Merge branch 'develop-pre-release' of develop.openfoam.com:Development/OpenFOAM-plus into develop-pre-release

applications/utilities/miscellaneous/foamRestoreFields/foamRestoreFields.C

@@ -144,13 +144,9 @@ label restoreFields
         }
     }
 
-    if (dryrun)
+    if (verbose)
     {
-        Info<< "dry-run: " << dirName << nl;
+        Info<< "directory " << dirName.name() << nl;
-    }
-    else if (verbose)
-    {
-        Info<< "directory " << dirName << nl;
     }
 
     // Count of files moved, including backups
@@ -296,7 +292,7 @@ int main(int argc, char *argv[])
     // command-line options
 
     label nProcs = 0;
-    instantList times;
+    wordList timeDirs;
 
     if (args.found("processor") && !Pstream::parRun())
     {
@@ -310,8 +306,11 @@ int main(int argc, char *argv[])
                 << exit(FatalError);
         }
 
-        // Obtain times from "processor0/" only
+        // Obtain time directory names from "processor0/" only
-        times = timeSelector::select
+
+        timeDirs = ListOps::create<word>
+        (
+            timeSelector::select
             (
                 Time
                 (
@@ -320,31 +319,34 @@ int main(int argc, char *argv[])
                     args.caseName()/"processor0"
                 ).times(),
                 args
+            ),
+            [](const instant& t){ return t.name(); }
         );
     }
     else
     {
-        if (Pstream::master())
+        timeDirs = ListOps::create<word>
-        {
+        (
-            times = timeSelector::select
+            timeSelector::select
             (
                 Time(Time::controlDictName, args).times(),
                 args
+            ),
+            [](const instant& t){ return t.name(); }
         );
-        }
 
-        Pstream::scatter(times);
+        Pstream::scatter(timeDirs);
     }
 
 
-    if (times.empty())
+    if (timeDirs.empty())
     {
         Info<< "no times selected" << nl;
     }
 
-    for (const instant& inst : times)
+    for (const word& dirName : timeDirs)
     {
-        Info<< "\nTime = " << inst.name() << nl;
+        Info<< "\nTime = " << dirName << nl;
 
         label count = 0;
 
@@ -352,7 +354,7 @@ int main(int argc, char *argv[])
         {
             const wordHashSet files
             (
-                getFiles(args.path()/"processor0", inst.name())
+                getFiles(args.path()/"processor0", dirName)
             );
 
             for (label proci=0; proci < nProcs; ++proci)
@@ -360,7 +362,7 @@ int main(int argc, char *argv[])
                 count += restoreFields
                 (
                     method,
-                    args.path()/("processor" + Foam::name(proci))/inst.name(),
+                    args.path()/("processor" + Foam::name(proci))/dirName,
                     files,
                     targetNames
                 );
@@ -371,14 +373,14 @@ int main(int argc, char *argv[])
             wordList files;
             if (Pstream::master())
             {
-                files = getFiles(args.path(), inst.name());
+                files = getFiles(args.path(), dirName);
             }
             Pstream::scatter(files);
 
             count += restoreFields
             (
                 method,
-                args.path()/inst.name(),
+                args.path()/dirName,
                 wordHashSet(files),
                 targetNames
             );

bin/tools/RunFunctions

@@ -94,7 +94,7 @@ getNumberOfProcessors()
 getApplication()
 {
     # Re-use positional parameters for automatic whitespace elimination
-    set -- $(foamDictionary -disableFunctionEntries -entry application -value system/controlDict)
+    set -- $(foamDictionary -disableFunctionEntries -entry application -value system/controlDict 2>/dev/null)
 
     if [ "$#" -eq 1 ]
     then

etc/bashrc

@@ -158,6 +158,7 @@ _foamEtc -config  vtk
 _foamEtc -config  ensight
 _foamEtc -config  gperftools
 ## _foamEtc -config  ADIOS
+## _foamEtc -config  ADIOS2
 _foamEtc -config  CGAL
 _foamEtc -config  scotch
 _foamEtc -config  FFTW

etc/config.csh/ADIOS2

@@ -2,7 +2,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
-#   \\  /    A nd           | Copyright (C) 2017 OpenCFD Ltd.
+#   \\  /    A nd           | Copyright (C) 2017-2018 OpenCFD Ltd.
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@@ -28,16 +28,12 @@ if ($?FOAM_VERBOSE && $?prompt) then
     echo "Using adios ($adios2_version)  ->  $ADIOS2_ARCH_PATH"
 endif
 
-# If *_ARCH_PATH does not end with '-system' or '-none',
+# - only add if the directory really exists
-# it is located within ThirdParty, or a central installation
+_foamAddLibAuto $ADIOS2_ARCH_PATH
-# outside of ThirdParty and should be added to the path.
+if ($status == 0) then
-
-set ending="${ADIOS2_ARCH_PATH:t}"
-if ( "$ending" != "adios-none" && "$ending" != "adios-system" ) then
-    # PATH was already cleaned by etc/cshrc caller
     _foamAddPath $ADIOS2_ARCH_PATH/bin
 endif
 
-unset adios_version ending
+unset adios2_version
 
 #------------------------------------------------------------------------------

etc/config.sh/ADIOS2

@@ -2,7 +2,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
-#   \\  /    A nd           | Copyright (C) 2017 OpenCFD Ltd.
+#   \\  /    A nd           | Copyright (C) 2017-2018 OpenCFD Ltd.
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@@ -16,6 +16,7 @@
 # Description
 #     Setup for ADIOS2 include/libraries (usually ThirdParty installation).
 #
+#     Use with -force when sourcing directly from the command-line
 #------------------------------------------------------------------------------
 # USER EDITABLE PART: Changes made here may be lost with the next upgrade
 
@@ -29,21 +30,30 @@ then
     echo "Using adios ($adios2_version)  ->  $ADIOS2_ARCH_PATH" 1>&2
 fi
 
-if command -v _foamAddPath >/dev/null 2>&1      # Normal sourcing
+if command -v _foamAddLibAuto > /dev/null 2>&1
 then
-    # If *_ARCH_PATH does not end with '-system' or '-none',
+    # Normal sourcing (not makeADIOS)
-    # it is located within ThirdParty, or a central installation
+    # - but only add if the directory really exists
-    # outside of ThirdParty and should be added to the path.
 
-    ending="${ADIOS2_ARCH_PATH##*-}"
+    if _foamAddLibAuto $ADIOS2_ARCH_PATH
-    if [ "$ending" != none -a "$ending" != system ]
     then
-        # PATH was already cleaned by etc/bashrc caller
         _foamAddPath $ADIOS2_ARCH_PATH/bin
     fi
 
-    unset adios2_version ending
+    unset adios2_version
 
+elif [ "$1" = "-force" ]
+then
+    # Forced command-line sourcing
+
+    if output="$($WM_PROJECT_DIR/bin/tools/lib-dir -sh $ADIOS2_ARCH_PATH 2>/dev/null)"
+    then
+        eval "$output"
+        PATH="$ADIOS2_ARCH_PATH/bin:$PATH"
+    fi
+
+    unset adios2_version output
 fi
 
+
 #------------------------------------------------------------------------------

etc/cshrc

@@ -200,6 +200,7 @@ _foamEtc -config  paraview -- "$FOAM_SETTINGS"  # Pass through for evaluation
 _foamEtc -config  vtk
 _foamEtc -config  ensight
 ## _foamEtc -config  ADIOS
+## _foamEtc -config  ADIOS2
 _foamEtc -config  CGAL
 _foamEtc -config  FFTW
 

src/functionObjects/lagrangian/vtkCloud/vtkCloud.C

@@ -330,7 +330,6 @@ Foam::functionObjects::vtkCloud::vtkCloud
     fvMeshFunctionObject(name, runTime, dict),
     writeOpts_(vtk::formatType::INLINE_BASE64),
     printf_(),
-    useTimeName_(false),
     useVerts_(false),
     selectClouds_(),
     selectFields_(),
@@ -394,7 +393,7 @@ bool Foam::functionObjects::vtkCloud::read(const dictionary& dict)
         printf_ = "%0" + std::to_string(padWidth) + "d";
     }
 
-    useTimeName_ = dict.lookupOrDefault<bool>("timeName", false);
+    // useTimeName_ = dict.lookupOrDefault<bool>("useTimeName", false);
 
     useVerts_ = dict.lookupOrDefault<bool>("cellData", false);
 
@@ -436,11 +435,18 @@ bool Foam::functionObjects::vtkCloud::write()
         return true;  // skip - not available
     }
 
+//     const word timeDesc =
+//     (
+//         useTimeName_
+//       ? time_.timeName()
+//       : printf_.empty()
+//       ? Foam::name(time_.timeIndex())
+//       : word::printf(printf_, time_.timeIndex())
+//     );
+
     const word timeDesc =
     (
-        useTimeName_
+        printf_.empty()
-      ? time_.timeName()
-      : printf_.empty()
       ? Foam::name(time_.timeIndex())
       : word::printf(printf_, time_.timeIndex())
     );

src/functionObjects/lagrangian/vtkCloud/vtkCloud.H

@@ -28,7 +28,8 @@ Group
     grpUtilitiesFunctionObjects
 
 Description
-    This functionObject writes cloud(s) in VTK format.
+    This functionObject writes cloud(s) in VTK PolyData format
+    (.vtp extension) with the time information saved in a '.series' file.
 
     Example of function object specification:
     \verbatim
@@ -38,11 +39,11 @@ Description
         libs            ("liblagrangianFunctionObjects.so");
         writeControl    writeTime;
         writeInterval   1;
-        format          binary;
+        format          ascii;
 
         cloud           myCloud;
-        width           12;
         fields          (T U rho);
+        width           4;  // file-padding
     }
     \endverbatim
 
@@ -57,20 +58,19 @@ Usage
         cellData     | Emit cellData instead of pointData | no        | false
         directory    | The output directory name        | no          | VTK
         width        | Padding width for file name      | no          | 8
-        timeName     | Use time-name instead of time-index | no       | false
         format       | ascii or binary format           | no          | binary
         writePrecision | write precision in ascii       | no | same as IOstream
     \endtable
 
-    The output filename and fields are added to the cloud's \c OutputProperties
+    The output filename and fields are added to the functionObjectProperties
-    dictionary. For the previous example specification:
+    information. For the previous example specification:
 
     \verbatim
     cloudWrite1
     {
         myCloud
         {
-            file    "<case>/VTK/myCloud_00001.vtp";
+            file    "<case>/VTK/myCloud_0001.vtp";
             fields  (T U rho);
         }
     }
@@ -122,9 +122,6 @@ class vtkCloud
         //- The printf format for zero-padding names
         string printf_;
 
-        //- Use time-name instead of time-index
-        bool useTimeName_;
-
         //- Write lagrangian as cell data (verts) instead of point data
         bool useVerts_;
 

tutorials/incompressible/pimpleFoam/RAS/wingMotion/wingMotion2D_pimpleFoam/system/ensightWrite

@@ -1,4 +1,10 @@
-// -*- C++ -*-
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  plus                                  |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
 
 ensightWrite
 {

tutorials/incompressible/pimpleFoam/RAS/wingMotion/wingMotion2D_simpleFoam/system/controlDict

@@ -47,19 +47,7 @@ runTimeModifiable true;
 
 functions
 {
-    forces
+    #include "forces"
-    {
-        type                forces;
-        libs                ("libforces.so");
-        writeControl        timeStep;
-        writeInterval       10;
-        patches             (wing);
-        rho                 rhoInf;
-        log                 true;
-        rhoInf              1;
-        CofR                (0.4974612746 -0.01671895744 0.125);
-    }
 }
 
-
 // ************************************************************************* //

tutorials/incompressible/pimpleFoam/RAS/wingMotion/wingMotion2D_simpleFoam/system/forces

@@ -0,0 +1,24 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  plus                                  |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+
+forces
+{
+    type            forces;
+    libs            ("libforces.so");
+
+    writeControl    timeStep;
+    writeInterval   10;
+    log             false;
+
+    patches         (wing);
+    rho             rhoInf;
+    rhoInf          1;
+    CofR            (0.4974612746 -0.01671895744 0.125);
+}
+
+// ************************************************************************* //

wmake/scripts/have_adios2

@@ -0,0 +1,143 @@
+#----------------------------------*-sh-*--------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2018 OpenCFD Ltd.
+#    \\/     M anipulation  |
+#------------------------------------------------------------------------------
+# License
+#     This file is part of OpenFOAM, licensed under GNU General Public License
+#     <http://www.gnu.org/licenses/>.
+#
+# Script
+#     have_adios2
+#
+# Description
+#     Detection/setup of ADIOS2
+#
+# Requires
+#     ADIOS2_ARCH_PATH
+#
+# Functions provided
+#     have_adios2, no_adios2, echo_adios2
+#
+# Variables set on success
+#     HAVE_ADIOS2
+#     ADIOS2_ARCH_PATH
+#     ADIOS2_INC_DIR
+#     ADIOS2_LIB_DIR
+#
+#------------------------------------------------------------------------------
+. $WM_PROJECT_DIR/wmake/scripts/sysFunctions # General system functions
+
+#------------------------------------------------------------------------------
+
+# Reset variables
+no_adios2()
+{
+    unset HAVE_ADIOS2 ADIOS2_INC_DIR ADIOS2_LIB_DIR
+    return 0
+}
+
+
+# Report
+echo_adios2()
+{
+    echo "adios2=${HAVE_ADIOS2:-false}"
+    echo "root=$ADIOS2_ARCH_PATH"
+    echo "include=$ADIOS2_INC_DIR"
+    echo "library=$ADIOS2_LIB_DIR"
+}
+
+
+# On success, return 0 and export variables
+# -> HAVE_ADIOS2, ADIOS2_INC_DIR, ADIOS2_LIB_DIR
+have_adios2()
+{
+    local header library static label settings warn
+    # warn="==> skip adios2"
+
+    # Basic setup/checks
+    settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/ADIOS2) || {
+        [ -n "$warn" ] && echo "$warn (no config.sh/ADIOS2 settings)"
+        return 1
+    }
+    . $settings
+    if isNone "$ADIOS2_ARCH_PATH"
+    then
+        [ -n "$warn" ] && echo "$warn (not available)"
+        return 1
+    fi
+
+
+    # Header/library names
+    header="adios2.h"
+    library="libadios2$extLibso"
+
+
+    if hasAbsdir "$ADIOS2_ARCH_PATH"
+    then
+        header=$(findFirstFile $ADIOS2_ARCH_PATH/include/$header)
+
+        # FOAM_EXT_LIBBIN is allowed to be unset
+        library=$(findFirstFile \
+            $FOAM_EXT_LIBBIN/$library \
+            $ADIOS2_ARCH_PATH/lib/$library \
+            $ADIOS2_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$library \
+        )
+    elif isSystem "$ADIOS2_ARCH_PATH"
+    then
+        header=$(findFirstFile /usr/local/include/$header /usr/include/$header)
+
+        case "$header" in
+        /usr/local/*)
+            library=$(findFirstFile \
+                /usr/local/lib/$library \
+                /usr/local/lib$WM_COMPILER_LIB_ARCH/$library \
+            )
+            ;;
+
+        *)
+            library=$(findFirstFile \
+                /usr/lib/$library \
+                /usr/lib$WM_COMPILER_LIB_ARCH/$library \
+            )
+            ;;
+        esac
+    else
+        unset header library
+    fi
+
+
+    # Header found?
+    [ -n "$header" ] || {
+        [ -n "$warn" ] && echo "$warn (no header)"
+        return 2
+    }
+
+    # Library found?
+    [ -n "$library" ] || {
+        [ -n "$warn" ] && echo "$warn (missing library)"
+        return 2
+    }
+
+    header="${header%/*}"     # Strip one-level (include/adios2/...)
+
+    export HAVE_ADIOS2=true
+    export ADIOS2_ARCH_PATH
+    export ADIOS2_INC_DIR="${header%/*}"     # Basename
+    export ADIOS2_LIB_DIR="${library%/*}"    # Basename
+}
+
+
+# Force reset of old variables
+no_adios2
+
+# Testing
+if [ "$1" = "-test" ]
+then
+    have_adios2
+    echo_adios2
+fi
+
+#------------------------------------------------------------------------------