Package schrodinger :: Package application :: Package matsci :: Module jaguarworkflows

Module jaguarworkflows

Classes

JaguarFailedException
An exception that is thrown when either reading the Jaguar output file fails for some reason, or a successful reading shows that Jaguar failed.

RobustSubmissionJob
A JobControlJob object that will retry to submit multiple times for fizzled, jobs (if the queue setting is such) but will not attempt to retry a job that died.

Results
A low memory results object - because the driver ends up holding on to results for a long time and can be simultaneously holding results for a large number of calculations, we want to keep the memory footprint of each result low.

Step
Manages the start, monitoring and finish of a single step in a workflow

FrozenStep
A step that does not perform geometry optimization but just runs a calculation at the geometry of the parent step.

OptStep
A step that performs a geometry optimization

WorkFlow
A class to hold the data for and shepherd a single structure through all the jobs required to gather its data.

Functions

[hide private]

bool

is_ompi_allowed()
Check to see if the OMPI feature flag is enabled

dict

keyword_string_to_dict(keystring)
Return a dictionary whose keys are keywords and values are keyword values

str

keyword_dict_to_string(keydict, fix_for_cmdline=False)
Return a string of keywords specified by keydict

schrodinger.application.jaguar.output.JaguarOutput

get_jaguar_output(path, step_info="")
Get a JaguarOutput object for the given path

schrodinger.structure.Structure

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

schrodinger.structure.Structure

get_jaguar_out_mae(path)
Get the output Maestro structure for the jaguar calculation given by path

add_jaguar_files_to_jc_backend(base_name, backend=None, spm=False, others=None, restart=True)
Add the typical jaguar files for a job to the backend so they are returned to the working directory.

jobclass

create_job(options, filename, jobclass=RobustSubmissionJob)
Create a job of class jobclass that will run the Jaguar input file filename with options

schrodinger.job.queue.JobDJ

create_queue(options=None, host=None, **kwargs)
Create a JobDJ job with some default values and the given keyword arguments Current defaults:

run_workflows(jobq, active_workflows, writer)
Run all the workflows and return when they are finished.

Variables

[hide private]

__doc__ = ...

_version = '$Revision 0.0 $'

UNFINISHED_JOB_STATES = set([queue.WAITING, queue.ACTIVE])

HARTREE_TO_J = constants.physical_constants ['hartree-joule re...

HARTREE_TO_KCAL = HARTREE_TO_J* constants.N_A/(1000* constants...

HARTREE_TO_EV = 27.21138506

GAS_PHASE_ENERGY_PROP = 'r_j_Gas_Phase_Energy'

SOLUTION_ENERGY_PROP = 'r_j_Solution_Phase_Energy'

Function Details

[hide private]

is_ompi_allowed()

Check to see if the OMPI feature flag is enabled

Returns: bool: If the flag is enabled

keyword_string_to_dict(keystring)

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

keyword_dict_to_string(keydict, fix_for_cmdline=False)

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_jaguar_output(path, step_info="")

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_jaguar_output_structure(path)

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_jaguar_out_mae(path)

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_jaguar_files_to_jc_backend(base_name, backend=None, spm=False, others=None, restart=True)

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_job(options, filename, jobclass=RobustSubmissionJob)

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

Returns: jobclass

The created job

create_queue(options=None, host=None, **kwargs)

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_workflows(jobq, active_workflows, writer)

Run all the workflows and return when they are finished. At the end of this function, active_workflows will be empty.

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

Variables Details

[hide private]

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
...

HARTREE_TO_J

Value:

constants.physical_constants ['hartree-joule relationship'] [0]

HARTREE_TO_KCAL

Value:

HARTREE_TO_J* constants.N_A/(1000* constants.calorie)