schrodinger.application.matsci.nano.tube module

Classes and functions for building single- and multi-walled nanotubes.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.nano.tube.CheckInput

Bases: CheckInput

Check user input.

checkAll(element1, element2, bondlength, nindex, mindex, ncells, no_double_bonds, termfrag, min_term_frags, up_to_nindex, up_to_mindex, nwalls, wallsep, logger=None, is_coarse_grain=False)

Manage all checks.

Parameters:

  • element1 (str) – elemental symbol of the first atom

  • element2 (str) – elemental symbol of the second atom

  • bondlength (float) – bond length between the first and second atoms in Angstrom

  • nindex (int) – first chiral index

  • mindex (int) – second chiral index

  • ncells (int) – number of unit cells

  • no_double_bonds (bool) – disable the formation of double bonds

  • termfrag (str) – terminate the lattice with a given fragment

  • min_term_frags (bool) – minimize the geometry of terminating fragments

  • up_to_nindex (bool) – enumerate nanotube structures on the n-index

  • up_to_mindex (bool) – enumerate nanotube structures on the m-index

  • nwalls (int) – number of walls in a multi-wall nanotube

  • wallsep (float) – wall separation in Angstrom for a multi-wall nanotube

  • logger (logging.getLogger) – output logger

  • is_coarse_grain (bool) – Whether a coarse grain structure is being created

class schrodinger.application.matsci.nano.tube.Rectangle(origin, bottom, left, end)

Bases: object

Manage the properties of a rectangle.

INSIDETHRESH = 1e-05
__init__(origin, bottom, left, end)

Create an instance.

Parameters:

  • origin (numpy.array) – lower left point

  • bottom (numpy.array) – lower right point

  • left (numpy.array) – upper left point

  • end (numpy.array) – upper right point

linear_equation(ixy, fxy, x)

Return y = m*x + b for m and b from the line formed by initial point ixy and final point fxy.

Parameters:

  • ixy (numpy.array) – initial point on line

  • fxy (numpy.array) – final point on line

  • x (float) – domain argument

Return type:

float

Returns:

y, range value

insideRectangle(xy, logger=None)

Return boolean specifying if the provided plane coordinates lie within the boundary.

Parameters:

  • xy (numpy.array) – plane coordinates

  • logger (logging.getLogger) – output logger

Return type:

bool, bool

Returns:

insidex, insidey, inside the x-boundary or not, same for y-boundary

class schrodinger.application.matsci.nano.tube.NanoSheet(nanotube_sheet_obj)

Bases: object

Create a sheet.HoneycombLattice that is large enough so that the nanotube sheet can be cut out from it.

ANGLEMEDIUM = 1.0471975511965976
__init__(nanotube_sheet_obj)

Create an instance.

Parameters:

nanotube_sheet_obj (NanoTubeSheet) – contains parameters of the nanotube sheet

defineVectors()

Define HoneycombLattice and NanoTubeSheet lattice, etc. vectors.

Return type:

numpy.array, numpy.array

Returns:

lattvec1, lattvec2, the HoneycombLattice lattice vectors

getGrowParams(lattvec1, lattvec2)

Get HoneycombLattice grow parameters.

Parameters:

  • lattvec1 (numpy.array) – lattice vector 1

  • lattvec2 (numpy.array) – lattice vector 2

Return type:

float, numpy.array, float, numpy.array

Returns:

grow1len, grow1unit, grow2len, grow2unit, the lengths and unit vectors of the grow vectors

changeBasis(grow1unit, grow2unit)

Change the basis of the NanoTubeSheet to that of the NanoSheet.

Parameters:

  • grow1unit (numpy.array) – unit vector of first grow vector

  • grow2unit (numpy.array) – unit vector of second grow vector

Return type:

float, float

Returns:

coef1, coef2, coefficients of the end vector in the grow basis

defineDimensions(coef1, grow1len, coef2, grow2len)

Define the dimensions of the NanoSheet.

Parameters:

  • coef1 (float) – coefficient of end vector on first grow vector

  • grow1len (float) – length of first grow vector

  • coef2 (float) – coefficient of end vector on second grow vector

  • grow2len (float) – length of second grow vector

rotateNanoSheet()

Rotate the nanosheet so that lattice edge 1 is along the x-axis.

getNanoSheet(logger=None)

Get the sheet.HoneycombLattice from which the nanotube sheet will be cut.

Parameters:

logger (logging.getLogger) – output logger

class schrodinger.application.matsci.nano.tube.NanoTubeSheet(element1, element2, bondlength, nindex, mindex, ncells, is_coarse_grain)

Bases: object

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

ZEROVEC = array([0., 0.])
__init__(element1, element2, bondlength, nindex, mindex, ncells, is_coarse_grain)

Create an instance.

Parameters:

  • element1 (str) – elemental symbol of the first atom

  • element2 (str) – elemental symbol of the second atom

  • bondlength (float) – bond length between the first and second atoms in Angstrom

  • nindex (int) – first chiral index

  • mindex (int) – second chiral index

  • ncells (int) – number of unit cells

  • is_coarse_grain (bool) – Whether a coarse grain structure is being created

static redefineLatticeVecs(lattvec1, lattvec2)

Redefine lattice vectors according to Dresselhaus.

Parameters:

  • lattvec1 (numpy.array) – first lattice vector

  • lattvec2 (numpy.array) – second lattice vector

Return type:

numpy.array, numpy.array

Returns:

nlattvec1, nlattvec2, first and second lattice vectors redefined

renumberAtomLists(renumbermap)

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

Parameters:

renumbermap (dict) – maps old indicies into new indicies

cutOutNanoSheet(logger=None)

Cut out the nanotube sheet from the nanosheet.

Parameters:

logger (logging.getLogger) – output logger

delDanglingTermAtoms()

Remove dangling atoms from the top and bottom of the nanotube sheet.

delZigZagMatchAtoms(logger=None)

Remove overlapping match atoms for the zigzag case.

Parameters:

logger (logging.getLogger) – output logger

delChiralMatchAtoms(logger=None)

Remove overlapping match atoms for the chiral case.

Parameters:

logger (logging.getLogger) – output logger

buildNanoTubeSheet(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 schrodinger.application.matsci.nano.tube.NanoTube(element1, element2, bondlength, no_double_bonds, nindex, mindex, ncells, termfrag, min_term_frags, is_coarse_grain)

Bases: object

Create a nanotube by rolling up a nanotube sheet.

TITLEKEY = 's_m_title'
ENTRYKEY = 's_m_entry_name'
TITLENAME = 'nanotube'
NINDEX = 'i_matsci_N_Index'
MINDEX = 'i_matsci_M_Index'
NCELLS = 'i_matsci_N_Cells'
RADIUS = 'r_matsci_Radius/Ang.'
LENGTH = 'r_matsci_Length/Ang.'
MSGWIDTH = 50
NUMDECIMAL = 3
__init__(element1, element2, bondlength, no_double_bonds, nindex, mindex, ncells, termfrag, min_term_frags, is_coarse_grain)

Create an instance.

Parameters:

  • element1 (str) – elemental symbol of the first atom

  • element2 (str) – elemental symbol of the second atom

  • bondlength (float) – bond length between the first and second atoms in Angstrom

  • no_double_bonds (bool) – disable the formation of double bonds

  • nindex (int) – first chiral index

  • mindex (int) – second chiral index

  • ncells (int) – number of unit cells

  • termfrag (str) – terminate the lattice with a given fragment

  • min_term_frags (bool) – minimize the geometry of terminating fragments

  • is_coarse_grain (bool) – Whether a coarse grain structure is being created

getChiralAngle(logger=None)

Determine the chiral angle of the tube in degrees where the chiral angle is angle(lattvec1, chiral) and is in [0.0, 30.0], 0.0 for zigzag and 30.0 for armchair and the rest are chiral.

Parameters:

logger (logging.getLogger) – output logger

tubularizeNanoTubeSheet(logger=None)

Tubularize the nanotube sheet.

Parameters:

logger (logging.getLogger) – output logger

rotateTube(logger=None)

Rotate the nanotube so that the tube axis is the translation vector.

preprocessMatchAtoms(inmatch)

Dangling match atoms require two bonding partners so make those atom indicies redundant in the list.

Parameters:

inmatch (list of ints) – non-redundant list

Return type:

list of ints

Returns:

outmatch, redundant list

bondMatchingEdges(matchleft, matchright)

Properly bond the left and right edges which meet each other after rolling.

Parameters:

  • matchleft (list of ints) – indicies of atoms on the left

  • matchright (list of ints) – indicies of atoms on the right

doTermination(nanosheet_obj, fragment)

Terminate the nanotube. Do this by hijacking the HoneycombLattice instance and overwriting some attributes.

Parameters:

  • nanosheet_obj (sheet.HoneycombLattice) – contains information shared between this instance and the nanotube instance

  • fragment (str) – fragment name

doBondOrders(logger=None)

Assign bond orders to the nanotube.

Parameters:

logger (logging.getLogger) – output logger

removeHydrogens()

Remove all hydrogens from the structure.

minTerminatingFrags(nanosheet_obj)

Minimize terminating fragments. Do this by hijacking the HoneycombLattice instance and overwriting some attributes.

Parameters:

nanosheet_obj (sheet.HoneycombLattice) – contains information shared between this instance and the nanotube instance

handleProps(chorus_properties)

Handle the structure properties of the tube.

Parameters:

chorus_properties (list) – contains the nine chorus properties, i.e. ax, ay, az, bx, …, cz

printProps(logger=None)

Print the properties of this nanotube.

Parameters:

logger (logging.getLogger) – output logger

getChorusPBC()

Return the chorus box PBC.

Return type:

list

Returns:

contains the nine chorus properties, i.e. ax, ay, az, bx, …, cz

buildTube(use_finite_bos=True, logger=None)

Build a tube.

Parameters:

  • use_finite_bos (bool) – use a bond order protocol meant for finite molecules

  • logger (logging.getLogger) – output logger

class schrodinger.application.matsci.nano.tube.MultiWalledNanoTube(innertube, nwalls, wallsep)

Bases: object

Build a multi-walled nanotube by assembling specific NanoTubes.

NWALLS = 'i_matsci_N_Walls'
WALLSEP = 'r_matsci_Wall_Sep./Ang.'
MSGWIDTH = 50
__init__(innertube, nwalls, wallsep)

Create an instance.

Parameters:

  • innertube (NanoTube) – tube object of inner most tube

  • nwalls (int) – number of walls in the multi-walled tube

  • wallsep (float) – wall separation in Angstrom for the multi-walled tube.

areSameLength()

Return True if the tubes in the multi-walled nanotube are the same length, False otherwise.

Return type:

bool

Returns:

True if the tubes in the multi-walled nanotube are the same length, False otherwise

getRadius()

Return the radius in Ang.

Return type:

float

Returns:

the radius in Ang.

getTerminatingIdxs()

Return the indices of terminating atoms.

Return type:

list

Returns:

indices of terminating atoms

getOuterChiralIndicies(wallindex, logger=None)

Get the chiral indicies for this outer tube.

Parameters:

  • wallindex (int) – index of this outer tube

  • logger (logging.getLogger) – output logger

Return type:

int, int

Return type:

nindex, mindex, chiral indicies for outer tube

getOuterTubeVectors(nindex, mindex)

Return the tube vectors for the given (n, m).

Parameters:

  • nindex (int) – first chiral index

  • mindex (int) – second chiral index

Return type:

numpy.array, numpy.array

Returns:

chiral, translat, the tube vectors

findLargestTranslat()

Return the length of the wall with the longest translation vector.

Return type:

float

Returns:

tmax, length of longest vector in Angstrom

getNumUnitCells(translat)

Return the number of unit cells to use for the given wall.

Parameters:

translat (numpy.array) – translation vector of the given wall

Return type:

int

Returns:

ncells, the number of cells to use for the given wall

alignCenterCollect()

Align and center the tubes and collect tubes into a single structure.

getTubeSpacings()

Determine actual tube spacings in units of Ang.

handleProps()

Handle the structure properties of the multi-walled tube.

printProps(logger=None)

Print the properties of this multi-walled nanotube.

Parameters:

logger (logging.getLogger) – output logger

buildMultiWallTube(use_finite_bos=True, logger=None)

Assemble the multi-walled tube.

Parameters:

  • use_finite_bos (bool) – use a bond order protocol meant for finite molecules

  • logger (logging.getLogger) – output logger

class schrodinger.application.matsci.nano.tube.NanoTubes(element1='C', element2='C', bondlength=1.418, no_double_bonds=False, nindex=6, mindex=6, ncells=2, termfrag='hydrogen', min_term_frags=False, up_to_nindex=False, up_to_mindex=False, nwalls=1, wallsep=3.35, orient=False, logger=None, is_coarse_grain=False)

Bases: object

Main class for making nanotubes.

MSGWIDTH = 50
__init__(element1='C', element2='C', bondlength=1.418, no_double_bonds=False, nindex=6, mindex=6, ncells=2, termfrag='hydrogen', min_term_frags=False, up_to_nindex=False, up_to_mindex=False, nwalls=1, wallsep=3.35, orient=False, logger=None, is_coarse_grain=False)
Parameters:

  • element1 (str) – elemental symbol of the first atom

  • element2 (str) – elemental symbol of the second atom

  • bondlength (float) – bond length between the first and second atoms in Angstrom

  • no_double_bonds (bool) – disable the formation of double bonds

  • nindex (int) – first chiral index

  • mindex (int) – second chiral index

  • ncells (int) – number of unit cells

  • termfrag (str) – terminate the lattice with a given fragment

  • min_term_frags (bool) – minimize the geometry of terminating fragments

  • up_to_nindex (bool) – enumerate nanotube structures on the n-index

  • up_to_mindex (bool) – enumerate nanotube structures on the m-index

  • nwalls (int) – number of walls in a multi-wall nanotube

  • wallsep (float) – wall separation in Angstrom in a multi-wall nanotube

  • orient (bool) – whether to orient the sheets for Maestro

  • logger (logging.getLogger) – output

  • is_coarse_grain (bool) – Whether a coarse grain structure is being created

printJobParams(logger=None)

Print job parameters.

Parameters:

logger (logging.getLogger) – output logger

makeSingleWalledTubes(use_finite_bos=True, logger=None)

Make single-walled nanotubes.

Parameters:

  • use_finite_bos (bool) – use a bond order protocol meant for finite molecules

  • logger (logging.getLogger) – output logger

Return type:

list of NanoTube

Returns:

singletubes, contains all created single-walled tubes

printSingleWalledTubes(logger=None)

Formatted print of single-walled tubes.

Parameters:

logger (logging.getLogger) – output logger

makeMultiWalledTubes(use_finite_bos=True, logger=None)

Make multi-walled nanotubes.

Parameters:

  • use_finite_bos (bool) – use a bond order protocol meant for finite molecules

  • logger (logging.getLogger) – output logger

Return type:

list of MultiWalledNanoTube

Returns:

multitubes, contains all created multi-walled tubes

printMultiWalledTubes(logger=None)

Formatted print of multi-walled tubes.

Parameters:

logger (logging.getLogger) – output logger

schrodinger.application.matsci.nano.tube.remove_pbc(astructure)

Remove the PBC definitions from the given structure.

Parameters:

astructure (schrodinger.structure.Structure) – the structure for which to remove the PBC

schrodinger.application.matsci.nano.tube.translate_tube(tube, radius)

Translate the tube so that it is inside the box.

Parameters:
schrodinger.application.matsci.nano.tube.get_tube_unit_cell(radius, length)

Get the a, b, and c vectors of the unit cell for a tube of given length and radius.

Parameters:

  • radius (float) – The radius of the tube in Angstroms

  • length (float) – The length of the tube in Angstroms

Return tuple(numpy.array):

Three numpy arrays each of length 3, corresponding to the a, b, and c vectors of the unit cell (in Angstroms)

schrodinger.application.matsci.nano.tube.get_tube_dimensions(chiral, translat)

Calculate the length and radius of a nanotube

Parameters:

  • chiral (numpy.array) – The chiral vector of the nanutube

  • translat (numpy.array) – The translat vector of the nanutube

Return tuple(float, float):

The length and radius of the nanotube, respectively. Units are in Angstroms.

schrodinger.application.matsci.nano.tube.get_tube_vectors(ncells, nindex, mindex, lattvec1, lattvec2)

Return chiral and translation vectors for a nanotube sheet.

Parameters:

  • ncells (int) – number of unit cells

  • nindex (int) – first chiral index

  • mindex (int) – second chiral index

  • lattvec1 (numpy.array) – first lattice vector

  • lattvec2 (numpy.array) – second lattice vector

Return tuple(numpy.array, numpy.array):

The chiral and translat tube vectors, respectively