Feature snappy hex mesh gap refinement

Adding automatic gap refinement capability

See merge request !2

Feature snappy hex mesh

It's got all of the VW snappyHexMesh developments in it.

Not yet the automatic-gap refinement.

See merge request !1

ENH: Adding humidityTemperatureCoupledMixed BC and directionalPressureGradientExplicitSource and the corresponding tutorial
tutorials/heatTransfer/chtMultiRegionFoam/windshieldCondensation

Original fix (http://www.openfoam.org/mantisbt/view.php?id=1780)
did an increment to create a new communicator. This might
access the communicator-to-mpi_structure tables in PstreamGlobals.H outside
range. Instead allocate and release communicator.

Initial implementation. Still goes wrong on r1 == r2.

- shoot rays to nearest point on surface and two perpendicular rays
  (instead of always shooting in the 3 coordinate directions)

- avoid bleeding through the surface intersection

1. multi-ray shooting. It now shoots rays in all the 3 coordinate directions
from the cell centre. Before it would shoot just a single ray from the
nearest point on the surface, going through the cell centre.

There is a cost overhead in that now it shoots 6 rays (+-x, +-y, +-z)
instead of just 1.

2. bleeding of refinement. It marks the cells inside a gap and walks out
the gap-size to neighbouring cells (which are just outside the gap). This
should make for a smoother refinement pattern.

Merge branch 'feature-snappyHexMesh' of develop.openfoam.com:Development/OpenFOAM-dev-OpenCFD into feature-snappyHexMesh

The start of the layer addition loop does a synchronisation of the wanted
displacement. This also does a truncation of the displacement if it is <
minThickness. At the first iteration the displacement was initialised to
vector::one which might trigger the truncation logic (and then disable
extrusion altogether). Instead we now initialise the displacement to
vector::GREAT before entering the synchronisation.

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1792

The built-in explicit symplectic integrator has been replaced by a
general framework supporting run-time selectable integrators.  Currently
the explicit symplectic, implicit Crank-Nicolson and implicit Newmark
methods are provided, all of which are 2nd-order in time:

Symplectic 2nd-order explicit time-integrator for 6DoF solid-body motion:

    Reference:
        Dullweber, A., Leimkuhler, B., & McLachlan, R. (1997).
        Symplectic splitting methods for rigid body molecular dynamics.
        The Journal of chemical physics, 107(15), 5840-5851.

    Can only be used for explicit integration of the motion of the body,
    i.e. may only be called once per time-step, no outer-correctors may be
    applied.  For implicit integration with outer-correctors choose either
    CrankNicolson or Newmark schemes.

    Example specification in dynamicMeshDict:
    solver
    {
        type    symplectic;
    }

Newmark 2nd-order time-integrator for 6DoF solid-body motion:

    Reference:
        Newmark, N. M. (1959).
        A method of computation for structural dynamics.
        Journal of the Engineering Mechanics Division, 85(3), 67-94.

    Example specification in dynamicMeshDict:
    solver
    {
        type    Newmark;
        gamma   0.5;    // Velocity integration coefficient
        beta    0.25;   // Position integration coefficient
    }

Crank-Nicolson 2nd-order time-integrator for 6DoF solid-body motion:

    The off-centering coefficients for acceleration (velocity integration) and
    velocity (position/orientation integration) may be specified but default
    values of 0.5 for each are used if they are not specified.  With the default
    off-centering this scheme is equivalent to the Newmark scheme with default
    coefficients.

    Example specification in dynamicMeshDict:
    solver
    {
        type    CrankNicolson;
        aoc     0.5;    // Acceleration off-centering coefficient
        voc     0.5;    // Velocity off-centering coefficient
    }

Both the Newmark and Crank-Nicolson are proving more robust and reliable
than the symplectic method for solving complex coupled problems and the
tutorial cases have been updated to utilize this.

In this new framework it would be straight forward to add other methods
should the need arise.

Henry G. Weller
CFD Direct

Ur can be generated using a functionObject or in the post-processor

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1868

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1870

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1872

Refinement:
-----------
// Optionally avoid patch merging - keeps hexahedral cells
// (to be used with automatic refinement/unrefinement)
//mergePatchFaces off;

// Optional multiple locationsInMesh with corresponding optional cellZone
// (automatically generates faceZones inbetween)
locationsInMesh
(
    ((-0.09 -0.039 -0.049)  bottomAir)  // cellZone bottomAir
    ((-0.09 0.009 -0.049)   topAir)     // cellZone topAir
);

// Optional faceType and patchType specification for these faceZones
faceZoneControls
{
    bottomAir_to_topAir
    {
        faceType baffle;
    }
}

/ Optional checking of 'bleeding' of mesh through a specifying a locations
// outside the mesh
locationsOutsideMesh ((0 0 0)(12.3 101.17 3.98));

// Improved refinement: refine all cells with all (or all but one) sides refined

// Improved refinement: refine all cells with opposing faces with different
// refinement level. These cells can happen on multiply curved surfaces.
// Default on, can be switched off with
//interfaceRefine false;

Snapping
--------
// Optional smoothing of points at refinement interfaces. This will reduce
// the non-orthogonality at refinement interfaces.
//nSmoothInternal $nSmoothPatch;

Layering
--------

// Layers can be added to patches or to any side of a faceZone.
// (Any faceZone internally gets represented as two patches)

// The angle to merge patch faces can be set independently of the
// featureAngle. This is especially useful for large feature angles
// Default is the same as the featureAngle.
//mergePatchFacesAngle 45;

// Optional mesh shrinking type 'displacementMotionSolver'. It uses any
// displacementMotionSolver, e.g. displacementSBRStress
// (default is the medial-axis algorithm, 'displacementMedialAxis')
//meshShrinker displacementMotionSolver;

mattijs authored 9 years ago and Andrew Heather committed 9 years ago

Refinement:
-----------
// Optionally avoid patch merging - keeps hexahedral cells
// (to be used with automatic refinement/unrefinement)
//mergePatchFaces off;

// Optional multiple locationsInMesh with corresponding optional cellZone
// (automatically generates faceZones inbetween)
locationsInMesh
(
    ((-0.09 -0.039 -0.049)  bottomAir)  // cellZone bottomAir
    ((-0.09 0.009 -0.049)   topAir)     // cellZone topAir
);

// Optional faceType and patchType specification for these faceZones
faceZoneControls
{
    bottomAir_to_topAir
    {
        faceType baffle;
    }
}

/ Optional checking of 'bleeding' of mesh through a specifying a locations
// outside the mesh
locationsOutsideMesh ((0 0 0)(12.3 101.17 3.98));

// Improved refinement: refine all cells with all (or all but one) sides refined

// Improved refinement: refine all cells with opposing faces with different
// refinement level. These cells can happen on multiply curved surfaces.
// Default on, can be switched off with
//interfaceRefine false;

Snapping
--------
// Optional smoothing of points at refinement interfaces. This will reduce
// the non-orthogonality at refinement interfaces.
//nSmoothInternal $nSmoothPatch;

Layering
--------

// Layers can be added to patches or to any side of a faceZone.
// (Any faceZone internally gets represented as two patches)

// The angle to merge patch faces can be set independently of the
// featureAngle. This is especially useful for large feature angles
// Default is the same as the featureAngle.
//mergePatchFacesAngle 45;

// Optional mesh shrinking type 'displacementMotionSolver'. It uses any
// displacementMotionSolver, e.g. displacementSBRStress
// (default is the medial-axis algorithm, 'displacementMedialAxis')
//meshShrinker displacementMotionSolver;