Rob's SGT inputs

Rob's SGT generation code (emod3d-mpi) takes inputs via command-line arguments (in name=value pairs). For CyberShake, we pass the following command-line parameters:

1. Station name (name)
2. Volume dimension in grid coordinates (nx, ny, nz)
3. Simulation parameters (nt, dt, xmom, etc) – these can be specified in a parameters file, but overridden via the command line
4. CyberShake site location in grid coordinates (xsrc, ysrc, zsrc)
5. Various directories (logdir, seisdir, main_dump_dir, vmoddir)
6. Coordinates of the middle of the volume and the rotation angle (modellon, modellat, modelrot)
7. Output options (SGT output, every 10 timesteps)

and use command-line arguments to point to the following input files:

1. Parameter file listing a variety of simulation parameters. We override these with some command-line arguments.
2. Velocity model vp, vs, rho files. Each binary file contains 4-byte floats in fast x, z, y format. These files are generated using a query code for either CVM-S4 or CVM-H which generates 1 output file per core, and then merged.
3. Cordfile listing the points to save SGTs for. This file is generated by reading through all the SRF files to extract their points, and including an adaptive mesh. The format is:

 # comment lines
 num_points
 i	j	k	ijk concatenated(“index”)	lon	lat	depth (km)

The output from emod3d-mpi is one SGT file per core (per component; the SGT simulation must be run once for X, Y, and Z). Each SGT file contains:

1 sgtmaster structure
num_global_pts sgtindex structures
num_local_pts sgtheader structures
num_local_pts xx, yy, zz, xy, xz, yz tensor values for timestep=0
num_local_pts xx, yy, zz, xy, xz, yz tensor values for timestep=1

…

These are then merged into a single SGT file (per component) and reordered using merge_sgt into:

1 sgtmaster structure
num_global_pts sgtindex structures
for num_global_pts in fast z, y, x:
   1 sgtheader structure
   num_output_timesteps xx, yy, zz, xy xz, yz tensor values