Subclass of Target for fitting force fields to hydration free energies. More...

Inheritance diagram for src.hydration.Hydration:

Collaboration diagram for src.hydration.Hydration:

Public Member Functions
def	__init__ (self, options, tgt_opts, forcefield)
	Initialization. More...

def	read_reference_data (self)
	Read the reference hydrational data from a file. More...

def	run_simulation (self, label, liq, AGrad=True)
	Submit a simulation to the Work Queue or run it locally. More...

def	submit_liq_gas (self, mvals, AGrad=True)
	Set up and submit/run sampling simulations in the liquid and gas phases. More...

def	submit_jobs (self, mvals, AGrad=True, AHess=True)

def	build_engines (self)
	Create a list of engines which are used to calculate HFEs using single point evaluation. More...

def	indicate (self)
	Print qualitative indicator. More...

def	hydration_driver_sp (self)
	Calculate HFEs using single point evaluation. More...

def	get_sp (self, mvals, AGrad=False, AHess=False)
	Get the hydration free energy and first parameteric derivatives using single point energy evaluations. More...

def	get_exp (self, mvals, AGrad=False, AHess=False)
	Get the hydration free energy using the Zwanzig formula. More...

def	get_ti2 (self, mvals, AGrad=False, AHess=False)
	Get the hydration free energy using two-point thermodynamic integration. More...

def	get (self, mvals, AGrad=False, AHess=False)
	Evaluate objective function. More...

Public Attributes
	last_traj

	extra_output

	loop_over_snapshots
	LPW 2018-02-11: This is set to True if the target calculates a single-point property over several existing snapshots. More...

	datafile
	The vdata.txt file that contains the hydrations. More...

	engine_opts
	Scripts to be copied from the ForceBalance installation directory. More...

	IDs

	expval

	experr

	nicknames

	have_nicks

	have_experr

	molecules

	whfe

	engines

	liq_engines

	gas_engines

	hfe_dict

	hfe_err

	hfemode

	calc

	calc_err

	objective

Detailed Description

Subclass of Target for fitting force fields to hydration free energies.

Definition at line 26 of file hydration.py.

Constructor & Destructor Documentation

◆ init()

def src.hydration.Hydration.__init__	(	self,
		options,
		tgt_opts,
		forcefield
	)

Initialization.

Definition at line 31 of file hydration.py.

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Member Function Documentation

◆ build_engines()

def src.hydration.Hydration.build_engines ( self )

Create a list of engines which are used to calculate HFEs using single point evaluation.

Definition at line 266 of file hydration.py.

◆ get()

def src.hydration.Hydration.get	(	self,
		mvals,
		AGrad = `False`,
		AHess = `False`
	)

Evaluate objective function.

Definition at line 438 of file hydration.py.

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◆ get_exp()

def src.hydration.Hydration.get_exp	(	self,
		mvals,
		AGrad = `False`,
		AHess = `False`
	)

Get the hydration free energy using the Zwanzig formula.

We will obtain two different estimates along with their uncertainties.

Definition at line 335 of file hydration.py.

◆ get_sp()

def src.hydration.Hydration.get_sp	(	self,
		mvals,
		AGrad = `False`,
		AHess = `False`
	)

Get the hydration free energy and first parameteric derivatives using single point energy evaluations.

Definition at line 320 of file hydration.py.

◆ get_ti2()

def src.hydration.Hydration.get_ti2	(	self,
		mvals,
		AGrad = `False`,
		AHess = `False`
	)

Get the hydration free energy using two-point thermodynamic integration.

Definition at line 403 of file hydration.py.

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◆ hydration_driver_sp()

def src.hydration.Hydration.hydration_driver_sp ( self )

Calculate HFEs using single point evaluation.

Definition at line 310 of file hydration.py.

◆ indicate()

def src.hydration.Hydration.indicate ( self )

Print qualitative indicator.

Definition at line 277 of file hydration.py.

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◆ read_reference_data()

def src.hydration.Hydration.read_reference_data ( self )

Read the reference hydrational data from a file.

Definition at line 114 of file hydration.py.

◆ run_simulation()

def src.hydration.Hydration.run_simulation	(	self,
		label,
		liq,
		AGrad = `True`
	)

Submit a simulation to the Work Queue or run it locally.

Inputs: label = The name of the molecule (and hopefully the folder name that you're running in) liq = True/false flag indicating whether to run in liquid or gas phase

Definition at line 169 of file hydration.py.

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◆ submit_jobs()

def src.hydration.Hydration.submit_jobs	(	self,
		mvals,
		AGrad = `True`,
		AHess = `True`
	)

Definition at line 253 of file hydration.py.

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◆ submit_liq_gas()

def src.hydration.Hydration.submit_liq_gas	(	self,
		mvals,
		AGrad = `True`
	)

Set up and submit/run sampling simulations in the liquid and gas phases.

Definition at line 227 of file hydration.py.

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Member Data Documentation

◆ calc

src.hydration.Hydration.calc

Definition at line 452 of file hydration.py.

◆ calc_err

src.hydration.Hydration.calc_err

Definition at line 454 of file hydration.py.

◆ datafile

src.hydration.Hydration.datafile

The vdata.txt file that contains the hydrations.

Definition at line 81 of file hydration.py.

◆ engine_opts

src.hydration.Hydration.engine_opts

Scripts to be copied from the ForceBalance installation directory.

Read in the reference data Set engname in OptionDict, which gets printed to disk. This is far from an ideal solution... Copy target options into engine options.

Definition at line 90 of file hydration.py.

◆ engines

src.hydration.Hydration.engines

Definition at line 267 of file hydration.py.

◆ experr

src.hydration.Hydration.experr

Definition at line 118 of file hydration.py.

◆ expval

src.hydration.Hydration.expval

Definition at line 117 of file hydration.py.

◆ extra_output

src.hydration.Hydration.extra_output

Definition at line 72 of file hydration.py.

◆ gas_engines

src.hydration.Hydration.gas_engines

Definition at line 269 of file hydration.py.

◆ have_experr

src.hydration.Hydration.have_experr

Definition at line 125 of file hydration.py.

◆ have_nicks

src.hydration.Hydration.have_nicks

Definition at line 123 of file hydration.py.

◆ hfe_dict

src.hydration.Hydration.hfe_dict

Definition at line 323 of file hydration.py.

◆ hfe_err

src.hydration.Hydration.hfe_err

Definition at line 337 of file hydration.py.

◆ hfemode

src.hydration.Hydration.hfemode

Definition at line 379 of file hydration.py.

◆ IDs

src.hydration.Hydration.IDs

Definition at line 116 of file hydration.py.

◆ last_traj

src.hydration.Hydration.last_traj

Definition at line 70 of file hydration.py.

◆ liq_engines

src.hydration.Hydration.liq_engines

Definition at line 268 of file hydration.py.

◆ loop_over_snapshots

src.hydration.Hydration.loop_over_snapshots

LPW 2018-02-11: This is set to True if the target calculates a single-point property over several existing snapshots.

Definition at line 79 of file hydration.py.

◆ molecules

src.hydration.Hydration.molecules

Definition at line 150 of file hydration.py.

◆ nicknames

src.hydration.Hydration.nicknames

Definition at line 119 of file hydration.py.

◆ objective

src.hydration.Hydration.objective

Definition at line 455 of file hydration.py.

◆ whfe

src.hydration.Hydration.whfe

Definition at line 157 of file hydration.py.

The documentation for this class was generated from the following file:

hydration.py

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ build_engines()

◆ get()

◆ get_exp()

◆ get_sp()

◆ get_ti2()

◆ hydration_driver_sp()

◆ indicate()

◆ read_reference_data()

◆ run_simulation()

◆ submit_jobs()

◆ submit_liq_gas()

Member Data Documentation

◆ calc

◆ calc_err

◆ datafile

◆ engine_opts

◆ engines

◆ experr

◆ expval

◆ extra_output

◆ gas_engines

◆ have_experr

◆ have_nicks

◆ hfe_dict

◆ hfe_err

◆ hfemode

◆ IDs

◆ last_traj

◆ liq_engines

◆ loop_over_snapshots

◆ molecules

◆ nicknames

◆ objective

◆ whfe

◆ init()