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When an OpenFOAM simulation runs in parallel, the data for decomposed fields and
mesh(es) has historically been stored in multiple files within separate
directories for each processor. Processor directories are named 'processorN',
where N is the processor number.
This commit introduces an alternative "collated" file format where the data for
each decomposed field (and mesh) is collated into a single file, which is
written and read on the master processor. The files are stored in a single
directory named 'processors'.
The new format produces significantly fewer files - one per field, instead of N
per field. For large parallel cases, this avoids the restriction on the number
of open files imposed by the operating system limits.
The file writing can be threaded allowing the simulation to continue running
while the data is being written to file. NFS (Network File System) is not
needed when using the the collated format and additionally, there is an option
to run without NFS with the original uncollated approach, known as
"masterUncollated".
The controls for the file handling are in the OptimisationSwitches of
etc/controlDict:
OptimisationSwitches
{
...
//- Parallel IO file handler
// uncollated (default), collated or masterUncollated
fileHandler uncollated;
//- collated: thread buffer size for queued file writes.
// If set to 0 or not sufficient for the file size threading is not used.
// Default: 2e9
maxThreadFileBufferSize 2e9;
//- masterUncollated: non-blocking buffer size.
// If the file exceeds this buffer size scheduled transfer is used.
// Default: 2e9
maxMasterFileBufferSize 2e9;
}
When using the collated file handling, memory is allocated for the data in the
thread. maxThreadFileBufferSize sets the maximum size of memory in bytes that
is allocated. If the data exceeds this size, the write does not use threading.
When using the masterUncollated file handling, non-blocking MPI communication
requires a sufficiently large memory buffer on the master node.
maxMasterFileBufferSize sets the maximum size in bytes of the buffer. If the
data exceeds this size, the system uses scheduled communication.
The installation defaults for the fileHandler choice, maxThreadFileBufferSize
and maxMasterFileBufferSize (set in etc/controlDict) can be over-ridden within
the case controlDict file, like other parameters. Additionally the fileHandler
can be set by:
- the "-fileHandler" command line argument;
- a FOAM_FILEHANDLER environment variable.
A foamFormatConvert utility allows users to convert files between the collated
and uncollated formats, e.g.
mpirun -np 2 foamFormatConvert -parallel -fileHandler uncollated
An example case demonstrating the file handling methods is provided in:
$FOAM_TUTORIALS/IO/fileHandling
The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
239 lines
7.1 KiB
C
239 lines
7.1 KiB
C
/*---------------------------------------------------------------------------*\
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========= |
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\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
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\\ / O peration |
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\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
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\\/ M anipulation |
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-------------------------------------------------------------------------------
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License
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This file is part of OpenFOAM.
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OpenFOAM is free software: you can redistribute it and/or modify it
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under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
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for more details.
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You should have received a copy of the GNU General Public License
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along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
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Application
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applyBoundaryLayer
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Description
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Apply a simplified boundary-layer model to the velocity and
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turbulence fields based on the 1/7th power-law.
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The uniform boundary-layer thickness is either provided via the -ybl option
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or calculated as the average of the distance to the wall scaled with
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the thickness coefficient supplied via the option -Cbl. If both options
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are provided -ybl is used.
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\*---------------------------------------------------------------------------*/
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#include "fvCFD.H"
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#include "singlePhaseTransportModel.H"
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#include "turbulentTransportModel.H"
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#include "wallDist.H"
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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// Turbulence constants - file-scope
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static const scalar Cmu(0.09);
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static const scalar kappa(0.41);
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int main(int argc, char *argv[])
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{
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argList::addNote
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(
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"apply a simplified boundary-layer model to the velocity and\n"
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"turbulence fields based on the 1/7th power-law."
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);
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argList::addOption
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(
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"ybl",
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"scalar",
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"specify the boundary-layer thickness"
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);
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argList::addOption
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(
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"Cbl",
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"scalar",
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"boundary-layer thickness as Cbl * mean distance to wall"
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);
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argList::addBoolOption
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(
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"writenut",
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"write nut field"
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);
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#include "setRootCase.H"
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if (!args.optionFound("ybl") && !args.optionFound("Cbl"))
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{
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FatalErrorInFunction
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<< "Neither option 'ybl' or 'Cbl' have been provided to calculate "
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<< "the boundary-layer thickness.\n"
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<< "Please choose either 'ybl' OR 'Cbl'."
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<< exit(FatalError);
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}
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else if (args.optionFound("ybl") && args.optionFound("Cbl"))
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{
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FatalErrorInFunction
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<< "Both 'ybl' and 'Cbl' have been provided to calculate "
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<< "the boundary-layer thickness.\n"
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<< "Please choose either 'ybl' OR 'Cbl'."
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<< exit(FatalError);
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}
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#include "createTime.H"
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#include "createMesh.H"
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#include "createFields.H"
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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// Modify velocity by applying a 1/7th power law boundary-layer
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// u/U0 = (y/ybl)^(1/7)
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// assumes U0 is the same as the current cell velocity
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Info<< "Setting boundary layer velocity" << nl << endl;
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scalar yblv = ybl.value();
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forAll(U, celli)
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{
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if (y[celli] <= yblv)
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{
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mask[celli] = 1;
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U[celli] *= ::pow(y[celli]/yblv, (1.0/7.0));
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}
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}
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mask.correctBoundaryConditions();
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Info<< "Writing U\n" << endl;
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U.write();
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// Update/re-write phi
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#include "createPhi.H"
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phi.write();
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singlePhaseTransportModel laminarTransport(U, phi);
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autoPtr<incompressible::turbulenceModel> turbulence
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(
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incompressible::turbulenceModel::New(U, phi, laminarTransport)
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);
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if (isA<incompressible::RASModel>(turbulence()))
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{
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// Calculate nut
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turbulence->validate();
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tmp<volScalarField> tnut = turbulence->nut();
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volScalarField& nut = const_cast<volScalarField&>(tnut());
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volScalarField S(mag(dev(symm(fvc::grad(U)))));
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nut = (1 - mask)*nut + mask*sqr(kappa*min(y, ybl))*::sqrt(2)*S;
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// Do not correct BC - wall functions will 'undo' manipulation above
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// by using nut from turbulence model
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if (args.optionFound("writenut"))
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{
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Info<< "Writing nut" << endl;
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nut.write();
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}
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//--- Read and modify turbulence fields
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// Turbulence k
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tmp<volScalarField> tk = turbulence->k();
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volScalarField& k = const_cast<volScalarField&>(tk());
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scalar ck0 = pow025(Cmu)*kappa;
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k = (1 - mask)*k + mask*sqr(nut/(ck0*min(y, ybl)));
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// Do not correct BC - operation may use inconsistent fields wrt these
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// local manipulations
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// k.correctBoundaryConditions();
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Info<< "Writing k\n" << endl;
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k.write();
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// Turbulence epsilon
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tmp<volScalarField> tepsilon = turbulence->epsilon();
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volScalarField& epsilon = const_cast<volScalarField&>(tepsilon());
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scalar ce0 = ::pow(Cmu, 0.75)/kappa;
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epsilon = (1 - mask)*epsilon + mask*ce0*k*sqrt(k)/min(y, ybl);
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// Do not correct BC - wall functions will use non-updated k from
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// turbulence model
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// epsilon.correctBoundaryConditions();
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Info<< "Writing epsilon\n" << endl;
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epsilon.write();
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// Turbulence omega
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IOobject omegaHeader
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(
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"omega",
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runTime.timeName(),
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mesh,
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IOobject::MUST_READ,
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IOobject::NO_WRITE,
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false
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);
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if (omegaHeader.typeHeaderOk<volScalarField>(true))
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{
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volScalarField omega(omegaHeader, mesh);
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dimensionedScalar k0("VSMALL", k.dimensions(), VSMALL);
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omega = (1 - mask)*omega + mask*epsilon/(Cmu*k + k0);
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// Do not correct BC - wall functions will use non-updated k from
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// turbulence model
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// omega.correctBoundaryConditions();
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Info<< "Writing omega\n" << endl;
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omega.write();
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}
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// Turbulence nuTilda
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IOobject nuTildaHeader
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(
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"nuTilda",
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runTime.timeName(),
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mesh,
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IOobject::MUST_READ,
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IOobject::NO_WRITE,
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false
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);
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if (nuTildaHeader.typeHeaderOk<volScalarField>(true))
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{
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volScalarField nuTilda(nuTildaHeader, mesh);
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nuTilda = nut;
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// Do not correct BC
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// nuTilda.correctBoundaryConditions();
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Info<< "Writing nuTilda\n" << endl;
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nuTilda.write();
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}
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}
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Info<< nl << "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
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<< " ClockTime = " << runTime.elapsedClockTime() << " s"
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<< nl << endl;
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Info<< "End\n" << endl;
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return 0;
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}
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// ************************************************************************* //
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