Package schrodinger :: Package application :: Package matsci :: Module mecp_mod :: Class JaguarJobs

Class JaguarJobs

object --+
         |
        JaguarJobs

Manages Jaguar jobs.

Instance Methods

[hide private]

__init__(self, data=[(0, 3, 0), (0, 1, 1)], scf_gs=False, kwargs=OrderedDict([('iuhf', 2), ('dftname', 'B3LYP'), ('basis', 'MID..., base_name='mecp', host='localhost', nproc=2, tpp=1, logger=None)
Create an instance.

clearJobs(self)
Clear the list of jobs attribute.

setStructure(self, astructure)
Set the structure to use for the jobs.

setInTemplates(self, in_templates=None)
Set the input templates to use for the jobs.

setUpLaunchDir(self, launch_dir=None)
Set up the launch directory for the jobs.

str

getBaseName(self, idx)
Return a base name for the given job.

dict

getKwargs(self, charge, multiplicity, state)
Return the kwargs for the given job.

list

getFileNames(self, base_name)
Return a list of files names for the given job.

str

getInTemplate(self, idx)
Return an input template file.

queue.JobControlJob

getJob(self, base_name, jag_input_file)
Return a queue.JobControlJob for the given job.

setUpInputFiles(self, job)
Set up the input files for the job.

runJobs(self)
Run the jobs.

processOutput(self)
Process the output from the jobs.

list

runIt(self, astructure, in_templates=None, launch_dir=None)
Main function to run the jobs.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, data=`[(`0`,` 3`,` 0`),` `(`0`,` 1`,` 1`)]`, scf_gs=False, kwargs=OrderedDict([('iuhf', 2), ('dftname', 'B3LYP'), ('basis', 'MID`...`, base_name=`'mecp'`, host=`'localhost'`, nproc=2, tpp=1, logger=None)
(Constructor)

Create an instance.

Parameters:

data (list) - contains (charge, multiplicity, state) tuples for all jobs, for electronic state 0 is the ground state and <N> is the N-th excited state
scf_gs (bool) - specify whether ground states should be determined using an SCF
kwargs (dict) - dictionary of Jaguar &gen section key-value pairs
base_name (str) - a base name used to name the jobs and their related files
host (str) - the host on which to run the jobs
nproc (int) - the number of processors to use for running the jobs, i.e. the number of simultaneous jobs
tpp (int) - the number of threads to use for the jobs, i.e. -TPP (threads-per-process)
logger (logging.Logger or None) - output logger or None if there isn't one

Overrides: object.__init__

setStructure(self, astructure)

Set the structure to use for the jobs.

Parameters:

astructure (schrodinger.structure.Structure) - the structure to use for the jobs

setInTemplates(self, in_templates=None)

Set the input templates to use for the jobs.

Parameters:

in_templates (list or None) - a list of Jaguar input files to use as templates for creating the jobs, if used then the length of this list should be equivalent to that of the data attribute, the first ZMAT section is overwritten with the input astructure argument, use None if there aren't any templates

setUpLaunchDir(self, launch_dir=None)

Set up the launch directory for the jobs.

Parameters:

launch_dir (str or None) - the directory from which to launch the jobs or None if there isn't one (in which case the CWD will be used)

getBaseName(self, idx)

Return a base name for the given job.

Parameters:

idx (int) - the job index

Returns: str

base name for the job

getKwargs(self, charge, multiplicity, state)

Return the kwargs for the given job.

Parameters:

charge (int) - net molecular charge
multiplicity (int) - molecular multiplicity
state (int) - the electronic state, 0 is the ground state and <N> is the N-th excited state

Returns: dict

Jaguar kwargs for the job

getFileNames(self, base_name)

Return a list of files names for the given job.

Parameters:

base_name (str) - base name for the job

Returns: list

file names for the job

getInTemplate(self, idx)

Return an input template file.

Parameters:

idx (int) - the job index

Returns: str

the input template file

getJob(self, base_name, jag_input_file)

Return a queue.JobControlJob for the given job.

Parameters:

base_name (str) - base name for the job
jag_input_file (str) - Jaguar input file for the job

Returns: queue.JobControlJob

the job object

setUpInputFiles(self, job)

Set up the input files for the job.

Parameters:

job (JaguarJob) - a JaguarJob object containing various job parameters

runIt(self, astructure, in_templates=None, launch_dir=None)

Main function to run the jobs.

Parameters:

astructure (schrodinger.structure.Structure) - the structure to use for the jobs
in_templates (list or None) - a list of Jaguar input files to use as templates for creating the jobs, if used then the length of this list should be equivalent to that of the data attribute, the first ZMAT section is overwritten with the input astructure argument, use None if there aren't any templates
launch_dir (str or None) - the directory from which to launch the jobs or None if there isn't one (in which case the CWD will be used)

Returns: list

contains JaguarJob objects for all jobs

Class JaguarJobs

__init__(self, data=[(0, 3, 0), (0, 1, 1)], scf_gs=False, kwargs=OrderedDict([('iuhf', 2), ('dftname', 'B3LYP'), ('basis', 'MID..., base_name='mecp', host='localhost', nproc=2, tpp=1, logger=None) (Constructor)

setStructure(self, astructure)

setInTemplates(self, in_templates=None)

setUpLaunchDir(self, launch_dir=None)

getBaseName(self, idx)

getKwargs(self, charge, multiplicity, state)

getFileNames(self, base_name)

getInTemplate(self, idx)

getJob(self, base_name, jag_input_file)

setUpInputFiles(self, job)

runIt(self, astructure, in_templates=None, launch_dir=None)

init(self, data=`[(`0`,` 3`,` 0`),` `(`0`,` 1`,` 1`)]`, scf_gs=False, kwargs=OrderedDict([('iuhf', 2), ('dftname', 'B3LYP'), ('basis', 'MID`...`, base_name=`'mecp'`, host=`'localhost'`, nproc=2, tpp=1, logger=None)
(Constructor)