Back to Input Deck Cards

DATASET

Specifies a dataset to be associated with parameters sets in the model.

Required Cards:

DATASET <optional string>

Opens the DATASET block with the name of the dataset in the string. If the name is not provided, the NAME entry below must be included.

FILENAME <string>

Name of file containing data.

HDF5_DATASET_NAME <string>

Name of the group within an HDF5 file where the data resides.

NAME <string>

Name of the dataset if not included with DATASET card. Note: this string overwrites the optional string specified after the DATASET card.

REALIZATION_DEPENDENT

A toggle card that will load the dataset based on the realization ID. For instance, if a dataset named “perm” is tied to PERMEABILITY within a MATERIAL_PROPERTY and the realization ID is 99, PFLOTRAN searches for an HDF5 dataset labeled “perm99”.

Cell-Indexed Datasets

Cell indexed datasets specify a value for each grid cell in the domain. These datasets may only be used for initial conditions and material properties. Within the HDF5 file, the dataset takes the following form:

  1. A top-level HDF5 dataset named Cell Ids lists the integer IDs of all cells as aligned with the dataset values, typically numbered 1-N, but theoretically, the user can list the IDs randomly and the data will end up in the correct location.

  2. A top level HDF5 dataset named after the dataset in the PFLOTRAN input file stores the data assigned to the cells. The name in the PFLOTRAN input file must match the dataset name in the HDF5 file. When realization-dependent, the realization id will be appended automatically in PFLOTRAN to match the name in the HDF5 file.

The attached cell_indexed_dataset.py generates a cell-indexed poros99 dataset.

Gridded Datasets

For most any location in an input file where the FILE or LIST keyword could be applied, the user may use the keyword DATASET followed by the name of the dataset entered under a DATASET block elsewhere in the input file. However, the user must exercise vigilance to ensure that the dataset is properly organized in the HDF5 file and is aligned spatially with the domain. Gridded Datasets are distributed on a uniform Cartesian grid in 1D, 2D or 3D from which PFLOTRAN may interpolate values. Within the HDF5 file, the dataset takes the following form (names used in these steps refer to the examples below):

  1. At the top of the HDF5 file (i.e. outside of any lower level groups), the user creates an HDF5 Group, in this case named river_head.

  2. Within the Group, two separate HDF5 Datasets are created: one named Data and the other Time, where Time is optional.

  1. The ‘’Data’’ Dataset is N dimensional array corresponding to the rank of the data plus a time dimension, if transient. The time dimension is indexed farthest to the right (dim1,dim2,…,t).

  2. The ‘’Time’’ Dataset is one dimensional and holds the times associated with the data in the Data dataset, if transient. It sized equal to the number of times in the Data dataset. See Time Units below.

  1. Add the following HDF5 Attributes to the HDF5 Group

  1. Dimension <string>: where options are X, Y, Z, XY, XZ, YZ, XYZ

  2. Discretization <double array>: the grid spacing for the dimensions in a

  3. Origin <double array>: the origin of the dimensions in a

  4. Max Buffer Size <int>: size of internal buffer storing (time) slices of a transient dataset when the entire dataset cannot be held in memory. Must be greater than 1 for non-STEP interpolation.

  5. Interpolation Method <string>: string = ‘STEP’ or ‘LINEAR’

  6. Cell Centered <bool>: the dataset is cell centered. Otherwise, it is node centered and you need an additional entry for each dimension (e.g. nx+1 values for X).

  7. Time Units <string>: time units for ‘’Time’’ Dataset. Required only only if time units are not seconds (s). Options include second, minute, hour, day, week, month, year. You can also use abbreviations: s,min,h,d,w,mo,y.

The attached gridded_dataset.h5 illustrates the usage.

Examples

Dataset use in FLOW_CONDITION

DATASET y_river_boundary_head
  FILENAME data.h5
  HDF5_DATASET_NAME river_head
END

FLOW_CONDITION river
  TYPE
    LIQUID_PRESSURE HYDROSTATIC
  /
  DATUM DATASET y_river_boundary_head
  LIQUID_PRESSURE 101325.d0
END

Porosity dataset used in MATERIAL_PROPERTY that is consistent with cell_indexed_dataset.py

DATASET por
  HDF5_DATASET_NAME poros99
  FILENAME cell_index_dataset.h5
END

MATERIAL_PROPERTY soil1
  ID 1
  POROSITY DATASET por
  TORTUOSITY 1.d0
END

Realization-dependent dataset use in MATERIAL_PROPERTY

DATASET perm
  FILENAME hanford_unit.h5
  REALIZATION_DEPENDENT
END

DATASET poros
  FILENAME hanford_unit.h5
  REALIZATION_DEPENDENT
END

MATERIAL_PROPERTY hanford_unit
  ...
  POROSITY DATASET poros
  PERMEABILITY
    ...
    DATASET perm
    ...
  /
  ...
END

Dataset use in a transport CONSTRAINT

DATASET initial_pH
  HDF5_DATASET_NAME pH
  FILENAME parameters-543.h5
END

DATASET initial_Calcite_vol_frac
  HDF5_DATASET_NAME Calcite_vol_frac
  FILENAME parameters-543.h5
END

CONSTRAINT initial
  CONCENTRATIONS
    H+     1.d-8      P  DATASET initial_pH
    HCO3-  1.d-3      G  CO2(g)
    Ca++   5.d-4      M  Calcite
  /
  MINERALS
    Calcite DATASET initial_Calcite_vol_frac 1.d0
  /
END