Command line options

Sassena is configured by an xml configuration file. By default, Sassena will look for a file scatter.xml in the current directory. Some settings of the configuration file can be overridden by command line options.

--help

show help message

--config=FILENAME

xml configuration file name (default: ./scatter.xml)

--sample.structure.file=FILENAME

Structure file name (default: ./sample.pdb)

--sample.structure.format=FORMAT

Structure file format (default: pdb)

--stager.file=FILENAME

Trajectory file name (default: ./dump.dcd)

--stager.format=FORMAT

Trajectory file format (default: dcd)

--scattering.signal.file=FILENAME

Output file name (default: ./signal.h5)

--stager.target=SELECTION

Atom selection producing the signal (default: system)

--stager.dump=BOOL

Do/Don’t dump the postprocessed coordinates to a file (default: false)

--limits.computation.threads=NUMBER

Number of OpenMP threads per MPI process (default: 1). Alternatively, the standard OMP_NUM_THREADS environment variable can be set to control the thread count.