Preliminary layout for OpenFOAM data within ADIOS

• This is a work-in-progress (proof-of-concept) for reading/writing OpenFOAM data with ADIOS.
• For development purposes, a function object is used for the implementation framework.
• Restart is with a 'fast-forward' principle: OpenFOAM is used for the Time=0 construction of meshes and fields, fields are overwritten with their values read from the adios file.
• Supports multiple regions, multiple clouds per region.
• Restarting with mesh changing is not yet fully implemented.

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2019-12-20

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• Storage directory: "adiosData/"

• Each "bp" (OpenFOAM binary packed) adios file is restricted to a single time-step/iteration. This makes for simple and efficient handling.

• In rare cases are values stored in global arrays with offsets.

  • Single values per-processor (eg, time index).
  • Cloud parcel data (currently).

  In all other cases, data are stored with their local dimensions only.

• Data stored as "unsigned byte" generally represent binary content that has been serialized via the OpenFOAM Ostream and are targeted for use by an Istream when reading. This binary content should be largely identical to a normal OpenFOAM field-file, but without the file-header.

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General Attributes

These attributes provide assistance when reading the data files. All entries are considered mandatory.

type	name	example
any	/constant/...	reserved
any	/system/...	reserved
int	/openfoam/api	1906
string	/openfoam/patch	"190401"
string	/openfoam/endian	"LSB"
int	/openfoam/label	32
int	/openfoam/scalar	64
int	/openfoam/nProcs	4
int	/openfoam/nRegions	2
string[]	/openfoam/regions	{"region0", "solid"}

The number of regions can either be obtained directly from the /openfoam/nRegions attribute, or aternatively from the list length of the /openfoam/regions attribute. No particular sort order is specified for the region names.

General Variables

Coordinated data for all mesh, fields and cloud information.

type	name	comment
any	/constant/...	reserved
any	/system/...	reserved

Time Attributes

Since each file is restricted to a single time-step/iteration, which inherently identical across all processes, the time management values are tracked as attributes rather than as variables. This additionally simplifies later post-processing, since the attribute values are available directly from the meta-data.

type	name	comment
int	/time/index	iteration value
double	/time/value	time-value
double	/time/deltaT	current time-step value
double	/time/deltaT0	previous time-step value
double	/time/faces	time-value of mesh topology (per region)
double	/time/points	time-value of mesh points (per region)

The order of the /time/faces and /time/points attributes must correspond exactly to the ordering used by the /openfoam/regions attribute.

The attribute /time/value can be considered to be a global time value for all fields and clouds contained within the file. When the /time/faces value for a particular region matches that of /time/value, the file will also contain a mesh description for that region. If only the /time/points value for a particular region matches, this indicates mesh motion (but with the same topology) and the file will correspondingly contain the updated points for that region.

This mechanism can be used to locate an appropriate mesh description from previously saved files. The following pseudocode illustrates part of the logic:

if /time/value == /time/faces/REGION
    # current file contains updated topology (points, faces, etc)
    REGION/polyMesh/points
    REGION/polyMesh/faces/...
    ...

elif /time/value == /time/points/REGION
    # current file contains updated mesh points
    REGION/polyMesh/points

else
    # mesh points, faces in an older file
    # - compare to currently loaded meshes to see if update is needed

Since the adios files are generally saved with names corresponding to their time state, it is possible to identify the file containing a particular mesh/time-state without searching the file contents.

Region Attributes

Basic information that applies to mesh and field information.

type	name	comment
int	<regionName>/nPatches	number of patches
string[]	<regionName>/patch-names	patch names
string[]	<regionName>/patch-types	patch types

The number of patches used in the mesh may be larger than the number of patch names and types attributes since these attributes do not include any processor patches.

Example

type	name	example
int	region0/nPatches	3
string[]	region0/patch-names	{"movingWall", "fixedWalls", "frontAndBack"}
string[]	region0/patch-types	{"wall", "wall", "empty" }
	solid/...

Meshes

These variables are only available when the updateMesh attribute is also true.

Global Array Variables

type	name	comment
int	<regionName>/polyMesh/nPoints	per processor
int	<regionName>/polyMesh/nCells	per processor
int	<regionName>/polyMesh/nFaces	per processor
int	<regionName>/polyMesh/nInternalFaces	per processor

Local Variables

type	name	comment
double	<regionName>/polyMesh/points	{nPoints x 3}
int	<regionName>/polyMesh/faces/indices	indices for compact faceList
int	<regionName>/polyMesh/faces/content	content for compact faceList
int	<regionName>/polyMesh/owner	face owners
int	<regionName>/polyMesh/neighbour	face neighbours
byte	<regionName>/polyMesh/boundary	boundary mesh information

Fields

Local Variables

type	name	comment
double	<regionName>/field/U	primitive field content
byte	<regionName>/field/U/boundaryField	internalField - primitive field content
double	<regionName>/field/p	internalField - primitive field content
byte	<regionName>/field/p/boundaryField	as per OPENFOAM binary file content
	...

Attributes

type	name	example
string	<regionName>/field/U/class	"volVectorField"
string[]	<regionName>/field/U/patch-types	{"fixedValue", "fixedValue", "empty"}
string	<regionName>/field/p/class	"volScalarField"
string[]	<regionName>/field/p/patch-types	{ "zeroGradient", "zeroGradient", "empty" }
	...

Clouds

These entries are only available when the region also has any active cloud information. A missing value of nClouds is equivalent to nClouds=0.

The cloud contents are written as their IOFields.

Region Cloud Attributes

type	name	comment
int	<regionName>/nClouds	number of associated clouds in region
string[]	<regionName>/clouds	{"name0", "name1", ...}

Cloud Variables (Globally-addressable)

type	name	comment
double	<regionName>/cloud/<cloudName>/position	cloud x,y,z positions

Cloud Attributes

type	name	example
string	<regionName>/cloud/<cloudName>/class	"Cloud<basicKinematicCollidingParcel>"
int	<regionName>/cloud/<cloudName>/nParcels	total count (sum of corresponding variable)

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