ENH: added adiosWrite code and tutorials

.gitignore

@@ -22,9 +22,6 @@
 # Derived files
 lex.yy.c
 
-# Corefiles
-core
-
 # Dependency files - anywhere
 *.dep
 

src/Allwmake

+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+. $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
+. $WM_PROJECT_DIR/wmake/scripts/have_adios2
+
+# -----------------------------------------------------------------------------
+
+if have_adios2
+then
+    adiosFoam/Allwmake
+    adiosWrite/Allwmake
+else
+    hint_adios2
+fi
+
+# -----------------------------------------------------------------------------

src/adiosFoam/Allwmake

+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+. $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
+. $WM_PROJECT_DIR/wmake/scripts/have_adios2
+
+# -----------------------------------------------------------------------------
+
+if have_adios2
+then
+    wmake libso
+else
+    echo "==> skip adiosFoam library"
+fi
+
+# -----------------------------------------------------------------------------

src/adiosFoam/Make/files

+adiosFoam.C
+
+core/adiosCore.C
+controls/adiosRegionControl.C
+
+read/adiosReader.C
+read/adiosReaderCloud.C
+read/adiosReaderField.C
+
+write/adiosCoreWrite.C
+write/adiosCoreWriteAttr.C
+write/adiosCoreWriteVar.C
+write/adiosCoreWriteMesh.C
+write/adiosCoreWriteField.C
+write/adiosCoreWriteCloud.C
+
+time/adiosTime.C
+
+LIB = $(FOAM_LIBBIN)/libadiosFoam

src/adiosFoam/Make/options

+sinclude $(GENERAL_RULES)/ADIOS2
+
+EXE_INC = \
+    $(PFLAGS) $(PINC) $(ADIOS_FLAGS) \
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/finiteArea/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude
+
+LIB_LIBS = \
+    $(PLIBS) $(ADIOS_LIBS) \
+    -lmeshTools \
+    -lfiniteVolume \
+    -lfiniteArea \
+    -llagrangian

src/adiosFoam/adiosFoam.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2019 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "adiosFoam.H"
+#include "OSspecific.H"
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+const Foam::word Foam::adiosFoam::defaultDirectory("adiosData");
+const Foam::string Foam::adiosFoam::foamAttribute("/openfoam");
+const Foam::string Foam::adiosFoam::timeAttribute("/time");
+
+
+// * * * * * * * * * * * * * * * Global Functions  * * * * * * * * * * * * * //
+
+Foam::instantList Foam::adiosFoam::findTimes
+(
+    const fileName& directory,
+    const word& constantName
+)
+{
+    // Read directory entries into a list
+    fileNameList dirEntries(readDir(directory, fileName::FILE, false));
+
+    // Initialise instant list
+    instantList Times(dirEntries.size() + 1);
+    label nTimes = 0;
+
+    // Check for "constant" - not yet useful
+    bool haveConstant = false;
+    for (const fileName& dirEntry : dirEntries)
+    {
+        if (dirEntry.hasExt("bp") && dirEntry.lessExt() == constantName)
+        {
+            Times[nTimes].value() = 0;
+            Times[nTimes].name()  = word(dirEntry);
+            ++nTimes;
+            haveConstant = true;
+            break;
+        }
+    }
+
+    // Read and parse all the entries in the directory
+    for (const fileName& dirEntry : dirEntries)
+    {
+        if (dirEntry.hasExt("bp"))
+        {
+            scalar val;
+            const word dirValue(dirEntry.lessExt());
+
+            if (readScalar(dirValue, val))
+            {
+                Times[nTimes].value() = val;
+                Times[nTimes].name()  = word(dirEntry);
+                ++nTimes;
+            }
+        }
+    }
+
+    // Reset the length of the times list
+    Times.setSize(nTimes);
+
+    if (haveConstant)
+    {
+        if (nTimes > 2)
+        {
+            std::sort(&Times[1], Times.end(), instant::less());
+        }
+    }
+    else if (nTimes > 1)
+    {
+        std::sort(&Times[0], Times.end(), instant::less());
+    }
+
+    return Times;
+}
+
+
+// ************************************************************************* //

src/adiosFoam/adiosFoam.H

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016-2019 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+Namespace
+    Foam::adiosFoam
+
+Description
+    Core routines and definitions for OpenFOAM ADIOS files.
+
+SourceFiles
+    adiosFoam.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef adiosFoam_H
+#define adiosFoam_H
+
+#include "fileName.H"
+#include "instantList.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace adiosFoam
+{
+
+/*---------------------------------------------------------------------------*\
+                        Namespace adiosFoam Declaration
+\*---------------------------------------------------------------------------*/
+
+//- The default directory name for ADIOS files ("adiosData")
+extern const word defaultDirectory;
+
+//- OpenFOAM global attributes within ADIOS file ("/openfoam")
+extern const string foamAttribute;
+
+//- OpenFOAM time attributes within ADIOS file ("/time")
+extern const string timeAttribute;
+
+
+//- Search a given directory for ADIOS time files
+instantList findTimes
+(
+    const fileName& directory,
+    const word& constantName  = "constant"
+);
+
+
+//- Path name for a region
+inline const word& regionPath
+(
+    const word& regionName
+)
+{
+    return regionName;
+}
+
+
+//- Extract region name from a variable name (somewhat fragile)
+inline word regionOf
+(
+    const fileName& varName
+)
+{
+    const auto i = varName.find('/');
+
+    return varName.substr(0, i);
+}
+
+
+//- Path name for fields
+inline fileName fieldPath
+(
+    const word& regionName,
+    const fileName& var = fileName::null
+)
+{
+    return regionPath(regionName) / "field" / var;
+}
+
+
+//- Path name for meshes
+inline fileName meshPath
+(
+    const word& regionName,
+    const fileName& var = fileName::null
+)
+{
+    return regionPath(regionName) / "polyMesh" / var;
+}
+
+
+//- Path name for clouds
+inline fileName cloudPath
+(
+    const word& regionName,
+    const word& cloudName = word::null
+)
+{
+    return regionPath(regionName) / "cloud" / cloudName;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace adiosFoam
+} // End namespace Foam
+
+#endif
+
+// ************************************************************************* //

src/adiosFoam/controls/adiosRegionControl.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016-2019 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "adiosRegionControl.H"
+#include "cloud.H"
+#include "fvMesh.H"
+#include "IOstreams.H"
+
+// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
+
+void Foam::adiosFoam::regionControl::read
+(
+    const fvMesh& mesh,
+    const dictionary& dict
+)
+{
+    resetAll();
+    name_ = mesh.name(); // ensure absolute consistency
+
+    Info<< " Region dict: " << name_ << endl;
+
+    const dictionary* writePtr  = dict.findDict("write");
+    const dictionary* ignorePtr = dict.findDict("ignore");
+
+    const dictionary& wrtDict = (writePtr  ? *writePtr  : dictionary::null);
+    const dictionary& ignDict = (ignorePtr ? *ignorePtr : dictionary::null);
+
+    explicitWrite_ = wrtDict.getOrDefault("explicit", false);
+
+    requestedFields_.clear();
+    requestedClouds_.clear();
+    ignoredFields_.clear();
+    ignoredClouds_.clear();
+
+    if (explicitWrite_)
+    {
+        wrtDict.readEntry("fields", requestedFields_);
+        wrtDict.readEntry("clouds", requestedClouds_);
+    }
+    else
+    {
+        wrtDict.readIfPresent("fields", requestedFields_);
+        wrtDict.readIfPresent("clouds", requestedClouds_);
+    }
+
+    ignDict.readIfPresent("fields", ignoredFields_);
+    ignDict.readIfPresent("clouds", ignoredClouds_);
+
+    // Check if the requested fields are actually accessible
+    DynamicList<word> missing(requestedFields_.size());
+    for (const wordRe& what : requestedFields_)
+    {
+        if (what.isLiteral())
+        {
+            if (mesh.foundObject<regIOobject>(what))
+            {
+                Info<< " " << what;
+            }
+            else
+            {
+                missing.append(what);
+            }
+        }
+    }
+
+    // Also print the cloud names
+    for (const auto& name : requestedClouds_)
+    {
+        Info<< ' ' << name;
+    }
+
+    Info<< nl << endl;
+
+    if (missing.size())
+    {
+        WarningInFunction
+            << nl
+            << missing.size() << " objects not found in database:" << nl
+            << "   " << flatOutput(missing) << endl;
+    }
+}
+
+
+void Foam::adiosFoam::regionControl::resetAll()
+{
+    explicitWrite_ = false;
+    requestedFields_.clear();
+    requestedClouds_.clear();
+    ignoredFields_.clear();
+    ignoredClouds_.clear();
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::adiosFoam::regionControl::regionControl()
+:
+    regionControl("")
+{}
+
+
+Foam::adiosFoam::regionControl::regionControl(const word& regionName)
+:
+    name_(regionName),
+    explicitWrite_(false),
+    requestedFields_(),
+    requestedClouds_(),
+    ignoredFields_(),
+    ignoredClouds_(),
+    topoTime_(0),
+    pointTime_(0),
+    facesName_(),
+    pointsName_()
+{}
+
+
+Foam::adiosFoam::regionControl::regionControl
+(
+    const fvMesh& mesh,
+    const dictionary& dict
+)
+:
+    regionControl(mesh.name())
+{
+    read(mesh, dict);
+    pointTime_ = topoTime_ = mesh.time().timeOutputValue();
+}
+
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+bool Foam::adiosFoam::regionControl::acceptCloudObject
+(
+    const cloud& c
+) const
+{
+    const word& name = c.name();
+
+    return
+    (
+        // Not explicitly ignored
+        !ignoredClouds_.match(name)
+     &&
+        (
+            // auto-write or explicitly requested
+            (autoWrite() && c.writeOpt() == IOobject::AUTO_WRITE)
+         || requestedClouds_.match(name)
+        )
+    );
+}
+
+
+bool Foam::adiosFoam::regionControl::acceptFieldObject
+(
+    const regIOobject& obj
+) const
+{
+    const word& name = obj.name();
+
+    return
+    (
+        // NO clouds and not explicitly ignored
+        !isA<cloud>(obj) && !ignoredFields_.match(name)
+     &&
+        (
+            // auto-write or explicitly requested
+            (autoWrite() && obj.writeOpt() == IOobject::AUTO_WRITE)
+         || requestedFields_.match(name)
+        )
+     && !name.endsWith("_0")  // ignore _0 fields
+    );
+}
+
+
+// TODO: handling mesh on input
+// void resetPrimitives
+// (
+// const Xfer<pointField>& points,
+// const Xfer<faceList>& faces,
+// const Xfer<labelList>& owner,
+// const Xfer<labelList>& neighbour,
+// const labelList& patchSizes,
+// const labelList& patchStarts,
+// const bool validBoundary = true
+// );
+// resetPrimitives(*face,
+// Foam::polyMesh::readUpdateState Foam::polyMesh::readUpdate()
+// {
+//     if (debug)
+//     {
+//         InfoInFunction << "Updating mesh based on saved data." << endl;
+//     }
+
+
+enum Foam::polyMesh::readUpdateState
+Foam::adiosFoam::regionControl::updateTimes(const fvMesh& mesh) const
+{
+    const double now = mesh.time().timeOutputValue();
+    const word pointsInstance = mesh.pointsInstance().name();
+    const word facesInstance  = mesh.facesInstance().name();
+
+    polyMesh::readUpdateState state = polyMesh::UNCHANGED;
+
+    if (pointsName_ != pointsInstance)
+    {
+        state = polyMesh::POINTS_MOVED;
+
+        pointsName_ = pointsInstance;
+        pointTime_  = now;
+    }
+
+    if (facesName_ != facesInstance)
+    {
+        state = polyMesh::TOPO_CHANGE;
+
+        facesName_ = facesInstance;
+        topoTime_  = now;
+    }
+
+    return state;
+}
+
+
+// ************************************************************************* //

src/adiosFoam/controls/adiosRegionControl.H

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016-2019 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+Class
+    Foam::adiosFoam::adiosRegionControl
+
+Description
+    Controls for managing region and cloud writing
+
+SourceFiles
+    adiosRegionControl.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef adiosFoamRegionControl_H
+#define adiosFoamRegionControl_H
+
+#include "adiosTime.H"
+#include "polyMesh.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// Forward Declarations
+class cloud;
+class fvMesh;
+
+namespace adiosFoam
+{
+
+/*---------------------------------------------------------------------------*\
+                        Class regionControl Declaration
+\*---------------------------------------------------------------------------*/
+
+//- Per-region info variables grouped together to be able
+//- to create a list of them
+class regionControl
+{