TUT: remove paraFoam hints from tutorials (mostly only need paraview now)

STYLE: remove reference to paraview _SM plugins (OpenFOAM-v1912 and earlier)

BUG: inconsistent "U" name on re-read (buoyancyEnergy)

STYLE: fix spelling inconsistencies

- for tracing tutorials execution

ENH: setTurbulenceFields: new automatic initialisation method for turbulence fields

See merge request !545

Kutalmış Berçin authored 2 years ago and Mark OLESEN committed 2 years ago

TUT: cylinder: fix the order in Allclean

species and heat adsorption BC's and fvOption source

See merge request !548

sergio authored 3 years ago and Kutalmış Berçin committed 2 years ago

speciesSorption is a zeroGradient BC which absorbs mass given by a first
order time derivative, absoprtion rate and an equilibrium value
calculated based on internal species values next to the wall.

patchCellsSource is a source fvOption which applies to the corresponding
species and apply the source calculated on the speciesSorption BC.

A new abstract virtual class was created to group BC's which
don't introduce a source to the matrix (i.e zeroGradient) but calculate
a mass sink/source which should be introduced into the matrix. This
is  done through the fvOption patchCellsSource.

support surface writer output transform (#2505)

See merge request !549

Mark OLESEN authored 2 years ago and Andrew Heather committed 2 years ago

- this allows the "relocation" of sampled surfaces. For example,
  to reposition into a different coordinate system for importing
  into CAD.

- incorporate output scaling for all surface writer types.

  This was previously done on an adhoc basis for different writers,
  but with now included in the base-level so that all writers
  can automatically use scale + transform.

  Example:

  formatOptions
  {
      vtk
      {
          scale 1000;  // m -> mm
          transform
          {
              origin  (0.05 0 0);
              rotation axisAngle;
              axis    (0 0 1);
              angle   -45;
          }
      }
  }

ENH: adjoint code review

See merge request !518

Vaggelis Papoutsis authored 2 years ago and Andrew Heather committed 2 years ago

Necessary when grad(Ua) is cached

Vaggelis Papoutsis authored 2 years ago and Andrew Heather committed 2 years ago

Partially fixes #2502 (see discussion there)

Vaggelis Papoutsis authored 2 years ago and Andrew Heather committed 2 years ago

in RASModelVariables were doing this by checking whether the
corresponding pointer was allocated. In some cases, however, even if the
field does not exist, the pointer is not null, leading to the wrong
output. Made the correspding functions virtual and overwritten their
return values in the derived classes. Kept the initial implementation in
base to facilitate the clone function.

Vaggelis Papoutsis authored 2 years ago and Andrew Heather committed 2 years ago

in cases with more than one primal or adjoint solvers

TUT: removed all occurances of useSolverNameForFields
from the optimisation tutorials since it is now set
automatically.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

to be in line with the changes in 00f46a2c52 and added the same tutorial
which performs the optimisation in one-go, for comparison.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

volBSplinesBase const, since the no private/protected
variable is changed there.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

in the sensitivity patches, symmetry::evaluate() needs access to the
internalField which does exist, leading to wrong memory access.

Fixed by specifying a calculated type fvPatchField for all patches when
creating a boundaryField<Type>

Using a symmetry(Plane) as a sensitivity patch is quite rare and
borderline wrong, but this provides a fix nonetheless.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

The multiplier of grad(dxdb) is a volTensorField which, by itself, is
memory consuming. The function computing it though was sloppy in terms
of memory management, constituting the peak memory consumption during an
adjoint optimisation. Initial changes to remedy the problem include the
deallocation of some of the volTensorFields included in the computation
of grad(dxdb) once unneeded, the utilisation of volSymmTensorFields
instead of volTensorFields where possible and avoiding allocating some
unnecessary intermediate fields.

Actions to further reduce memory consumption:

- For historical reasons, the code computes/stores the transpose of
  grad(dxdb), which is then transposed when used in the computation of
  the FI or the ESI sensitivity derivatives.  This redundant
  transposition can be avoid, saving the allocation of an additional
  volTensorField, but the changes need to permeate a number of places in
  the code that contribute to grad(dxdb) (e.g.  ATC, adjoint turbulence
  models, adjoint MRF, etc).
- Allocation of unnecessary pointers in the objective class should be
  avoided.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

- ATCstandard, ATCUaGradU:
  the ATC is now added as a dimensioned field and not as an fvMatrix
  to UaEqn. This get rid of many unnecessary allocations.

- ATCstandard:
  gradU is cached within the class to avoid its re-computation in
  every adjoint iteration of the steady state solver.

- Inlined a number of functions within the primal and adjoint solvers.
  This probably has a negligible effect since they likely were inlined
  by the compiler either way.

- The momentum diffusivity at the boundary, used by the adjoint boundary
  conditions, was computed for the entire field and, then, only the
  boundary field of each adjoint boundary condition was used. If many
  outlet boundaries exist, the entire nuEff field would be computed as
  many times as the number of boundaries, leading to an unnecessary
  computational overhead.

- Outlet boundary conditions (both pressure and velocity) use the local
  patch gradient to compute their fluxes. This patch gradient requires
  the computation of the adjacent cell gradient, which is done on the
  fly, on a per patch basis. To compute this patch adjacent gradient
  however, the field under the grad sign is interpolated on the entire
  mesh. If many outlets exist, this leads to a huge computational
  overhead. Solved by caching the interpolated field to the database and
  re-using it, in a way similar to the caching of gradient fields (see
  fvc::grad).

WIP: functions returning references to primal and adjoint boundary
fields within boundaryAdjointContributions seem to have a non-negligible
overhead for cases with many patches. No easy work-around here since
these are virtual and cannot be inlined.

WIP: introduced the code structure for caching the contributions to
the adjoint boundary conditions that depend only on the primal fields
and reusing. The process needs to be completed and evaluated, to make
sure that the extra code complexity is justified by gains in
performance.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

from the equivalent entry of the primal eikonal equation solver, unless
specified in the corresponding adjoint dictionary.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

is now appended by the name of the adjoint solver, if more than one
exist. This was necessary for an accurate continuation since, before
these changes, only the ma field of the last solver was written. As a
result, when restarting the first adjoint solver was reading the ma
field of the last one. No changes are needed in fvSolution and fvSchemes
w.r.t. the previous code version.

Vaggelis Papoutsis authored 4 years ago and Andrew Heather committed 2 years ago

as a step towards machine-accuracy continuation of the optimisation
loop.

Additionally, control points are now written under the time/uniform
folder, to be in-line with rest of the code structure for continuation.
As a side-effect, the controlPointsDefinition in
constant/dynamicMeshDict does not need to be changed to 'fromFile'
anymore in order to perform the continuation. The 'fromFile' option is
still valid if the user wants to supply the control points manually but,
as with all other controlPointsDefinitions, it will be disregarded if the
proper file exists under the time/uniform/volumetricBSplines folder.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

Before the commit, the sensitivity classes were receiving references of
the (incompressible) primal and adjoint variables.  However, if
additional physics was added (energy equation, multiphase, etc), the
infrastructure wasn't convenient for accommodating (new terms in the FI
and E-SI formulations, new terms in the sensitivity map, etc).

Now, the sensitivity classes receive a reference to an
incompressibleAdjointSolver and receive the terms for the FI and
sensitivity maps through there. The latter is still WIP.

Modified adjointSimple to incorporate these changes as well.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

Each solver now writes its sensitivity derivatives to its dictionary,
enabling also a binary format. If present, the sensitivities are then
re-read from the dictionary, avoiding thus possible loss of information
due to re-computation.

As a side-effect, sensitivities are computed after the completion of
each adjoint solver, instead of being computed after all adjoint solvers
have been completed.

Vaggelis Papoutsis authored 3 years ago and Andrew Heather committed 2 years ago

- computation of lift sensitivity derivatives for the NACA0012 airfoil
- optimisation of an s-bend duct for min. total pressure losses