schrodinger.application.matsci.nano.space_groups module

Classes and functions for creating crystals by unit cell.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.nano.space_groups.get_spacegroups()

Get space groups object.

Return type:

SpaceGroups

Returns:

Cached space groups object, do not modify!!

schrodinger.application.matsci.nano.space_groups.get_symmops_from_spglib(symm)

Get set of symmetry operators from a set of rotations and translations. Symmetry operator is defined with a 4 x 4 matrix, top left 3 x 3 is rotation matrix, top right column 1 x 3 is translation, rest, bottom row is [0 0 0 1]

Parameters:

symm (dict of two keys: 'rotations': list of 3 x 3 matrices, 'translations': list of 1 x 3 matrices) – dictionary of list of rotations and translations

Returns:

list of 4x4 matrices

Return type:

list of symmetry operators

class schrodinger.application.matsci.nano.space_groups.CrystalSystems

Bases: object

Manage the properties of the seven crystal systems.

TRICLINIC_NAME = 'triclinic'

MONOCLINIC_NAME = 'monoclinic'

ORTHORHOMBIC_NAME = 'orthorhombic'

TETRAGONAL_NAME = 'tetragonal'

TRIGONAL_NAME = 'trigonal'

HEXAGONAL_NAME = 'hexagonal'

CUBIC_NAME = 'cubic'

class Triclinic(name)

Bases: object

Manage the triclinic system.

__init__(name)

Create an instance.

Parameters:

name (str) – crystal system name

class Monoclinic(name)

Bases: object

Manage the monoclinic system.

__init__(name)

Create an instance.

Parameters:

name (str) – crystal system name

class Orthorhombic(name)

Bases: object

Manage the orthorhombic system.

__init__(name)

Create an instance.

Parameters:

name (str) – crystal system name

class Tetragonal(name)

Bases: object

Manage the tetragonal system.

__init__(name)

Create an instance.

Parameters:

name (str) – crystal system name

class Trigonal(name)

Bases: object

Manage the trigonal system.

__init__(name)

Create an instance.

Parameters:

name (str) – crystal system name

class Hexagonal(name)

Bases: object

Manage the hexagonal system.

__init__(name)

Create an instance.

Parameters:

name (str) – crystal system name

class Cubic(name)

Bases: object

Manage the cubic system.

__init__(name)

Create an instance.

Parameters:

name (str) – crystal system name

getCrystalSystem(name)

Return the crystal system object for the crystem system of the provided name.

Parameters:

name (str) – crystal system name

Return type:

one of the seven crystal system objects

Returns:

crystal_system_obj

class schrodinger.application.matsci.nano.space_groups.SpaceGroup(definition_id: int, space_group_id: int, ichoice: int, num_choices: int, space_group_short_name: str, space_group_full_name: str, point_group_name: str, centering_opers: List, primary_opers: List, symmetry_opers: List, num_centering_opers: int, num_primary_opers: int, num_symmetry_opers: int, centering_opers_strs: List, primary_opers_strs: List, symmetry_opers_strs: List, crystal_system: CrystalSystems, xyzasu: str, spg_setting: str)

Bases: NamedTuple

Collect the properties of a space group.

DEFINITION_ID = 'Def. ID'

SPACE_GROUP_ID = 'Space Group ID'

CRYSTAL_SYSTEM = 'Crystal System'

SHORT_HERMANN_MAUGUIN_SYMBOL = 'Short H.-M. Symbol'

FULL_HERMANN_MAUGUIN_SYMBOL = 'Full H.-M. Symbol'

POINT_GROUP_NAME = 'Point Group'

NUM_CENTERING_OPERS = 'N Centering Ops.'

NUM_PRIMARY_OPERS = 'N Primary Ops.'

NUM_SYMMETRY_OPERS = 'N Symmetry Ops.'

CENTERING_OPERS = 'Centering Operators'

PRIMARY_OPERS = 'Primary Operators'

SYMMETRY_OPERS = 'Symmetry Operators'

SPACE_GROUP_SETTING = 'Space Group Setting'

ID_TAG = 'spgid  '

SHORT_NAME_TAG = 'sspgname  '

FULL_NAME_TAG = 'fspgname  '

POINT_GROUP_TAG = 'pgname    '

CRYSTAL_SYSTEM_TAG = 'crysym    '

SETTING_TAG = 'setting   '

ASU_TAG = 'xyzasu    '

PRIMARY_OPERATIONS_TAG = 'primoper  '

CENTERING_OPERATIONS_TAG = 'centoper  '

END_OF_DEF_TAG = 'endofdef'

definition_id: int

Alias for field number 0

space_group_id: int

Alias for field number 1

ichoice: int

Alias for field number 2

num_choices: int

Alias for field number 3

space_group_short_name: str

Alias for field number 4

space_group_full_name: str

Alias for field number 5

point_group_name: str

Alias for field number 6

centering_opers: List

Alias for field number 7

primary_opers: List

Alias for field number 8

symmetry_opers: List

Alias for field number 9

num_centering_opers: int

Alias for field number 10

num_primary_opers: int

Alias for field number 11

num_symmetry_opers: int

Alias for field number 12

centering_opers_strs: List

Alias for field number 13

primary_opers_strs: List

Alias for field number 14

symmetry_opers_strs: List

Alias for field number 15

crystal_system: CrystalSystems

Alias for field number 16

xyzasu: str

Alias for field number 17

spg_setting: str

Alias for field number 18

classmethod fromData(definition_id, space_group_id, ichoice, num_choices, space_group_short_name, space_group_full_name, point_group_name, centering_opers, primary_opers, symmetry_opers, centering_opers_strs, primary_opers_strs, symmetry_opers_strs, crystal_system, xyzasu, spg_setting)

Create an instance.

Parameters:

• definition_id (int) – the id of the definition, i.e. a number ranging from 1 to 291 (some of the 230 space groups have more than a single unit cell definition).

• space_group_id (int) – the id of the space group, i.e. a number ranging from 1 to 230, which the number of space groups.

• ichoice (int) – the space group setting index

• num_choices (int) – the number of different unit cell settings for this space group. For example, a setting may be a choice of axes, etc.

• space_group_short_name (string) – the short Hermann-Mauguin symbol of the space group.

• space_group_full_name (string) – the full Hermann-Mauguin symbol of the space group.

• point_group_name (string) – the name of the point group of the space group.

• centering_opers (list of numpy.array) – contains the centering matricies of the space group.

• primary_opers (list of numpy.array) – contains the primary matricies of the space group.

• symmetry_opers (list of numpy.array) – contains the symmetry matricies of the space group, i.e. the combinations of the centering and primary matricies.

• centering_opers_strs (list) – string representation of the centering operators.

• primary_opers_strs (list) – string representation of the primary operators.

• symmetry_opers_strs (list) – string representation of the symmetry operators, i.e. the combination of the centering and primary string representations.

• crystal_system (one of the sevel crystal system objects) – the crystal system.

• xyzasu (str) – the xyzasu descriptor which will be parsed but not used

• spgsetting – the setting of the space group

isSohnckeGroup()

Return whether this group is Sohncke or not.

:rtype bool :return: Whether this group is Sohncke or not.

printSymmetryOpers(logger=None)

Log a formatted print of all of the symmetry operators for this space group.

Parameters:

logger (logging.getLogger) – output logger

printDatabaseEntry(logger=None)

Print a space group object in mmspg/spgbase.dat format.

Parameters:

logger (logging.getLogger) – output logger

class schrodinger.application.matsci.nano.space_groups.SpaceGroups

Bases: object

Manage space group objects.

NUM_SPACE_GROUPS = 230

CRYSTAL_SYSTEMS = <schrodinger.application.matsci.nano.space_groups.CrystalSystems object>

CENTERING = 'centering'

PRIMARY = 'primary'

SYMMETRY = 'symmetry'

__init__()

Create an instance.

getAllSpaceGroups()

Make a list of all SpaceGroup objects each of which contains some space group parameters from mmspg/spgbase.dat.

getSpgObjByName(name, first=True)

Get a space group object by name.

Parameters:

• name (str) – short name (HM symbol) checked first. If short_only=False, long symbol checked second. The first space group encountered with such a name is returned.

• first (bool) – If True, returns the first occurrence based on the symmetry operators

Return type:

SpaceGroup or None

Returns:

Space group object or None if not found

printAllSpgInfo(verbose, logger)

Print all space group information.

Parameters:

• verbose (bool) – verbose log

• logger (logging.getLogger) – output logger

schrodinger.application.matsci.nano.space_groups.equal_rotations(rotations1, rotations2)

Check if rotations are equal.

Parameters:

• rotations1 (3D numpy.array) – Array of rotation matrices (2D arrays) associated with a space group

• rotations2 (3D numpy.array) – Array of rotation matrices (2D arrays) associated with a space group

Return type:

bool

Returns:

True, if rotations are the same, otherwise False