Package schrodinger :: Package application :: Package matsci :: Package nano :: Module tube :: Class NanoTubeSheet

Class NanoTubeSheet

object --+
         |
        NanoTubeSheet

Preprocess a nanosheet into a nanotube sheet which will be rolled up into a nanotube.

Instance Methods

[hide private]

__init__(self, element1, element2, bondlength, nindex, mindex, ncells)
Create an instance.

numpy.array, numpy.array

redefineLatticeVecs(self, lattvec1, lattvec2)
Redefine lattice vectors according to Dresselhaus.

numpy.array, numpy.array

getTubeVectors(self)
Return chiral and translation vectors for the nanotube sheet.

renumberAtomLists(self, renumbermap)
Apply the given renumbering map to the terminating and matching atom lists.

cutOutNanoSheet(self, logger=None)
Cut out the nanotube sheet from the nanosheet.

delDanglingTermAtoms(self)
Remove dangling atoms from the top and bottom of the nanotube sheet.

delZigZagMatchAtoms(self, logger=None)
Remove overlapping match atoms for the zigzag case.

delChiralMatchAtoms(self, logger=None)
Remove overlapping match atoms for the chiral case.

buildNanoTubeSheet(self, termfrag, use_finite_bos=True, logger=None)
Build the nanotube sheet.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

ZEROVEC = array([ 0., 0.])

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, element1, element2, bondlength, nindex, mindex, ncells)
(Constructor)

Create an instance.

Overrides: object.__init__

redefineLatticeVecs(self, lattvec1, lattvec2)

Redefine lattice vectors according to Dresselhaus.

Parameters:

lattvec1 (numpy.array) - first lattice vector
lattvec2 (numpy.array) - second lattice vector

Returns: numpy.array, numpy.array

nlattvec1, nlattvec2, first and second lattice vectors redefined

getTubeVectors(self)

Return chiral and translation vectors for the nanotube sheet.

Returns: numpy.array, numpy.array: chiral, translat, tube vectors

renumberAtomLists(self, renumbermap)

Apply the given renumbering map to the terminating and matching atom lists.

Parameters:

renumbermap (dict) - maps old indicies into new indicies

cutOutNanoSheet(self, logger=None)

Cut out the nanotube sheet from the nanosheet.

Parameters:

logger (logging.getLogger) - output logger

delZigZagMatchAtoms(self, logger=None)

Remove overlapping match atoms for the zigzag case.

Parameters:

logger (logging.getLogger) - output logger

delChiralMatchAtoms(self, logger=None)

Remove overlapping match atoms for the chiral case.

Parameters:

logger (logging.getLogger) - output logger

buildNanoTubeSheet(self, termfrag, use_finite_bos=True, logger=None)

Build the nanotube sheet.

Parameters:

termfrag (str) - terminate the lattice with a given fragment
use_finite_bos (bool) - use a bond order protocol meant for finite molecules
logger (logging.getLogger) - output logger

Class NanoTubeSheet

__init__(self, element1, element2, bondlength, nindex, mindex, ncells) (Constructor)

redefineLatticeVecs(self, lattvec1, lattvec2)

getTubeVectors(self)

renumberAtomLists(self, renumbermap)

cutOutNanoSheet(self, logger=None)

delZigZagMatchAtoms(self, logger=None)

delChiralMatchAtoms(self, logger=None)

buildNanoTubeSheet(self, termfrag, use_finite_bos=True, logger=None)

init(self, element1, element2, bondlength, nindex, mindex, ncells)
(Constructor)