As mentioned in the installation and availability section, the main APBS binary is installed in ${APBS_PREFIX}/bin where ${APBS_PREFIX} is the top-level directory you chose for the installation. Of course, you can move the binary to any directory you choose. APBS is invoked with a very simple syntax: apbs [options] input-file
Command line options include: - --outputfile=name Sets the output logging path (as described in the output logging section of the manual) to name, or name_N for parallel runs, where N is the processor ID. If --outputformat is not specified, a flat-file format will be used as the default.
- --outputformat=type Sets the output logging format. Accepted values are:
- flat Flat-file format (default).
- xml XML format
- --help Displays command line usage
- --version Displays the current APBS version
input-file is an input file with a specific syntax described in the section Input files. Besides the output files specified from within input-file and the optional logs as specified by use of the --output-file command line option, APBS writes data to three additional places: - Standard output. This will appear on your screen (if you don't redirect it somewhere) and will contain all the basic information about the electrostatics calculation.
- Standard error. This will also appear on your screen (if you don't redirect it somewhere) and will contain warnings and error messages.
- The file io.mc (or io.mc_N for parallel runs, where N is the processor ID. This gives you detailed information about the progress of the run with a particular focus on the numerical solver.
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