SalvusCompute API Documentation

Release: 0.12.16

SalvusCompute is steered by input files. These can be either TOML files or equivalent JSON files. Both are shown here. Navigate to the corresponding group on the right hand side. Note that we recommend using SalvusFlow to generate the input files but you can also do it manually, of course.

Example file with all the options. Please note that many of these might be mutally exclusive and/or optional. A detailed description of all parameters follows.

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[adjoint]
    forward_meta_json_filename = "meta-json.json"
    [adjoint.point_source_block]
        filename = "sources.h5"
        groups = ["sources_1", "sources_2"]
    [[adjoint.point_source]]
        location = [0.0, 1.0]
        spatial_type = "scalar"
        spatial_weights = [1.0]
        [adjoint.point_source.rotation_on_input]
            matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
        [adjoint.point_source.source_time_function]
            wavelet = "custom"
            filename = "source.h5"
            dataset_name = "/stf"
    [adjoint.gradient]
        parameterization = "rho-vp-vs"
        output_filename = "gradient.h5"
        format = "hdf5"
[domain]
    dimension = 3
    polynomial_order = 4
    [domain.mesh]
        filename = "mesh.h5"
        format = "hdf5"
    [domain.model]
        filename = "model.h5"
        format = "hdf5"
    [domain.geometry]
        filename = "geometry.h5"
        format = "hdf5"
[hardware]
    gpu = false
[output]
    memory_per_rank_in_MB = 1000.0
    [output.meta_data]
        meta_json_filename = "meta.json"
        progress_json_filename = "salvus_progress.json"
    [output.point_data]
        filename = "receivers.h5"
        format = "asdf"
        sampling_interval_in_time_steps = 10
        [[output.point_data.receiver]]
            location = "XXX"
            network_code = "AB"
            station_code = "0000"
            location_code = ""
            fields = ["displacement", "gradient-of-displacement"]
            [output.point_data.receiver.rotation_on_output]
                matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
                components = ["Z", "N", "E"]
    [output.surface_data]
        filename = "boundary_output.h5"
        format = "hdf5"
        fields = ["displacement", "strain"]
        sampling_interval_in_time_steps = 10
        side_sets = ["x0", "y0", "z0"]
        start_time_in_seconds = "0.0"
        end_time_in_seconds = "1.0"
    [output.volume_data]
        filename = "volume_output.h5"
        format = "hdf5"
        fields = ["u", "grad_u"]
        sampling_interval_in_time_steps = "10"
        start_time_in_seconds = "0.0"
        end_time_in_seconds = "1.0"
    [output.frequency_domain]
        filename = "frequency_domain.h5"
        format = "hdf5"
        fields = ["phi", "displacement"]
        frequencies = [1.0, 2.0]
        start_time_in_seconds = -0.12
        end_time_in_seconds = 1234.56
    [output.final_time_data]
        filename = "final_time_values.h5"
        format = "hdf5"
        fields = ["phi", "displacement"]
[physics]
    [physics.wave_equation]
        time_stepping_scheme = "newmark"
        start_time_in_seconds = -0.12
        end_time_in_seconds = 1234.56
        time_step_in_seconds = 0.01
        reference_time_in_seconds = 1000.0
        courant_number = 0.6
        attenuation = false
        point_source_chunk_size = 1000
        point_source_buffer_memory_in_MB_per_rank = 1000.0
        [physics.wave_equation.point_source_block]
            filename = "sources.h5"
            groups = ["sources_1", "sources_2"]
        [[physics.wave_equation.point_source]]
            location = [0.0, 1.0]
            spatial_type = "scalar"
            spatial_weights = [1.0]
            [physics.wave_equation.point_source.rotation_on_input]
                matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
            [physics.wave_equation.point_source.source_time_function]
                wavelet = "ricker"
                center_frequency = 1.0
                time_shift_in_seconds = 1.0
        [[physics.wave_equation.boundaries]]
            type = "homogeneous-dirichlet"
            side_sets = ["y0", "x1"]
            components = "XXX"
        [[physics.wave_equation.boundaries]]
            type = "ocean-loading"
            side_sets = ["y0", "x1"]
        [[physics.wave_equation.boundaries]]
            type = "absorbing"
            side_sets = ["x0", "x1", "y1"]
            width_in_meters = 1.06
            taper_amplitude = 1.07
            side_sets_are_axis_aligned = "true"
    [physics.diffusion_equation]
        time_stepping_scheme = "euler"
        start_time_in_seconds = -0.12
        end_time_in_seconds = 1234.56
        time_step_in_seconds = 0.01
        courant_number = 0.6
        [physics.diffusion_equation.initial_values]
            filename = "model.h5"
            format = "hdf5"
            field = "VP"
        [physics.diffusion_equation.final_values]
            filename = "final.h5"
    [physics.poisson_equation]
        [physics.poisson_equation.right_hand_side]
            filename = "model.h5"
            format = "hdf5"
            field = "values"
            fields = ["field1", "field2"]
        [physics.poisson_equation.initial_values]
            filename = "model.h5"
            format = "hdf5"
            field = "VP"
            fields = ["field1", "field2"]
        [[physics.poisson_equation.boundaries]]
            type = "homogeneous-dirichlet"
            side_sets = ["y0", "x1"]
            components = "XXX"
        [[physics.poisson_equation.boundaries]]
            type = "neumann"
            side_sets = ["y0", "x1"]
        [physics.poisson_equation.solution]
            filename = "solution.h5"
            fields = ["solution", "residuals"]
[solver]
    type = "cg"
    preconditioner = true
    max_iterations = 10
    relative_tolerance = 1e-06
    absolute_tolerance = 1.0
    monitor = true

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{
  "adjoint": {
    "forward_meta_json_filename": "meta-json.json",
    "point_source_block": {
      "filename": "sources.h5",
      "groups": [
        "sources_1",
        "sources_2"
      ]
    },
    "point_source": [
      {
        "location": [
          0.0,
          1.0
        ],
        "spatial_type": "scalar",
        "spatial_weights": [
          1.0
        ],
        "rotation_on_input": {
          "matrix": [
            [
              1,
              0,
              0
            ],
            [
              0,
              1,
              0
            ],
            [
              0,
              0,
              1
            ]
          ]
        },
        "source_time_function": {
          "wavelet": "custom",
          "filename": "source.h5",
          "dataset_name": "/stf"
        }
      }
    ],
    "gradient": {
      "parameterization": "rho-vp-vs",
      "output_filename": "gradient.h5",
      "format": "hdf5"
    }
  },
  "domain": {
    "dimension": 3,
    "polynomial_order": 4,
    "mesh": {
      "filename": "mesh.h5",
      "format": "hdf5"
    },
    "model": {
      "filename": "model.h5",
      "format": "hdf5"
    },
    "geometry": {
      "filename": "geometry.h5",
      "format": "hdf5"
    }
  },
  "hardware": {
    "gpu": false
  },
  "output": {
    "memory_per_rank_in_MB": 1000.0,
    "meta_data": {
      "meta_json_filename": "meta.json",
      "progress_json_filename": "salvus_progress.json"
    },
    "point_data": {
      "filename": "receivers.h5",
      "format": "asdf",
      "sampling_interval_in_time_steps": 10,
      "receiver": [
        {
          "location": "XXX",
          "network_code": "AB",
          "station_code": "0000",
          "location_code": "",
          "fields": [
            "displacement",
            "gradient-of-displacement"
          ],
          "rotation_on_output": {
            "matrix": [
              [
                1,
                0,
                0
              ],
              [
                0,
                1,
                0
              ],
              [
                0,
                0,
                1
              ]
            ],
            "components": [
              "Z",
              "N",
              "E"
            ]
          }
        }
      ]
    },
    "surface_data": {
      "filename": "boundary_output.h5",
      "format": "hdf5",
      "fields": [
        "displacement",
        "strain"
      ],
      "sampling_interval_in_time_steps": 10,
      "side_sets": [
        "x0",
        "y0",
        "z0"
      ],
      "start_time_in_seconds": "0.0",
      "end_time_in_seconds": "1.0"
    },
    "volume_data": {
      "filename": "volume_output.h5",
      "format": "hdf5",
      "fields": [
        "u",
        "grad_u"
      ],
      "sampling_interval_in_time_steps": "10",
      "start_time_in_seconds": "0.0",
      "end_time_in_seconds": "1.0"
    },
    "frequency_domain": {
      "filename": "frequency_domain.h5",
      "format": "hdf5",
      "fields": [
        "phi",
        "displacement"
      ],
      "frequencies": [
        1.0,
        2.0
      ],
      "start_time_in_seconds": -0.12,
      "end_time_in_seconds": 1234.56
    },
    "final_time_data": {
      "filename": "final_time_values.h5",
      "format": "hdf5",
      "fields": [
        "phi",
        "displacement"
      ]
    }
  },
  "physics": {
    "wave_equation": {
      "time_stepping_scheme": "newmark",
      "start_time_in_seconds": -0.12,
      "end_time_in_seconds": 1234.56,
      "time_step_in_seconds": 0.01,
      "reference_time_in_seconds": 1000.0,
      "courant_number": 0.6,
      "attenuation": false,
      "point_source_chunk_size": 1000,
      "point_source_buffer_memory_in_MB_per_rank": 1000.0,
      "point_source_block": {
        "filename": "sources.h5",
        "groups": [
          "sources_1",
          "sources_2"
        ]
      },
      "point_source": [
        {
          "location": [
            0.0,
            1.0
          ],
          "spatial_type": "scalar",
          "spatial_weights": [
            1.0
          ],
          "rotation_on_input": {
            "matrix": [
              [
                1,
                0,
                0
              ],
              [
                0,
                1,
                0
              ],
              [
                0,
                0,
                1
              ]
            ]
          },
          "source_time_function": {
            "wavelet": "ricker",
            "center_frequency": 1.0,
            "time_shift_in_seconds": 1.0
          }
        }
      ],
      "boundaries": [
        [
          {
            "type": "homogeneous-dirichlet",
            "side_sets": [
              "y0",
              "x1"
            ],
            "components": "XXX"
          },
          {
            "type": "ocean-loading",
            "side_sets": [
              "y0",
              "x1"
            ]
          },
          {
            "type": "absorbing",
            "side_sets": [
              "x0",
              "x1",
              "y1"
            ],
            "width_in_meters": 1.06,
            "taper_amplitude": 1.07,
            "side_sets_are_axis_aligned": "true"
          }
        ]
      ]
    },
    "diffusion_equation": {
      "time_stepping_scheme": "euler",
      "start_time_in_seconds": -0.12,
      "end_time_in_seconds": 1234.56,
      "time_step_in_seconds": 0.01,
      "courant_number": 0.6,
      "initial_values": {
        "filename": "model.h5",
        "format": "hdf5",
        "field": "VP"
      },
      "final_values": {
        "filename": "final.h5"
      }
    },
    "poisson_equation": {
      "right_hand_side": {
        "filename": "model.h5",
        "format": "hdf5",
        "field": "values",
        "fields": [
          "field1",
          "field2"
        ]
      },
      "initial_values": {
        "filename": "model.h5",
        "format": "hdf5",
        "field": "VP",
        "fields": [
          "field1",
          "field2"
        ]
      },
      "boundaries": [
        [
          {
            "type": "homogeneous-dirichlet",
            "side_sets": [
              "y0",
              "x1"
            ],
            "components": "XXX"
          },
          {
            "type": "neumann",
            "side_sets": [
              "y0",
              "x1"
            ]
          }
        ]
      ],
      "solution": {
        "filename": "solution.h5",
        "fields": [
          "solution",
          "residuals"
        ]
      }
    }
  },
  "solver": {
    "type": "cg",
    "preconditioner": true,
    "max_iterations": 10,
    "relative_tolerance": 1e-06,
    "absolute_tolerance": 1.0,
    "monitor": true
  }
}

Adjoint group [adjoint]

If this group is present with its required members, Salvus will solve the adjoint-state problem for the specified physics and domain.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[adjoint]
    forward_meta_json_filename = "meta-json.json"
    [adjoint.point_source_block]
        filename = "sources.h5"
        groups = ["sources_1", "sources_2"]
    [[adjoint.point_source]]
        location = [0.0, 1.0]
        spatial_type = "scalar"
        spatial_weights = [1.0]
        [adjoint.point_source.rotation_on_input]
            matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
        [adjoint.point_source.source_time_function]
            wavelet = "custom"
            filename = "source.h5"
            dataset_name = "/stf"
    [adjoint.gradient]
        parameterization = "rho-vp-vs"
        output_filename = "gradient.h5"
        format = "hdf5"

Copy
{
  "adjoint": {
    "forward_meta_json_filename": "meta-json.json",
    "point_source_block": {
      "filename": "sources.h5",
      "groups": [
        "sources_1",
        "sources_2"
      ]
    },
    "point_source": [
      {
        "location": [
          0.0,
          1.0
        ],
        "spatial_type": "scalar",
        "spatial_weights": [
          1.0
        ],
        "rotation_on_input": {
          "matrix": [
            [
              1,
              0,
              0
            ],
            [
              0,
              1,
              0
            ],
            [
              0,
              0,
              1
            ]
          ]
        },
        "source_time_function": {
          "wavelet": "custom",
          "filename": "source.h5",
          "dataset_name": "/stf"
        }
      }
    ],
    "gradient": {
      "parameterization": "rho-vp-vs",
      "output_filename": "gradient.h5",
      "format": "hdf5"
    }
  }
}

Detailed description of all parameters:

• forward_meta_json_filename

  • Pretty name: Forward meta json

  • Description: The json file describing the forward run

  • Parameter type: string

  • Required: True

Block of point sources. subgroup [adjoint.point_source_block]

Reads all source characteristics from a group in an HDF5 file.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[adjoint.point_source_block]
    filename = "sources.h5"
    groups = ["sources_1", "sources_2"]

Copy
{
  "point_source_block": {
    "filename": "sources.h5",
    "groups": [
      "sources_1",
      "sources_2"
    ]
  }
}

Detailed description of all parameters:

• filename

  • Pretty name: Filename

  • Description: Filename containing sources

  • Parameter type: string

  • Required: True

• groups

  • Pretty name: Groups

  • Description: Array of groups in the HDF5 file containing source information

  • Parameter type: array of strings

  • Required: True

Point source subgroup [adjoint.point_source]

Point sources for the wave equation.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[[adjoint.point_source]]
    location = [0.0, 1.0]
    spatial_type = "scalar"
    spatial_weights = [1.0]
    [adjoint.point_source.rotation_on_input]
        matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
    [adjoint.point_source.source_time_function]
        wavelet = "custom"
        filename = "source.h5"
        dataset_name = "/stf"

Copy
{
  "point_source": {
    "location": [
      0.0,
      1.0
    ],
    "spatial_type": "scalar",
    "spatial_weights": [
      1.0
    ],
    "rotation_on_input": {
      "matrix": [
        [
          1,
          0,
          0
        ],
        [
          0,
          1,
          0
        ],
        [
          0,
          0,
          1
        ]
      ]
    },
    "source_time_function": {
      "wavelet": "custom",
      "filename": "source.h5",
      "dataset_name": "/stf"
    }
  }
}

Detailed description of all parameters:

• location

  • Pretty name: Source location

  • Description: The source location in Cartesian coordinates.

  • Parameter type: array of numbers

  • Required: False

• spatial_type

  • Pretty name: Spatial type of the source

  • Description: The spatial type of the point source.

  • Parameter type: string

  • Required: False

  • Possible values: "scalar", "vector", "moment_tensor", "scalar_gradient", "vector_gradient"

• spatial_weights

  • Pretty name: Spatial weights of the source

  • Description: The spatial weights and scale of the point source.

  • Parameter type: array of numbers

  • Required: False

subgroup [adjoint.point_source.rotation_on_input]

Optionally rotate the output. The specified rotation matrix will be applied to the final output of the receiver. It should thus rotate from Cartesian X,Y,Z to the coordinate system of your choice.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[adjoint.point_source.rotation_on_input]
    matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]

Copy
{
  "rotation_on_input": {
    "matrix": [
      [
        1,
        0,
        0
      ],
      [
        0,
        1,
        0
      ],
      [
        0,
        0,
        1
      ]
    ]
  }
}

Detailed description of all parameters:

• matrix

  • Pretty name: Rotation Matrix

  • Description: A 2x2 or 3x3 rotation matrix.

  • Parameter type: array of arrays

  • Required: True

Source time function subgroup [adjoint.point_source.source_time_function]

The temporal evolution of the source.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[adjoint.point_source.source_time_function]
    wavelet = "custom"
    filename = "source.h5"
    dataset_name = "/stf"

Copy
{
  "source_time_function": {
    "wavelet": "custom",
    "filename": "source.h5",
    "dataset_name": "/stf"
  }
}

Detailed description of all parameters:

• wavelet

  • Pretty name: Source time function

  • Description: The type of the source time function

  • Parameter type: string

  • Required: True

  • Possible values: "custom"

• filename

  • Pretty name: Source filename

  • Description: The hdf5 filename of the source.

  • Parameter type: string

  • Required: True

• dataset_name

  • Pretty name: Dataset name

  • Description: The hdf5 dataset name containing the source time function.

  • Parameter type: string

  • Required: True

Gradient subgroup [adjoint.gradient]

Model parameters and output filename for gradient computation.

Required: True

Full example (Please note that some options might be mutally exclusive):

Copy
[adjoint.gradient]
    parameterization = "rho-vp-vs"
    output_filename = "gradient.h5"
    format = "hdf5"

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{
  "gradient": {
    "parameterization": "rho-vp-vs",
    "output_filename": "gradient.h5",
    "format": "hdf5"
  }
}

Detailed description of all parameters:

• parameterization

  • Pretty name: Parameterization

  • Description: Parameterization of this gradeint

  • Parameter type: string

  • Required: True

  • Possible values: "linear", "rho-vp", "rho-vp-vs", "impedance", "love-parameters", "tti"

• output_filename

  • Pretty name: Output file name

  • Description: File within which to store the gradient

  • Parameter type: string

  • Required: True

• format

  • Pretty name: File format

  • Description: The file format for the gradient output.

  • Parameter type: string

  • Required: False

  • Possible values: "hdf5", "hdf5-full", "hdf5-minimal"

Domain group [domain]

This groups describes the physical domain in which to run simulations.

Required: True

Full example (Please note that some options might be mutally exclusive):

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[domain]
    dimension = 3
    polynomial_order = 4
    [domain.mesh]
        filename = "mesh.h5"
        format = "hdf5"
    [domain.model]
        filename = "model.h5"
        format = "hdf5"
    [domain.geometry]
        filename = "geometry.h5"
        format = "hdf5"

Copy
{
  "domain": {
    "dimension": 3,
    "polynomial_order": 4,
    "mesh": {
      "filename": "mesh.h5",
      "format": "hdf5"
    },
    "model": {
      "filename": "model.h5",
      "format": "hdf5"
    },
    "geometry": {
      "filename": "geometry.h5",
      "format": "hdf5"
    }
  }
}

Detailed description of all parameters:

• dimension

  • Pretty name: Dimension

  • Description: The spatial dimension of the problem.

  • Parameter type: integer

  • Required: True

  • Possible values: 2, 3

• polynomial_order

  • Pretty name: Polynomial order

  • Description: Polynomial order of the spectral elements.

  • Parameter type: integer

  • Required: True

  • Possible values: 1, 2, 3, 4, 5, 6, 7

Mesh subgroup [domain.mesh]

Specify the domain topology.

Required: True

Full example (Please note that some options might be mutally exclusive):

Copy
[domain.mesh]
    filename = "mesh.h5"
    format = "hdf5"

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{
  "mesh": {
    "filename": "mesh.h5",
    "format": "hdf5"
  }
}

Detailed description of all parameters:

• filename

  • Pretty name: Mesh filename

  • Description: The filename of the mesh.

  • Parameter type: string

  • Required: True

• format

  • Pretty name: Mesh format

  • Description: The format of the mesh.

  • Parameter type: string

  • Required: True

  • Possible values: "hdf5"

Model subgroup [domain.model]

Specify the physical parameters of the domain.

Required: True

Full example (Please note that some options might be mutally exclusive):

Copy
[domain.model]
    filename = "model.h5"
    format = "hdf5"

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{
  "model": {
    "filename": "model.h5",
    "format": "hdf5"
  }
}

Detailed description of all parameters:

• filename

  • Pretty name: Model filename

  • Description: The filename of the model.

  • Parameter type: string

  • Required: True

• format

  • Pretty name: Model format

  • Description: The format of the model.

  • Parameter type: string

  • Required: True

  • Possible values: "hdf5"

Geometry subgroup [domain.geometry]

Specify the geometry of the domain.

Required: True

Full example (Please note that some options might be mutally exclusive):

Copy
[domain.geometry]
    filename = "geometry.h5"
    format = "hdf5"

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{
  "geometry": {
    "filename": "geometry.h5",
    "format": "hdf5"
  }
}

Detailed description of all parameters:

• filename

  • Pretty name: Filename

  • Description: The filename containing the geometry information.

  • Parameter type: string

  • Required: True

• format

  • Pretty name: Geometry format

  • Description: The format of the geometry.

  • Parameter type: string

  • Required: True

  • Possible values: "hdf5"

Hardware group [hardware]

This groups describes the hardware and job specific parameters.

Required: False

Full example (Please note that some options might be mutally exclusive):

Copy
[hardware]
    gpu = false

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{
  "hardware": {
    "gpu": false
  }
}

Detailed description of all parameters:

• gpu

  • Pretty name: Enable GPU support

  • Description: Run simulation on GPUs

  • Parameter type: boolean

  • Required: True

Output group [output]

Simulation without output only have limited use. Specify point, surface, and volumetric outputs here.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[output]
    memory_per_rank_in_MB = 1000.0
    [output.meta_data]
        meta_json_filename = "meta.json"
        progress_json_filename = "salvus_progress.json"
    [output.point_data]
        filename = "receivers.h5"
        format = "asdf"
        sampling_interval_in_time_steps = 10
        [[output.point_data.receiver]]
            location = "XXX"
            network_code = "AB"
            station_code = "0000"
            location_code = ""
            fields = ["displacement", "gradient-of-displacement"]
            [output.point_data.receiver.rotation_on_output]
                matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
                components = ["Z", "N", "E"]
    [output.surface_data]
        filename = "boundary_output.h5"
        format = "hdf5"
        fields = ["displacement", "strain"]
        sampling_interval_in_time_steps = 10
        side_sets = ["x0", "y0", "z0"]
        start_time_in_seconds = "0.0"
        end_time_in_seconds = "1.0"
    [output.volume_data]
        filename = "volume_output.h5"
        format = "hdf5"
        fields = ["u", "grad_u"]
        sampling_interval_in_time_steps = "10"
        start_time_in_seconds = "0.0"
        end_time_in_seconds = "1.0"
    [output.frequency_domain]
        filename = "frequency_domain.h5"
        format = "hdf5"
        fields = ["phi", "displacement"]
        frequencies = [1.0, 2.0]
        start_time_in_seconds = -0.12
        end_time_in_seconds = 1234.56
    [output.final_time_data]
        filename = "final_time_values.h5"
        format = "hdf5"
        fields = ["phi", "displacement"]

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{
  "output": {
    "memory_per_rank_in_MB": 1000.0,
    "meta_data": {
      "meta_json_filename": "meta.json",
      "progress_json_filename": "salvus_progress.json"
    },
    "point_data": {
      "filename": "receivers.h5",
      "format": "asdf",
      "sampling_interval_in_time_steps": 10,
      "receiver": [
        {
          "location": "XXX",
          "network_code": "AB",
          "station_code": "0000",
          "location_code": "",
          "fields": [
            "displacement",
            "gradient-of-displacement"
          ],
          "rotation_on_output": {
            "matrix": [
              [
                1,
                0,
                0
              ],
              [
                0,
                1,
                0
              ],
              [
                0,
                0,
                1
              ]
            ],
            "components": [
              "Z",
              "N",
              "E"
            ]
          }
        }
      ]
    },
    "surface_data": {
      "filename": "boundary_output.h5",
      "format": "hdf5",
      "fields": [
        "displacement",
        "strain"
      ],
      "sampling_interval_in_time_steps": 10,
      "side_sets": [
        "x0",
        "y0",
        "z0"
      ],
      "start_time_in_seconds": "0.0",
      "end_time_in_seconds": "1.0"
    },
    "volume_data": {
      "filename": "volume_output.h5",
      "format": "hdf5",
      "fields": [
        "u",
        "grad_u"
      ],
      "sampling_interval_in_time_steps": "10",
      "start_time_in_seconds": "0.0",
      "end_time_in_seconds": "1.0"
    },
    "frequency_domain": {
      "filename": "frequency_domain.h5",
      "format": "hdf5",
      "fields": [
        "phi",
        "displacement"
      ],
      "frequencies": [
        1.0,
        2.0
      ],
      "start_time_in_seconds": -0.12,
      "end_time_in_seconds": 1234.56
    },
    "final_time_data": {
      "filename": "final_time_values.h5",
      "format": "hdf5",
      "fields": [
        "phi",
        "displacement"
      ]
    }
  }
}

Detailed description of all parameters:

• memory_per_rank_in_MB

  • Pretty name: Memory for output buffers per rank

  • Description: Memory for output buffers per rank

  • Parameter type: number

  • Required: False

Informational metadata output subgroup [output.meta_data]

Specify additional non-physical output like runtime information about the simulations.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[output.meta_data]
    meta_json_filename = "meta.json"
    progress_json_filename = "salvus_progress.json"

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{
  "meta_data": {
    "meta_json_filename": "meta.json",
    "progress_json_filename": "salvus_progress.json"
  }
}

Detailed description of all parameters:

• meta_json_filename

  • Pretty name: Meta JSON filename

  • Description: Store machine-readable information about successful runs in this file.

  • Parameter type: string

  • Required: True

• progress_json_filename

  • Pretty name: Progress JSON filename

  • Description: JSON file that output information about the current Salvus progress during the simulations.

  • Parameter type: string

  • Required: False

Point data output subgroup [output.point_data]

Store pointwise evaluations of various dynamic fields.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[output.point_data]
    filename = "receivers.h5"
    format = "asdf"
    sampling_interval_in_time_steps = 10
    [[output.point_data.receiver]]
        location = "XXX"
        network_code = "AB"
        station_code = "0000"
        location_code = ""
        fields = ["displacement", "gradient-of-displacement"]
        [output.point_data.receiver.rotation_on_output]
            matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
            components = ["Z", "N", "E"]

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{
  "point_data": {
    "filename": "receivers.h5",
    "format": "asdf",
    "sampling_interval_in_time_steps": 10,
    "receiver": [
      {
        "location": "XXX",
        "network_code": "AB",
        "station_code": "0000",
        "location_code": "",
        "fields": [
          "displacement",
          "gradient-of-displacement"
        ],
        "rotation_on_output": {
          "matrix": [
            [
              1,
              0,
              0
            ],
            [
              0,
              1,
              0
            ],
            [
              0,
              0,
              1
            ]
          ],
          "components": [
            "Z",
            "N",
            "E"
          ]
        }
      }
    ]
  }
}

Detailed description of all parameters:

• filename

  • Pretty name: Filename

  • Description: Output filename.

  • Parameter type: string

  • Required: True

• format

  • Pretty name: File format

  • Description: The file format for the receiver data.

  • Parameter type: string

  • Required: True

  • Possible values: "asdf", "hdf5"

• sampling_interval_in_time_steps

  • Pretty name: Sampling interval in time steps

  • Description: Only store every X time steps.

  • Parameter type: integer

  • Required: True

Receiver subgroup [output.point_data.receiver]

Receiver specification for point measurements

Required: False

Full example (Please note that some options might be mutally exclusive):

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[[output.point_data.receiver]]
    location = "XXX"
    network_code = "AB"
    station_code = "0000"
    location_code = ""
    fields = ["displacement", "gradient-of-displacement"]
    [output.point_data.receiver.rotation_on_output]
        matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
        components = ["Z", "N", "E"]

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{
  "receiver": {
    "location": "XXX",
    "network_code": "AB",
    "station_code": "0000",
    "location_code": "",
    "fields": [
      "displacement",
      "gradient-of-displacement"
    ],
    "rotation_on_output": {
      "matrix": [
        [
          1,
          0,
          0
        ],
        [
          0,
          1,
          0
        ],
        [
          0,
          0,
          1
        ]
      ],
      "components": [
        "Z",
        "N",
        "E"
      ]
    }
  }
}

Detailed description of all parameters:

• location

  • Pretty name: Receiver location

  • Description: The receiver location in Cartesian coordinates.

  • Parameter type: array of numbers

  • Required: False

• network_code

  • Pretty name: Network code

  • Description: Network code

  • Parameter type: string

  • Required: False

• station_code

  • Pretty name: Station code

  • Description: Station code

  • Parameter type: string

  • Required: False

• location_code

  • Pretty name: Location code

  • Description: Location code

  • Parameter type: string

  • Required: False

• fields

  • Pretty name: Fields

  • Description: Choose which parameters to store.

  • Parameter type: array of strings

  • Required: False

  • Possible values: "displacement", "velocity", "acceleration", "gradient-of-displacement", "strain", "stress-tensor", "stress", "phi", "phi_t", "phi_tt", "gradient-of-phi"

subgroup [output.point_data.receiver.rotation_on_output]

Optionally rotate the output. The specified rotation matrix will be applied to the final output of the receiver. It should thus rotate from Cartesian X,Y,Z to the coordinate system of your choice.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[output.point_data.receiver.rotation_on_output]
    matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
    components = ["Z", "N", "E"]

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{
  "rotation_on_output": {
    "matrix": [
      [
        1,
        0,
        0
      ],
      [
        0,
        1,
        0
      ],
      [
        0,
        0,
        1
      ]
    ],
    "components": [
      "Z",
      "N",
      "E"
    ]
  }
}

Detailed description of all parameters:

• matrix

  • Pretty name: Rotation Matrix

  • Description: A 2x2 or 3x3 rotation matrix.

  • Parameter type: array of arrays

  • Required: True

• components

  • Pretty name: Components

  • Description: The component names of the rotated output. Will be used in the output files.

  • Parameter type: array of strings

  • Required: True

Surface data output subgroup [output.surface_data]

Store various dynamic fields at surfaces.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[output.surface_data]
    filename = "boundary_output.h5"
    format = "hdf5"
    fields = ["displacement", "strain"]
    sampling_interval_in_time_steps = 10
    side_sets = ["x0", "y0", "z0"]
    start_time_in_seconds = "0.0"
    end_time_in_seconds = "1.0"

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{
  "surface_data": {
    "filename": "boundary_output.h5",
    "format": "hdf5",
    "fields": [
      "displacement",
      "strain"
    ],
    "sampling_interval_in_time_steps": 10,
    "side_sets": [
      "x0",
      "y0",
      "z0"
    ],
    "start_time_in_seconds": "0.0",
    "end_time_in_seconds": "1.0"
  }
}

Detailed description of all parameters:

• filename

  • Pretty name: Filename

  • Description: Output filename.

  • Parameter type: string

  • Required: True

• format

  • Pretty name: File format

  • Description: The file format for the boundary data.

  • Parameter type: string

  • Required: True

  • Possible values: "hdf5"

• fields

  • Pretty name: Fields

  • Description: Choose which parameters to store.

  • Parameter type: array of strings

  • Required: True

  • Possible values: "displacement", "velocity", "acceleration", "fem-ku-elastic", "inverse-mass-matrix-elastic", "gradient-of-displacement", "stress-tensor", "stress", "strain", "phi", "phi_t", "phi_tt", "fem-ku-acoustic", "inverse-mass-matrix-acoustic", "gradient-of-phi", "m1-times-gradient-of-phi", "frequency-domain"

• sampling_interval_in_time_steps

  • Pretty name: Sampling interval in time steps

  • Description: Only store every X time steps.

  • Parameter type: integer

  • Required: True

• side_sets

  • Pretty name: Side sets

  • Description: Specify side sets at which to store the boundary wavefield.

  • Parameter type: array of strings

  • Required: True

• start_time_in_seconds

  • Pretty name: Start of time to record surface output

  • Description: A number in seconds that specifies when recording of the surface output should start.

  • Parameter type: number

  • Required: False

• end_time_in_seconds

  • Pretty name: Don't record surface output after this time.

  • Description: A number in seconds that specifies when recording of the surface output should end.

  • Parameter type: number

  • Required: False

Volume data output subgroup [output.volume_data]

Output fully volumetric fields. Be aware that the output can be very large.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[output.volume_data]
    filename = "volume_output.h5"
    format = "hdf5"
    fields = ["u", "grad_u"]
    sampling_interval_in_time_steps = "10"
    start_time_in_seconds = "0.0"
    end_time_in_seconds = "1.0"

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{
  "volume_data": {
    "filename": "volume_output.h5",
    "format": "hdf5",
    "fields": [
      "u",
      "grad_u"
    ],
    "sampling_interval_in_time_steps": "10",
    "start_time_in_seconds": "0.0",
    "end_time_in_seconds": "1.0"
  }
}

Detailed description of all parameters:

• filename

  • Pretty name: Filename

  • Description: Output filename.

  • Parameter type: string

  • Required: True

• format

  • Pretty name: File format

  • Description: The file format for the volume data.

  • Parameter type: string

  • Required: True

  • Possible values: "hdf5"

• fields

  • Pretty name: Fields

  • Description: Choose which parameters to store.

  • Parameter type: array of strings

  • Required: True

  • Possible values: "displacement", "velocity", "acceleration", "fem-ku-acoustic", "inverse-mass-matrix-acoustic", "fem-ku-elastic", "inverse-mass-matrix-elastic", "gradient-of-displacement", "stress-tensor", "stress", "strain", "phi", "phi_t", "phi_tt", "gradient-of-phi", "m1-times-gradient-of-phi", "absorbing-gamma-elastic", "absorbing-gamma-acoustic", "frequency-domain", "adjoint-checkpoint", "ls-0", "ls-1", "ls-2", "ls-3", "ls-4", "ls-0-acoustic", "ls-1-acoustic", "ls-2-acoustic", "ls-3-acoustic", "ls-4-acoustic"

• sampling_interval_in_time_steps

  • Pretty name: Sampling interval in time steps

  • Description: If an integer N is passed, output volumetric wavefield data every N times steps. If 'auto-for-checkpointing' is passed, Salvus will use the 'memory_per_rank_in_MB' field to determine what the optimal checkpointing snapshot interval will be.

  • Parameter type: ['integer', 'string', 'object']

  • Required: True

• start_time_in_seconds

  • Pretty name: Start of time to record volumetric output

  • Description: A number in seconds that specifies when recording of the volumetric output should start.

  • Parameter type: number

  • Required: False

• end_time_in_seconds

  • Pretty name: Don't record volumetric output after this time.

  • Description: A number in seconds that specifies when recording of the volumetric output should end.

  • Parameter type: number

  • Required: False

Volumetric output in the frequency domain subgroup [output.frequency_domain]

Output real and imaginary part of Fourier-transformed volumetric fields.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[output.frequency_domain]
    filename = "frequency_domain.h5"
    format = "hdf5"
    fields = ["phi", "displacement"]
    frequencies = [1.0, 2.0]
    start_time_in_seconds = -0.12
    end_time_in_seconds = 1234.56

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{
  "frequency_domain": {
    "filename": "frequency_domain.h5",
    "format": "hdf5",
    "fields": [
      "phi",
      "displacement"
    ],
    "frequencies": [
      1.0,
      2.0
    ],
    "start_time_in_seconds": -0.12,
    "end_time_in_seconds": 1234.56
  }
}

Detailed description of all parameters:

• filename

  • Pretty name: Filename

  • Description: Output filename.

  • Parameter type: string

  • Required: True

• format

  • Pretty name: File format

  • Description: The file format.

  • Parameter type: string

  • Required: True

  • Possible values: "hdf5", "hdf5-minimal", "hdf5-full"

• fields

  • Pretty name: Fields

  • Description: Choose which parameters to store.

  • Parameter type: array of strings

  • Required: True

  • Possible values: "displacement", "phi"

• frequencies

  • Pretty name: Frequencies

  • Description: Choose set of discrete frequencies to output the fields.

  • Parameter type: array of numbers

  • Required: True

• start_time_in_seconds

  • Pretty name: Start time of the on-the-fly Fourier transform

  • Description: The time stamp in seconds at which the DFT starts. Must be greater or equal than the simulation start time. It will snap to the closest time step greater or equal to the specified time. If not set the DFT will begin at the start time of the simulation.

  • Parameter type: number

  • Required: False

• end_time_in_seconds

  • Pretty name: End time of the on-the-fly Fourier transform

  • Description: The time stamp in seconds at which the DFT ends. Must be smaller or equal than the simulation end time. It will snap to the closest time step smaller or equal to the specified time. If not set the DFT will stop at the end time of the simulation.

  • Parameter type: number

  • Required: False

Output final time values subgroup [output.final_time_data]

Volumetric output at the end time of the simulation.

Required: False

Full example (Please note that some options might be mutally exclusive):

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[output.final_time_data]
    filename = "final_time_values.h5"
    format = "hdf5"
    fields = ["phi", "displacement"]

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{
  "final_time_data": {
    "filename": "final_time_values.h5",
    "format": "hdf5",
    "fields": [
      "phi",
      "displacement"
    ]
  }
}

Detailed description of all parameters:

• filename

  • Pretty name: Filename

  • Description: Output filename.

  • Parameter type: string

  • Required: True

• format

  • Pretty name: File format

  • Description: The file format.

  • Parameter type: string

  • Required: True

  • Possible values: "hdf5", "hdf5-minimal", "hdf5-full"

• fields

  • Pretty name: Fields

  • Description: Choose which parameters to store.

  • Parameter type: array of strings

  • Required: True

  • Possible values: "displacement", "velocity", "phi", "phi_t"

Physics group [physics]

Which equation do you want to solve?

Required: True

Full example (Please note that some options might be mutally exclusive):

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[physics]
    [physics.wave_equation]
        time_stepping_scheme = "newmark"
        start_time_in_seconds = -0.12
        end_time_in_seconds = 1234.56
        time_step_in_seconds = 0.01
        reference_time_in_seconds = 1000.0
        courant_number = 0.6
        attenuation = false
        point_source_chunk_size = 1000
        point_source_buffer_memory_in_MB_per_rank = 1000.0
        [physics.wave_equation.point_source_block]
            filename = "sources.h5"
            groups = ["sources_1", "sources_2"]
        [[physics.wave_equation.point_source]]
            location = [0.0, 1.0]
            spatial_type = "scalar"
            spatial_weights = [1.0]
            [physics.wave_equation.point_source.rotation_on_input]
                matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
            [physics.wave_equation.point_source.source_time_function]
                wavelet = "ricker"
                center_frequency = 1.0
                time_shift_in_seconds = 1.0
        [[physics.wave_equation.boundaries]]
            type = "homogeneous-dirichlet"
            side_sets = ["y0", "x1"]
            components = "XXX"
        [[physics.wave_equation.boundaries]]
            type = "ocean-loading"
            side_sets = ["y0", "x1"]
        [[physics.wave_equation.boundaries]]
            type = "absorbing"
            side_sets = ["x0", "x1", "y1"]
            width_in_meters = 1.06
            taper_amplitude = 1.07
            side_sets_are_axis_aligned = "true"
    [physics.diffusion_equation]
        time_stepping_scheme = "euler"
        start_time_in_seconds = -0.12
        end_time_in_seconds = 1234.56
        time_step_in_seconds = 0.01
        courant_number = 0.6
        [physics.diffusion_equation.initial_values]
            filename = "model.h5"
            format = "hdf5"
            field = "VP"
        [physics.diffusion_equation.final_values]
            filename = "final.h5"
    [physics.poisson_equation]
        [physics.poisson_equation.right_hand_side]
            filename = "model.h5"
            format = "hdf5"
            field = "values"
            fields = ["field1", "field2"]
        [physics.poisson_equation.initial_values]
            filename = "model.h5"
            format = "hdf5"
            field = "VP"
            fields = ["field1", "field2"]
        [[physics.poisson_equation.boundaries]]
            type = "homogeneous-dirichlet"
            side_sets = ["y0", "x1"]
            components = "XXX"
        [[physics.poisson_equation.boundaries]]
            type = "neumann"
            side_sets = ["y0", "x1"]
        [physics.poisson_equation.solution]
            filename = "solution.h5"
            fields = ["solution", "residuals"]