User Documentation

Publications and presentations

• Milner, K., Becker, T. W., Boschi, L., Sain, J., Schorlemmer, D. and H. Waterhouse: The Solid Earth Research and Teaching Environment: a new software framework to share research tools in the classroom and across disciplines. Eos Trans. AGU, 90, 12, 2009.  PDF

• Waterhouse, H. D., K. Milner, T. W. Becker, J. Sain, and D. Schorlemmer: A Solid Earth Research and Teaching Environment, Opportunities and Challenges in Computational Geophysics workshop, Caltech, 2009.  PDF

Download and Installation

See our download and installation page

Module documentation

Follow these links for documentation on the science background behind the individual modules and references to original papers and background reading.

• hc
• larry
• larry3d
• Syn2D
• ConMan

GUI documentation

The SEATREE graphical user interface is divided into a module settings panel to the left, a module output panel to the right, and GMT plotting settings panel on the bottom. New script output is created by user-interaction with the module panel, the GMT panel will only replot the same output. The actual computations are done by calling python subroutines and issuing shell commands, whose progress can be monitored in the terminal where SEATREE was started.

The file menu allows switching between modules, saving and loading global SEATREE settings as an XML file, and saving plots as either PS or PNG formats.

The script menu can be used to display the actual shell commands issued by SEATREE for automatization. However, using python drivers is preferred.

hc flow calculator panel

See the hc technical documentation for background information.

• Calculation settings
  • Density scaling factor: assuming density model is a spherical harmonic expansion of a mantle tomography, velocity anomaly model in %, this factor will convert velocity anomalies into density anomalies. hc and the python drivers can also read depth-dependent scaling factors, but those are not implemented in the GUI yet. Use the  pdens.py script to edit density scaling files.

• Density type: dshs is the short spherical harmonics format used for the  Becker & Boschi (2002) compilation. Alternatively, leave free to use  the new HC format.

• Density model: spherical harmonics expansion of tomographic anomalies. SEATREE comes with a few examples from the  Becker & Boschi (2002) compilation
  • pmean/smean: P and S composite mantle tomography averages from  Becker & Boschi (2002)
  • s20rts: S wave model by Ritsema, J., H.J. van Heijst & J.H. Woodhouse, J. Geophys. Res., 109, 2004.
  • s362wmani: isotropic part of radially anisotropic S model by Kustowski et al. (JGR, submitted)
  • saw24b16: SH model by Mégnin, C. and Romanowicz , B. Geophys. J. Int, 143, 2000.
  • vox5p: P model by Boschi et al., as used in  Boschi et al., 2007

• Viscosity file: radial mantle viscosity structure in the format that can be handled and edited by  pvisc.py. visc.sh08 is the best-fit viscosity from  Steinberger, B. and A. Calderwood, Geophys. J. Int., 167, 2006., visc.C is a simplified three layer viscosity.

• Free slip/no-slip/plate velocity toggle: surface mechanical boundary condition. If plates are selected, will read pvel.sh.dat in the  the HC format.The file that is supplied are NUVEL-1 plate velocities from Gripp, A. E. and R.G. Gordon (Geophys. Res. Lett. 17, 1990), expanded up to L=63.

• Solution files from a computation can be saved and loaded.
• Compute velocities: will compute velocity solutions everywhere in the mantle, and the geoid
• Compute tractions: will compute traction on a surface with normal in radial direction, and the geoid

• Plot setting
  • Plot geoid: will expand the spherical harmonics solution for the geoid into a Netcdf grd file, plot it with GMT, and display a converted PS file
  • Plot plate velocities/radial tractions: will plot the velocity or traction solution at the selected layer number. The actual depth depends on the density input file and is displayed in the plot.

Larry

See the larry technical background information for details.

• Resolution: resolution of the tomographic parameterization in degrees at the equator
• Norm damping: Amount of norm damping applied to the least squares solution.
• Roughness damping: Amount of roughness damping applied to the least squares solution.
• Data file: Selection of Love and Rayleigh wave phase velocity measurements, numbers indicate period.
• Compute D Matrix: Compute the design matrix, only needed when resolution or dataset changes
• Compute solution: compute the least squares solution of the inverse problem, needed every time the damping changes.

The plot shows velocity anomalies as produced by the least squares solution. VR is variance reduction, |x| the model norm.

Larry3D

See the larry3d technical background information for details.

• Resolution: resolution of the tomographic parameterization in degrees at the equator (lower is better, but slower).
• Norm damping: Amount of norm damping applied to the least squares solution.
• Roughness damping: Amount of roughness damping applied to the least squares solution.
• Number of layers: Number of layers to be included in the model (more is better, but slower).
• Data type: Choose between available sets of data, sources, and receivers. Currently Harvard, Houser, or Ritsema.
• Ray type: Choose type of waves to consider. Currently limited to P and S waves.
• Compute D Matrix: Compute the design matrix, not affected by damping.
• Compute solution: Compute the least squares solution of the inverse problem.
• Layer to plot: Choose which layer to plot using GMT.
• Plot layer: Creates and displays a GMT plot of the solution for that layer.

Syn2D

See the Syn2D technical background information for details.

• Plot Type: switches between postscript based/GMT output and Matplotlib direct plotting
• Input Model Type: select a checkerboard model, or a square raster image gray scale file for synthetic "Earth" structure
• Checkerboard size: control box size if checkerboard is selected
• Make model / Plot model: create synthetic Earth model, and display a plot of it
• Station mode: allows for different geometries for the station (seismometer) and event (earthquake) distributions
• Synth Gen Data Pnts: Total number of traveltime observations generated from the station-event geometry
• Num Recordings per Event: number of stations which record each event
• Make data / Plot data: generate the dataset of synthetic travel times, and display data (by selecting stations, events, or raypaths)
• Damping value: roughness damping value for the inversion of the synthetic data
• Invert Data / Plot inversion: perform and visualize the inversion.

GMT settings panel

• Colormap type: GMT colormaps as in  this GMT cpt overview
• Adjust scale: will automatically adjust background colors and vector lengths. Switch this off to compare results for different settings on the same scale.
• Pbound: switch NUVEL plate boundaries on and off
• Grid lines: add grid lines to the map, useful to see the properties of the global projection
• Pound and vectors color buttons: modify the color of those polygons
• Projection: choose between different projections, center longitudes and PS map width in inches.

Sreenshots

Screenshots of the SEATREE GUI in action

Bug reports, feedback, and release history