schrodinger.application.desmond.stage.app.matsci module¶
Various multisim concrete stage classes.
Copyright Schrodinger, LLC. All rights reserved.
- 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)¶