- local data to be written is now transferable into the
OFstreamCollator. This avoids making a full copy when threading is
active.
- use plain lists for managing proc data
* storage: List<List<char>> instead of PtrList<List<char>>
* views: List<stdFoam::span<char>> instead of PtrList<SubList<char>>
- use gather/write (unthreaded) as backstop if the output is too big
to fit in the buffer size. Emit warning instead of FatalError
- OCharStream for serializing
- skip intermediate blocks without reading
- support character spans
- read and distribute with direct non-blocking send/recv
instead of PstreamBuffers or with IPstream/OPstream streaming
operators.
- non-blocking gather/write when using intermediate buffer space
- use OCharStream instead of OStringStream to avoid copying char data.
- direct non-blocking send/recv with probing instead of PstreamBuffers
to avoid serialization/de-serialization of char data and reduce the
memory footprint somewhat.
- polling dispatch to write file content as it becomes available,
which should improve communication and IO overlap
- range(proci) instead of localStart(proci), localSize(proci) combination.
* does the same thing, can be used directly with various other
routines for slicing etc.
Eg,
Foam::identity(globalNumbering.range(myProci))
- globalIndex::calcOffset() instead of constructing a globalIndex and
taking the localStart(). Avoids intermediate resizing and storing of
an offsets table (which is then discarded) as well as the subsequent
lookup into that table
- creates an IOobject at the current time instance (timeName) with
NO_READ/NO_WRITE/NO_REGISTER characteristics.
This generalises and replaces the Cloud fieldIOobject() to simplify
some common use.
// Shorter version (new):
volScalarField fld
(
mesh.newIOobject(name),
...
);
// Longer version:
volScalarField fld
(
IOobject
(
name,
mesh.time().timeName(),
mesh,
IOobject::NO_READ,
IOobject::NO_WRITE
IOobject::NO_REGISTER
),
...
);
- can be useful when using memory-based streams for buffering,
in which case the name() can be used to specify the filesystem
location instead of the default stream names ("input", "output").
- shape optimisation: SQP failed due to wrong divScheme for the adjoint
equations
- shape optimisation: tutorials designed to show the impact of different flow
conditions were actually using the same U
- topology optimisation: tutorials designed to show the impact of the
flow rate distribution were actually using the same target
fractions
- topology optimisation: updated old fvSolution syntax
- had max(std::streamsize, label) but this does not resolve properly
on OSX, so write out in long form instead.
The similar logic in DynamicList is okay since there it compares
max(label, label) instead
In steadyOptimisation mode, each time-step corresponds to an
optimisation cycle and is sub-cycled, to allow for iterating the flow
and adjoint equations. This sub-cycling does not allow the execution of
function objects. This was circumvented in 8947735b1d, by explicitly
calling the execution of the function objects in the simple solver
of adjointOptimisationFoam.
However, each sub-cycled iteration is a writeTime, if the current
optimisation cycle corresponds to a writeTime. This means that function
objects with a
writeControl write;
will be executed in each iteration of the flow equations, within this
specific optimisation cycle, leading to a lot of disc space and file
clutter, if the function object outputs fields (e.g. yPlus).
8947735b1d is partially rolled back, by protecting the call to the
execution of the function objects with a bool that defaults to false.
- 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
The solution of the QP subproblem can become quite expensive, especially
for cases with many design variables (e.g. topology optimisation).
A (potentially dense) matrix with the size of the design variables is
solved using a matrix-free CG solver. The convergence speed greatly
depends on the used preconditioner. This commit adds
preconditioner-vector products based on the L-BFGS inverse Hessian and,
more importantly, a preconditioner computed using the Sherman-Morrison
formula. The latter is applicable here since the LHS of the QP problem
is computed as the sum of rank-2 L-BFGS updates, a sum of rank-1 updates
(as many as the flow-related constraints) and a diagonal matrix
depending on the bound constraints.
Additionally, the QP subproblem could have no feasible points. To relax
this, constraints can be applied gradually through the
targetConstraintReduction enty (typical value of 0.1 for topology
optimisation).
Most cases now rely on the nullSpace update method, instead of MMA,
since it has proven more reliable.
Also, added some constrained optimisation cases, including constraints
on the flow rate partition and total pressure losses as well as cases
targeting uniformity as the objective function.
Added a 3D topology optimisation case which also includes constraints.
of the STL written by topology optimisation.
BUG: when determining which mesh faces are cut by iso-surface faces,
only append the latter if it contains more than two points
by a small amount, if all of them lay on the lower or upper bounds at
the beginning of the optimisation, to avoid singular matrices when
computing the update of the design variables.
and the Jacobian of the objective function wrt the turbulence variables
is called (rare/unorthodox case).
Additionally, objectivePowerDissipation dissipation can now be used in
topology optimisation, adding the necessary blockage dependency to it.
- Building the iso-surface spliting fluid and solid parts in topology
optimisation has been re-worked to obtain an iso-surface with unique
point numbering
- The mechanism behind marchingCells for dynamicTopODesignVariables has
been slightly reworked
The derivatives of the objective and constraint functions can optionally
be normalised in each optimisation cycle, so that MMA does not put an
excesive stress on the constraints, which can negatively affect the
course of the optimisation
A 1-Inlet-2-Outlet geometry is showcased for laminar and turbulent
flows, set-up with different variants of porosity-based and
level-set-based topology optimisation
Both porosity-based and level-set-based topO frameworks are included
through the topO and levelSet designVariables, respectively.
Both frameworks work by manipulating an underlying field of design
variables, defined in all cells of the computational domain. That field
is then regularised through a Helmholtz-like filter, before being
processed in a different way from the two topO frameworks (the
porosity-based topO sharpens/projects it while the level-set-based topO
computes signed distances around its zero iso-surface). The result of
this processing is then fed into functions that define source terms to
be added to the mean flow and turbulence model equations, to block
off/solidify parts of the mesh that are counterproductive with respect
to the objective function. These source terms are added through
fvOptions.
Since the designed walls are only simulated through source terms, the
outcome of topO should be re-analyzed on a body-fitted grid, to quantify
the actual gain in the objective function. Both topO frameworks output
the designed wall in STL format which can be used, for instance with
snappyHexMesh, to construct such a body fitted grid.
This provides a list of faces (can be internal ones) to act as
additional seeds for the wave algorithm. The default argument provides
an empty list, so the behaviour of patchWave should not change.
Useful in topology optimisation, for propagating the active design
variables from the seed faces to the interior, with a given number of
cells at a time.
- advectionDiffusion is frequently used within optimisation loops since
it is differentiable. In shape optimisation, the re-computation of
mesh distances is performed at the very beginning of a new
optimisation cycle, due to inheriting from MeshObject. If the mesh
quality is poor enough, the advectionDiffusion PDE might diverge and
crash the run, before the problematic mesh is written to files for
inspection. The default behaviour now is to check the mesh before
solving the advectionDiffusion PDE and write the mesh points if some
mesh check fails.
- fvOptions can now be included in advectionDiffusion (necessary for
topology optimisation of turbulent flows for models that include the
distance field)
- Minor changes in the numerical treatment of the diffusion term, to
enhance stability
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
- for clang-based compilers the default linker may be lld or simply ld.
Support '+link-ld' to explicitly select use of the ld linker.
- consolidate linker rules into single files
STYLE: adjust SPDX Identifier
redistributePar -decompose switches communicator when
reading on master. However other processors still get
constructed with the worldComm. >v2306 AMI stores the communicator
from construction time there was a mismatch
- regression introduced by commit 0ff86ee2
(only affects recent develop).
- now split off first/final iterations into a separate
"controls" dictionary (instead of lumping them into "solver") to
make them persistent between iterations.
- updating the header information (by copying) was closing the stream,
removing all watches and doing a checkOut/checkIn, which could lead to
dangling references.
Now just close the stream and simply copy the IOobject header
information directly.
STYLE: mark regIOobject assignment operator as possibly deprecated
- will revisit to revise or remove in the future
- the faMesh/fvMesh copy constructors were using the readOption from
the base-mesh schemes/solution instead of copying their contents.
This would not really affect fvMesh (since it has its own IOobject
for the constructor), but did affect faMesh. However, the problem
only shows up with collated + redistribute, since that is where
the ranks can be doing uncoordinated IO.
Only consider as a bug for recent develop since previous versions
had other problems with collated+redistribute with finite-area
anyhow.
- 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.
- give precedence to ~openmp (-no-openmp) over +openmp (-openmp)
in the general rules and in the Makefile. This makes it robuster
when specifying +openmp in general, but ~openmp for specific build
components.
- disable openmp for OSspecific and Pstream components.
Neither should contain any openmp code anyhow.
Additionally, since OSspecific is generally built as a static
object, it can become problematic (eg, with AMD ROCm) if the
compiler generates information that openmp is required but then uses
static linkage.
- the fields for finite-area are currently stored directly on the
polyMesh registry, but for future relocation to a sub-registry
provide a uniform accessor.
ENH: use thisDb() for faMatrix access and extrapolatedCalculated
- 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)
Generates sample positions from points specified in a file as Abaqus mesh
points.
Example usage:
sets
{
cone25 // user-specified set name
{
type abaqusMesh;
file "abaqusMesh.inp";
// Optional entries
// Scale, e.g. mm to m
scale 0.001;
// Search distance when the sample point is not located in a cell
maxDist 0.25;
...
}
}
Write coordSet(s) as Abaqus point fields
Example usage
T
{
type sets;
setFormat abaqus;
fields (T);
sets
{
...
}
}
\endverbatim
Optional format options
\verbatim
formatOptions
{
abaqus
{
format ascii;
// Optional entries
// Custom header: $ entries are substituions
header
(
"** OpenFOAM abaqus output"
"** Project $FOAM_CASE"
"** File $FILE_NAME"
"** $FIELD_NAME Time t=$TIME"
);
// Write geometry in addition to field data
writeGeometry yes;
// Null value when sample value is not found
// Default is scalar::min
nullValue 0;
// Insert additional time sub-directory in the output path
// - yes : postProcessing/<fo-name>/<time>/<file>
// - no : postProcessing/<fo-name>/<file>
useTimeDir no;
// Available when 'useTimeDir' is 'no' to disambiguate file names
// Time base for output file names:
// - 'time' : <base>.inp_<field>.<time>
// - 'iteration' : <base>.inp_<field>.<iteration>
timeBase iteration;
// Optional start counters when using timeBase iteration
writeIndex
(
T 1
);
...
}
}
Example:
formatOptions
{
<writer>
{
// Apply offsets to field values
fieldLevel
{
T 273.15; // Convert from K to C by subtracting 273.15
}
// Note: scale applied after application of field level
fieldScale
{
p 0.001; // Convert pressure from Pa to kPa by scaling by 0.001
}
}
}
Added -writeChecks <format> option
- writes computed mesh metrics to file in using <format>
- currently supported formats are OpenFOAM dictionary and JSON
Collects and writes case information to file in OpenFOAM dictionary or JSON
format. Data includes:
- meta: case name, path, regions, parallel etc.
- dictionaries: entries retrieved from dictionaries - registered or from file
- per region: mesh metrics, boundary and boundary field types
- function object results
Example of function object specification:
caseInfo
{
type caseInfo;
libs (utilityFunctionObjects);
// Warn when entries are not found
lookupMode warn; // none | warn | error;
// Write format
writeFormat json; // dictionary | json;
dictionaries
{
USolver // User-specified names
{
// Look up using registered name
name "fvSolution";
// Optionally limit to specific entries
include
(
"solvers/U/solver"
);
}
fvSchemes
{
name "fvSchemes";
// include all entries by default
}
timeScheme
{
name "fvSchemes";
include
(
"/ddtSchemes/default"
);
}
turbulence
{
name "turbulenceProperties";
// include all entries by default
}
controlDict
{
// Look up using file path
path "<case>/system/controlDict";
include
(
"application"
"deltaT"
"startTime"
"endTime"
);
}
}
functionObjects (minMax1);
}
Quality metrics, e.g. non-orthogonality, skewness etc are calculated/reported
in polyMeshCheck functions. These results are now added to the meshState/mesh
dictionary to enable external access.
ENH: added 'mesh' dictionary to meshState to hold mesh properties
- solver information now stored in a 'solver' dictionary (was solverPerformance)
- {first|final}Iteration entry now stored in solver dict instead of top level
- mesh data (new) stored in 'mesh' dictionary
- code is compiled dynamically on the master node.
In the normal (non-distributed) case, simply poll the NFS
to see when it appears on the sub-procs.
For a case with distributed roots, first broadcast it (via MPI)
to the IO master nodes and then poll afterwards.
- on startup, detect and create missing processorXXX/ subdirectories
on distributed filesystems
- 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 <>
- was previously limited to 'char' whereas gatherv/scatterv
already supported various integer and float types
STYLE: rebundle allToAll declarations with macros
ENH: provide a version of allToAllConsensus returning the Map
- simplifies use and avoids ambiguities in the send/recv parameters
- the Map version will now also transmit zero value data if they exist
in the Map. Unlike the List version, zero values are not necessary to
signal connectivity with a Map.
COMP: forwarding template parameters for NBX routines
ENH: consolidate PstreamBuffers size exchange options
- had a variety of nearly identical backends for all-to-all,
gather/scatter. Now combined internally with a dispatch enumeration
which provides better control over which size exchange algorithm
is used.
DEFEATURE: remove experimental full-NBX PstreamBuffers variant
- no advantages seen compared to the hybrid NBX/PEX approach.
Removal reduces some code cruft.
DEFEATURE: remove experimental "double non-blocking" NBX version
- the idea was to avoid blocking receives for very large data transfers,
but that is usually better accomplished with a hybrid NBX/PEX approach
like PstreamBuffers allows
- 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.
- report location with previous good offset and the new count that
would cause overflow. Simpler to report and the (very long) list
of input sizes is not particularly useful for diagnostics either.
ENH: add globalIndex comparison operators
- for outputting lists of globalIndex
- 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.
- the default returns -1 (ie, not found/available). This is overridden
by processorCyclicPolyPatch to actually perform a search
COMP: explicitly define polyMesh::writeObject in the header
- currently no special treatment, but allows future adjustments
without affecting the header.
- extends the enumeration (NO_REGISTER, REGISTER, LEGACY_REGISTER).
Can be used to tweak registration preference where required and
potentially (TDB) to define a different default value in the future
- 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.
- 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
- remnant was left in the NBX implementation for Map<Type>.
Still not entirely certain which vendors/versions handle message
probe/recv properly, but using the "regular" probe and recv is OK
since everything is without threaded race conditions.
STYLE: adjust file extension of UPstreamWrapping templates
- avoids it being exposed via lnInclude
- 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
- 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.
- it seems that both sides of the ternary are evaluated despite
the divide-by-zero protection. Use volatile to force the compiler
to use in-order evaluation.
- attempt to minimize rounding in the cached time values
since these are also used to re-populate the case files
STYLE: remove ancient handling of "meshes" entry
- was superseded by "geometry" entry in OpenFOAM-1912 and later.
Now remove the transitional shim, which was in place for
restart migration from 1906.
CONFIG: downgrade non-uniform time from error to warning
- can be a spurious error when the deltaT is very small
CONFIG: support keywords 'minFreq', 'maxFreq'
- these are the updated naming for 'fl' and 'fu' (still supported)
- new format option keywords: timeFormat, timePrecision
CONFIG: default ensight output is now consistently BINARY
- this removes some uncertainty with the ensightWrite functionObject
which was previously dependent on the simulation writeFormat
and makes its behaviour consistent with foamToEnsight
Note: binary Ensight output is consistent with the
defaults for VTP output (inline binary)
ENH: minor adjustment of ensight writing methods
- retain group information when copying zones
- support construct empty (add details later)
- improve consistency for zone and boundaryMesh construction
- support front/back/both selection for faceZoneToCell
STYLE: prefer faceZone patch() method instead of operator()
STYLE: use std::unique_ptr instead of manual pointer management
- for zones and core patch types.
Easier data management, allows default destructors (for example)
- use add_tokens() instead of the old multi-parameter
append(.., bool) method which was misleading since it added tokens
at the current tokenIndex, not at the end.
- stringify ITstream contents with CharStream instead of StringStream.
Allows string_view for copying out the content.
ENH: set namedDictionary dictionary name from Istream
- provides context for error messages etc (#2990)
- 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
- default construct is now identical to HashTable(Foam::zero).
It performs no allocation and is also noexcept.
The previously used default capacity (128) was a holdover from
much older versions where set/insert did not properly handle
insertion into a table with zero capacity (number of buckets).
- earlier deletion of unpopulated HashTable on resizing:
If the table is already clear (ie, has no entries),
can immediately remove the old internal table before reallocating
the newly sized table, which may avoid a needless memory spike.
- reserve() method:
Naming and general behaviour as per std::unordered_map.
It behaves similarly to the resize() method but is supplied the
number of elements instead of the capacity, which can be a more
natural way of specifying the storage requirements.
Additionally, reserve() will only increase the table capacity for
behaviour similar to DynamicList and std::vector, std::string etc.
Old:
labelHashSet set;
set.resize(2*nElems);
Now:
labelHashSet set;
set.reserve(nElems);
- remove unused HashTable(Istream&, label) constructor
STYLE: static_cast of (nullptr) and std::fill_n for filling table
- 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())
- when running with "errors warn;" it will reset the warnings counter
(if any) when it returns to a good state.
This re-enables un-suppressed warnings for the next cycle.
Also reset the warnings counter on end().
ENH: add short-circuit in HashTable::erase(key)
- skip and return false if the table is empty or the key is not found.
This makes for faster no-op behaviour.
- for workflows with appearing/disappearing patches (for example)
can specify that empty surfaces should be ignored or warned about
instead of raising a FatalError.
Note that this handling is additional to the regular top-level
"errors" specification. So specifying 'strict' will only actually
result in a FatalError if the "errors" does not trap errors.
- "ignore" : any empty surfaces are simply ignored and no
file output (besides the header).
- "warn" : empty surfaces are warned about a few times (10)
and the file output contains a NaN entry
- "strict" : corresponds to the default behaviour.
Throws a FatalError if the surface is empty.
This error may still be caught by the top-level "errors" handling.
- support UList shallowCopy with pointer/size
(eg, for slicing into or from span)
ENH: add SubList::reset() functionality
- allows modification of a SubList after construction.
Previously a SubList had an immutable location after construction
and there was no way to shift or change its location.
BUG: missed special handling for DynamicList<char>::readList (fixes#2974)
- equivalent to List<char>::readList, in which the stream is
temporarily toggled from ASCII to BINARY when reading in a List of
char data.
This specialization was missed when DynamicList<T>::readList() was
fully implemented.
- defines values for EMPTY, UNIFORM, NONUNIFORM and MIXED
that allow bitwise OR reduction and provide an algorithm
for calculating uniformity
ENH: consolidate more efficient uniformity checks in PackedList
ENH: improve linebreak handling when outputting small matrices
- use ignore instead of seekg/tellg to swallow input (robuster)
- check for bad gcount() values
- wrap Foam::fileSize() compressed/uncompressed handling into IFstream.
- improve handling of compressed files in masterUncollatedFileOperation.
Previously read into a string via stream iterators.
Now read chunk-wise into a List of char for fewer reallocations.
- soft renames (ie, old names still available via typedefs) for more
reasonable names and more coverage with std stream variants.
The old names could be a bit cryptic.
For example, uiliststream (== an unallocated/external list storage),
which is written as std::ispanstream for C++23.
Could similarly argue that IListStream is better named as
ICharStream, since it is an input stream of characters and the
internal storage mechanism (List or something else) is mostly
irrelevant.
Extending the coverage to include all std stream variants, and
simply rewrap them for OpenFOAM IOstream types. This simplifies the
inheritance patterns and allows reuse of icharstream/ocharstream as
a drop-in replace for istringstream/ostringstream in other wrappers.
Classes:
* icharstream / ICharStream [old: none / IListStream]
* ocharstream / OCharStream [old: none / OListStream]
* ispanstream / ISpanStream [old: uiliststream / UIListStream]
* ospanstream / OSpanStream [old: none / UOListStream]
Possible new uses : read file contents into a buffer, broadcast
buffer contents to other ranks and then transfer into an icharstream
to be read from. This avoid the multiple intermediate copies that
would be associated when using an istringstream.
- Use size doubling instead of block-wise incremental for ocharstream
(OCharStream). This corresponds to the sizing behaviour as per
std::stringstream (according to gcc-11 includes)
STYLE: drop Foam_IOstream_extras constructors for memory streams
- transitional/legacy constructors but not used in any code
- nonBlocking: receive before send
- nonBlocking: wait for receive requests, process and then wait for
other requests. Can be extended to use polling...
- the 'fake' send (to self) now send copies into recv buffers instead
of send buffers.
This provides a clear separation of send and receive fields
- avoid unnecessary reallocations with PtrList of send/recv buffers
- remove outer looping for accessAndFlip and pass target field
as parameter for inner looping instead
ENH: refine mapDistribute send/recv requests handling
- separate send/recv requests for finer control
- receive does not need access to PtrList of sendBuffers, since the
send-to-self now uses the recvBuffers
- totalSize() returns retrieve the linear (total) size
(naming as per globalIndex)
- operator[] retrieves the referenced value (linear indexing)
- labels() returns a flattened labelList (as per labelRange itself)
- broadcasts list contiguous content as a two-step process:
1. broadcast the size, and resize for receiver list
2. broadcast contiguous contents (if non-empty)
This avoids serialization/de-serialization memory overhead but at
the expense of an additional broadcast call.
The trade-off of the extra broadcast of the size will be less
important than avoiding a memory peak for large contiguous mesh data.
REVERT: unstable MPI_Mprobe/MPI_Mrecv on intelmpi + PMI-2 (#2796)
- partial revert of commit c6f528588b, for NBX implementation.
Not yet flagged as causing errors here, but eliminated for
consistency.
- simplifies use with other allocators (eg, memory pools).
Can also be used with other containers.
vectorField fld = ...;
sigFpe::fillNan(fld.data_bytes(), fld.size_bytes());
COMP: inline sigFpe::ignore helper class
- now unused (may be removed in the future), but can avoid compiling
code for it
COMP: missing sigStopAtWriteNow() definition for MSwindows
- simplifies internal handling (like a fileName) and allows the
dictionary name to be used with unambiguous addressing.
The previous dot (.) separator is ambiguous (ie, as dictionary
separator or as part of a keyword).
ENH: foamDictionary report -add/-set to stderr
- selected with '+strict' in WM_COMPILE_CONTROL or 'wmake -strict', it
enables the FOAM_DEPRECATED_STRICT() macro, which can be used to
mark methods that are implicitly deprecated, but are not yet marked
as full deprecated (eg, API modification is too recent, generates
too many warnings). Can be considered a developer option.
- since the Apple SIP (System Integrity Protection) clears environment
variables such as DYLD_LIBRARY_PATH, a number of workarounds have
been used to provide shadow values. However, for a more robust
installation using -rpath at compilation time appears to be the
better solution.
In addition to the usual -rpath specification with absolute file
paths, MacOS supports (@loader_path, @executable_path) as well.
Now default to link with rpath information for MacOS, which can be
disabled by adding `~rpath` in WM_COMPILE_CONTROL
Explicit library paths handled:
- FOAM_FOAM_EXT_LIBBIN, FOAM_EXT_LIBBIN/FOAM_MPI
The executable rpaths are handled assuming a structure of
install-path/bin
install-path/lib/$(FOAM_MPI)
install-path/lib
Absolute compile-time paths for FOAM_USER_LIBBIN, FOAM_SITE_LIBBIN
and FOAM_LIBBIN are not handled since these are either too fragile
(FOAM_USER_LIBBIN and FOAM_SITE_LIBBIN values) or covered via
@loader_path anyhow (FOAM_LIBBIN).
Since the value of FOAM_MPI is a compile-time value, this rpath
treatment makes the installation less suitable for runtime changes
to the MPI vendor/version.
Note: no rpath added for c-only compilations since there are
currently no c-only libraries or executables with dynamic loading
- eliminate ClassName in favour of simple debug
- include Apple-specific FPE handling after local definition
to allow for more redefinitions
COMP: remove stray <csignal> includes
- naming like std::map::try_emplace(), it behaves like emplace_set()
if there is no element at the given location otherwise a no-op
ENH: reuse existing HashPtrTable 'slot' when setting pointers
- avoids extra HashTable operations
- the construction of compound tokens is now split into two stages:
- default construct
- read contents
This permits a larger variety of handling.
- the new token::readCompoundToken(..) method allows for simpler
more failsafe invocations.
- forward resize(), read() methods for compound tokens to support
separate read and population.
Top-level refCompoundToken() method for modify access.
ENH: split off a private readCompoundToken() method within ISstream
- this allows overloading and alternative tokenisation handling for
derived classes
- simplifies iteration of ITstream using nRemainingTokens() and skip()
methods or directly as a list of tokens.
The currentToken() method returns const or non-const access to
the token at the current tokenIndex.
The peekToken(label) method provides failsafe read access to tokens
at given locations.
ENH: add primitiveEntry construct with moving a single token
Increase usage of std algoritms within the OpenFOAM List classes. Remove reliance on linked-list during reading
See merge request Development/openfoam!620
- drop unnecessary Foam::Swap specializations when MoveConstructible
and MoveAssignable already apply. The explicit redirect to swap
member functions was needed before proper move semantics where
added.
Removed specializations: autoPtr, refPtr, tmp, UList.
Retained specialization: DynamicList, FixedList.
Special handling for DynamicList is only to accommodate dissimilar
sizing template parameters (which probably doesn't occur in
practice).
Special handling for FixedList to apply element-wise swapping.
- use std::swap for primitives. No need to mask with Foam::Swap wrapper
- fully implement DynamicList::readList() instead of simply
redirecting to List::readList(). This also benefits DynamicField.
Leverage DynamicList reading to simplify and improve CircularBuffer
reading.
- bracket lists are now read chunk-wise instead of using a
singly-linked list. For integral and vector-space types
(eg, scalar, vector, etc) this avoids intermediate allocations
for each element.
ENH: add CircularBuffer emplace_front/emplace_back
STYLE: isolate to-be-deprecated construct/assign forms
- still have construct/assign FixedList from a C-array.
This is not really needed, can use std::initializer_list
- still have construct/assign List from SLList.
Prefer to avoid these in the future.
DEFEATURE: remove construct/assign FixedList from SLList
- never used
DEFEATURE: remove move construct/assign List from SLList
- now unused. Retain copy construct/assign from SLList for transition
purposes.
- test for existing globalData() or perhaps use DIY globalIndex instead
STYLE: check for non-ASCII instead of BINARY with compression
- allows for other non-ASCII formats
- is_vectorspace :
test existence and non-zero value of the Type 'rank' static variable
- pTraits_rank :
value of 'rank' static variable (if it exists), 0 otherwise
- pTraits_nComponents :
value of 'nComponents' static variable (if it exists), 1 otherwise
- pTraits_has_zero :
test for pTraits<T>::zero member, which probably means that it also
has one, min, max members as well
Note that these traits are usable with any classes. For example,
- is_vectorspace<std::string>::value ==> false
- pTraits_nComponents<std::string>::value ==> 1
- pTraits<std::string>::nComponents ==> fails to compile
Thus also allows testing pTraits_rank<...>::value with items
for which pTraits<...>::rank fails to compile.
Eg, cyclicAMIPolyPatch::interpolate called by FaceCellWave with a
wallPoint.
pTraits<wallPoint>::rank ==> fails to compile
is_vectorspace<wallPoint>::value ==> false
GIT: relocate ListLoopM.H to src/OpenFOAM/fields/Fields (future isolation)
- in most cases a parallel-consistent order is required.
Even when the order is not important, it will generally require
fewer allocations to create a UPtrList of entries instead of a
HashTable or even a wordList.
- prefer csorted() method for const access since it ensures that the
return values are also const pointers (for example) even if
the object itself can be accessed as a non-const.
- the csorted() method already existed for HashTable and
objectRegistry, but now added to IOobjectList for method name
consistency (even although the IOobjectList only has a const-access
version)
ENH: objectRegistry with templated strict lookup
- for lookupClass and csorted/sorted. Allows isType restriction as a
compile-time specification.
* resize_null() methods for PtrList variants
- for cases where an existing PtrList needs a specific size and
but not retain any existing entries.
Eg,
ptrs.resize_null(100);
vs. ptrs.free(); ptr.resize(100);
or ptr.resize(100); ptrs.free();
* remove stored pointer before emplacing PtrList elements
- may reduce memory peaks
* STYLE: static_cast of (nullptr) instead of reinterpret_cast of (0)
* COMP: implement emplace_set() for PtrDynList
- previously missing, which meant it would have leaked through to the
underlying PtrList definition
* emplace methods for autoPtr, refPtr, tmp
- applies reset() with forwarding arguments.
For example,
tmp<GeoField> tfld = ...;
later...
tfld.emplace(io, mesh);
vs.
tfld.reset(new GeoField(io, mesh));
or
tfld.reset(tmp<GeoField>::New(io, mesh));
The emplace() obviously has reduced typing, but also allows the
existing stored pointer to be deleted *before* creating its
replacement (reduces memory peaks).
- this simplifies polling receives and allows separation from
the sends
ENH: add UPstream::removeRequests(pos, len)
- cancel/free of outstanding requests and remove segment from the
internal list of outstanding requests
- removed gatherv control.
The globalIndex information is cached on the merged surface
and thus not triggered often.
- strip out debug mergeField method which was a precursor to
what is now within surfaceWriter itself.
- add 'merge' true/false handling to allow testing without
parallel merging (implies no writing)
- continue to support spherical by default (for compatibility)
but add the 'spherical' switch to disable that and use a cubic
distribution instead.
STYLE: reduce number of inline files
Co-authored-by: Mark Olesen <>
- can be used, for example, to track global states:
// Encode as 0:empty, 1:uniform, 2:nonuniform, 3:mixed
PackedList<2> uniformity(fields.size());
forAll(fields, i)
{
uniformity.set(i, fields[i].whichUniformity());
}
reduce
(
uniformity.data(),
uniformity.size_data(),
bitOrOp<unsigned>()
);
- can reduce communication by only sending non-zero data (especially
when using NBX for size exchanges), but proper synchronisation with
multiply-connected processor/processor patches (eg, processorCyclic)
may still require speculative sends.
Can now setup for PstreamBuffers 'registered' sends to avoid
ad hoc bookkeeping within the caller.
- simplifies code by avoiding code duplication:
* parLagrangianDistributor
* meshToMesh (processorLOD and AABBTree methods)
BUG: inconsistent mapping when using processorLOD boxes (fixes#2932)
- internally the processorLODs createMap() method used a 'localFirst'
layout whereas a 'linear' order is what is actually expected for the
meshToMesh mapping. This will cause of incorrect behaviour
if using processorLOD instead of AABBTree.
A dormant bug since processorLOD is not currently selectable.
- when constructing from a sendMap, can now also specify a linear
receive layout instead of a localFirst layout
This will make it easier to reduce some code (#2932)
- add missing interface for simple distribute of List/DynamicList
with a specified commsType. Was previously restricted to
defaultCommsType only.
ENH: mapDistribute distribute/reverseDistribute with specified commsType
STYLE: prefer UPstream vs Pstream within mapDistribute
- replaces previous (similar) union but leverages the type tag for
handling logic
STYLE: remove unneeded refCount from exprResult
COMP: operator!= as member operator (exprResultDelayed, exprResultStored)
- the operator!= as a free function failed to resolve after removing
the refCount inheritance
- primarily for handling expression results,
but can also be used as a universal value holder.
Has some characteristics suitable for type-less IO:
eg, is_integral(), nComponents()
ENH: add is_pointer() check for expression scanToken
- handle existence/non-existence of a FoamFile header automatically
- support an upper limit when getting the number of blocks and
use that for a hasBlock(...) method, which will stop reading sooner.
- Time is normally constructed with READ_MODIFIED for its controlDict
and objectRegistry, but for certain applications (eg, redistributePar)
it can be useful to construct without file monitoring and specifying
MUST_READ instead.
Example,
Info<< "Create time\n" << Foam::endl;
Time runTime
(
Time::controlDictName,
args,
false, // Disallow functionObjects
true, // Allow controlDict "libs"
IOobjectOption::MUST_READ // Instead of READ_MODIFIED
);
- update TimeState access methods
- use writeTime() instead of old method name outputTime()
- use deltaTValue() instead of deltaT().value()
to avoids pointless construct of intermediate
- no change in behaviour except to emit a warning when called with the
a non-reading readOption
STYLE: remove redundant size check
- size checking is already done by Field::assign() within the
DimensionedField::readField
2023-07-04 17:25:22 +02:00
12181 changed files with 156776 additions and 54498 deletions
Info<<"Total energy absorbed [W]: "<<totalQ<<endl;
if(mesh_.time().outputTime())
if(mesh_.time().writeTime())
{
reflectingCellsVol.write();
nHat.write();
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