src.vibration.Vibration Class Reference

Subclass of Target for fitting force fields to vibrational spectra (from experiment or theory). More...

Inheritance diagram for src.vibration.Vibration:

Collaboration diagram for src.vibration.Vibration:

Public Member Functions
def	__init__ (self, options, tgt_opts, forcefield)
	Initialization. More...
def	read_reference_data (self)
	Read the reference vibrational data from a file. More...
def	indicate (self)
	Print qualitative indicator. More...
def	vibration_driver (self)
def	vib_overlap (self, v1, v2)
	Calculate overlap between vibrational modes for two Cartesian displacements. More...
def	get (self, mvals, AGrad=False, AHess=False)
	Evaluate objective function. More...

Public Attributes
	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...
	vfnm
	The vdata.txt file that contains the vibrations. More...
	engine
	Read in the reference data. More...
	na
	Number of atoms. More...
	ref_eigvals
	ref_eigvecs
	reassign
	c2r
	overlaps
	calc_eigvals
	objective

Detailed Description

Subclass of Target for fitting force fields to vibrational spectra (from experiment or theory).

Currently Tinker is supported.

Definition at line 40 of file vibration.py.

Constructor & Destructor Documentation

__init__()

def src.vibration.Vibration.__init__	(		self,
			options,
			tgt_opts,
			forcefield
	)

Initialization.

Definition at line 45 of file vibration.py.

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Member Function Documentation

get()

def src.vibration.Vibration.get	(		self,
			mvals,
			AGrad = False,
			AHess = False
	)

Evaluate objective function.

Definition at line 166 of file vibration.py.

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indicate()

def src.vibration.Vibration.indicate

(

self

)

Print qualitative indicator.

Definition at line 124 of file vibration.py.

read_reference_data()

def src.vibration.Vibration.read_reference_data

(

self

)

Read the reference vibrational data from a file.

Definition at line 78 of file vibration.py.

vib_overlap()

def src.vibration.Vibration.vib_overlap	(		self,
			v1,
			v2
	)

Calculate overlap between vibrational modes for two Cartesian displacements.

Parameters

v1, v2 : np.ndarray The two sets of Cartesian displacements to compute overlap for, 3*N_atoms values each.

Returns

float Overlap between mass-weighted eigenvectors

Definition at line 154 of file vibration.py.

vibration_driver()

def src.vibration.Vibration.vibration_driver

(

self

)

Definition at line 132 of file vibration.py.

Member Data Documentation

c2r

src.vibration.Vibration.c2r

Definition at line 198 of file vibration.py.

calc_eigvals

src.vibration.Vibration.calc_eigvals

Definition at line 218 of file vibration.py.

engine

src.vibration.Vibration.engine

Read in the reference data.

Build keyword dictionaries to pass to engine. Create engine object.

Definition at line 71 of file vibration.py.

loop_over_snapshots

src.vibration.Vibration.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 62 of file vibration.py.

na

src.vibration.Vibration.na

Number of atoms.

Definition at line 80 of file vibration.py.

objective

src.vibration.Vibration.objective

Definition at line 219 of file vibration.py.

overlaps

src.vibration.Vibration.overlaps

Definition at line 203 of file vibration.py.

reassign

src.vibration.Vibration.reassign

Definition at line 125 of file vibration.py.

ref_eigvals

src.vibration.Vibration.ref_eigvals

Definition at line 81 of file vibration.py.

ref_eigvecs

src.vibration.Vibration.ref_eigvecs

Definition at line 82 of file vibration.py.

vfnm

src.vibration.Vibration.vfnm

The vdata.txt file that contains the vibrations.

Definition at line 64 of file vibration.py.

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

• vibration.py