yPlus > 11.6)
-                {
-                    G[faceCelli] +=
-                        nuw[facei]*magFaceGradU[facei]
-                        *Cmu25*::sqrt(k[faceCelli])
-                        /(kappa*y[patchi][facei]);
-                }
-            }
-        }
-    }
-
-
-    // perform the averaging
-
-    forAll(patches, patchi)
-    {
-        const fvPatch& curPatch = patches[patchi];
-
-        if (isType<wallFvPatch>(curPatch))
-        {
-            forAll(curPatch, facei)
-            {
-                label faceCelli = curPatch.faceCells()[facei];
-
-                epsilon[faceCelli] /= cellBoundaryFaceCount[faceCelli];
-                G[faceCelli] /= cellBoundaryFaceCount[faceCelli];
-            }
-        }
-    }
-}

applications/solvers/multiphase/twoPhaseEulerFoam/turbulenceModel/wallViscosity.H

@@ -1,38 +0,0 @@
-{
-    scalar Cmu25 = ::pow(Cmu, 0.25);
-
-    const fvPatchList& patches = mesh.boundary();
-
-    forAll(patches, patchi)
-    {
-        const fvPatch& currPatch = patches[patchi];
-
-        if (isType<wallFvPatch>(currPatch))
-        {
-            scalarField& nutw = nutb.boundaryField()[patchi];
-
-            forAll(currPatch, facei)
-            {
-                label faceCelli = currPatch.faceCells()[facei];
-
-                // calculate yPlus
-                scalar yPlus =
-                    Cmu25*y[patchi][facei]
-                   *::sqrt(k[faceCelli])
-                   /nub.value();
-
-                if (yPlus > 11.6)
-                {
-                    nutw[facei] =
-                        yPlus*nub.value()*kappa
-                       /::log(E*yPlus)
-                      - nub.value();
-                }
-                else
-                {
-                    nutw[facei] = 0.0;
-                }
-            }
-        }
-    }
-}

applications/test/PackedList/Make/options

@@ -0,0 +1,7 @@
+/*
+  check for consistent behaviour with non-optimized code
+  */
+
+EXE_INC = \
+    -DFULLDEBUG -g -O0
+

applications/test/PackedList/PackedListTest.C

@@ -28,320 +28,146 @@ Description
 
 \*---------------------------------------------------------------------------*/
 
+#include "argList.H"
 #include "uLabel.H"
+#include "IOobject.H"
 #include "IOstreams.H"
+#include "IFstream.H"
 #include "PackedBoolList.H"
+#include <climits>
+
 
 using namespace Foam;
 
+template<unsigned nBits>
+inline void reportInfo()
+{
+    unsigned offset = PackedList<nBits>::packing();
+
+    unsigned useSHL = ((1u << (nBits * offset)) - 1);
+    unsigned useSHR = (~0u >> (sizeof(unsigned)*CHAR_BIT - nBits * offset));
+
+    Info<< nl
+        << "PackedList<" << nBits << ">" << nl
+        << " max_value: " << PackedList<nBits>::max_value() << nl
+        << " packing: " << PackedList<nBits>::packing() << nl
+        << " utilization: " << (nBits * offset) << nl;
+
+    Info<< " Masking:" << nl
+        << "  shift << " << unsigned(nBits * offset) << nl
+        << "  shift >> " << unsigned((sizeof(unsigned)*CHAR_BIT) - nBits * offset)
+        << nl;
+
+    hex(Info);
+    Info<< "   maskLower: " << PackedList<nBits>::maskLower(PackedList<nBits>::packing())
+        << nl
+        << "      useSHL: " << useSHL << nl
+        << "      useSHR: " << useSHR << nl;
+
+    if (useSHL != useSHR)
+    {
+        Info<< "WARNING:  different results for SHL and SHR" << nl;
+    }
+
+    Info<< nl;
+    dec(Info);
+}
+
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 //  Main program:
 
 int main(int argc, char *argv[])
 {
-    Info<< "PackedList max_bits() = " << PackedList<>::max_bits() << nl;
+    argList::noParallel();
+    argList::validArgs.insert("file .. fileN");
 
-    Info<< "\ntest allocation with value\n";
+    argList::validOptions.insert("mask", "");
-    PackedList<3> list1(5,1);
+    argList::validOptions.insert("count", "");
-    list1.print(Info);
+    argList::validOptions.insert("info", "");
 
-    Info<< "\ntest assign uniform value\n";
+    argList args(argc, argv, false, true);
-    list1 = 3;
-    list1.print(Info);
-
-    Info<< "\ntest assign uniform value (with overflow)\n";
-    list1 = -1;
-    list1.print(Info);
-
-    Info<< "\ntest zero\n";
-    list1 = 0;
-    list1.print(Info);
-
-    Info<< "\ntest set() with default argument (max_value)\n";
-    list1.set(3);
-    list1.print(Info);
-
-    Info<< "\ntest assign between references\n";
-    list1[2] = 3;
-    list1[4] = list1[2];
-    list1.print(Info);
-
-    Info<< "\ntest assign between references, with chaining\n";
-    list1[0] = list1[4] = 1;
-    list1.print(Info);
-
-    Info<< "\ntest assign between references, with chaining and auto-vivify\n";
-    list1[1] = list1[8] = list1[10] = list1[14] = 2;
-    list1.print(Info);
 
 
-    Info<< "\ntest operator== between references\n";
+    if (args.optionFound("mask"))
-    if (list1[1] == list1[8])
     {
-        Info<< "[1] == [8] (expected)\n";
+        Info<< "bit width: " << unsigned(sizeof(unsigned)*CHAR_BIT) << endl;
+        reportInfo<1>();
+        reportInfo<2>();
+        reportInfo<3>();
+        reportInfo<4>();
+        reportInfo<5>();
+        reportInfo<6>();
+        reportInfo<7>();
+        reportInfo<8>();
+        reportInfo<9>();
+        reportInfo<10>();
+        reportInfo<11>();
+        reportInfo<12>();
+        reportInfo<13>();
+        reportInfo<14>();
+        reportInfo<15>();
+        reportInfo<16>();
+        reportInfo<17>();
+        reportInfo<18>();
+        reportInfo<19>();
+        reportInfo<20>();
+        reportInfo<21>();
+        reportInfo<22>();
+        reportInfo<23>();
+        reportInfo<24>();
+        reportInfo<25>();
+        reportInfo<26>();
+        reportInfo<27>();
+        reportInfo<28>();
+        reportInfo<29>();
+        reportInfo<30>();
+        reportInfo<31>();
+
+        return 0;
     }
-    else
+    else if (args.additionalArgs().empty())
     {
-        Info<< "[1] != [8] (unexpected)\n";
+        args.printUsage();
-    }
-
-    if (list1[0] != list1[1])
-    {
-        Info<< "[0] != [1] (expected)\n";
-    }
-    else
-    {
-        Info<< "[0] == [1] (unexpected)\n";
-    }
-
-    Info<< "\ntest operator== with iterator\n";
-    {
-        PackedList<3>::iterator iter = list1[1];
-
-        if (iter != list1[8])
-        {
-            Info<< "iter != [8] (expected)\n";
-        }
-        else
-        {
-            Info<< "iter == [8] (unexpected)\n";
-        }
-
-        if (*iter != list1[8])
-        {
-            Info<< "*iter != [8] (unexpected)\n";
-        }
-        else
-        {
-            Info<< "*iter == [8] (expected)\n";
-        }
     }
 
 
+    forAll(args.additionalArgs(), argI)
     {
-        const PackedList<3>& constLst = list1;
+        const string& srcFile = args.additionalArgs()[argI];
-        Info<< "\ntest operator[] const with out-of-range index\n";
+        Info<< nl << "reading " << srcFile << nl;
-        constLst.print(Info);
-        if (constLst[20])
-        {
-            Info<< "[20] is true (unexpected)\n";
-        }
-        else
-        {
-            Info<< "[20] is false (expected) list size should be unchanged (const)\n";
-        }
-        constLst.print(Info);
 
-        Info<< "\ntest operator[] non-const with out-of-range index\n";
+        IFstream ifs(srcFile);
-        if (list1[20])
+        List<label> rawLst(ifs);
+
+        PackedBoolList packLst(rawLst);
+
+        Info<< "size: " << packLst.size() << nl;
+
+        if (args.optionFound("count"))
         {
-            Info<< "[20] is true (unexpected)\n";
+            unsigned int rawCount = 0;
+            forAll(rawLst, elemI)
+            {
+                if (rawLst[elemI])
+                {
+                    rawCount++;
+                }
+            }
+            Info<< "raw count: " << rawCount << nl
+                << "packed count: " << packLst.count() << nl;
         }
-        else
+
+        if (args.optionFound("info"))
         {
-            Info<< "[20] is false (expected) but list was resized?? (non-const)\n";
+            packLst.print(Info);
         }
-        list1.print(Info);
+
+        Info<< nl;
+        IOobject::writeDivider(Info);
     }
 
-
-    Info<< "\ntest operator[] with out-of-range index\n";
-    if (!list1[20])
-    {
-        Info<< "[20] is false, as expected\n";
-    }
-    list1.print(Info);
-
-    Info<< "\ntest resize with value (without reallocation)\n";
-    list1.resize(8, list1.max_value());
-    list1.print(Info);
-
-    Info<< "\ntest flip() function\n";
-    list1.flip();
-    list1.print(Info);
-
-    Info<< "\nre-flip()\n";
-    list1.flip();
-    list1.print(Info);
-
-    Info<< "\ntest set() function\n";
-    list1.set(1, 5);
-    list1.print(Info);
-
-    Info<< "\ntest assign bool\n";
-    list1 = false;
-    list1.print(Info);
-
-    Info<< "\ntest assign bool\n";
-    list1 = true;
-    list1.print(Info);
-
-    Info<< "\ntest resize without value (with reallocation)\n";
-    list1.resize(12);
-    list1.print(Info);
-
-    Info<< "\ntest resize with value (with reallocation)\n";
-    list1.resize(25, list1.max_value());
-    list1.print(Info);
-
-    Info<< "\ntest resize smaller (should not touch allocation)\n";
-    list1.resize(8);
-    list1.print(Info);
-
-    Info<< "\ntest append() operation\n";
-    list1.append(2);
-    list1.append(3);
-    list1.append(4);
-    list1.print(Info);
-
-    Info<< "\ntest reserve() operation\n";
-    list1.reserve(32);
-    list1.print(Info);
-
-    Info<< "\ntest shrink() operation\n";
-    list1.shrink();
-    list1.print(Info);
-
-    Info<< "\ntest setCapacity() operation\n";
-    list1.setCapacity(15);
-    list1.print(Info);
-
-    Info<< "\ntest setCapacity() operation\n";
-    list1.setCapacity(100);
-    list1.print(Info);
-
-    Info<< "\ntest operator[] assignment\n";
-    list1[16] = 5;
-    list1.print(Info);
-
-    Info<< "\ntest operator[] assignment with auto-vivify\n";
-    list1[36] = list1.max_value();
-    list1.print(Info);
-
-    Info<< "\ntest setCapacity smaller\n";
-    list1.setCapacity(24);
-    list1.print(Info);
-
-    Info<< "\ntest resize much smaller\n";
-    list1.resize(150);
-    list1.print(Info);
-
-    Info<< "\ntest trim\n";
-    list1.trim();
-    list1.print(Info);
-
-    // add in some misc values
-    list1[31] = 1;
-    list1[32] = 2;
-    list1[33] = 3;
-
-    Info<< "\ntest iterator\n";
-    PackedList<3>::iterator iter = list1.begin();
-    Info<< "begin():";
-    iter.print(Info) << "\n";
-
-    Info<< "iterator:" << iter() << "\n";
-    iter() = 5;
-    iter.print(Info);
-    list1.print(Info);
-
-    iter = list1[31];
-    Info<< "iterator:" << iter() << "\n";
-    iter.print(Info);
-
-
-    Info<< "\ntest get() method\n";
-    Info<< "get(10):" << list1.get(10) << " and list[10]:" << list1[10] << "\n";
-    list1.print(Info);
-
-    Info<< "\ntest iterator indexing\n";
-    Info<< "cend() ";
-    list1.cend().print(Info) << "\n";
-
-    {
-        Info<< "\ntest assignment of iterator\n";
-        list1.print(Info);
-        Info<< "cend()\n";
-        list1.end().print(Info);
-        PackedList<3>::iterator cit = list1[100];
-        Info<< "out-of-range: ";
-        cit.print(Info);
-        cit = list1[15];
-        Info<< "in-range: ";
-        cit.print(Info);
-        Info<< "out-of-range: ";
-        cit = list1[1000];
-        cit.print(Info);
-    }
-
-
-    for
-    (
-        PackedList<3>::iterator cit = list1[30];
-        cit != list1.end();
-        ++cit
-    )
-    {
-        cit.print(Info);
-    }
-
-    Info<< "\ntest operator[] auto-vivify\n";
-    Info<< "size:" << list1.size() << "\n";
-
-    const unsigned int val = list1[45];
-
-    Info<< "list[45]:" << val << "\n";
-    Info<< "size after read:" << list1.size() << "\n";
-
-    list1[45] = list1.max_value();
-    Info<< "size after write:" << list1.size() << "\n";
-    Info<< "list[45]:" << list1[45] << "\n";
-    list1[49] = list1[100];
-    list1.print(Info);
-
-
-    Info<< "\ntest copy constructor + append\n";
-    PackedList<3> list2(list1);
-    list2.append(4);
-    Info<< "source list:\n";
-    list1.print(Info);
-    Info<< "destination list:\n";
-    list2.print(Info);
-
-    Info<< "\ntest pattern that fills all bits\n";
-    PackedList<4> list3(8, 8);
-
-    label pos = list3.size() - 1;
-
-    list3[pos--] = list3.max_value();
-    list3[pos--] = 0;
-    list3[pos--] = list3.max_value();
-    list3.print(Info);
-
-    Info<< "removed final value: " << list3.remove() << endl;
-    list3.print(Info);
-
-
-    List<bool> list4(4, true);
-    {
-        const List<bool>& constLst = list4;
-        Info<< "\ntest operator[] const with out-of-range index\n";
-        Info<< constLst << endl;
-        if (constLst[20])
-        {
-            Info<< "[20] is true (unexpected)\n";
-        }
-        else
-        {
-            Info<< "[20] is false (expected) list size should be unchanged (const)\n";
-        }
-        Info<< constLst << endl;
-    }
-
-    Info<< "\n\nDone.\n";
-
     return 0;
 }
 
-
 // ************************************************************************* //

applications/test/PackedList1/Make/files

@@ -0,0 +1,3 @@
+PackedListTest1.C
+
+EXE = $(FOAM_USER_APPBIN)/PackedListTest1

applications/test/PackedList1/PackedListTest1.C

@@ -0,0 +1,347 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2009 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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+
+Description
+
+\*---------------------------------------------------------------------------*/
+
+#include "uLabel.H"
+#include "IOstreams.H"
+#include "PackedBoolList.H"
+
+using namespace Foam;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+//  Main program:
+
+int main(int argc, char *argv[])
+{
+    Info<< "PackedList max_bits() = " << PackedList<>::max_bits() << nl;
+
+    Info<< "\ntest allocation with value\n";
+    PackedList<3> list1(5,1);
+    list1.print(Info);
+
+    Info<< "\ntest assign uniform value\n";
+    list1 = 3;
+    list1.print(Info);
+
+    Info<< "\ntest assign uniform value (with overflow)\n";
+    list1 = -1;
+    list1.print(Info);
+
+    Info<< "\ntest zero\n";
+    list1 = 0;
+    list1.print(Info);
+
+    Info<< "\ntest set() with default argument (max_value)\n";
+    list1.set(3);
+    list1.print(Info);
+
+    Info<< "\ntest assign between references\n";
+    list1[2] = 3;
+    list1[4] = list1[2];
+    list1.print(Info);
+
+    Info<< "\ntest assign between references, with chaining\n";
+    list1[0] = list1[4] = 1;
+    list1.print(Info);
+
+    Info<< "\ntest assign between references, with chaining and auto-vivify\n";
+    list1[1] = list1[8] = list1[10] = list1[14] = 2;
+    list1.print(Info);
+
+
+    Info<< "\ntest operator== between references\n";
+    if (list1[1] == list1[8])
+    {
+        Info<< "[1] == [8] (expected)\n";
+    }
+    else
+    {
+        Info<< "[1] != [8] (unexpected)\n";
+    }
+
+    if (list1[0] != list1[1])
+    {
+        Info<< "[0] != [1] (expected)\n";
+    }
+    else
+    {
+        Info<< "[0] == [1] (unexpected)\n";
+    }
+
+    Info<< "\ntest operator== with iterator\n";
+    {
+        PackedList<3>::iterator iter = list1[1];
+
+        if (iter != list1[8])
+        {
+            Info<< "iter != [8] (expected)\n";
+        }
+        else
+        {
+            Info<< "iter == [8] (unexpected)\n";
+        }
+
+        if (*iter != list1[8])
+        {
+            Info<< "*iter != [8] (unexpected)\n";
+        }
+        else
+        {
+            Info<< "*iter == [8] (expected)\n";
+        }
+    }
+
+
+    {
+        const PackedList<3>& constLst = list1;
+        Info<< "\ntest operator[] const with out-of-range index\n";
+        constLst.print(Info);
+        if (constLst[20])
+        {
+            Info<< "[20] is true (unexpected)\n";
+        }
+        else
+        {
+            Info<< "[20] is false (expected) list size should be unchanged (const)\n";
+        }
+        constLst.print(Info);
+
+        Info<< "\ntest operator[] non-const with out-of-range index\n";
+        if (list1[20])
+        {
+            Info<< "[20] is true (unexpected)\n";
+        }
+        else
+        {
+            Info<< "[20] is false (expected) but list was resized?? (non-const)\n";
+        }
+        list1.print(Info);
+    }
+
+
+    Info<< "\ntest operator[] with out-of-range index\n";
+    if (!list1[20])
+    {
+        Info<< "[20] is false, as expected\n";
+    }
+    list1.print(Info);
+
+    Info<< "\ntest resize with value (without reallocation)\n";
+    list1.resize(8, list1.max_value());
+    list1.print(Info);
+
+    Info<< "\ntest flip() function\n";
+    list1.flip();
+    list1.print(Info);
+
+    Info<< "\nre-flip()\n";
+    list1.flip();
+    list1.print(Info);
+
+    Info<< "\ntest set() function\n";
+    list1.set(1, 5);
+    list1.print(Info);
+
+    Info<< "\ntest assign bool\n";
+    list1 = false;
+    list1.print(Info);
+
+    Info<< "\ntest assign bool\n";
+    list1 = true;
+    list1.print(Info);
+
+    Info<< "\ntest resize without value (with reallocation)\n";
+    list1.resize(12);
+    list1.print(Info);
+
+    Info<< "\ntest resize with value (with reallocation)\n";
+    list1.resize(25, list1.max_value());
+    list1.print(Info);
+
+    Info<< "\ntest resize smaller (should not touch allocation)\n";
+    list1.resize(8);
+    list1.print(Info);
+
+    Info<< "\ntest append() operation\n";
+    list1.append(2);
+    list1.append(3);
+    list1.append(4);
+    list1.print(Info);
+
+    Info<< "\ntest reserve() operation\n";
+    list1.reserve(32);
+    list1.print(Info);
+
+    Info<< "\ntest shrink() operation\n";
+    list1.shrink();
+    list1.print(Info);
+
+    Info<< "\ntest setCapacity() operation\n";
+    list1.setCapacity(15);
+    list1.print(Info);
+
+    Info<< "\ntest setCapacity() operation\n";
+    list1.setCapacity(100);
+    list1.print(Info);
+
+    Info<< "\ntest operator[] assignment\n";
+    list1[16] = 5;
+    list1.print(Info);
+
+    Info<< "\ntest operator[] assignment with auto-vivify\n";
+    list1[36] = list1.max_value();
+    list1.print(Info);
+
+    Info<< "\ntest setCapacity smaller\n";
+    list1.setCapacity(24);
+    list1.print(Info);
+
+    Info<< "\ntest resize much smaller\n";
+    list1.resize(150);
+    list1.print(Info);
+
+    Info<< "\ntest trim\n";
+    list1.trim();
+    list1.print(Info);
+
+    // add in some misc values
+    list1[31] = 1;
+    list1[32] = 2;
+    list1[33] = 3;
+
+    Info<< "\ntest iterator\n";
+    PackedList<3>::iterator iter = list1.begin();
+    Info<< "begin():";
+    iter.print(Info) << "\n";
+
+    Info<< "iterator:" << iter() << "\n";
+    iter() = 5;
+    iter.print(Info);
+    list1.print(Info);
+
+    iter = list1[31];
+    Info<< "iterator:" << iter() << "\n";
+    iter.print(Info);
+
+
+    Info<< "\ntest get() method\n";
+    Info<< "get(10):" << list1.get(10) << " and list[10]:" << list1[10] << "\n";
+    list1.print(Info);
+
+    Info<< "\ntest iterator indexing\n";
+    Info<< "cend() ";
+    list1.cend().print(Info) << "\n";
+
+    {
+        Info<< "\ntest assignment of iterator\n";
+        list1.print(Info);
+        Info<< "cend()\n";
+        list1.end().print(Info);
+        PackedList<3>::iterator cit = list1[100];
+        Info<< "out-of-range: ";
+        cit.print(Info);
+        cit = list1[15];
+        Info<< "in-range: ";
+        cit.print(Info);
+        Info<< "out-of-range: ";
+        cit = list1[1000];
+        cit.print(Info);
+    }
+
+
+    for
+    (
+        PackedList<3>::iterator cit = list1[30];
+        cit != list1.end();
+        ++cit
+    )
+    {
+        cit.print(Info);
+    }
+
+    Info<< "\ntest operator[] auto-vivify\n";
+    Info<< "size:" << list1.size() << "\n";
+
+    const unsigned int val = list1[45];
+
+    Info<< "list[45]:" << val << "\n";
+    Info<< "size after read:" << list1.size() << "\n";
+
+    list1[45] = list1.max_value();
+    Info<< "size after write:" << list1.size() << "\n";
+    Info<< "list[45]:" << list1[45] << "\n";
+    list1[49] = list1[100];
+    list1.print(Info);
+
+
+    Info<< "\ntest copy constructor + append\n";
+    PackedList<3> list2(list1);
+    list2.append(4);
+    Info<< "source list:\n";
+    list1.print(Info);
+    Info<< "destination list:\n";
+    list2.print(Info);
+
+    Info<< "\ntest pattern that fills all bits\n";
+    PackedList<4> list3(8, 8);
+
+    label pos = list3.size() - 1;
+
+    list3[pos--] = list3.max_value();
+    list3[pos--] = 0;
+    list3[pos--] = list3.max_value();
+    list3.print(Info);
+
+    Info<< "removed final value: " << list3.remove() << endl;
+    list3.print(Info);
+
+
+    List<bool> list4(4, true);
+    {
+        const List<bool>& constLst = list4;
+        Info<< "\ntest operator[] const with out-of-range index\n";
+        Info<< constLst << endl;
+        if (constLst[20])
+        {
+            Info<< "[20] is true (unexpected)\n";
+        }
+        else
+        {
+            Info<< "[20] is false (expected) list size should be unchanged (const)\n";
+        }
+        Info<< constLst << endl;
+    }
+
+    Info<< "\n\nDone.\n";
+
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/test/dictionary/dictionaryTest.C

@@ -29,6 +29,7 @@ Description
 
 \*---------------------------------------------------------------------------*/
 
+#include "argList.H"
 #include "IOstreams.H"
 #include "IOobject.H"
 #include "IFstream.H"
@@ -41,6 +42,15 @@ using namespace Foam;
 
 int main(int argc, char *argv[])
 {
+    argList::noParallel();
+    argList args(argc, argv);
+
+    Info<< nl
+        << "FOAM_CASE=" << getEnv("FOAM_CASE") << nl
+        << "FOAM_CASENAME=" << getEnv("FOAM_CASENAME") << nl
+        << endl;
+
+
     {
         dictionary dict1(IFstream("testDict")());
         Info<< "dict1: " << dict1 << nl

applications/test/dictionary/testDict

@@ -14,6 +14,9 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 #inputMode  merge
+#includeIfPresent "someUnknownFile"
+#includeIfPresent "$FOAM_CASE/someUnknownFile"
+#includeIfPresent "$FOAM_CASE/someUnknownFile-$FOAM_CASENAME"
 
 internalField   uniform 1;
 

applications/test/fileNameClean/Make/files

@@ -0,0 +1,3 @@
+fileNameCleanTest.C
+
+EXE = $(FOAM_USER_APPBIN)/fileNameCleanTest

applications/test/fileNameClean/fileNameCleanTest.C

@@ -0,0 +1,104 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2009 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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+    fileNameCleanTest
+
+Description
+
+
+\*---------------------------------------------------------------------------*/
+
+#include "argList.H"
+#include "fileName.H"
+#include "SubList.H"
+#include "IOobject.H"
+#include "IOstreams.H"
+#include "OSspecific.H"
+
+
+using namespace Foam;
+
+void printCleaning(fileName& pathName)
+{
+    Info<< "fileName = " << pathName << nl
+        << "  path() = " << pathName.path() << nl
+        << "  name() = " << pathName.name() << nl
+        << "  joined = " << pathName.path()/pathName.name() << nl << nl;
+
+    pathName.clean();
+
+    Info<< "cleaned  = " << pathName << nl
+        << "  path() = " << pathName.path() << nl
+        << "  name() = " << pathName.name() << nl
+        << "  joined = " << pathName.path()/pathName.name() << nl << nl;
+
+    IOobject::writeDivider(Info);
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Main program:
+
+int main(int argc, char *argv[])
+{
+    argList::noBanner();
+    argList::noParallel();
+    argList::validArgs.insert("fileName .. fileNameN");
+
+    argList args(argc, argv, false, true);
+
+    if (args.additionalArgs().empty())
+    {
+        args.printUsage();
+    }
+
+    if (args.optionFound("case"))
+    {
+        fileName pathName = args.option("case");
+        Info<< nl
+            << "-case" << nl
+            << "path = " << args.path() << nl
+            << "root = " << args.rootPath() << nl
+            << "case = " << args.caseName() << nl
+            << "FOAM_CASE=" << getEnv("FOAM_CASE") << nl
+            << "FOAM_CASENAME=" << getEnv("FOAM_CASENAME") << nl
+            << endl;
+
+        printCleaning(pathName);
+    }
+
+    forAll(args.additionalArgs(), argI)
+    {
+        fileName pathName = args.additionalArgs()[argI];
+        printCleaning(pathName);
+    }
+
+    Info<< "\nEnd" << endl;
+
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/test/foamVersion/foamVersionString.C

@@ -27,6 +27,7 @@ Application
 
 Description
     Print the OpenFOAM version strings.
+
     Simultaneously the smallest possible program to use a minimal bit of
     the OpenFOAM library
 
@@ -37,9 +38,9 @@ Description
 
 int main()
 {
-    std::cerr
+    std::cout
-        << "build   " << Foam::FOAMbuild << "\n"
+        << "version " << Foam::FOAMversion << "\n"
-        << "version " << Foam::FOAMversion << "\n";
+        << "build   " << Foam::FOAMbuild << "\n";
 
     return 0;
 }

applications/test/mvBak/Make/files

@@ -0,0 +1,3 @@
+mvBakTest.C
+
+EXE = $(FOAM_USER_APPBIN)/mvBakTest

applications/test/mvBak/Make/options

@@ -0,0 +1,2 @@
+/* EXE_INC = -I$(LIB_SRC)/cfdTools/include */
+/* EXE_LIBS = -lfiniteVolume */

applications/test/mvBak/mvBakTest.C

@@ -23,46 +23,59 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Write primitive and binary block from OPstream using pvm.
 
 \*---------------------------------------------------------------------------*/
 
-#include "error.H"
+#include "OSspecific.H"
+#include "argList.H"
 
-#include "OPstream.H"
+using namespace Foam;
-
-#include <pvm3.h>
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Main program:
 
-namespace Foam
+int main(int argc, char *argv[])
 {
+    argList::noBanner();
+    argList::noParallel();
+    argList::validArgs.insert("file .. fileN");
+    argList::validOptions.erase("case");
+    argList::validOptions.insert("ext", "bak");
 
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+    argList args(argc, argv, false, true);
 
-OPstream::~OPstream()
+    if (args.additionalArgs().empty())
-{
-    if
-    (
-        pvm_psend
-        (
-            procID(toProcNo_),
-            msgType(),
-            buf_.begin(),
-            bufPosition_,
-            PVM_BYTE
-        ) != PvmOk
-    )
     {
-        FatalErrorIn("OPstream::~OPstream()")
+        args.printUsage();
-            << "pvm_psend cannot send outgoing message"
-            << ::abort;
     }
+
+    label ok = 0;
+
+    forAll(args.additionalArgs(), argI)
+    {
+        const string& srcFile = args.additionalArgs()[argI];
+
+        if (args.optionFound("ext"))
+        {
+            if (mvBak(srcFile, args.option("ext")))
+            {
+                ok++;
+            }
+        }
+        else
+        {
+            if (mvBak(srcFile))
+            {
+                ok++;
+            }
+        }
+    }
+
+    Info<< "mvBak called for " << args.additionalArgs().size()
+        << " files (moved " << ok << ")\n" << endl;
+
+    return 0;
 }
 
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
 // ************************************************************************* //

applications/test/router/routerDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/advanced/autoRefineMesh/autoRefineMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/advanced/modifyMesh/modifyMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/advanced/refineHexMesh/refineHexMesh.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Hex 2x2x2 refiner
+    Refines a hex mesh by 2x2x2 cell splitting.
 
 \*---------------------------------------------------------------------------*/
 

applications/utilities/mesh/advanced/refineWallLayer/refineWallLayer.C

@@ -23,9 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Utility to refine cells next to patches. Takes a patchName
+    Utility to refine cells next to patches.
-    and number of layers to refine. Works out cells within these layers
+
-    and refines those in the wall-normal direction.
+    Takes a patchName and number of layers to refine. Works out cells within
+    these layers and refines those in the wall-normal direction.
 
 \*---------------------------------------------------------------------------*/
 

applications/utilities/mesh/advanced/selectCells/selectCellsDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/advanced/splitCells/splitCells.C

@@ -23,10 +23,11 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Utility to split cells with flat faces. Uses a geometric cut with a plane
+    Utility to split cells with flat faces.
-    dividing the edge angle into two so might produce funny cells. For hexes
+
-    it will use by default a cut from edge onto opposite edge (i.e. purely
+    Uses a geometric cut with a plane dividing the edge angle into two so
-    topological).
+    might produce funny cells. For hexes it will use by default a cut from
+    edge onto opposite edge (i.e. purely topological).
 
     Options:
     - split cells from cellSet only

applications/utilities/mesh/conversion/Optional/Allwmake

@@ -5,9 +5,8 @@
 cd ${0%/*} || exit 1    # run from this directory
 set -x
 
-
 # build libccmio and create lnInclude directory
-( cd $WM_THIRD_PARTY_DIR && ./AllwmakeLibccmio )
+$WM_THIRD_PARTY_DIR/AllwmakeLibccmio
 
 # if the library built properly, the headers should exist too
 if [ -e $FOAM_LIBBIN/libccmio.so ]

applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L

@@ -47,6 +47,7 @@ Description
 #include "cyclicPolyPatch.H"
 #include "Swap.H"
 #include "IFstream.H"
+#include "readHexLabel.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -92,6 +93,9 @@ DynamicList<label> cellGroupStartIndex;
 DynamicList<label> cellGroupEndIndex;
 DynamicList<label> cellGroupType;
 
+// Special parsing of (incorrect) Cubit files
+bool cubitFile = false;
+
 
 void uniquify(word& name, HashSet<word>& patchNames)
 {
@@ -622,11 +626,20 @@ endOfSection               {space}")"{space}
         BEGIN(readZoneGroupData);
     }
 
-<readZoneGroupData>{space}{label}{space}{word}{space}{word}{space}{label}? {
+<readZoneGroupData>{space}{hexLabel}{space}{word}{space}{word}{space}{label}? {
         IStringStream zoneDataStream(YYText());
 
         // cell zone-ID not in hexadecimal!!! Inconsistency
-        label zoneID(readLabel(zoneDataStream));
+        label zoneID = -1;
+
+        if (cubitFile)
+        {
+            zoneID = readHexLabel(zoneDataStream);
+        }
+        else
+        {
+            zoneID = readLabel(zoneDataStream);
+        }
 
         groupType.insert(zoneID, word(zoneDataStream));
         groupName.insert(zoneID, word(zoneDataStream));
@@ -752,6 +765,7 @@ int main(int argc, char *argv[])
     argList::validOptions.insert("scale", "scale factor");
     argList::validOptions.insert("ignoreCellGroups", "cell group names");
     argList::validOptions.insert("ignoreFaceGroups", "face group names");
+    argList::validOptions.insert("cubit", "");
 
     argList args(argc, argv);
 
@@ -774,6 +788,17 @@ int main(int argc, char *argv[])
         args.optionLookup("ignoreFaceGroups")() >> ignoreFaceGroups;
     }
 
+    cubitFile = args.options().found("cubit");
+
+    if (cubitFile)
+    {
+        Info<< nl
+            << "Assuming Cubit generated file"
+            << " (incorrect face orientation; hexadecimal zoneIDs)."
+            << nl << endl;
+    }
+
+
 #   include "createTime.H"
 
     fileName fluentFile(args.additionalArgs()[0]);
@@ -827,7 +852,10 @@ int main(int argc, char *argv[])
         )
         {
             fm[facei] = true;
-            faces[facei] = faces[facei].reverseFace();
+            if (!cubitFile)
+            {
+                faces[facei] = faces[facei].reverseFace();
+            }
             Swap(owner[facei], neighbour[facei]);
         }
     }

applications/utilities/mesh/conversion/mshToFoam/mshToFoam.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Reads .msh format generated by the Adventure system.
+    Converts .msh file generated by the Adventure system.
 
     Note: the .msh format does not contain any boundary information. It is
     purely a description of the internal mesh.

applications/utilities/mesh/conversion/netgenNeutralToFoam/netgenNeutralToFoam.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    read Neutral file format as written by Netgen4.4.
+    Converts neutral file format as written by Netgen v4.4.
 
     Example:
 

applications/utilities/mesh/conversion/polyDualMesh/polyDualMeshApp.C

@@ -23,8 +23,8 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Calculate the dual of a polyMesh. Adheres to all the feature&patch edges.
+    Calculate the dual of a polyMesh. Adheres to all the feature and patch
-
+    edges.
 
 Usage
 

applications/utilities/mesh/conversion/star4ToFoam/star4ToFoam.C

@@ -79,7 +79,7 @@ int main(int argc, char *argv[])
             scaleFactor = 1;
         }
     }
-    
+
     if (args.optionFound("solids"))
     {
         meshReaders::STARCD::keepSolids = true;

applications/utilities/mesh/conversion/tetgenToFoam/tetgenToFoam.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Reads .ele and .node and .face files as written by tetgen.
+    Converts .ele and .node and .face files, written by tetgen.
 
     Make sure to use add boundary attributes to the smesh file
     (5 fifth column in the element section)

applications/utilities/mesh/generation/blockMesh/setEdge.C

@@ -100,7 +100,7 @@ void blockDescriptor::setEdge(label edgeI, label start, label end, label dim)
                 scalar gExp = calcGexp(expand_[edgeI], dim);
 
                 // divide the line
-                lineDivide divEdge(curvedEdges_[nCEI], dim, 1.0/gExp);
+                lineDivide divEdge(curvedEdges_[nCEI], dim, 1.0/(gExp+SMALL));
 
                 pointField p = divEdge.points();
                 scalarList d = divEdge.lambdaDivisions();

applications/utilities/mesh/generation/extrudeMesh/Allwclean

@@ -1,6 +1,8 @@
 #!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
 set -x
 
 wclean libso extrudeModel
 wclean
 
+# ----------------------------------------------------------------- end-of-file

applications/utilities/mesh/generation/extrudeMesh/extrudeMesh.C

@@ -24,8 +24,8 @@ License
 
 Description
     Extrude mesh from existing patch (by default outwards facing normals;
-    optional flips faces)
+    optional flips faces) or from patch read from file.
-    or from patch read from file.
+
     Note: Merges close points so be careful.
 
     Type of extrusion prescribed by run-time selectable model.

applications/utilities/mesh/generation/extrudeMesh/extrudeProperties

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/cellSet/cellSetDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/createBaffles/createBaffles.C

@@ -23,11 +23,11 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Makes internal faces into boundary faces. Does not duplicate points. Use
+    Makes internal faces into boundary faces. Does not duplicate points, unlike
-    mergeOrSplitBaffles if you want this.
+    mergeOrSplitBaffles.
 
-    Note: if any coupled patch face is selected for baffling automatically
+    Note: if any coupled patch face is selected for baffling the opposite
-    the opposite member is selected for baffling as well. Note that this
+    member has to be selected for baffling as well. Note that this
     is the same as repatching. This was added only for convenience so
     you don't have to filter coupled boundary out of your set.
 
@@ -128,6 +128,7 @@ int main(int argc, char *argv[])
     argList::validArgs.append("faceZone");
     argList::validArgs.append("patch");
     argList::validOptions.insert("additionalPatches", "(patch2 .. patchN)");
+    argList::validOptions.insert("internalFacesOnly", "");
     argList::validOptions.insert("overwrite", "");
 
 #   include "setRootCase.H"
@@ -183,6 +184,12 @@ int main(int argc, char *argv[])
 
     bool overwrite = args.optionFound("overwrite");
 
+    bool internalFacesOnly = args.optionFound("internalFacesOnly");
+
+    if (internalFacesOnly)
+    {
+        Info<< "Not converting faces on non-coupled patches." << nl << endl;
+    }
 
 
     // Read objects in time directory
@@ -234,7 +241,21 @@ int main(int argc, char *argv[])
     //   guarantees that when e.g. creating a cyclic all faces from one
     //   side come first and faces from the other side next.
 
+    // Whether first use of face (modify) or consecutive (add)
     PackedBoolList modifiedFace(mesh.nFaces());
+    // Never modify coupled faces
+    forAll(patches, patchI)
+    {
+        const polyPatch& pp = patches[patchI];
+        if (pp.coupled())
+        {
+            forAll(pp, i)
+            {
+                modifiedFace[pp.start()+i] = 1;
+            }
+        }
+    }
+    label nModified = 0;
 
     forAll(newPatches, i)
     {
@@ -281,6 +302,8 @@ int main(int argc, char *argv[])
                         modifiedFace                // modify or add status
                     );
                 }
+
+                nModified++;
             }
         }
 
@@ -333,16 +356,27 @@ int main(int argc, char *argv[])
         // Modify any boundary faces
         // ~~~~~~~~~~~~~~~~~~~~~~~~~
 
+        // Normal boundary:
+        // - move to new patch. Might already be back-to-back baffle
+        // you want to add cyclic to. Do warn though.
+        //
+        // Processor boundary:
+        // - do not move to cyclic
+        // - add normal patches though.
+
+        // For warning once per patch.
+        labelHashSet patchWarned;
+
         forAll(patches, patchI)
         {
             const polyPatch& pp = patches[patchI];
 
-            if (patches[newPatchI].coupled() && pp.coupled())
+            if (pp.coupled() && patches[newPatchI].coupled())
             {
                 // Do not allow coupled faces to be moved to different coupled
                 // patches.
             }
-            else
+            else if (pp.coupled() || !internalFacesOnly)
             {
                 forAll(pp, i)
                 {
@@ -352,6 +386,19 @@ int main(int argc, char *argv[])
 
                     if (zoneFaceI != -1)
                     {
+                        if (patchWarned.insert(patchI))
+                        {
+                            WarningIn(args.executable())
+                                << "Found boundary face (in patch " << pp.name()
+                                << ") in faceZone " << fZone.name()
+                                << " to convert to baffle patch "
+                                << patches[newPatchI].name()
+                                << endl
+                                << "    Run with -internalFacesOnly option"
+                                << " if you don't wish to convert"
+                                << " boundary faces." << endl;
+                        }
+
                         modifyOrAddFace
                         (
                             meshMod,
@@ -364,6 +411,7 @@ int main(int argc, char *argv[])
                             fZone.flipMap()[zoneFaceI], // face flip in zone
                             modifiedFace                // modify or add status
                         );
+                        nModified++;
                     }
                 }
             }
@@ -371,7 +419,7 @@ int main(int argc, char *argv[])
     }
 
 
-    Info<< "Converted " << returnReduce(modifiedFace.count(), sumOp<label>())
+    Info<< "Converted " << returnReduce(nModified, sumOp<label>())
         << " faces into boundary faces on patch " << patchName << nl << endl;
 
     if (!overwrite)

applications/utilities/mesh/manipulation/createPatch/createPatchDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/faceSet/faceSetDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/flattenMesh/flattenMesh.C

@@ -26,7 +26,7 @@ Application
     flattenMesh
 
 Description
-    Flatten the front and back planes of a 2D cartesian mesh.
+    Flattens the front and back planes of a 2D cartesian mesh.
 
 \*---------------------------------------------------------------------------*/
 
@@ -90,7 +90,7 @@ int main(int argc, char *argv[])
         }
     }
 
-    twoDCorr.correctPoints(points); 
+    twoDCorr.correctPoints(points);
 
     // Set the precision of the points data to 10
     IOstream::defaultPrecision(10);

applications/utilities/mesh/manipulation/insideCells/insideCells.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Pick up cells with cell centre 'inside' of surface. Requires surface
+    Picks up cells with cell centre 'inside' of surface. Requires surface
     to be closed and singly connected.
 
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/mergeOrSplitBaffles/mergeOrSplitBaffles.C

@@ -26,7 +26,7 @@ Application
     mergeOrSplitBaffles
 
 Description
-    Detect faces that share points (baffles). Either merge them or
+    Detects faces that share points (baffles). Either merge them or
     duplicate the points.
 
     Notes:

applications/utilities/mesh/manipulation/mirrorMesh/mirrorMesh.C

@@ -23,7 +23,6 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-
     Mirrors a mesh around a given plane.
 
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/mirrorMesh/mirrorMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/pointSet/pointSetDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/refineMesh/refineMesh.C

@@ -23,9 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Utility to refine cells in multiple directions. Either supply -all
+    Utility to refine cells in multiple directions.
-    option to refine all cells (3D refinement for 3D cases; 2D for 2D cases)
+
-    or reads a refineMeshDict with
+    Either supply -all option to refine all cells (3D refinement for 3D
+    cases; 2D for 2D cases) or reads a refineMeshDict with
     - cellSet to refine
     - directions to refine
 

applications/utilities/mesh/manipulation/refineMesh/refineMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/setSet/setSet.C

@@ -31,12 +31,11 @@ Description
 #include "Time.H"
 #include "polyMesh.H"
 #include "globalMeshData.H"
-#include "topoSetSource.H"
-#include "topoSet.H"
 #include "IStringStream.H"
-#include "topoSet.H"
 #include "cellSet.H"
 #include "faceSet.H"
+#include "pointSet.H"
+#include "topoSetSource.H"
 #include "OFstream.H"
 #include "IFstream.H"
 #include "demandDrivenData.H"

applications/utilities/mesh/manipulation/splitMeshRegions/splitMeshRegions.C

@@ -23,8 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Splits mesh into multiple regions. Each region is defined as a domain
+    Splits mesh into multiple regions.
-    whose cells can all be reached by cell-face-cell walking without crossing
+
+    Each region is defined as a domain whose cells can all be reached by
+    cell-face-cell walking without crossing
     - boundary faces
     - additional faces from faceset (-blockedFaces faceSet).
     - any face inbetween differing cellZones (-cellZones)

applications/utilities/mesh/manipulation/transformPoints/transformPoints.C

@@ -27,7 +27,10 @@ Application
 
 Description
     Transforms the mesh points in the polyMesh directory according to the
-    options:
+    translate, rotate and scale options.
+
+Usage
+    Options are:
 
     -translate vector
         Translates the points by the given vector,

applications/utilities/parallelProcessing/reconstructParMesh/reconstructParMesh.C

@@ -26,9 +26,10 @@ Application
     reconstructParMesh
 
 Description
-    Reconstructs a mesh using geometric information only. Writes
+    Reconstructs a mesh using geometric information only.
-    point/face/cell procAddressing so afterwards reconstructPar can be used to
+
-    reconstruct fields.
+    Writes point/face/cell procAddressing so afterwards reconstructPar can be
+    used to reconstruct fields.
 
     Note:
     - uses geometric matching tolerance (set with -mergeTol option)

applications/utilities/parallelProcessing/redistributeMeshPar/redistributeMeshPar.C

@@ -26,7 +26,17 @@ Application
     redistributeMeshPar
 
 Description
-    Parallel redecomposition of mesh.
+    Redistributes existing decomposed mesh and fields according to the current
+    settings in the decomposeParDict file.
+
+    Must be run on maximum number of source and destination processors.
+    Balances mesh and writes new mesh to new time directory.
+
+    Can also work like decomposePar:
+
+        mkdir processor0
+        cp -r constant processor0
+        mpirun -np ddd redistributeMeshPar -parallel
 
 \*---------------------------------------------------------------------------*/
 

applications/utilities/postProcessing/dataConversion/foamDataToFluent/foamDataToFluentDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.5                                   |
+|  \\    /   O peration     | Version:  1.6                                   |
 |   \\  /    A nd           | Web:      http://www.OpenFOAM.org               |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/postProcessing/dataConversion/foamToEnsightParts/foamToEnsightParts.C

@@ -36,8 +36,8 @@ Usage
     @param -ascii \n
     Write Ensight data in ASCII format instead of "C Binary"
 
-    @param -zeroTime \n
+    @param -noZero \n
-    Include the often incomplete initial conditions.
+    Exclude the often incomplete initial conditions.
 
     @param -index \<start\>\n
     Ignore the time index contained in the time file and use a