You're reading an old version (v5.0) of this documentation. If you want up-to-date information, please have a look at master.

Command Line Arguments

Normally MARE2DEM is called with just the name of the input resistivity file:

mpirun -n <np> MARE2DEM <resistivity file>

where <resistivity file> is the name of the required input Resistivity File (.resistivity). By convention, this file should have the extension .resistivity. For example inputModel.0.resistivity. The model found by each inversion iteration is then output to a new resistivity file with the iteration number incremented. For example: inputModel.1.resistivity, inputModel.2.resistivity, … The corresponding model responses are written to inputModel.1.resp, inputModel.2.resp,…

The command mpirun starts up the parallel message passing interface environment and has argument -n <np> where <np> should be the number of processing cores on your system (laptop, desktop, etc).

For inversion models, MARE2DEM will also outputs the normalized data sensitivities to the free parameters (see Normalized Sensitivity). The sensitivity is output to the file <resistivity file>.<iter#>.sensitivity. plotMARE2DEM.m can be used to plot the sensitivity; it can be overlain as contours or shading on inversion models. The sensitivity can be used as a relative measure of data sensitivity to structure, but be aware this is a linearized approximation for what is a non-linear inverse problem, so results should be taken with a grain of salt.

MARE2DEM has a few other command line options for more advanced usage, but most users won’t need to use these:

mpirun -n <np>  MARE2DEM [-F] [-J] [-scratch <scratchfolder>] <resistivity file> [<output file>]

where the arguments in brackets [] are optional:

<output file> - With this option, the output files are named <output file>.1.resistivity, <output file>.1.resp, <output file>.2.resistivity, <output file>.2.resp,…

-F Computes the forward response of the input model only. The forward response is output to <resistivity file>.resp. Note that if MARE2DEM detects no free parameters in the input model it will only compute the forward response; thus, typically the -F is only required when you want to compute the forward response of an inversion model (say when doing sensitivity tests of anomalous features found by inversion, where you paint over the anomaly using Mamba2D and then see how the MT or CSEM responses change).

-J Outputs the full Jacobian matrix of the input model for each iteration. This flag is provided for advanced users wishing to use the Jacobian matrix in other calculations and normal users do not need to use this; further, the output Jacobian files can be quite large. The Jacobian matrix is written to an unformatted binary data file columnwise with the naming convention <resistivity file>.<iter#>.jacobianBin. Note that the saved J is unweighted (i.e. it has NOT been normalized by the data uncertainties).

-scratch <scratchfolder> Use the specified directory for the scratch files required for 2.5D CSEM inversion (but not needed for MT). Optimally this should be a local directory on each compute node and not a networked directory.