pele.angleaxis._otp_bulk

class pele.angleaxis._otp_bulk.OTPBulk

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class OTPBulk(RBSystem):

This will build a system class for a system of OTP (Ortho Ter Phenyl) molecules

OTP is a very simple rigid body molecule described as 3 Lennard-Jones particles connected in a rigid isosceles triangle

OTPBulk.make_otp()

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def make_otp(self):

this constructs a single OTP molecule

OTPBulk.setup_aatopology()

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def setup_aatopology(self):

this sets up the topology for the whole rigid body system

OTPBulk.get_random_configuration()

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def get_random_configuration(self):

Returns an array containing random periodic com/aa coordinates.

OTPBulk.configuration_from_file()

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def configuration_from_file(self, fileobj, angleaxis=True):

Returns an array of com/aa coordinates as read in from a file.

Parameters:

fileobj - file

A file object corresponding to the input file

angleaxis - boolean, optional

If this is true, the input file should consist of 3*nrigid

centre-of-mass coordinates followed by 3*nrigid angle-axis vector components.

The exact shape does not matter.

Otherwise, the input file consists of 9*nrigid atomistic cartesian coordinates.

OTPBulk.setup_params()

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def setup_params(self, params):

set some system dependent parameters to improve algorithm performance

OTPBulk.get_potential()

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def get_potential(self):

construct the rigid body potential