Module jaguarworkflows

Check to see if the OMPI feature flag is enabled

Returns: bool

If the flag is enabled

Get maximum number of atoms currently supported by Jaguar

Returns: int

Maximum number of atoms

Return a dictionary whose keys are keywords and values are keyword values

Parameters:

• keystring (str) - The keywords are taken from this string - keywords must be in the keyword=value format and whitespace delimited.

Returns: dict

Dictionary of keyword/value pairs

Raises:

• ValueError - if any tokens do not match the keyword=value format

Return a string of keywords specified by keydict

Parameters:

• keydict (dict) - Dictionary - keys are Jaguar keywords, values are keyword values of str type
• fix_for_cmdline (bool) - True if the string should have special characters such as *, + and () preceeded by a backslash, False if the values should be unmodified. Use this if the keywords will eventually be passed to Jaguar on the command line (such as vcd_workflow_gui.py, JAGUAR-5164), but not if the keywords will be added to a JaguarInput object. The latter applies even if the keywords will be passed on the command line to a backend before being added (MATSCI-1088).

Returns: str

A string of space-separated keyword=value pairs

Get a JaguarOutput object for the given path

Parameters:

• path (str) - The path to the output file. May be just the base name of the output file (file instead of file.out)
• step_info (str) - The step name - optional, and only used to create more informative error messages.

Returns: schrodinger.application.jaguar.output.JaguarOutput

The JaguarOutput object for path

Raises:

• JaguarFailedException - If a problem is detected with the output

Get the structure associated with the .out results file indicated by path.

Parameters:

• path (str) - The path to the Jaguar output file - does not need to include the .out part of the output file name - can be absolute or relative

Returns: schrodinger.structure.Structure

The output structure object for the indicated .out file

Get the output Maestro structure for the jaguar calculation given by path

Parameters:

• path (str) - The path to the desired .mae file or the base name of the Jaguar job

Returns: schrodinger.structure.Structure

The output structure, or None if the file doesn't exist

Add the typical jaguar files for a job to the backend so they are returned to the working directory.

Parameters:

• base_name (str) - The base name of the files
• backend (schrodinger.job.jobcontrol._Backend) - The jobcontrol backend (from jobcontrol.get_backend()). If not supplied, an attempt will be made to obtain one.
• spm (bool) - Whether to add the _uvv_singlet.spm file
• others (list) - List of additional extensions for files named base_name.extension that should be added to the job control backend. For example: others=['_vib.spm', '_vcd.spm'] will add base_name_vib.spm and basename_vcd.spm. Note that any extensions need to include the leading '.'.
• restart (bool) - Whether to include the .0x.in file. These files are very large, so it's best not to keep them unless necessary.

Create a job of class jobclass that will run the Jaguar input file filename with options

Parameters:

• options (argparse.Namespace) - The input options.
• filename (str) - The name of the input file
• jobclass (schrodinger.job.JobControlJob) - The class used to create the job
• serial_only (bool) - Whether to force the job to run in serial. If False (default), parallel options will be used if available in options.

Returns: jobclass

The created job

Create a JobDJ job with some default values and the given keyword arguments Current defaults:

• verbosty: normal
• max_failures: NOLIMIT
• max_retries: 3

Parameters:

• options (argparse Namespace object) - the hostlist will be formed from the options.host property if not supplied by the host argument
• host (str) - The host string to use to create the queue

  All other keyword arguments will be passed on to the JobDJ object

Returns: schrodinger.job.queue.JobDJ

The JobDJ object

Run all the workflows and return when they are finished. At the end of this function, active_workflows will be empty. Returns True if at least one job did not fail (or there were no jobs to run), otherwise False.

Parameters:

• jobq (schrodinger.job.queue.JobDJ) - The JobDJ object to which jobs are added
• active_workflows (list) - List of Workflow objects that should be run
• writer (schrodinger.structure.StructureWriter) - The StructureWriter object to use to right output structures

Returns: bool

True if at least one job did not fail, otherwise False

__doc__

Value:

""" Workflow and Step classes to aid in running a series of Jaguar jobs. For each molecule, a Workflow object is established. The Steps the Wor kflow will run depend on the options chosen. Some Steps depend on other Steps to finish before starting. It is the job of the Workflow to submit jobs when al ...