Class SystemBuilder

General class used for system builder workups.

Instance Methods

[hide private]

__init__(self, root=None)

outIons(self, log)
Get the ion, positive and negative salt counts from log.

outMolarity(self, log)
Gets molarity from system builder log

getSolventVolume(self)
Calculates approx.

outLatticeVectors(self, log)
Returns the lattice vectors as an array

outBoundary(self, log)
This will return a dict of terms depending on the boundary conditions.

workupBoundary(self, bound_cfg, buffer=5)
Generalized workup for boundary conditions.

workupIon(self, ion_cfg, buffer=0)
Generalized workup for ions.

workupExclude(self, asl1, asl2, dist, sel)

workupDensity(self, density_cfg)
Calculated density from: Desmond density = ((#mols * MM)/Na)/(Water Vol * 10^-24)

workupMolarity(self, molarity_workup)
Molarity workup

Method Details

[hide private]

getSolventVolume(self)

Calculates approx. water (not other solvents) from system builder log

outBoundary(self, log)

This will return a dict of terms depending on the boundary conditions. For cubic and orthorhombic it returns (shape, volume) and for all triclinic shapes it returns (shape, volume, alpha, beta, gamma)

workupBoundary(self, bound_cfg, buffer=5)

Generalized workup for boundary conditions. Uses config.

Parameters:

bound_cfg (dict) - boundary paramters from cfg file

workupIon(self, ion_cfg, buffer=0)

Generalized workup for ions. Uses config.

Parameters:

ion_cfg (dict) - ion parameters from cfg file

workupDensity(self, density_cfg)

Calculated density from: Desmond density = ((#mols * MM)/Na)/(Water Vol * 10^-24)

MM = molar mass Na = Avagadro's number water = volume of water

workupMolarity(self, molarity_workup)

Molarity workup

self.L - converts 1L = 10^27 A^3 self.Na - Avagadro's number