Merge pull request #5393 from prckent/nexus_options

Nexus: document command line options

Author: prckent

nexus/sphinx_docs/user-scripts.rst

@@ -674,6 +674,30 @@ Currently, only workflows that use Quantum ESPRESSO (PWSCF) are supported by ``g
 
 Please contact the developers if any of these issues are critical for research.
 
-
+.. _command-line-options:
+
+Nexus command line options
+--------------------------
+
+Nexus user scripts process a number of command line options. These override settings in the script.  They are most commonly used to check the status of workflows (``--status_only``) and to check
+the generated workflows during development (``--generate_only``).
+
+- ``--status_only`` : Report status of all simulations and then exit.
+- ``--status`` : Controls displayed simulation status information.  May be set to one of 'standard', 'active', 'failed', or 'ready'.
+- ``--generate_only`` : Write inputs to all simulations and then exit.  Note that no dependencies are processed, e.g., if one simulation depends on another for an orbital file location or for a relaxed structure, this information will not be present in the generated input file for that simulation since no simulations are actually run with this option.
+- ``--graph_sims`` : Display a graph of simulation workflows, then exit.
+- ``--progress_tty`` : Print abbreviated polling messages. The polling message normally written to a newline every polling period will instead be overwritten in place, greatly shortening the output.
+- ``--sleep`` : Number of seconds between polls.  At each poll, new simulations are run once all simulations they depend on have successfully completed. A status line is printed every poll.
+- ``--machine`` : Name of the machine the simulations will be run on.  Workstations with between 1 and 128 cores may be specified by 'ws1' to 'ws128' (works for any machine where only mpirun is used).
+- ``--account`` : Account name required to submit jobs at some HPC centers.
+- ``--runs`` : Directory name to perform all runs in.  Simulation paths are appended to this directory.
+- ``--results`` : Directory to copy out lightweight results data.  If set to '', results will not be stored outside of the runs directory.
+- ``--local_directory`` : Base path where runs and results directories will be created
+- ``--pseudo_dir`` : Path to directory containing pseudopotential files.
+- ``--basis_dir`` : Path to directory containing basis set files (useful if running Gaussian-basis based QMC workflows).'
+- ``--ericfmt`` : Path to the ericfmt file used with GAMESS (required by GAMESS).
+- ``--mcppath`` : Path to the mcpdata file used with GAMESS (optional for most workflows).
+- ``--vdw_table`` : Path to the vdw_table file used with Quantum ESPRESSO (required only if running Quantum ESPRESSO with van der Waals functionals).
+- ``--qprc`` : Path to the quantum_package.rc file used with Quantum Package.
 
 .. bibliography:: bibs/methods.bib