src.quantity Namespace Reference

Classes
class	Quantity
	Base class for thermodynamical quantity used for fitting. More...
class	Quantity_Density
class	Quantity_H_vap

Functions
def	mean_stderr (ts)
	Return mean and standard deviation of a time series ts. More...
def	energy_derivatives (engine, FF, mvals, h, pgrad, length, AGrad=True)
	Compute the first derivatives of a set of snapshot energies with respect to the force field parameters. More...

Variables
	logger = getLogger(__name__)

Function Documentation

energy_derivatives()

def src.quantity.energy_derivatives	(		engine,
			FF,
			mvals,
			h,
			pgrad,
			length,
			AGrad = True
	)

Compute the first derivatives of a set of snapshot energies with respect to the force field parameters.

The function calls the finite difference subroutine on the energy_driver subroutine also in this script.

Parameters

engine : Engine Use this Engine (GMX,TINKER,OPENMM etc.) object to get the energy snapshots. FF : FF Force field object. mvals : list Mathematical parameter values. h : float Finite difference step size. length : int Number of snapshots (length of energy trajectory). AGrad : Boolean Switch that turns derivatives on or off; if off, return all zeros.

Returns

G : np.array Derivative of the energy in a FF.np x length array.

Definition at line 52 of file quantity.py.

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mean_stderr()

def src.quantity.mean_stderr

(

ts

)

Return mean and standard deviation of a time series ts.

Definition at line 19 of file quantity.py.

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Variable Documentation

logger

src.quantity.logger = getLogger(__name__)

Definition at line 14 of file quantity.py.