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)

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

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.

ALLINDICIES = [1, 2, 3, 4, 5, 6]
ARMCHAIR_BY_ONE_BASE = [1, 2]
GROWINDICIES = [3, 4, 5]
ONE_BY_ARMCHAIR_BASE = [1, 6]
ONE_BY_ZIGZAG_BASE = [6]
TERMINDICIES = [1, 2, 6]
TYPE1NEIGHBOR = (-1, 0)
TYPE2NEIGHBOR = (0, -1)
TYPEAANEIGHBOR = (-1, -1)
TYPEZZNEIGHBOR = (-1, 1)
ZIGZAG_BY_ONE_BASE = [2]
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
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 along with the maximum possible bond order as the last entry. Pairs are given using the unit cell numbering rather than the lattice numbering.
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
index = 6
organizeDoubleBonds(growindex1, growindex2, cellstructure)

Organize double bonds in the cell so that they do not conflict with neighboring cells.

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

Bases: object

Create honeycomb bilayers.

STACK_DIRECTION = -1
ZEROVEC = array([ 0., 0., 0.])
buildBilayer()

Build the bilayer.

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
stackBilayers()

Stack the bilayers.

translateLayers()

Translate the layers to be inside the box.

updatePBC()

Update the PBC.

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

Bases: object

Manage cells in the honeycomb lattice.

createCell()

Make a 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
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
class schrodinger.application.matsci.nano.sheet.HoneycombLattice(element1, element2, bondlength, ncell1, edgetype1, ncell2, edgetype2, no_double_bonds, termfrag, min_term_frags)

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'
CAPPING_BOND_LENGTH = 1.103
C_VACUUM = 3.35
DIRECTION = 'forward'
ENTRYKEY = 's_m_entry_name'
NCELL1 = 'i_matsci_N_Cell_1'
NCELL2 = 'i_matsci_N_Cell_2'
TITLEKEY = 's_m_title'
TITLENAME = 'nanosheet'
buildLattice(logger=None)

Build a honeycomb lattice.

Parameters:logger (logging.getLogger) – output logger
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
getLatticeVectors()

Return the two honeycomb lattice vectors.

Return type:numpy.array, numpy.array
Returns:lattvec1, lattvec2, the two lattice vectors
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
terminateLattice(logger=None)

Terminate the lattice with the given fragments.

Parameters:logger (logging.getLogger) – output logger
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
class schrodinger.application.matsci.nano.sheet.HoneycombUnitCell(element1, element2, bondlength, no_double_bonds)

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 to pairs of adjacent atoms. Unless disabled by the user bonds [1, 2], [3, 4], and [5, 6] will be double bonds.

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'
buildUnitCell()

Build the unit cell.

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, no_double_bonds)

Create Structure for the unit cell.

Parameters:
  • symgroup1 (SymmetryEquiv) – first equivalent group
  • symgroup2 (SymmetryEquiv) – second equivalent group
  • no_double_bonds (bool) – disables the formation of double bonds
Return type:

schrodinger.structure.Structure
Returns:

unitcell, structure for the unit cell
setAtomProps()

Create structure.atom properties for later use.

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)

Bases: object

Main class for making nanosheets.

MSGWIDTH = 50
makeNanoSheets(logger=None)

Make nanosheets.

Parameters:logger (logging.getLogger) – output logger
printJobParams(logger=None)

Print job parameters.

Parameters:logger (logging.getLogger) – output logger
class schrodinger.application.matsci.nano.sheet.NeighborType(edgetype, bondingatoms)

Bases: object

Manage the properties of a neighbor type.

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

Bases: object

Manage symmetry equivalent positions in the unit cell.

generateSymmetryEquiv()

Generate symmetry equivalent positions in the unit cell.

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