- previously would always return "constant" as the instance for
an optional dir/file that wasn't found.
However, this meant retesting to screen out false positives.
Now support an additional parameter
'bool constant_fallback = ...'
to return "constant" or an empty word.
The method signature changes slightly with a new optional bool
parameter:
//! Return \c "constant" instead of \c "" if the search failed
const bool constant_fallback = true
ENH: code consolidation for findInstancePath
- relocate from Time to TimePaths and provide an additional static
version that is reused in fileOperations
BUG: distributedTriSurfaceMesh:::findLocalInstance broken (#3135)
- was not checking the parent at all.
COMP: remove unused findInstancePath(const fileName&, ..) method
- in renumberMesh replace calculation of a subMesh connectivity
with calculation of the full mesh connectivity followed by subsetting
of the full adjacency matrix. This should reduce the overall number of
operations. (MR !669)
- provide no_topology() characteristic to avoid triggering potentially
expensive mesh connectivity calculations when they are not required.
- remove/deprecate unused pointField references from the renumber
methods. These appear to have crept in from outer similarities
with decompositionMethod, but have no meaning for renumbering.
- remove/deprecate various unused aggregation renumberings since these
have been previously replaced by pre-calling calcCellCells, or
using bandCompression directly.
- make regionFaceOrder for block-wise renumbering optional and
treat as experimental (ie, default is now disabled).
The original idea was to sort the intra-region and inter-region faces
separately. However, this will mostly lead to non-upper triangular
ordering between regions, which checkMesh and others don't really like.
ENH: add timing information for various renumberMesh stages
ENH: add reset of clockTime and cpuTime increment
- simplifies section-wise timings
ENH: add globalIndex::null() and fieldTypes::processorType conveniences
- provides more central management of these characteristics
- particularly useful in these combinations:
1.
OCharStream buf;
// populate
ISpanStream is(buf.view());
// parse
2.
// read from file
ifile.getLine(str);
ISpanStream is(str);
// parse
These avoid making a copy of the character content, compared to
versions with stringstream:
OStringStream buf;
IStringStream is(buf.str());
- renumberMesh now has -dry-run, -write-maps, -no-fields,
-renumber-method, -renumber-coeffs options.
* Use -dry-run with -write-maps to visualize the before/after
effects of renumbering (creates a VTK file).
* -no-fields to renumber the mesh only.
This is useful and faster when the input fields are uniform
and the -overwrite option is specified.
* -renumber-method allows a quick means of specifying a different
default renumber method (instead of Cuthill-McKee).
The -renumber-coeffs option allows passing of dictionary content
for the method.
Examples,
// Different ways to specify reverse Cuthill-McKee
* -renumber-method RCM
* -renumber-coeffs 'reverse true;'
* -renumber-method CuthillMcKee
* -renumber-coeffs 'reverse true;'
* -renumber-coeffs 'method CuthillMcKee; reverse true;'
// Other (without dictionary coefficients)
* renumberMesh -renumber-method random
// Other (with dictionary coefficients)
renumberMesh \
-renumber-method spring \
-renumber-coeffs 'maxCo 0.1; maxIter 1000; freezeFraction 0.99;'
// Other (with additional libraries)
renumberMesh -renumber-method zoltan -lib zoltanRenumber
COMP: build zoltan renumbering to MPI-specific location
- zoltan and Sloan renumbering are now longer automatically linked to
the renumberMesh utility but must be separately loaded by a
command-line option or through a dictionary "libs" entry.
ENH: add output cellID for decomposePar -dry-run -cellDist
ENH: eliminate unnecessary duplicate communicator
- in globalMeshData previously had a comm_dup hack to avoid clashes
with deltaCoeffs calculations. However, this was largely due to a
manual implementation of reduce() that used point-to-point
communication. This has since been updated to use an MPI_Allreduce
and now an MPI_Allgather, neither of which need this hack.
- this was previously a UList instead of SubList,
but SubList supports better assignment of values
ENH: add invertOneToManyCompact
- returns a CompactListList<label> instead of labelListList, which
allows for reuse as partitioning table etc and/or slightly reduced
memory overhead
- add convenience forms for common combinations
- avoid allocation for 1:1 identity agglomerations
- support subsetting forms (avoids an intermediate fvMeshSubset)
that also return the cellMap
- refactored to eliminate code duplication between weighted and
unweighted forms
- construct Map/HashTable from key/value lists.
- invertToMap() : like invert() but returns a Map<label>,
which is useful for sparse numbering
- inplaceRenumber() : taking a Map<label> for the mapper
ENH: construct/reset CStringList for list of C-strings
- can use UList signature since the routines do not resize the list
or attempt to broadcast it: useful for SubList handling.
ENH: add IPstream/OPstream send/recv static methods
- the old Pstream::scatter routines (which were largely a misnomer)
have been superseded by various broadcast routines, but were left in
the code with #ifndef/#ifdef Foam_Pstream_scatter_nobroadcast
guards. Now noisily deprecate them, and remove the old manual tree
communication in favour of MPI broadcast and/or
serialize/de-serialize with wrapped Pstream::broadcast
- consolidate various gather methods to include the communication
structure directly. No functional change, but reduces the number of
methods.
ENH: add parallel guard to UPstream::whichCommunication() method
- returns List::null() as the schedule for non-parallel instead
of an inappropriate linear or tree schedule
ENH: Pstream::listGatherValues, Pstream::listScatterValues
- like the existing UPstream versions but supporting non-contiguous
- adjointOptimisation : missing link to fileFormats
- snappyHexMesh : add fvMotionSolvers link (#3058)
STYLE: remove remnant -DFULLDEBUG hints
- now more easily covered with wmake -debug ...
- the fileHandler changes included setting cacheLevel(0) to avoid
blocking with redistributePar. However, this meant if clouds
were not uniformly present on all ranks the fileHandler would follow
different code paths and lead to blocking.
Now switch to distributed mode for the lagrangian operations within
redistributePar based on the cacheLevel information.
FIX: avoid triggering a false processor check in argList
- when redistributing to few ranks
Parts of the adjoint optimisation library were re-designed to generalise
the way sensitivity derivatives (SDs) are computed and to allow easier
extension to primal problems other than the ones governed by
incompressible flows. In specific:
- the adjoint solver now holds virtual functions returning the part of
SDs that depends only on the primal and the adjoint fields.
- a new class named designVariables was introduced which, apart from
defining the design variables of the optimisation problem and
providing hooks for updating them in an optimisation loop, provides
the part of the SDs that affects directly the flow residuals (e.g.
geometric variations in shape optimisation, derivatives of source
terms in topology optimisation, etc). The final assembly of the SDs
happens here, with the updated sensitivity class acting as an
intermediate.
With the new structure, when the primal problem changes (for instance,
passive scalars are included), the same design variables and sensitivity
classes can be re-used for all physics, with additional contributions to
the SDs being limited (and contained) to the new adjoint solver to be
implemented. The old code structure would require new SD classes for
each additional primal problem.
As a side-effect, setting up a case has arguably become a bit easier and
more intuitive.
Additional changes include:
---------------------------
- Changes in the formulation and computation of shape sensitivity derivatives
using the E-SI approach. The latter is now derived directly from the
FI approach, with proper discretization for the terms and boundary
conditions that emerge from applying the Gauss divergence theorem used
to transition from FI to E-SI. When E-SI and FI are based on the same
Laplace grid displacement model, they are now numerically equivalent
(the previous formulation proved the theoretical equivalence of the
two approaches but numerical results could differ, depending on the
case).
- Sensitivity maps at faces are now computed based (and are deriving
from) sensitivity maps at points, with a constistent point-to-face
interpolation (requires the differentiation of volPointInterpolation).
- The objective class now allocates only the member pointers that
correspond to the non-zero derivatives of the objective w.r.t. the
flow and geometric quantities, leading to a reduced memory footprint.
Additionally, contributions from volume-based objectives to the
adjoint equations have been re-worked, removing the need for
objectiveManager to be virtual.
- In constrained optimisation, an adjoint solver needs to be present for
each constraint function. For geometric constraints though, no adjoint
equations need to solved. This is now accounted for through the null
adjoint solver and the geometric objectives which do not allocate
adjoint fields for this kind of constraints, reducing memory
requirements and file clutter.
- Refactoring of the updateMethod to collaborate with the new
designVariables. Additionally, all updateMethods can now read and
write restart data in binary, facilitating exact continuation.
Furthermore, code shared by various quasi-Newton methods (BFGS, DBFGS,
LBFGS, SR1) has been organised in the namesake class. Over and above,
an SQP variant capable of tackling inequality constraints has been
added (ISQP, with I indicating that the QP problem in the presence of
inequality constraints is solved through an interior point method).
Inequality constraints can be one-sided (constraint < upper-value)
or double-sided (lower-value < constraint < upper-value).
- Bounds can now be defined for the design variables.
For volumetricBSplines in specific, these can be computed as the
mid-points of the control points and their neighbouring ones. This
usually leads to better-defined optimisation problems and reduces the
chances of an invalid mesh during optimisation.
- Convergence criteria can now be defined for the optimisation loop
which will stop if the relative objective function reduction over
the last objective value is lower than a given threshold and
constraints are satisfied within a give tolerance. If no criteria are
defined, the optimisation will run for the max. given number of cycles
provided in controlDict.
- Added a new grid displacement method based on the p-Laplacian
equation, which seems to outperform other PDE-based approaches.
TUT: updated the shape optimisation tutorials and added a new one
showcasing the use of double-sided constraints, ISQP, applying
no-overlapping constraints to volumetric B-Splines control points
and defining convergence criteria for the optimisation loop.
- enhance POSIX compliance
- apply distinct colours and dash type for each line
- standardize the frame size to 1200x627
- dynamically replace the title with <function-object-name>/<file-name>
- address underscore character issues
- introduce legend components for tensors
- resolve a bug caused by parentheses in tensor files
BUG: particleTrackProperties: correct the typo (fixes#3050)
- on large memory systems (eg, 6TB) the process information
exceeds an 'int' range, so adjust parsing of the /proc/..
to use int64
ENH: update/modernize OSspecific system information
ENH: minor update of profiling code
- std::string, noexcept, lazier evaluations
STYLE: use direct call of memInfo
- use Foam::zero as a dispatch tag
FIX: return moleculeCloud::constProps() List by reference not copy
STYLE: range-for when iterating cloud parcels
STYLE: more consistent typedefs / declarations for Clouds
- better code style and seems to avoid triggering a gcc warning about
possibly uninitialized values
COMP: JSONformatter writeEntry missing a return value
STYLE: accept 'json' for checkMesh write format
- consistent with caseInfo functionObject
- simplifies handling.
* enables unprotecting to avoid accidentally cloning.
* removes the need for dedicated constructor or factory forms.
* simplfies DimensionedField and GeometricField New factory methods
- update objectRegistry management method (internal use)
old: bool cacheTemporaryObject(...)
new: bool is_cacheTemporaryObject(...)
to clarify that it is a query, not a request for caching etc.
- replace typeGlobal() global function with is_globalIOobject
traits for more consistent and easier overriding.
- relocate typeFilePath() global function as a member of IOobject
for consistency with typeHeaderOk.
BUG: faSchemes, fvSchemes not marked as global file types
- caused issues with collated
- static version of polyMesh::meshDir(), which takes a region name
polyMesh::meshDir(regionName)
vs
polyMesh::regionName(regionName)/polyMesh::meshSubDir
STYLE: use polyMesh::regionName(..) instead of comparing to defaultRegion
STYLE: use getOrDefault when retrieving various -region options
FIX: polyMesh::dbDir() now checks registry name, not full path (#3033)
Added -writeChecks <format> option
- writes computed mesh metrics to file in using <format>
- currently supported formats are OpenFOAM dictionary and JSON
- when reading, detect all clouds on all processors and uses this when
reading fields. Similarly, when writing it uses writeOnProc to skip
clouds that are empty on any particular processor.
Co-authored-by: Mark Olesen <>
- provide a globalIndex::calcOffsets() taking an indirect list, which
enables convenient offsets calculation from a variety of inputs.
- new CompactListList unpack variant: copy_unpack()
The copy_unpack() works somewhat like std::copy() in that it writes
the generated sublists to iterator positions, which makes this
type of code possible:
CompactListList<label> compact = ...;
DynamicList<face> extracted;
compact.copy_unpack<face>
(
std::back_inserter(extracted),
labelRange(4, 10)
);
-and-
const label nOldFaces = allFaces.size();
allFaces.resize(allFaces + nNewFaces);
auto iter = allFaces.begin(nOldFaces);
iter = compact.copy_unpack<face>(iter, /* selection 1 */);
...
iter = compact.copy_unpack<face>(iter, /* selection 2 */);
ENH: globalIndex resize()
- can be used to shrink or grow the offsets table.
Any extension of the offsets table corresponds to 'slots'
with 0 local size.
- allows construction of string tokens holding character content.
For example, data that has been serialized and buffered and that
now needs to be written or sent to another process.
- avoids clutter of argList::envGlobalPath() ...
ENH: allow temporary overwriting of output writeFormat
- allows switching for particular output routines
COMP: explicitly use TimePaths methods with Time
- this simplifies any overloading done at a later stage
- this makes it easier to split creation into a two-stage process
as required
- extend handling for polyBoundaryMeshEntries, faBoundaryMeshEntries
with more functionality. Ensure that these are never registered.
ENH: addition writeEntry methods for polyBoundaryMesh
- simplifies streaming and collating into other files
ENH: polyMesh rereading - update owner/neighbour header information
- this avoids accidentally reading the "cells" file if the mesh has
been created with NO_READ and then updated
STYLE: less vertical space when outputting empty PtrList
- combined most of the unweighted and weighted decomposition routines
such that an empty weight field is treated as uniform weighting.
This allows default parameters and cuts down on the number of
decompose methods.
- for topology-driven decomposition, it is now possible to pass in the
owner/neighbour connectivity as a CompactListList directly instead
of first creating a labelListList (which was internally repacked into
a CompactListList in many cases).
However, multiLevelDecomp still uses unpacking (to avoid a larger
reworking of code).
- support direct creation of some methods (eg, random, scotch etc)
without a dictionary
- fix incorrect neighbour face weighting (fixes#3019)
ENH: relocate calcCellCells from decompositionMethod to globalMeshData
- makes it more universally available
- CompactListList::size() corresponds to the number of sub-lists
whereas globalIndex::size() corresponds to the totalSize().
This difference can lead to potential coding errors when switching
between pure addressing (eg globalIndex) and addressing with content
(eg, CompactListList).
Within the source tree, there are no longer any occurances of
globalIndex::size() but it is nonetheless unsafe to change its
meaning now. Instead provide a commonly named length() method that
corresponds to the natural length: ie, the number of offsets minus 1
(with guards).
- add CompactListList::writeMatrix for writing the compact contents
in an unpacked form (eg, for debugging) without actually needing to
unpack into storage.
- provide globalIndex::whichProcID() two-parameter version
with myProcNo as the first argument.
Symmetric with isLocal etc, useful when using a communicator
that is not worldComm.
- usually only need big/little defines (which are now in the Fwd)
and rarely need byte-swapping.
Provide endian.H compatibility include, but foamEndianFwd.H or
foamEndian.H to avoid potential name clashes.
- The pTraits_cmptType returns the data type of 'cmptType' (for
arithmetic and VectorSpace types) or is simply a pass-through.
This can be combined with the pTraits_nComponents for casting.
For example,
function
(
reinterpret_cast<pTraits_cmptType<Type>::type*>(buf.data()),
(buf.size()/pTraits_nComponents<Type>::value)
);
ENH: extend Foam::identityOp so support array indexing (pass-through)
- single() method : simply tests if the globalIndex has nProcs == 1,
which is typically from a gatherNone invocation.
For example,
globalIndex gi;
if (...) gi.reset(localSize);
else gi.reset(globalIndex::gatherNone{}, localSize);
// later...
const label begin = (gi.single() ? 0 : gi.localStart());
const label count = (gi.single() ? gi.totalSize() : gi.localSize());
- add front() and back() methods to return the begin/end ranges,
and begin_value(), end_value() - as per labelRange.
- make more methods noexcept
- calcOffset(), calcRange() helper functions to determine
the processor-local of a numbering range without the overhead of
creating a list of offsets.
For example,
label myOffset = globalIndex::calcOffset(mesh.nCells());
labelRange mySlice = globalIndex::calcRange(mesh.nCells());
- add globalIndex localEnd() as per CompactListList method
STYLE: align looping constructs in CompactListList with List
- make more methods noexcept
- becoming more frequently used and there is no ambiguity in calling
parameters either - identity(label) vs identity(labelUList&).
Provide both int32 and int64 versions.
- now mark methods with strict deprecation, to make it easier to find
their use but without adding extra compilation noise for others
ENH: minor update for Enum methods and iterator
- add warnOnly (failsafe) option for readEntry and getOrDefault
- add good() method to Enum iterator (simliar to HashTable)
- replace unused/fragile Enum find() methods with iterator return
that can be used more generally
- explicit use of UPstream::worldComm in globalIndex methods
for more clarity
- adjust method declaration ordering:
de-emphasize the processor-local convenience methods
- consistent use of leading tag dispatch,
remove unused enum-based dispatch tag
- add begin()/cbegin() with offset (as per List containers)
BUG: missing use of communicator in globalIndex gatherNonLocal
- does not affect any existing code (which all use worldComm anyhow)
- support std::string_view (c++17) or span view (older c++) of stream
buffer contents. This simplifies formatting + reparsing.
Example,
OCharStream os;
os << ...;
ISpanStream is(os.view());
is >> ...;
- additional release() method for ICharStream, OCharStream
that returns the contents as a DynamicList<char> and resets the stream.
- provide a str() method for API compatibility with older
std::ostringstream etc.
- change write(const string&) to write(const std::string&).
This allows output of std::string without an intermediate copy.
- additional writeQuoted method to handle range of char data:
writeQuoted(const char* str, std::streamsize len, bool)
This helps with supporting string_view and span<char>
- add operator<< for stdFoam::span<char> and std::string_view (c++17)
- avoid duplicate code in OBJstream
STYLE: add override keyword for IO stream methods
- changes the addressed list size without affecting list allocation.
Can be useful for the following type of coding pattern:
- pre-allocate a List with some max content length
- populate with some content (likely not the entire pre-allocated size)
- truncate the list to the length of valid content
- process the List
- discard the List
Since the List is being discarded, using resize_unsafe() instead of
resize() avoids an additional allocation with the new size and
copying/moving of the elements.
This programming pattern can also be used when the List is being
returned from a subroutine, and carrying about a bit of unused memory
is less important than avoiding reallocation + copy/move.
If used improperly, it can obviously result in addressing into
unmanaged memory regions (ie, 'unsafe').
- shrink_to_fit()
corresponds to std::vector naming.
For DynamicList it is a *binding* request.
- shrink_unsafe()
simply adjusts the capacity() to match the
current size() without forcing a re-allocation.
Useful when collapsing to a non-dynamic list to avoid reallocation
and copying contents. The memory cleanup will still occur properly
at a later stage.
- DynamicList::swap(List&)
simple recovery of content into a non-dynamic List that also
ensures that the capacity is correctly updated.
STYLE: promote List::capacity() to public visibility (like std::vector)
STYLE: remove unused expandStorage() method
- simply a wrapper for resize(capacity())
