schrodinger.application.matsci.nano.sheet module

Classes and functions for making honeycomb nanosheets.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.nano.sheet.CheckInput

Bases: schrodinger.application.matsci.nano.check.CheckInput

Check user input.

checkAll(element1, element2, bondlength, ncell1, edgetype1, ncell2, edgetype2, no_double_bonds, termfrag, min_term_frags, bilayersep, nbilayers, stacktype, bilayershift, 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

  • ncell1 (int) – number of cells along lattice side 1

  • edgetype1 (str) – type of edge for lattice side 1

  • ncell2 (int) – number of cells along lattice side 2

  • edgetype2 (str) – type of edge for lattice side 2

  • 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

  • bilayersep (float) – bilayer separation

  • nbilayers (int) – number of bilayers

  • stacktype (str) – bilayer stacking type

  • bilayershift (float) – offset of bilayers in terms of the number of unit cells

  • logger (logging.getLogger) – output logger

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

DEFAULTMSG = '\n        You have specified a value for flag %s that is not supported.  Values\n        must be %s.  Proceeding with the default value of %s.'
MIDFIX = '-'
checkBilayerSep(bilayersep, logger=None)
checkBilayerShift(bilayershift, logger=None)
checkBilayerStackType(stacktype, logger=None)
checkBondlength(bondlength, logger=None)
checkCellDims(ncell1, ncell2, logger=None)
checkEdgetypes(edgetype1, edgetype2, logger=None)
checkElements(element1, element2, logger=None)
checkExistingFile(infile)

Check if the infile already exists and find a new name if it does.

Parameters

infile (str) – file name to check

Return type

str

Returns

outfile, if infile is bad return new file name

checkIndicies(nindex, mindex, logger=None)

Check n-index and m-index.

Parameters

  • nindex (int) – the first chiral index

  • mindex (int) – the second chiral index

  • logger (logging.getLogger) – output logger

checkMaeExt(infile)

Check that the infile has a supported Maestro extension.

Parameters

infile (str) – file name to check

Return type

str

Returns

outfile, if infile is bad return its basename plus constants.DEFAULT_MAE_EXT

checkNumBilayers(nbilayers, logger=None)
checkNumCells(ncells, logger=None)

Check the number of unit cells.

Parameters

  • ncells (int) – the number of unit cells

  • logger (logging.getLogger) – output logger

checkNumWalls(nwalls, logger=None)

Check the number of walls.

Parameters

  • nwalls (int) – the number of walls

  • logger (logging.getLogger) – output logger

checkTermFrag(termfrag, logger=None)
checkUpToIndex(up_to_nindex, up_to_mindex, logger=None)

Check the enumeration options.

Parameters

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

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

  • logger (logging.getLogger) – output logger

checkWallSep(wallsep, logger=None)

Check the desired wall separation.

Parameters

  • wallsep (float) – wall separation in Angstrom

  • logger (logging.getLogger) – output logger

class schrodinger.application.matsci.nano.sheet.SymmetryEquiv(element, genvec, indicies, is_coarse_grain=False)

Bases: object

Manage symmetry equivalent positions in the unit cell.

__init__(element, genvec, indicies, is_coarse_grain=False)

Create an instance.

Parameters

  • element (str) – atom for this symmetry type

  • genvec (numpy.array) – vector to generate symmetry equivalent positions

  • indicies (list of ints) – atom indicies to use for the symmetry equivalent atoms

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

generateSymmetryEquiv()

Generate symmetry equivalent positions in the unit cell.

class schrodinger.application.matsci.nano.sheet.HoneycombUnitCell(element1, element2, bondlength, is_coarse_grain=False)

Bases: object

Create a unit cell of a honeycomb lattice. The unit cell will be a regular hexagon according to the following coordinate system:

-----------------------------------------
|                  Y                    |
|         --------------------          |
|        / 6                5 \         |
|       /                      \        |
|      /                        \       |
|     /                          \      |
|    /                            \     |
|   /                              \    |
|  | 1             O              4 | X |
|   \                              /    |
|    \                            /     |
|     \                          /      |
|      \                        /       |
|       \                      /        |
|        \ 2                3 /         |
|         --------------------          |
-----------------------------------------

The hexagon will be centered on the origin O where vec(X, O) and vec(Y, O) are the X- and Y-axes and the Z-coordinate is zero. All edge lengths are equivalent and internal small triangles, i.e. triangle(1, O, 2) are equilateral. The following angles will be important: angle(1, 2, 3) = 120 degrees, angle(1, 2, O) = 60 degrees, and angle(1, 2, 6) = 30 degrees. In general the asymmetric unit will contain two atoms. The symmetry operation is C3 and thus symmetry equivalent positions fall into two sets, i.e. [1, 3, 5] and [2, 4, 6]. This unit cell will have single bonds assigned.

ANGLELARGE = 2.0943951023931953
ANGLEMEDIUM = 1.0471975511965976
ANGLESMALL = 0.5235987755982988
NUMATOMS = 6
NUM_EQUIV_SETS = 2
NUM_SYM_ATOMS = 3
SYMATOMS = [[1, 3, 5], [2, 4, 6]]
UNITCELLINDEX = 'i_matsci_Unit_Cell_Index'
__init__(element1, element2, bondlength, is_coarse_grain=False)

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

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

getAsymmetricUnit()

Return two vectors to the atoms in the asymmetric unit.

Return type

numpy.array, numpy.array

Returns

asupos1, asupos2, positions of the two atoms in the asymmetric unit

getStructure(symgroup1, symgroup2)

Create Structure for the unit cell.

Parameters
Return type

schrodinger.structure.Structure

Returns

unitcell, structure for the unit cell

setAtomProps()

Create structure.atom properties for later use.

buildUnitCell()

Build the unit cell.

class schrodinger.application.matsci.nano.sheet.NeighborType(edgetype, bondingatoms)

Bases: object

Manage the properties of a neighbor type.

__init__(edgetype, bondingatoms)

Create an instance.

Parameters

  • edgetype (str) – neighbor connection type

  • bondingatoms (list of ints) – bonding atom indices, in unit cell numbering, of the neighbor

class schrodinger.application.matsci.nano.sheet.Grow(edgetype1, edgetype2, ncell1, ncell2)

Bases: object

Manage the details of how to attach cells to the lattice of the desired shape. Most of this class is really just to manage grow parameters which are derived by applying the symmetry operations on a set of basic grow parameters given below.

TERMINDICIES = [1, 2, 6]
GROWINDICIES = [3, 4, 5]
ALLINDICIES = [1, 2, 3, 4, 5, 6]
ZIGZAG_BY_ONE_BASE = [2]
ARMCHAIR_BY_ONE_BASE = [1, 2]
ONE_BY_ZIGZAG_BASE = [6]
ONE_BY_ARMCHAIR_BASE = [1, 6]
TYPE1NEIGHBOR = (-1, 0)
TYPE2NEIGHBOR = (0, -1)
TYPEZZNEIGHBOR = (-1, 1)
TYPEAANEIGHBOR = (-1, -1)
__init__(edgetype1, edgetype2, ncell1, ncell2)

Create an instance.

Parameters

  • edgetype1 (str) – type of edge for lattice side 1

  • edgetype2 (str) – type of edge for lattice side 2

  • ncell1 (int) – number of cells along lattice side 1

  • ncell2 (int) – number of cells along lattice side 2

getGrowVectors(lattvec1, lattvec2)

Return the two vectors needed to grow the honeycomb lattice with the specified types of edges.

Parameters

  • lattvec1 (numpy.array) – lattice vector 1

  • lattvec2 (numpy.array) – lattice vector 2

Return type

numpy.array, numpy.array

Returns

growvec1, growvec2, the two lattice grow vectors

getNeighborTypes()

Return a dictionary of neighbor types.

Return type

dict

Returns

neighbortypes, as keys has tuples of deltas to neighboring positions and as values has NeighborTypes

getRedundantAtoms(deltas, neighbortypes)

Return a list of atoms in the current cell that will be redundant with its neighboring cells when placed in the lattice. Unit cell numbering, rather than lattice numbering, is used.

Parameters

  • deltas (list of tuples) – deltas to neighboring cells

  • neighbortypes (dict) – contains as keys the deltas for potential neighbors and as values NeighborTypes

Return type

list of ints

Returns

redundantatoms, list of redundant atoms

getBondingInfo(deltas, neighbortypes)

Return the details for attaching cells to the lattice.

Parameters

  • deltas (list of tuples) – deltas to neighboring cells

  • neighbortypes (dict) – contains as keys the deltas for potential neighbors and as values NeighborTypes

Return type

dict

Returns

bonds_to_neighbors, dictionary containing as keys the deltas to neighboring cells from cell (growindex1, growindex2) and as values a list of neighbor-cell atom pairs to bond. Pairs are given using the unit cell numbering rather than the lattice numbering.

getAtomsToTerminate(growindex1, growindex2, logger=None)

Return a list of atoms in the current cell that are not shared with any other cell. Unit cell numbering, rather than lattice numbering, is used.

Parameters

  • growindex1 (int) – grow index 1

  • growindex2 (int) – grow index 2

  • logger (logging.getLogger) – output logger

Return type

list of ints

Returns

atoms_to_terminate, list of unshared atoms

class schrodinger.application.matsci.nano.sheet.HoneycombCell(unit_cell_structure, center, growindex1, growindex2)

Bases: object

Manage cells in the honeycomb lattice.

__init__(unit_cell_structure, center, growindex1, growindex2)

Create an instance.

Parameters

  • unit_cell_structure (schrodinger.structure.Structure) – unit cell structure

  • center (numpy.array) – center of cell

  • growindex1 (int) – index along first grow vector

  • growindex2 (int) – index along second grow vector

createCell()

Make a cell.

findNeighboringCells(cells, deltas)

For the current cell find the neighboring cells.

makeFragment(redundantatoms)

Create the cell fragment to be merged with the honeycomb lattice.

Parameters

redundantatoms (list of ints) – indicies of redundant atoms present in the cell

determineLatticeNumbering(latticelen)

Determine the map of cell fragment unit cell atom indicies to lattice atom indicies.

Parameters

latticelen (int) – current number of atoms in lattice

class schrodinger.application.matsci.nano.sheet.HoneycombLattice(element1, element2, bondlength, ncell1, edgetype1, ncell2, edgetype2, termfrag, min_term_frags, is_coarse_grain=False)

Bases: object

Create the honeycomb lattice according to the following coordinate system:

----------------------------------------------------------------------
|                 Y                                                  |
|                                   --------------------             |
|                                  /                    \            |
|                                 /                      \           |
|                                /                        \          |
|                               /                          \         |
|                              /                            \        |
|                             /                              \       |
|         --------------------              P2                |      |
|        / 6                5 \                              /       |
|       /                      \                            /        |
|      /                        \                          /         |
|     /                          \                        /          |
|    /                            \                      /           |
|   /                              \                    /            |
|  | 1             O              4 --------------------           X |
|   \                              /                    \            |
|    \                            /                      \           |
|     \                          /                        \          |
|      \                        /                          \         |
|       \                      /                            \        |
|        \ 2                3 /                              \       |
|         --------------------              P1                |      |
|                             \                              /       |
|                              \                            /        |
|                               \                          /         |
|                                \                        /          |
|                                 \                      /           |
|                                  \                    /            |
|                                   --------------------             |
----------------------------------------------------------------------

where in addition to the parameters specified in the HoneycombUnitCell class the two lattice vectors are given by vec(P1, O) and vec(P2, O) with angle(P1, O, P2) = 60 degrees.

CAPPINGELEMENT = 'H'
CG_CAPPING_ELEMENT = 'C'
CAPPING_BOND_LENGTH = 1.103
DIRECTION = 'forward'
TITLEKEY = 's_m_title'
ENTRYKEY = 's_m_entry_name'
TITLENAME = 'nanosheet'
NCELL1 = 'i_matsci_N_Cell_1'
NCELL2 = 'i_matsci_N_Cell_2'
C_VACUUM = 3.35
__init__(element1, element2, bondlength, ncell1, edgetype1, ncell2, edgetype2, termfrag, min_term_frags, is_coarse_grain=False)

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

  • ncell1 (int) – number of cells along lattice side 1

  • edgetype1 (str) – type of edge for lattice side 1

  • ncell2 (int) – number of cells along lattice side 2

  • edgetype2 (str) – type of edge for lattice side 2

  • 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

updateLatticeBonding(cell, bonds_to_neighbors)

Update the bonding between the lattice and the newly added fragment.

Parameters

  • cell (HoneycombCell) – recently added cell

  • bonds_to_neighbors (dict) – keys are tuples to neighboring cells and values are lists of bonding atom pairs using the unit cell numbering

terminateLattice(logger=None)

Terminate the lattice with the given fragments.

Parameters

logger (logging.getLogger) – output logger

minTerminatingFragments(logger=None)

Minimize the geometry of all atoms in the terminating fragments with the exception of the lattice bound atoms.

Parameters

logger (logging.getLogger) – output logger

setLatticeProperties(chorus_properties)

Set some structure properties of the lattice.

Parameters

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

getChorusPBC(growvec1, growvec2)

Return the chorus box PBC.

Parameters

  • growvec1 (numpy.array) – the first lattice grow vector

  • growvec2 (numpy.array) – the second lattice grow vector

Return type

list

Returns

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

buildLattice(logger=None)

Build a honeycomb lattice.

Parameters

logger (logging.getLogger) – output logger

schrodinger.application.matsci.nano.sheet.get_lattice_vectors(bondlength)

Return the two honeycomb lattice vectors for a nanosheet. We build the lattice in XY-plane, where Z = 0

Parameters

bondlength (float) – The bond length between the atoms comprising the nanosheet (an Angstroms)

Return (numpy.array, numpy.array)

A 2-tuple of the two lattice vectors

class schrodinger.application.matsci.nano.sheet.HoneycombBilayers(lattice, separation, bondlength, stacktype, nbilayers, bilayershift)

Bases: object

Create honeycomb bilayers.

ZEROVEC = array([0., 0., 0.])
STACK_DIRECTION = -1
__init__(lattice, separation, bondlength, stacktype, nbilayers, bilayershift)

Create an instance.

Parameters

  • lattice (schrodinger.structure.Structure) – lattice structure

  • separation (float) – bilayer separation

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

  • stacktype (str) – type of bilayer stacking to be used

  • nbilayers (int) – number of bilayers

  • bilayershift (float) – offset of bilayers in terms of the number of unit cells

buildBilayer()

Build the bilayer.

stackBilayers()

Stack the bilayers.

updatePBC()

Update the PBC.

translateLayers()

Translate the layers to be inside the box.

getTerminatingAtoms(terminatingatoms)

Return the terminating atoms for all layers.

Parameters

termiatingatoms – terminating atoms for the first layer

Return type

list

Returns

terminating atoms for all layers

class schrodinger.application.matsci.nano.sheet.NanoSheets(element1='C', element2='C', bondlength=1.418, ncell1=10, edgetype1='armchair', ncell2=10, edgetype2='zigzag', no_double_bonds=False, termfrag='hydrogen', min_term_frags=False, bilayersep=3.35, nbilayers=0, stacktype='ABAB', bilayershift=0.5, orient=False, logger=None, is_coarse_grain=False)

Bases: object

Main class for making nanosheets.

MSGWIDTH = 50
__init__(element1='C', element2='C', bondlength=1.418, ncell1=10, edgetype1='armchair', ncell2=10, edgetype2='zigzag', no_double_bonds=False, termfrag='hydrogen', min_term_frags=False, bilayersep=3.35, nbilayers=0, stacktype='ABAB', bilayershift=0.5, 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

  • ncell1 (int) – number of cells along lattice side 1

  • edgetype1 (str) – type of edge for lattice side 1

  • ncell2 (int) – number of cells along lattice side 2

  • edgetype2 (str) – type of edge for lattice side 2

  • 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

  • bilayersep (float) – bilayer separation

  • nbilayers (int) – number of bilayers

  • stacktype (str) – bilayer stacking type

  • bilayershift (float) – offset of bilayer in terms of the number of unit cells

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

  • logger (logging.getLogger) – output logger

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

printJobParams(logger=None)

Print job parameters.

Parameters

logger (logging.getLogger) – output logger

makeNanoSheets(logger=None)

Make nanosheets.

Parameters

logger (logging.getLogger) – output logger

schrodinger.application.matsci.nano.sheet.build_cell(astructure, terminatingatoms, atomic_number1, atomic_number2, bondlength, no_bonding_along=None)

Build the cell.

Parameters

  • astructure (schrodinger.structure.Structure) – the structure for which to build the cell

  • terminatingatoms (list) – the terminating atoms for which PBC bonds will be needed

  • atomic_number1 (int) – the atomic number of the first element

  • atomic_number2 (int) – the atomic number of the second element

  • bondlength (float) – the bond length

  • no_bonding_along (list or None) – contains the indices of the lattice vectors along which to not form bonds, indices are 0 (a-vector), 1 (b-vector), and 2 (c-vector), if None then [2] will be used which is the default for sheets

Return type

schrodinger.structure.Structure

Returns

the built cell