Data Model Generation

Fides can now generate a data model based on some attributes that are written by ADIOS, instead of requiring the user to write their own data model. Currently they must be written as ADIOS Attributes and not Variables, and they can either be written in the same file as your ADIOS data or you could have ADIOS write them in a separate file that contains only the attributes.

Note

If the attributes are written in a file separate from the actual data, Fides expects that it is in the same directory as the data to be read.

General Attributes

This attribute can be used with any data model to use one of your ADIOS Variables as the time values. For instance, in ParaView (whether it’s post-processing or using Catalyst), specifying the time variable will use the values in the specified array instead of just the ADIOS step numbers.

Attributes

Attribute Name	Possible types/values	Default
Fides_Time_Variable	string: name of variable to use for time	none

Supported Data Models

For each supported data model there is a table of attributes and possible types/values listed below. If an attribute does not list a default value, it must be specified in the data given to Fides.

Uniform Data Model

The data model uses uniform point coordinates for the coordinate system, needing the origin and spacing to be specified. The cell set is structured based on the dimensions of the data.

Attributes

Attribute Name	Possible types/values	Default
Fides_Data_Model	string: uniform	none
Fides_Origin	3 integer or floating points	none
Fides_Spacing	3 integer or floating points	none
Fides_Dimension_Variable	string: name of variable to use for determining dimensions	none

Example JSON

The following JSON shows an example of what Fides generates for this data model.

{
    "uniform_grid": {
        "data_sources": [
            {
                "name": "source",
                "filename_mode": "input"
            }
        ],
        "coordinate_system": {
            "array": {
                "array_type": "uniform_point_coordinates",
                "dimensions": {
                    "source": "variable_dimensions",
                    "data_source": "source",
                    "variable": "density"
                },
                "origin": {
                    "source": "array",
                    "values": [
                        0,
                        0,
                        0
                    ]
                },
                "spacing": {
                    "source": "array",
                    "values": [
                        0.1,
                        0.1,
                        0.1
                    ]
                }
            }
        },
        "cell_set": {
            "cell_set_type": "structured",
            "dimensions": {
                "source": "variable_dimensions",
                "data_source": "source",
                "variable": "density"
            }
        }
    }
}

Rectilinear Data Model

This data model creates a rectilinear data model where the coordinate system is specified by a cartesian product of (separate) arrays for the x, y, and z. The cell set is structured based on the dimensions of the data.

Attributes

Attribute Name	Possible types/values	Default
Fides_Data_Model	string: rectilinear	none
Fides_X_Variable	string: name of variable representing x values	x
Fides_Y_Variable	string: name of variable representing y values	y
Fides_Z_Variable	string: name of variable representing z values	z
Fides_Dimension_Variable	string: name of variable to use for determining dimensions	none

Example JSON

The following JSON shows an example of what Fides generates for this data model.

{
    "rectilinear_grid": {
        "data_sources": [
            {
                "name": "source",
                "filename_mode": "input"
            }
        ],
        "coordinate_system": {
            "array": {
                "array_type": "cartesian_product",
                "x_array": {
                    "array_type": "basic",
                    "data_source": "source",
                    "variable": "x",
                    "static": true
                },
                "y_array": {
                    "array_type": "basic",
                    "data_source": "source",
                    "variable": "y",
                    "static": true
                },
                "z_array": {
                    "array_type": "basic",
                    "data_source": "source",
                    "variable": "z",
                    "static": true
                }
            }
        },
        "cell_set": {
            "cell_set_type": "structured",
            "dimensions": {
                "source": "variable_dimensions",
                "data_source": "source",
                "variable": "scalars"
            }
        }
    }
}

Unstructured Data Model

An unstructured or explicit mesh that expects arrays containing the coordinates, connectivity, cell types, and number of vertices for each cell.

Attributes

Attribute Name	Possible types/values	Default
Fides_Data_Model	string: unstructured	none
Fides_Coordinates_Variable	string: name of variable containing coordinates	points
Fides_Connectivity_Variable	string: name of connectivity variable	connectivity
Fides_Cell_Types_Variable	string: name of cell types variable	cell_types
Fides_Num_Vertices_Variable	string: name of variable listing number of vertices for each cell	num_verts

Example JSON

The following JSON shows an example of what Fides generates for this data model.

{
    "unstructured_grid": {
        "data_sources": [
            {
                "name": "source",
                "filename_mode": "input"
            }
        ],
        "coordinate_system": {
            "array": {
                "array_type": "basic",
                "data_source": "source",
                "variable": "points",
                "static": true
            }
        },
        "cell_set": {
            "cell_set_type": "explicit",
            "connectivity": {
                "array_type": "basic",
                "data_source": "source",
                "variable": "connectivity"
            },
            "cell_types": {
                "array_type": "basic",
                "data_source": "source",
                "variable": "cell_types"
            },
            "number_of_vertices": {
                "array_type": "basic",
                "data_source": "source",
                "variable": "num_verts"
            }
        }
    }
}

Unstructured with Single Cell Type Data Model

Similar to unstructured, except that there is only a single cell type used in the data, so we don’t need to store arrays of the cell types and number of vertices.

Attributes

Attribute Name	Possible types/values	Default
Fides_Data_Model	string: unstructured_single	none
Fides_Cell_Type	string: one of vertex, line, triangle, quad, tetrahedron, hexahedron, wedge, pyramid	none
Fides_Coordinates_Variable	string: name of variable containing coordinates	points
Fides_Connectivity_Variable	string: name of connectivity variable	connectivity

Example JSON

The following JSON shows an example of what Fides generates for this data model.

{
    "unstructured_grid_single_cell_type": {
        "data_sources": [
            {
                "name": "source",
                "filename_mode": "input"
            }
        ],
        "coordinate_system": {
            "array": {
                "array_type": "basic",
                "data_source": "source",
                "variable": "points",
                "static": true
            }
        },
        "cell_set": {
            "cell_set_type": "single_type",
            "cell_type": "triangle",
            "data_source": "source",
            "variable": "connectivity",
            "static": true
        }
    }
}

XGC Data Model

Attributes

Attribute Name	Possible types/values	Default
Fides_Data_Model	string: xgc	none
Fides_XGC_Mesh_Filename	string: filename of mesh data (not full path)	xgc.mesh.bp
Fides_XGC_3d_Filename	string: filename of 3d data (not full path)	xgc.3d.bp
Fides_XGC_Diag_Filename	string: filename of diag data (not full path)	xgc.oneddiag.bp
Fides_Coordinates_Variable	string: name of plane coordinates variable	rz
Fides_Triangle_Connectivity_Variable	string: name of variable containing triangle connectivity	nd_connect_list
Fides_Plane_Connectivity_Variable	string: name of variable containing connectivity between planes	nextnode
Fides_Number_Of_Planes_Variable	string: name of variable for number of planes	nphi

Example JSON

The following JSON shows an example of what Fides generates for this data model.

{
    "xgc": {
        "data_sources": [
            {
                "name": "mesh",
                "filename_mode": "relative",
                "filename": "xgc.mesh.bp"
            },
            {
                "name": "3d",
                "filename_mode": "relative",
                "filename": "xgc.3d.bp"
            },
            {
                "name": "diag",
                "filename_mode": "relative",
                "filename": "xgc.oneddiag.bp"
            }
        ],
        "coordinate_system": {
            "array": {
                "array_type": "xgc_coordinates",
                "data_source": "mesh",
                "variable": "rz",
                "static": true,
                "is_cylindrical": false
            }
        },
        "cell_set": {
            "cell_set_type": "xgc",
            "periodic": true,
            "cells": {
                "array_type": "basic",
                "data_source": "mesh",
                "variable": "nd_connect_list",
                "static": true,
                "is_vector": "false"
            },
            "plane_connectivity": {
                "array_type": "basic",
                "data_source": "mesh",
                "variable": "nextnode",
                "static": true,
                "is_vector": "false"
            }
        },
        "fields": [
            {
                "variable_list_attribute_name": "Fides_Variable_List",
                "variable_association_attribute_name": "Fides_Variable_Associations",
                "variable_sources_attribute_name": "Fides_Variable_Sources",
                "variable_arrays_attribute_name": "Fides_Variable_Array_Types",
                "array": {
                    "array_type": "",
                    "data_source": "",
                    "variable": ""
                }
            }
        ],
        "number_of_planes": {
            "source": "scalar",
            "data_source": "3d",
            "variable": "nphi"
        }
    }
}