src.interaction.Interaction Class Reference

Subclass of Target for fitting force fields to interaction energies. More...

Inheritance diagram for src.interaction.Interaction:

Collaboration diagram for src.interaction.Interaction:

Public Member Functions
def	__init__ (self, options, tgt_opts, forcefield)
def	read_reference_data (self)
	Read the reference ab initio data from a file such as qdata.txt. More...
def	indicate (self)
def	get (self, mvals, AGrad=False, AHess=False)
	Evaluate objective function. More...

Public Attributes
	select1
	Number of snapshots. More...
	select2
	Set fragment 2. More...
	loop_over_snapshots
	Set upper cutoff energy. More...
	eqm
	Reference (QM) interaction energies. More...
	label
	Snapshot label, useful for graphing. More...
	qfnm
	The qdata.txt file that contains the QM energies and forces. More...
	e_err
	e_err_pct
	mol
	Read in the trajectory file. More...
	ns
	engine
	Build keyword dictionaries to pass to engine. More...
	divisor
	Read in the reference data. More...
	prefactor
	weight
	emm
	objective

Detailed Description

Subclass of Target for fitting force fields to interaction energies.

Currently TINKER is supported.

We introduce the following concepts:

• The number of snapshots
• The reference interaction energies and the file they belong in (qdata.txt)

This subclass contains the 'get' method for building the objective function from any simulation software (a driver to run the program and read output is still required).

Definition at line 38 of file interaction.py.

Constructor & Destructor Documentation

__init__()

def src.interaction.Interaction.__init__	(		self,
			options,
			tgt_opts,
			forcefield
	)

Definition at line 41 of file interaction.py.

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Member Function Documentation

get()

def src.interaction.Interaction.get	(		self,
			mvals,
			AGrad = False,
			AHess = False
	)

Evaluate objective function.

Definition at line 185 of file interaction.py.

indicate()

def src.interaction.Interaction.indicate

(

self

)

Definition at line 160 of file interaction.py.

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read_reference_data()

def src.interaction.Interaction.read_reference_data

(

self

)

Read the reference ab initio data from a file such as qdata.txt.

After reading in the information from qdata.txt, it is converted into kcal/mol.

Definition at line 143 of file interaction.py.

Member Data Documentation

divisor

src.interaction.Interaction.divisor

Read in the reference data.

Definition at line 110 of file interaction.py.

e_err

src.interaction.Interaction.e_err

Definition at line 89 of file interaction.py.

e_err_pct

src.interaction.Interaction.e_err_pct

Definition at line 90 of file interaction.py.

emm

src.interaction.Interaction.emm

Definition at line 232 of file interaction.py.

engine

src.interaction.Interaction.engine

Build keyword dictionaries to pass to engine.

Definition at line 103 of file interaction.py.

eqm

src.interaction.Interaction.eqm

Reference (QM) interaction energies.

Definition at line 84 of file interaction.py.

label

src.interaction.Interaction.label

Snapshot label, useful for graphing.

Definition at line 86 of file interaction.py.

loop_over_snapshots

src.interaction.Interaction.loop_over_snapshots

Set upper cutoff energy.

Option for how much data to write to disk. LPW 2018-02-11: This is set to True if the target calculates a single-point property over several existing snapshots.

Definition at line 82 of file interaction.py.

mol

src.interaction.Interaction.mol

Read in the trajectory file.

Definition at line 92 of file interaction.py.

ns

src.interaction.Interaction.ns

Definition at line 96 of file interaction.py.

objective

src.interaction.Interaction.objective

Definition at line 233 of file interaction.py.

prefactor

src.interaction.Interaction.prefactor

Definition at line 129 of file interaction.py.

qfnm

src.interaction.Interaction.qfnm

The qdata.txt file that contains the QM energies and forces.

Definition at line 88 of file interaction.py.

select1

src.interaction.Interaction.select1

Number of snapshots.

Do we call Q-Chem for dielectric energies? (Currently needs to be fixed) Do we put the reference energy into the denominator? Do we put the reference energy into the denominator? Divide by the number of snapshots? What is the energy denominator? Set fragment 1

Definition at line 66 of file interaction.py.

select2

src.interaction.Interaction.select2

Set fragment 2.

Definition at line 70 of file interaction.py.

weight

src.interaction.Interaction.weight

Definition at line 189 of file interaction.py.

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

• interaction.py