spin_states.py Command Help

Command: $SCHRODINGER/jaguar run spin_states.py

usage: $SCHRODINGER/jaguar run spin_states.py [-h]
                                              [-multiplicity {low,intermediate,high,ground,excited,all}]
                                              [-k =<key>=<value> pairs]
                                              [-noistate] [-norun]
                                              [-noatomicsect]
                                              [-auxfile AUXFILE]
                                              input_files [input_files ...]

This workflow is intended to use DFT to explore the density of
states of molecules.  It can be used for any molecule. However,
it's most advanced settings are for mononuclear octahedral
transition metal complexes for which the flag '-multiplicity=
ground' may be used to predict the ground state multiplicity
using a simplified physical model.  Among other things the script can
be used to find the ground states of systems for which it is
otherwise difficult to do so.  It works by creating several Jaguar
jobs which use different options for the SCF initial guesses, for
example different multiplicities and possibly different initial
electronic configurations of the d-manifold.  The user may need
to use the Maestro build toolbar to assign atomic formal charges.
By default the B3LYP functional is used in a medium sized basis
set that employs a relativistic ECP and the use of molecular point 
point group symmetry is disabled.

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  input_files           White space delimited list of input
                        *mae file(s), i.e. <file1>.mae <file2>.mae
                        etc., where each *mae file may contain
                        multiple structures.

options:
  -h, --help            show this help message and exit
  -multiplicity {low,intermediate,high,ground,excited,all}
                        Choose the desired spin state of the calculations.
                        The choices 'low', 'intermediate', and 'high' specify
                        singlets or doublets, triplets or quartets, and
                        quintets and sextets, respectively.  For certain
                        cases 'intermediate' and 'high' are equivalent.  For octahedral
                        mononuclear transition metal complexes the choices
                        'ground' and 'excited' specify that the ground or excited
                        state multiplicities will be obtained using a spin
                        multiplicity prediction model.
  -k =<key>=<value> pairs, -keyword =<key>=<value> pairs, --keyword =<key>=<value> pairs
                        Set the listed Jaguar &gen section keyword,
                        for example '-keyword dftname=B3LYP',
                        '-keyword maxit=100', etc.
  -noistate             For systems containing a single transition
                        metal do not perform Jaguar calculations for
                        every possible value of the &gen section
                        keyword 'istate'.  Use this keyword to run
                        only a single SCF initial guess per multiplicity.
  -norun                Create Jaguar input files but do not run
                        the Jaguar calculations.
  -noatomicsect         Do not create an &atomic section in the
                        Jaguar input files.
  -auxfile AUXFILE      Specify extra files to be transferred remotely.

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.