schrodinger.application.matsci.espresso.qeinput module

Classes and functions to deal with XML input generation for Quantum Espresso.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.espresso.qeinput.DataType(engine, path)

Bases: tuple

__add__

Return self+value.

__class__

alias of builtins.type

__contains__

Return key in self.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__

Return self[key].

__getnewargs__()

Return self as a plain tuple. Used by copy and pickle.

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__

Implement iter(self).

__le__

Return self<=value.

__len__

Return len(self).

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__mul__

Return self*value.n

__ne__

Return self!=value.

static __new__(_cls, engine, path)

Create new instance of DataType(engine, path)

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()

Return a nicely formatted representation string

__rmul__

Return self*value.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

count(value) → integer -- return number of occurrences of value

engine

Alias for field number 0

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

path

Alias for field number 1

schrodinger.application.matsci.espresso.qeinput.deep_update(source, overrides)

Override/append source dict values using overrides dict, return a new dict. Everything is deepcopied to prevent unexpected changes.

Parameters:

• source (dict) – Source dictionary
• overrides (dict) – Dictionary to override with

Return type:

dict

Returns:

Updated dictionary

schrodinger.application.matsci.espresso.qeinput.validate_value(name, value, allowed_values)

Check that value is in list of allowed values.

Parameters:

• name (str) – Name of the variable
• value (str or int or float) – Value of the variable
• allowed_values (list) – List of values

Raises:

ValueError – If value is not in list

class schrodinger.application.matsci.espresso.qeinput.GenericType

Bases: object

Generic class for different input types.

__init__()

Initialize GenericType object and update attributes from data.

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Generic class for different input types.\n ', '__init__': <function GenericType.__init__>, 'updateWithData': <function GenericType.updateWithData>, '_cleanData': <function GenericType._cleanData>, '__dict__': <attribute '__dict__' of 'GenericType' objects>, '__weakref__': <attribute '__weakref__' of 'GenericType' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.espresso.qeinput.BandsType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to bands.

TOT_CHARGE_KEY = 'total_charge'

TOT_MAG_KEY = 'total_magnetization'

MIN_EMPTY_BANDS = 10

DEFAULTS = {'nbnd': 0, 'nbnd_empty_percent': 20.0, 'occupations': 'smearing', 'smearing_degauss': 0.01, 'smearing_type': 'gaussian', 'total_charge': 0.0, 'total_magnetization': -1.0}

__str__()

Return XML.

Return type:str Returns:XML string Raise:ValueError if self.nbnd is not set (or zero)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to bands.\n ', 'TOT_CHARGE_KEY': 'total_charge', 'TOT_MAG_KEY': 'total_magnetization', 'MIN_EMPTY_BANDS': 10, 'DEFAULTS': {'nbnd': 0, 'nbnd_empty_percent': 20.0, 'smearing_degauss': 0.01, 'total_charge': 0.0, 'total_magnetization': -1.0, 'smearing_type': 'gaussian', 'occupations': 'smearing'}, '__str__': <function BandsType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.BasisType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to basis.

GAMMA_ONLY_KEY = 'gamma_only'

DEFAULTS = {'ecutrho': 0.0, 'ecutwfc': 0.0, 'fft_grid': [], 'fft_smooth_grid': [], 'gamma_only': False}

__str__()

Return XML.

Return type:str Returns:XML string Raise:ValueError if self.ecutwfc or self.ecutrho is not set (or zero)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to basis.\n ', 'GAMMA_ONLY_KEY': 'gamma_only', 'DEFAULTS': {'ecutwfc': 0.0, 'ecutrho': 0.0, 'gamma_only': False, 'fft_grid': [], 'fft_smooth_grid': []}, '_validateGrid': <function BasisType._validateGrid>, '__str__': <function BasisType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.ElectronControlType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to electron control.

DEFAULTS = {'conv_thr': 1e-06, 'diago_cg_maxiter': 20, 'diago_full_acc': False, 'diago_thr_init': 0.0, 'diagonalization': 'davidson', 'max_steps': 100, 'mixing_beta': 0.7, 'mixing_mode': 'plain', 'mixing_ndim': 8, 'real_space_q': False}

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to electron control.\n ', 'DEFAULTS': {'diagonalization': 'davidson', 'mixing_mode': 'plain', 'mixing_beta': 0.7, 'conv_thr': 1e-06, 'mixing_ndim': 8, 'max_steps': 100, 'real_space_q': False, 'diago_thr_init': 0.0, 'diago_full_acc': False, 'diago_cg_maxiter': 20}, '__str__': <function ElectronControlType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.KpointsType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to k-points.

KPTS_MESH_KEY = 'kpts_mesh'

AUTOMATIC_BAND = 'automatic'

DEFAULTS = {'kpts_band': False, 'kpts_band_line_density': 20, 'kpts_dens': 0, 'kpts_dens_force_gamma': False, 'kpts_list': [], 'kpts_mesh': [6, 6, 6, 1, 1, 1]}

KPTS_TYPES = {'kpts_mesh', 'kpts_dens', 'kpts_band', 'kpts_list'}

setStructure(struct)

Set structure in self.struct and several other attributes: self.vecs and self.alat.

Parameters:struct (structure.Structure) – Structure used for k-point generation (‘kpts_dens’ case)

getNKpts()

Get total number of k-points based on k-points definition. If k-points type is defined, throw a ValueError.

Return type:int Returns:Number of k-points Raises:ValueError – If k-points type is not defined

matdynStr()

Get kpoint list suitable for matdyn input.

Return type:str Returns:Kpoint list

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to k-points.\n ', 'KPTS_MESH_KEY': 'kpts_mesh', 'AUTOMATIC_BAND': 'automatic', 'DEFAULTS': {'kpts_mesh': [6, 6, 6, 1, 1, 1], 'kpts_list': [], 'kpts_dens': 0, 'kpts_band': False, 'kpts_dens_force_gamma': False, 'kpts_band_line_density': 20}, 'KPTS_TYPES': {'kpts_mesh', 'kpts_dens', 'kpts_band', 'kpts_list'}, 'setStructure': <function KpointsType.setStructure>, '_cleanData': <function KpointsType._cleanData>, '_validateKpoints': <function KpointsType._validateKpoints>, '_generateBandPath': <function KpointsType._generateBandPath>, '_generateDensity': <function KpointsType._generateDensity>, 'getNKpts': <function KpointsType.getNKpts>, 'matdynStr': <function KpointsType.matdynStr>, '__str__': <function KpointsType.__str__>, '_toCart': <function KpointsType._toCart>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.SpinType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to spin.

DEFAULTS = {'spin_type': ''}

SPIN_NON_LSDA_ID = 1

SPIN_LSDA_ID = 2

__init__()

Initialize SpinType object from string.

Parameters:data (dict) – Dictionary of settings

getNSpin()

Get nspin based on the spin settings.

Returns:Spin type in the PW integer representation Return type:int

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to spin.\n ', 'DEFAULTS': {'spin_type': ''}, 'SPIN_NON_LSDA_ID': 1, 'SPIN_LSDA_ID': 2, '__init__': <function SpinType.__init__>, '_validateSpin': <function SpinType._validateSpin>, '_get_tag': <function SpinType._get_tag>, 'getNSpin': <function SpinType.getNSpin>, '__str__': <function SpinType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.VdwType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to vdw type.

DEFAULTS = {'correction': '', 'london_rcut': 200, 'london_s6': 0.75, 'xdm_a1': 0.6836, 'xdm_a2': 1.5045}

__init__()

Initialize VdwType object from dictionary.

Parameters:data (dict) – Dictionary of settings

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to vdw type.\n ', 'DEFAULTS': {'correction': '', 'london_s6': 0.75, 'london_rcut': 200, 'xdm_a1': 0.6836, 'xdm_a2': 1.5045}, '__init__': <function VdwType.__init__>, '_validateVdw': <function VdwType._validateVdw>, '__str__': <function VdwType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.HybridType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to hybrid functional type.

SCREEN_PARAM_KEY = 'screening_parameter'

DEFAULTS = {'ecutvcut': 0.7, 'exxdiv_treatment': 'gygi-baldereschi', 'qpts_mesh': [1, 1, 1], 'screening_parameter': 0.106, 'x_gamma_extrapolation': True}

__str__()

Return XML from attributes.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to hybrid functional type.\n ', 'SCREEN_PARAM_KEY': 'screening_parameter', 'DEFAULTS': {'qpts_mesh': [1, 1, 1], 'ecutvcut': 0.7, 'x_gamma_extrapolation': True, 'exxdiv_treatment': 'gygi-baldereschi', 'screening_parameter': 0.106}, '__str__': <function HybridType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.DftUType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to Dft U.

DEFAULTS = {'structure_type': None}

__init__()

Initialize DftUType object.

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to Dft U.\n ', 'DEFAULTS': {'structure_type': None}, '__init__': <function DftUType.__init__>, '__str__': <function DftUType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.DftType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to dft type.

DEFAULTS = {'dftu': {'structure_type': None}, 'functional': '', 'hybrid': {'qpts_mesh': [1, 1, 1], 'ecutvcut': 0.7, 'x_gamma_extrapolation': True, 'exxdiv_treatment': 'gygi-baldereschi', 'screening_parameter': 0.106}, 'vdw': {'correction': '', 'london_s6': 0.75, 'london_rcut': 200, 'xdm_a1': 0.6836, 'xdm_a2': 1.5045}}

vdw

hybrid

Get hybrid attribute (self._hybrid).

Returns:Hybrid attribute Return type:HybridType

dftu

Get DftU attribute from self._dftu.

Returns:Hybrid attribute Return type:HybridType

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to dft type.\n ', 'DEFAULTS': {'functional': '', 'vdw': {'correction': '', 'london_s6': 0.75, 'london_rcut': 200, 'xdm_a1': 0.6836, 'xdm_a2': 1.5045}, 'hybrid': {'qpts_mesh': [1, 1, 1], 'ecutvcut': 0.7, 'x_gamma_extrapolation': True, 'exxdiv_treatment': 'gygi-baldereschi', 'screening_parameter': 0.106}, 'dftu': {'structure_type': None}}, 'vdw': <property object>, 'hybrid': <property object>, 'dftu': <property object>, '__str__': <function DftType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.PseudopotentialsType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to pseudopotentials.

DEFAULTS = {'species': {}}

setStructureType(struct_type)

Set structure_type in self.struct_type and atom types in self.st_species.

Parameters:struct_type (StructureType) – Structure type used to calculate number of valence electrons in the cell

getData()

Get pseudopotentials file paths and other related data from the database having the same functional and family.

Return type:dict, float, float, float Returns:Dict with paths to PPs ({‘element’: ‘path’}), number of valence electrons, max ecutwfc, max ecutrho for elements

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to pseudopotentials.\n ', 'DEFAULTS': {'species': {}}, 'setStructureType': <function PseudopotentialsType.setStructureType>, 'getData': <function PseudopotentialsType.getData>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.MagSpecies

Bases: object

Class that defines species with starting magnetization.

__init__()

Initialize MagSpecies class.

createUniqueElement(element, mag, hubb_u)

Fill self.data dict. Keys of the self.data are elements. Values are dicts with magnetization as key and unique element as value. Unique element is just the atomic symbol plus (if element has more than one magnetization value) a unique integer. Example: {‘C’: {0.0: ‘C’}, ‘H’: {0.0: ‘H’, 0.1: ‘H1’}}

self.species is a dict where unique elements are keys and elements are values. Example (based on the example above): {‘C’: ‘C’, ‘H’: ‘H’, ‘H1’: ‘H’}

Parameters:

• element (str) – Element
• mag (float) – Starting magnetization
• hubb_u (float) – Hubbard U parameter

Return type:

str

Returns:

Unique element

getMag(element, unique_element)

Get magnetization given element and unique element values.

Parameters:

• element (str) – Element
• unique_element (str) – Unique element

Return type:

tuple

Returns:

Starting magnetization and Hubbard U

Raises:

ValueError – If element, unique_element combination is not found

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class that defines species with starting magnetization.\n ', '__init__': <function MagSpecies.__init__>, 'createUniqueElement': <function MagSpecies.createUniqueElement>, 'getMag': <function MagSpecies.getMag>, '__dict__': <attribute '__dict__' of 'MagSpecies' objects>, '__weakref__': <attribute '__weakref__' of 'MagSpecies' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.espresso.qeinput.StructureType(struct, use_symmetry)

Bases: object

Class to generate QE input XML section related to structure.

X = 0

Y = 1

Z = 2

__init__(struct, use_symmetry)

Initialize StructureType object.

Parameters:

• struct (List of structure.Structure) – Structures to generate XML from
• use_symmetry (bool) – If true, try to convert structure to primitive cell

setPrimitiveCell()

Set and use primitive cell found by spglib, if any.

setElements()

Set elements in self.elements and atomic numbers for spglib in self.anums.

getAtomicStructure()

Generate XML input related to atomic_structure.

Return type:str Returns:cell xml data

getAtomicSpecies(ppfiles)

Generate XML input related to atomic species.

Param:Dictionary containing paths to PPs ({‘Element’: ‘Path’}) Return type:str Returns:species xml data

fetchPPDB(functional)

Get pseudopotentials file paths and other related data from the database having the same functional and family.

Parameters:functional (str) – DFT Functional (one of the DFT_FUNCTIONALS) Return type:dict, float, float, float Returns:Dict with paths to PPs ({‘element’: ‘path’}), number of valence electrons, max ecutwfc, max ecutrho for elements

alignStructWithPlane(vector_index)

Slide structure (self.struct) along the axis such that all atoms are on top of the plane perpendicular to the axis defined by vector_index.

Parameters:vector_index (int) – Vector index (X or Y or Z) to align structure to the perpendicular plane

validateStruct(struct)

Validate provided structure against self.struct.

Parameters:struct (schrodinger.structure.Structure) – Structure to validate Raises:ValueError – If number of atoms or atomic types differ compared to the initial structure (self.structure)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to structure.\n ', 'X': 0, 'Y': 1, 'Z': 2, '__init__': <function StructureType.__init__>, 'setPrimitiveCell': <function StructureType.setPrimitiveCell>, 'setElements': <function StructureType.setElements>, 'getAtomicStructure': <function StructureType.getAtomicStructure>, 'getAtomicSpecies': <function StructureType.getAtomicSpecies>, '_getPPNelect': <function StructureType._getPPNelect>, 'fetchPPDB': <function StructureType.fetchPPDB>, '_getAtomicSpecies': <function StructureType._getAtomicSpecies>, '_getCell': <function StructureType._getCell>, '_validatePBCs': <function StructureType._validatePBCs>, 'alignStructWithPlane': <function StructureType.alignStructWithPlane>, 'validateStruct': <function StructureType.validateStruct>, '__dict__': <attribute '__dict__' of 'StructureType' objects>, '__weakref__': <attribute '__weakref__' of 'StructureType' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.espresso.qeinput.ControlType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to control.

DEFAULTS = {'calculation_type': '', 'etot_conv_thr': 1e-05, 'forc_conv_thr': 0.001, 'forces': False, 'prefix': '', 'press_conv_thr': 0.5, 'relax_steps': 50, 'stress': False, 'title': 'Default Title', 'wf_collect': False, 'wf_keep': False}

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to control.\n ', 'DEFAULTS': {'stress': False, 'forces': False, 'relax_steps': 50, 'etot_conv_thr': 1e-05, 'forc_conv_thr': 0.001, 'press_conv_thr': 0.5, 'title': 'Default Title', 'calculation_type': '', 'prefix': '', 'wf_collect': False, 'wf_keep': False}, '__str__': <function ControlType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.SymmetryType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to symmetry.

USE_SYMM_KEY = 'use_symmetry'

USE_PRIM_KEY = 'use_primitive'

GET_STD_CELL = 'get_std_cell'

USE_ALL_FRAC_KEY = 'use_all_frac'

DEFAULTS = {'get_std_cell': False, 'use_all_frac': False, 'use_primitive': False, 'use_symmetry': False}

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to symmetry.\n ', 'USE_SYMM_KEY': 'use_symmetry', 'USE_PRIM_KEY': 'use_primitive', 'GET_STD_CELL': 'get_std_cell', 'USE_ALL_FRAC_KEY': 'use_all_frac', 'DEFAULTS': {'use_symmetry': False, 'use_primitive': False, 'get_std_cell': False, 'use_all_frac': False}, '__str__': <function SymmetryType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.FreePositionsType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to Cartesian atomic constraints.

DEFAULTS = {}

static saveConstraint(data, atom)

Static method to save Cartesian atomic constraint.

Parameters:

• data (list of 3 integers) – Cartesian constraints for each coordinate: 1 - not constrained, 0 - constrained (QE convention)
• atom (structure._StructureAtom) – Atom to add/modify constraint to

Raises:

ValueError – If data is not a list of 3 elements

static saveTorsionConstraint(struct, indices)

Static method to save torsion angle constraint.

Parameters:

• struct (structure.Structure) – Structure to add constraint to as a property
• indices (list) – Atomic indices that describe a torsion angle

Raises:

ValueError – If data is not a list of 3 elements

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to Cartesian atomic\n constraints.\n ', 'DEFAULTS': {}, 'saveConstraint': <staticmethod object>, 'saveTorsionConstraint': <staticmethod object>, '__str__': <function FreePositionsType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.InputType(data)

Bases: object

Class to generate QE input XML section related to input.

__init__(data)

Initialize InputType object from the string.

Param:Tuple that contains XML for different part of the input

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to input.\n ', '__init__': <function InputType.__init__>, '__str__': <function InputType.__str__>, '__dict__': <attribute '__dict__' of 'InputType' objects>, '__weakref__': <attribute '__weakref__' of 'InputType' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.espresso.qeinput.NEBInputType(data)

Bases: schrodinger.application.matsci.espresso.qeinput.InputType

Class to generate QE input XML section related to NEB input.

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to NEB input.\n ', '__str__': <function NEBInputType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(data)

Initialize InputType object from the string.

Param:Tuple that contains XML for different part of the input

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.espresso.qeinput.PHInputType(data)

Bases: schrodinger.application.matsci.espresso.qeinput.InputType

Class to generate QE input XML section related to PHonon input.

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to PHonon input.\n ', '__str__': <function PHInputType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(data)

Initialize InputType object from the string.

Param:Tuple that contains XML for different part of the input

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.espresso.qeinput.MdType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate XML section related to MD control.

DEFAULTS = {'deltat': 1.0, 'ion_temperature': 'rescale-v', 'nraise': 1, 'tempw': 300.0, 'timestep': 2.0}

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate XML section related to MD control.\n ', 'DEFAULTS': {'ion_temperature': 'rescale-v', 'timestep': 2.0, 'tempw': 300.0, 'deltat': 1.0, 'nraise': 1}, '__str__': <function MdType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.IonControlType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE ionic control XML section related to control.

ION_DYNAMICS_KEY = 'ion_dynamics'

DEFAULTS = {'dynamics': {'ion_temperature': 'rescale-v', 'timestep': 2.0, 'tempw': 300.0, 'deltat': 1.0, 'nraise': 1}, 'ion_dynamics': 'bfgs'}

dynamics

Getter for the dynamics attribute.

Return type:MdType Returns:dynamics object

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE ionic control XML section related to control.\n ', 'ION_DYNAMICS_KEY': 'ion_dynamics', 'DEFAULTS': {'ion_dynamics': 'bfgs', 'dynamics': {'ion_temperature': 'rescale-v', 'timestep': 2.0, 'tempw': 300.0, 'deltat': 1.0, 'nraise': 1}}, 'dynamics': <property object>, '__str__': <function IonControlType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.CellControlType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE cell control XML section related to control.

CELL_DYNAMICS_KEY = 'cell_dynamics'

PRESSURE_KEY = 'pressure'

CELL_FACTOR_KEY = 'cell_factor'

CELL_DOFREE_KEY = 'cell_dofree'

DEFAULTS = {'cell_dofree': 'all', 'cell_dynamics': 'bfgs', 'cell_factor': 2.0, 'pressure': 0.0}

CELL_DOFREE_XML = {'2Dshape': 'fix_area', '2Dxy': 'fix_xy', 'shape': 'fix_volume'}

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE cell control XML section related to control.\n ', 'CELL_DYNAMICS_KEY': 'cell_dynamics', 'PRESSURE_KEY': 'pressure', 'CELL_FACTOR_KEY': 'cell_factor', 'CELL_DOFREE_KEY': 'cell_dofree', 'DEFAULTS': {'cell_dynamics': 'bfgs', 'pressure': 0.0, 'cell_factor': 2.0, 'cell_dofree': 'all'}, 'CELL_DOFREE_XML': {'shape': 'fix_volume', '2Dshape': 'fix_area', '2Dxy': 'fix_xy'}, '__str__': <function CellControlType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.EsmType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to esm type.

BC_KEY = 'bc'

BC_W_KEY = 'offset'

BC_EFIELD_KEY = 'efield'

DEFAULTS = {'bc': 'bc1', 'efield': 0.0, 'offset': 0.0}

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to esm type.\n ', 'BC_KEY': 'bc', 'BC_W_KEY': 'offset', 'BC_EFIELD_KEY': 'efield', 'DEFAULTS': {'bc': 'bc1', 'offset': 0.0, 'efield': 0.0}, '__str__': <function EsmType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.BoundaryType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to boundary conditions type.

ASSUME_ISOLATED_KEY = 'assume_isolated'

ESM_KEY = 'esm'

EFERMI_KEY = 'efermi'

RELATIVE_POT_KEY = 'relative_pot'

DEFAULTS = {'assume_isolated': '', 'efermi': 0.0, 'esm': {'bc': 'bc1', 'offset': 0.0, 'efield': 0.0}, 'relative_pot': None}

esm

Getter for the esm attribute.

Return type:EsmType Returns:esm object

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to boundary conditions type.\n ', 'ASSUME_ISOLATED_KEY': 'assume_isolated', 'ESM_KEY': 'esm', 'EFERMI_KEY': 'efermi', 'RELATIVE_POT_KEY': 'relative_pot', 'DEFAULTS': {'assume_isolated': '', 'esm': {'bc': 'bc1', 'offset': 0.0, 'efield': 0.0}, 'efermi': 0.0, 'relative_pot': None}, 'esm': <property object>, '_validateAssumeIsolated': <function BoundaryType._validateAssumeIsolated>, '__str__': <function BoundaryType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.NEBPathType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate QE input XML section related to the NEB path.

DEFAULTS = {'climbing_image': 'no-CI', 'esm': False, 'esm_efermi': 0.0, 'esm_first_image_charge': 0.0, 'esm_last_image_charge': 0.0, 'nimages': 4, 'nsteps': 50, 'optimization_scheme': 'broyden', 'optimize_first_last': False, 'string_method': 'neb', 'use_masses': False}

__str__()

Return XML.

Return type:str Returns:XML string

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate QE input XML section related to the NEB path.\n ', 'DEFAULTS': {'string_method': 'neb', 'nimages': 4, 'nsteps': 50, 'optimization_scheme': 'broyden', 'climbing_image': 'no-CI', 'use_masses': False, 'optimize_first_last': False, 'esm': False, 'esm_efermi': 0.0, 'esm_first_image_charge': 0.0, 'esm_last_image_charge': 0.0}, '_validate': <function NEBPathType._validate>, '__str__': <function NEBPathType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

class schrodinger.application.matsci.espresso.qeinput.PHControlType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate phonon control input XML section related to control.

DEFAULTS = {'epsil': False, 'prefix': '', 'qpts_mesh': [1, 1, 1]}

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate phonon control input XML section related to control.\n ', 'DEFAULTS': {'prefix': '', 'epsil': False, 'qpts_mesh': [1, 1, 1]}, '__str__': <function PHControlType.__str__>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

__str__()

Return XML.

Return type:str Returns:XML string

class schrodinger.application.matsci.espresso.qeinput.ElasticType

Bases: schrodinger.application.matsci.espresso.qeinput.GenericType

Class to generate phonon control input XML section related to control.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.espresso.qeinput', '__doc__': '\n Class to generate phonon control input XML section related to control.\n ', 'STRAIN_IDX_KEY': 'strain_index', 'STRAIN_AMOUNT_KEY': 'strain_amount', 'DEFAULTS': {'strain_index': [], 'strain_amount': 0.0}})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__()

Initialize GenericType object and update attributes from data.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.espresso.qeinput'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

updateWithData(data)

Update attributes from data. Set object attribute from data. Example: self.attribute = self.data.get(attribute)

Parameters:data (dict) – Dictionary of settings

STRAIN_IDX_KEY = 'strain_index'

STRAIN_AMOUNT_KEY = 'strain_amount'

DEFAULTS = {'strain_amount': 0.0, 'strain_index': []}