fukui.py Command Help

Command: $SCHRODINGER/jaguar run fukui.py

usage: $SCHRODINGER/jaguar run fukui.py [-h] [-plus] [-minus] [-k KEYWORDS]
                                        [-delta DELTA] [-WAIT] [-DEBUG]
                                        [-jobname <name>] [-subdir] [-recover]
                                        [-no_subjob_files]
                                        [-scr <absolute path>] [-PARALLEL <N>]
                                        [-max_threads <T>]
                                        [-procs_per_node <N>]
                                        [-use_one_node | -use_multiple_nodes]
                                        [-HOST <host>:<M>]
                                        [-SUBHOST <host>:<M>] [-SAVE]
                                        [-NOJOBID] [-OPLSDIR <oplsdir>]
                                        infile

Calculate Fukui functions (difference densities) for each input structure
and write the data to a .vis file

positional arguments:
  infile                Please specify a single .mae file (can contain multiple structures) or .in file.

options:
  -h, --help            show this help message and exit
  -plus                 Calculate f+ = rho(N+1) - rho(N). If both -plus and -minus are given, f0 = 1/2(f+ + f-) is also calculated.
  -minus                Calculate f- = rho(N) - rho(N-1). If both -plus and -minus are given, f0 = 1/2(f+ + f-) is also calculated.
  -k KEYWORDS, -keyword KEYWORDS, --keyword KEYWORDS
                        set Jaguar &gen section keywords
  -delta DELTA          Fraction of electron to use for perturbations [default = 0.01]

other options:
  -WAIT                 Wait for job to finish before returning prompt.
  -DEBUG, -D            Print detailed information about job launch.
  -jobname <name>       Set the job name.
  -subdir               Run Jaguar in a sub-directory.
  -recover              Manually re-run a job using the recover mechanism. NOTE this option is not recommended for default recovery jobs.
                        Use "jaguar run <filename>.recover" instead (see documentation for more details).
  -no_subjob_files      Do not return subjob output files to launch directory.
  -scr <absolute path>  Specify a scratch directory (must not already exist). Directory must be given as an absolute path.
                        Note this will be used by the Fortran backend and is independent of the specification of -TMPDIR.
  -PARALLEL <N>         Use up to <N> CPUs simultaneously for the whole workflow, automatically allocated among subjobs, including threaded subjobs.
  -max_threads <T>      Use no more than <T> OpenMP threads for each Jaguar subjob. Default 8.
  -procs_per_node <N>   Use no more than <N> CPUs per node. Default is taken from the schrodinger.hosts file; if undefined 8.
  -use_one_node         Force CPU resources to be requested upfront on one node. 
                        This pool of CPUs will be used for the duration of the job instead of resubmitting to the queue.
  -use_multiple_nodes   Force CPU resources to be requested dynamically from the queue (if available) instead of upfront on one node.

commonly used Schrodinger Suite options:
  -HOST <host>:<M>      Run job remotely on host <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs. 
                        May be combined with -PARALLEL <N>.
  -SUBHOST <host>:<M>   Run any subjobs remotely on subhost <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs. 
                        May be combined with -PARALLEL <N>.
  -SAVE                 Return .zip file of scratch directory.
  -NOJOBID              Run Jaguar interactively without jobserver (not available with python workflows).
  -OPLSDIR <oplsdir>    Use custom FF parameters from specified directory for workflows which support it.