schrodinger.application.desmond.stage.app.matsci module¶

Various multisim concrete stage classes.

class schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob(*arg, **kwarg)¶

Bases: schrodinger.application.desmond.cmj.StageBase

This class runs multiple SiteMap jobs for mixed resolution cosolvent simulations

NAME = 'aacg_sitemap'¶

SITEMAP_CMD = '/scr/buildbot/savedbuilds/2024-3/NB/build-133/sitemap'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

__init__(*arg, **kwarg)¶: Initialize the aacg-sitemap-multijob stage

crunch()¶: Submit the multiple SiteMap jobs

class schrodinger.application.desmond.stage.app.matsci.AverageCell(*args, **kwargs)¶

Bases: schrodinger.application.desmond.cmj.StructureStageBase

NAME = 'average_cell'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

run(jobname: str, input_fname: str) → Optional[str]¶

Run stage, return filename of the CMS model with scaled FFIO parameters

Parameters

jobname (str) – Jobname for this stage.
input_fname (str) – Filename for the input structure.

Return type

str

Returns

Filename for the output structure.

class schrodinger.application.desmond.stage.app.matsci.DeformCell(*args, **kwargs)¶

Bases: schrodinger.application.desmond.cmj.StructureStageBase

Deform cell axes based on the deformation.

NAME = 'deform_cell'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

run(jobname: str, input_fname: str) → Optional[str]¶

Run stage, return filename of the deformed CMS model.

Parameters

jobname (str) – Jobname for this stage.
input_fname (str) – Filename for the input structure.

Return type

str

Returns

Filename for the output structure.

class schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder(*args, **kwargs)¶

Bases: schrodinger.application.desmond.cmj.StructureStageBase

Add solvent to the slab. Slab must be along the Z direction.

NAME = 'solvate_slab_builder'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

run(jobname: str, input_fname: str) → Optional[str]¶

Parameters

jobname – Jobname for this stage.
input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

class schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis(*arg, **kwarg)¶

Bases: schrodinger.application.desmond.cmj.StageBase

This class sets up and runs automatic analysis for material-science related jobs.

NAME = 'matsci_analysis'¶

DEFAULT_BULK_TYPE = 'cohes_e density heat_vap specific_heat pressure_tensor sol_param volume'¶

BULK_TYPE_NUM = 7¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

__init__(*arg, **kwarg)¶: initialization of Material Science Analysis stage

getMSJobKeywords()¶

This returns the keywords used for this job type.

Returns: Standard job keywords
Return type: list of ark objects

crunch()¶: do all the setup and submit the calculations

class schrodinger.application.desmond.stage.app.matsci.ScaleEffectiveSolvent(*args, **kwargs)¶

Bases: schrodinger.application.desmond.cmj.StructureStageBase

Scale all nonbonded interactions by the passed scaling factor.

NAME = 'ses_stage'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

run(jobname: str, input_fname: str) → Optional[str]¶

Run stage, return filename of the CMS model with scaled FFIO parameters

Parameters

jobname (str) – Jobname for this stage.
input_fname (str) – Filename for the input structure.

Return type

str

Returns

Filename for the output structure.

class schrodinger.application.desmond.stage.app.matsci.ExtractSubSystem(should_pack=True)¶

Bases: schrodinger.application.desmond.cmj.StageBase

This stage extract subsystem from cms and trajectory from the previous simulation stage based on asl string. The stage essentially perform the same operation as trj_extract_subsystem.py script.

NAME = 'extract_subsystem'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

crunch()¶: do all the setup and submit the calculations

class schrodinger.application.desmond.stage.app.matsci.FrozenPhononCorrection(should_pack=True)¶

Bases: schrodinger.application.desmond.cmj.StageBase

Compute the frozen phonon correction for the given structure.

NAME = 'frozen_phonon_correction'¶

PARAM = <schrodinger.utils.sea.sea.Map object>¶

crunch()¶: do all the setup and submit the calculations

hook_captured_successful_job(job: schrodinger.application.desmond.cmj.Job)¶