schrodinger.application.matsci.qexsd.qespresso.documents module¶
-
class
schrodinger.application.matsci.qexsd.qespresso.documents.
QeDocument
(xsd_file, input_builder)¶ Bases:
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument
Abstract class for XML schema based configurations.
-
__init__
(xsd_file, input_builder)¶ Initialize self. See help(type(self)) for accurate signature.
-
read_qe_input
(filename)¶ Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.
Parameters: filename – Returns:
-
write_qe_input
(filename)¶ Write the XML configuration to a Fortran input.
Parameters: filename – Returns:
-
get_input_path
()¶
-
get_qe_input
(use_defaults=True)¶
-
load_fortran_input
(filename)¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Abstract class for XML schema based configurations.\n ', '__init__': <function QeDocument.__init__>, 'read_qe_input': <function QeDocument.read_qe_input>, 'write_qe_input': <function QeDocument.write_qe_input>, 'get_input_path': <function QeDocument.get_input_path>, 'get_qe_input': <function QeDocument.get_qe_input>, 'load_fortran_input': <function QeDocument.load_fortran_input>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__getitem__
(section)¶
-
__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.qexsd.qespresso.documents'¶
-
__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)
-
extra_validations
(xlm_tree)¶ Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.
-
find
(path, namespaces=None)¶ Find first matching element by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
findall
(path, namespaces=None)¶ Find all matching subelements by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
from_dict
()¶ Build an ElementTree object from a dictionary
-
get
(qualified_name)¶
-
iter
(tag=None)¶
-
parse_json
(filename)¶ Build an ElementTree object representing a YAML file
-
parse_xml
(filename)¶ Return an ElementTree object representing an XML file
-
parse_yaml
(filename)¶ Build an ElementTree object representing a YAML file
-
read
(filename, data_format='XML')¶ Read configuration from a text file in a specific data format.
Parameters: - filename – Name of the text file containing the configuration
- data_format – Input file data format (XML, JSON or YAML)
-
read_string
(text)¶
-
to_dict
()¶
-
to_json
()¶ Converts the configuration to to json.
-
validate
(filename=None)¶
-
write
(filename, output_format='XML')¶ Write configuration to a text file in a specific data format.
Parameters: - filename –
- output_format –
Returns:
-
-
class
schrodinger.application.matsci.qexsd.qespresso.documents.
PwDocument
¶ Bases:
schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument
Class to manage PW XML documents.
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
get_input_path
()¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage PW XML documents.\n ', '__init__': <function PwDocument.__init__>, 'get_input_path': <function PwDocument.get_input_path>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__getitem__
(section)¶
-
__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.qexsd.qespresso.documents'¶
-
__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)
-
extra_validations
(xlm_tree)¶ Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.
-
find
(path, namespaces=None)¶ Find first matching element by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
findall
(path, namespaces=None)¶ Find all matching subelements by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
from_dict
()¶ Build an ElementTree object from a dictionary
-
get
(qualified_name)¶
-
get_qe_input
(use_defaults=True)¶
-
iter
(tag=None)¶
-
load_fortran_input
(filename)¶
-
parse_json
(filename)¶ Build an ElementTree object representing a YAML file
-
parse_xml
(filename)¶ Return an ElementTree object representing an XML file
-
parse_yaml
(filename)¶ Build an ElementTree object representing a YAML file
-
read
(filename, data_format='XML')¶ Read configuration from a text file in a specific data format.
Parameters: - filename – Name of the text file containing the configuration
- data_format – Input file data format (XML, JSON or YAML)
-
read_qe_input
(filename)¶ Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.
Parameters: filename – Returns:
-
read_string
(text)¶
-
to_dict
()¶
-
to_json
()¶ Converts the configuration to to json.
-
validate
(filename=None)¶
-
write
(filename, output_format='XML')¶ Write configuration to a text file in a specific data format.
Parameters: - filename –
- output_format –
Returns:
-
write_qe_input
(filename)¶ Write the XML configuration to a Fortran input.
Parameters: filename – Returns:
-
-
class
schrodinger.application.matsci.qexsd.qespresso.documents.
PhononDocument
¶ Bases:
schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument
Class to manage Phonon XML documents.
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
get_input_path
()¶
-
get_qe_input
(use_defaults=False)¶ overrides get_qe_input calling super get_qe_input with use_defaults set to False. :param use_defaults: :return: the input as obtained from its input builder
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage Phonon XML documents.\n ', '__init__': <function PhononDocument.__init__>, 'get_input_path': <function PhononDocument.get_input_path>, 'get_qe_input': <function PhononDocument.get_qe_input>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__getitem__
(section)¶
-
__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.qexsd.qespresso.documents'¶
-
__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)
-
extra_validations
(xlm_tree)¶ Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.
-
find
(path, namespaces=None)¶ Find first matching element by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
findall
(path, namespaces=None)¶ Find all matching subelements by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
from_dict
()¶ Build an ElementTree object from a dictionary
-
get
(qualified_name)¶
-
iter
(tag=None)¶
-
load_fortran_input
(filename)¶
-
parse_json
(filename)¶ Build an ElementTree object representing a YAML file
-
parse_xml
(filename)¶ Return an ElementTree object representing an XML file
-
parse_yaml
(filename)¶ Build an ElementTree object representing a YAML file
-
read
(filename, data_format='XML')¶ Read configuration from a text file in a specific data format.
Parameters: - filename – Name of the text file containing the configuration
- data_format – Input file data format (XML, JSON or YAML)
-
read_qe_input
(filename)¶ Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.
Parameters: filename – Returns:
-
read_string
(text)¶
-
to_dict
()¶
-
to_json
()¶ Converts the configuration to to json.
-
validate
(filename=None)¶
-
write
(filename, output_format='XML')¶ Write configuration to a text file in a specific data format.
Parameters: - filename –
- output_format –
Returns:
-
write_qe_input
(filename)¶ Write the XML configuration to a Fortran input.
Parameters: filename – Returns:
-
-
class
schrodinger.application.matsci.qexsd.qespresso.documents.
NebDocument
¶ Bases:
schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument
Class to manage NEB XML documents.
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
get_input_path
()¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage NEB XML documents.\n ', '__init__': <function NebDocument.__init__>, 'get_input_path': <function NebDocument.get_input_path>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__getitem__
(section)¶
-
__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.qexsd.qespresso.documents'¶
-
__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)
-
extra_validations
(xlm_tree)¶ Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.
-
find
(path, namespaces=None)¶ Find first matching element by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
findall
(path, namespaces=None)¶ Find all matching subelements by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
from_dict
()¶ Build an ElementTree object from a dictionary
-
get
(qualified_name)¶
-
get_qe_input
(use_defaults=True)¶
-
iter
(tag=None)¶
-
load_fortran_input
(filename)¶
-
parse_json
(filename)¶ Build an ElementTree object representing a YAML file
-
parse_xml
(filename)¶ Return an ElementTree object representing an XML file
-
parse_yaml
(filename)¶ Build an ElementTree object representing a YAML file
-
read
(filename, data_format='XML')¶ Read configuration from a text file in a specific data format.
Parameters: - filename – Name of the text file containing the configuration
- data_format – Input file data format (XML, JSON or YAML)
-
read_qe_input
(filename)¶ Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.
Parameters: filename – Returns:
-
read_string
(text)¶
-
to_dict
()¶
-
to_json
()¶ Converts the configuration to to json.
-
validate
(filename=None)¶
-
write
(filename, output_format='XML')¶ Write configuration to a text file in a specific data format.
Parameters: - filename –
- output_format –
Returns:
-
write_qe_input
(filename)¶ Write the XML configuration to a Fortran input.
Parameters: filename – Returns:
-
-
class
schrodinger.application.matsci.qexsd.qespresso.documents.
TdDocument
¶ Bases:
schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument
Class to manage TDDFPT
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
get_input_path
()¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage TDDFPT\n ', '__init__': <function TdDocument.__init__>, 'get_input_path': <function TdDocument.get_input_path>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__getitem__
(section)¶
-
__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.qexsd.qespresso.documents'¶
-
__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)
-
extra_validations
(xlm_tree)¶ Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.
-
find
(path, namespaces=None)¶ Find first matching element by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
findall
(path, namespaces=None)¶ Find all matching subelements by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
from_dict
()¶ Build an ElementTree object from a dictionary
-
get
(qualified_name)¶
-
get_qe_input
(use_defaults=True)¶
-
iter
(tag=None)¶
-
load_fortran_input
(filename)¶
-
parse_json
(filename)¶ Build an ElementTree object representing a YAML file
-
parse_xml
(filename)¶ Return an ElementTree object representing an XML file
-
parse_yaml
(filename)¶ Build an ElementTree object representing a YAML file
-
read
(filename, data_format='XML')¶ Read configuration from a text file in a specific data format.
Parameters: - filename – Name of the text file containing the configuration
- data_format – Input file data format (XML, JSON or YAML)
-
read_qe_input
(filename)¶ Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.
Parameters: filename – Returns:
-
read_string
(text)¶
-
to_dict
()¶
-
to_json
()¶ Converts the configuration to to json.
-
validate
(filename=None)¶
-
write
(filename, output_format='XML')¶ Write configuration to a text file in a specific data format.
Parameters: - filename –
- output_format –
Returns:
-
write_qe_input
(filename)¶ Write the XML configuration to a Fortran input.
Parameters: filename – Returns:
-
-
class
schrodinger.application.matsci.qexsd.qespresso.documents.
SpectrumDocument
¶ Bases:
schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument
Class to manage turbo-spectrum inputs
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
get_input_path
()¶
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage turbo-spectrum inputs\n ', '__init__': <function SpectrumDocument.__init__>, 'get_input_path': <function SpectrumDocument.get_input_path>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__getitem__
(section)¶
-
__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.qexsd.qespresso.documents'¶
-
__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)
-
extra_validations
(xlm_tree)¶ Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.
-
find
(path, namespaces=None)¶ Find first matching element by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
findall
(path, namespaces=None)¶ Find all matching subelements by tag name or path.
Parameters: - path – is a string having either an element tag or an XPath,
- namespaces – is an optional mapping from namespace prefix to full name.
Returns: the first matching element, or None if no element was found
-
from_dict
()¶ Build an ElementTree object from a dictionary
-
get
(qualified_name)¶
-
get_qe_input
(use_defaults=True)¶
-
iter
(tag=None)¶
-
load_fortran_input
(filename)¶
-
parse_json
(filename)¶ Build an ElementTree object representing a YAML file
-
parse_xml
(filename)¶ Return an ElementTree object representing an XML file
-
parse_yaml
(filename)¶ Build an ElementTree object representing a YAML file
-
read
(filename, data_format='XML')¶ Read configuration from a text file in a specific data format.
Parameters: - filename – Name of the text file containing the configuration
- data_format – Input file data format (XML, JSON or YAML)
-
read_qe_input
(filename)¶ Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.
Parameters: filename – Returns:
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read_string
(text)¶
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to_dict
()¶
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to_json
()¶ Converts the configuration to to json.
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validate
(filename=None)¶
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write
(filename, output_format='XML')¶ Write configuration to a text file in a specific data format.
Parameters: - filename –
- output_format –
Returns:
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write_qe_input
(filename)¶ Write the XML configuration to a Fortran input.
Parameters: filename – Returns:
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