Specification ↩ Back

Each task is defined in a single configuration file in the YAML format.

Options:

• modflow — the input is an S3D file – configure the modflow_options section
• msh — the input is an MSH file – configure the msh_options section

Example: source_type: modflow

This section applies only if source_type: msh. If source_type: modflow is used, this section is ignored.

Input file (Gmsh format, *.msh)

Example: source_file: ./inputs/stoneflow3d_v2.msh

Interpolation method for computing point values from mesh element values.

Options:

• constant — The value is taken
  • from the element in which the point lies.
• IDW_element_neighbors — The value is interpolated from
  • the element in which the point lies and from
  • its neighboring elements.
• IDW_element_neighbors_of_neighbors — The value is interpolated from
  • the element in which the point lies,
  • its neighbors, and
  • the neighbors of those neighbors.

The second and third options use the Inverse Distance Weighting (IDW) method.

Example: interpolation_method: IDW_element_neighbors

Number of elements included in interpolation (ignored if interpolation_method: constant)

A value of 1 is equivalent to setting interpolation_method: constant.

Example: IDW_maximum_included_elements: 40

Exponent value n for computing the weight W in the IDW interpolation method (ignored if interpolation_method: constant)

W_pe = 1/(D_peⁿ),

where D_pe is the distance between point p and the centroid of element e.

Example: IDW_distance_exponent: 3

Enables or disables low-memory computation mode (reduces memory usage at the cost of speed)

Example: memory_optimization: no

Ignored if source_type: msh.

Input file (Groundwater Vistas format, *.s3d)

Example: source_file: ./inputs/varB_xyz_head.csv

Example: IDW_maximum_point_distance: 8

Example: IDW_minimum_points_count: 3

See IDW_distance_exponent

Example: IDW_distance_exponent: 3

Name of the grid

Example: name: horizontal_verze

Coordinates of the center of the OUTGRIF grid

Example: center_position: {x: 2500, y: 50, z: 50}

Size of the cuboid grid along x, y, z directions

Example: range: {x: 4995, y: 99.99, z: 99.99}

Grid discretization in x, y, z directions (cell edge sizes)

The number of points in each grid direction must satisfy: N * d < r where:

• N is the number of points
• d is the value of discretization for the given axis,
• r is the value of range for the same axis

Example: discretization: {dx: 10, dy: 10, dz: 10}

Options:

• no — Grid points are at cell corners
• yes — Grid points are at cell centers

💡 Quotes from the PFLOTRAN documentation are highlighted with a vertical bar on the left.

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).

Example: point_as_cell_center: no

Rotation angle of the grid around the z-axis passing through center_position.

Example: rotate_around_z_axis_degree: 0

Tilt angle of the grid relative to the XY plane. Rotation is around the axis parallel to the y edge and passing through center_position.

Example: incline_to_xy_plane_degree: 0

Output HDF5 file name for PFLOTRAN (“Gridded Dataset”)

Example: hdf5_file: AM_data_2.h5

name of the grid used

Example: grid: grid A

Quantity name – as it appears in the input file

Example: quantity: Head

Transformation formula for the input value

Example: result_formula: (value-z)*9804.198 + 101325

Whether a Times dataset is created in the resulting HDF5 file¹⁾

Example: time_dependance: no

Time value(s) for which the dataset is stored.

• for MSH, it must match the value(s) in the $ElementData header of the source MSH file:
  • time_dependance: no: times can have exactly one value
  • time_dependance: yes: times may contain one or more time values
    Example: times: [0,273,3789]
• for S3D:
  • time_dependance: no: the times parameter is ignored
  • time_dependance: yes: times must contain only one value (grid values are written/appended to HDF5 for that time) — see append_to_group

Example: times: [0]

Group name (like a “folder” in the HDF5 file). This defines the quantity for PFLOTRAN.

Example: group_name: pressure

• yes – if S3D values should be added as another time step
• no – in all other cases

Example: append_to_group: yes

Add the following HDF5 Attributes to the HDF5 Group

HDF5 file attributes according to the PFLOTRAN documentation.

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

Options:

• e.g. {x: 12, y: 35, z: 70}
• auto — uses the origin from the source data

Example: origin: auto

Interpolation Method <string>: string = STEP or LINEAR

Example: interpolation_method: LINEAR

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.

Example: max_buffer_size: 1000

Note

Example: note: pressure

Whether to generate the HDF5 file.

Options:

• yes
• no

Optional parameter. Default value is yes.

Example: execute: yes

Auxiliary outputs:

• image and
• table (text file)

name of the grid used

Example: grid: grid A

Slice plane (orientation and location)

Example: plane: {type: XZ, local_y: 0}

Name of the quantity to use

Example: quantity: pressure_p0

Time value [s] for the export

Example: time: 0

Transformation formula for the input value

Example: result_formula: (value-z)*9804.198 + 101325

Name of the output image

Example: file: pokus.png

Example: file: ./output/pokus.png

Color scale definition

Example: colors: ["white", "blue", "red", "yellow", "black"]

Quantity values corresponding to color transitions in the scale

Example: colors_borders: [-20, -10, 0, 10]

Options:

• contours
• linear_interpolation

Example: colors_view: contours

Example: origin: {x: 0, y: 0}

Name of the output text file

Example: file: pokus.csv

Column separator

Example: column_separator: comma

Decimal separator

Options:

• comma — ,
• point — .

Example: decimal_separator: point

Number format

Example: number_format: .4E

Whether to generate auxiliary outputs

Options:

• yes
• no

Optional parameter. Default value is yes.

Example: execute: no