pyPRISM.core.System module¶

class pyPRISM.core.System.System(types, kT=1.0)[source]¶

Bases: object

Primary class used to spawn PRISM calculations

Description

The system object contains tables that fully describe a system to be simulated. This includes the domain definition, all site densities, site diameters, interaction potentials, intra-molecular correlation functions (\(\hat{\omega}(k)\)), and closures. This class also contains a convenience function for spawning a PRISM object.

Example

import pyPRISM

sys = pyPRISM.System(['A','B'])

sys.domain = pyPRISM.Domain(dr=0.1,length=1024)

sys.density['A'] = 0.1
sys.density['B'] = 0.75

sys.diameter[sys.types] = 1.0

sys.closure[sys.types,sys.types] = pyPRISM.closure.PercusYevick()

sys.potential[sys.types,sys.types] = pyPRISM.potential.HardSphere()

sys.omega['A','A'] = pyPRISM.omega.SingleSite()
sys.omega['A','B'] = pyPRISM.omega.InterMolecular()
sys.omega['B','B'] = pyPRISM.omega.Gaussian(sigma=1.0,length=10000)

PRISM = sys.createPRISM()

PRISM.solve()

__init__(types, kT=1.0)[source]¶

Parameters:	types (list) – Lists of the site types that define the system kT (float) – Thermal temperature where \(k\) is the Boltzmann constant and \(T\) temperature. This is typicaly specified in reduced units where \(k_{B}=1.0\).

types¶

List of site types

Type:	list

rank¶

Number of site types

Type:	int

density¶

Container for all density values

Type:	`pyPRISM.core.Density`

potential¶

Table of pair potentials between all site pairs in real space

Type:	`pyPRISM.core.PairTable`

closure¶

Table of closures between all site pairs

Type:	`pyPRISM.core.PairTable`

omega¶

Table of omega correlation functions in Fourier-space

Type:	`pyPRISM.core.PairTable`

domain¶

Domain object which specifies the Real and Fourier space solution grid.

Type:	`pyPRISM.core.Domain`

kT¶

Value of the thermal energy level. Used to vary temperature and scale the potential energy functions.

Type:	float

diameter¶

Site diameters.

Warning

These diameters are currently only passed to the closures. They are not passed to potentials and it is up to the user to set sane sigma values that match these diameters.

Type:	`pyPRISM.core.ValueTable`

check()[source]¶

Is everything in the system specified?

Raises:	ValueError if all values are not set

createPRISM()[source]¶

Construct a PRISM object

Note

This method calls check() before creating the PRISM object.

Returns:	PRISM – Fully specified PRISM object
Return type:	pyPRISM.core.PRISM

iterpairs(full=False, diagonal=True)[source]¶

Convenience function for looping over type pairs.

Parameters:	full (bool) – If True, all i,j pairs (upper and lower diagonal) will be looped over diagonal (bool) – If True, only the i==j (on-diagonal) pairs will be considered when looping

solve(*args, **kwargs)[source]¶

Construct a PRISM object and attempt a numerical solution

Note

See solve() for arguments to this function

Note

This method calls check() before creating the PRISM object.

Returns:	PRISM – Solved PRISM object
Return type:	pyPRISM.core.PRISM