Release: 2024.1.2
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.
[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
{ "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]
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):
[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"
{ "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
[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):
[adjoint.point_source_block] filename = "sources.h5" groups = ["sources_1", "sources_2"]
{ "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
[adjoint.point_source]
Point sources for the wave equation.
Required: False
Full example (Please note that some options might be mutally exclusive):
[[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"
{ "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
[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):
[adjoint.point_source.rotation_on_input] matrix = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
{ "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
[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):
[adjoint.point_source.source_time_function] wavelet = "custom" filename = "source.h5" dataset_name = "/stf"
{ "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
[adjoint.gradient]
Model parameters and output filename for gradient computation.
Required: True
Full example (Please note that some options might be mutally exclusive):
[adjoint.gradient] parameterization = "rho-vp-vs" output_filename = "gradient.h5" format = "hdf5"
{ "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]
This groups describes the physical domain in which to run simulations.
Required: True
Full example (Please note that some options might be mutally exclusive):
[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"
{ "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
[domain.mesh]
Specify the domain topology.
Required: True
Full example (Please note that some options might be mutally exclusive):
[domain.mesh] filename = "mesh.h5" format = "hdf5"
{ "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"
[domain.model]
Specify the physical parameters of the domain.
Required: True
Full example (Please note that some options might be mutally exclusive):
[domain.model] filename = "model.h5" format = "hdf5"
{ "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"
[domain.geometry]
Specify the geometry of the domain.
Required: True
Full example (Please note that some options might be mutally exclusive):
[domain.geometry] filename = "geometry.h5" format = "hdf5"
{ "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]
This groups describes the hardware and job specific parameters.
Required: False
Full example (Please note that some options might be mutally exclusive):
[hardware]