inputparsing.py 14.7 KB
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import numpy as np
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import logging
from collections import defaultdict
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logger = logging.getLogger("nomad")
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#===============================================================================
class CP2KInput(object):
    """The contents of a CP2K simulation including default values and default
    units from the version-specific xml file.
    """

    def __init__(self, root_section):
        self.root_section = root_section

    @staticmethod
    def decode_cp2k_unit(unit):
        """Given a CP2K unit name, decode it as Pint unit definition.
        """
        map = {
            # Length
            "bohr": "bohr",
            "m": "meter",
            "pm": "picometer",
            "nm": "nanometer",
            "angstrom": "angstrom",

            # Angle
            "rad": "radian",
            "deg": "degree",

            #Energy
            "Ry": "rydberg"
        }
        pint_unit = map.get(unit)
        if pint_unit:
            return pint_unit
        else:
            logger.error("Unknown CP2K unit definition '{}'.".format(unit))

    def set_parameter(self, path, value):
        parameter, section = self.get_parameter_and_section(path)
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        if section is None:
            message = "The CP2K input does not contain a section {}".format(path)
            logger.warning(message)
        if parameter is None:
            message = "The CP2K input section {} does not contain a SECTION_PARAMETER".format(path)
            logger.warning(message)
        else:
            parameter.value = value
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    def set_keyword(self, path, value):
        keyword, section = self.get_keyword_and_section(path)
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        # If keyword found, put data in there
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        if keyword and section:
            keyword.value = value
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        # Keyword not found in the input tree, assuming it is a default keyword
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        elif section is not None:
            split_path = path.rsplit("/", 1)
            keyword = split_path[1]
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            if section.default_keyword is not None:
                # print "Saving default keyword at path '{}'".format(path)
                section.default_keyword.value += keyword + " " + value + "\n"
            else:
                message = "The CP2K input does not contain the keyword {}, and there is no default keyword for the section {}".format(path, split_path[0])
                logger.warning(message)
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    def get_section(self, path):
        split_path = path.split("/")
        section = self.root_section
        for part in split_path:
            section = section.get_subsection(part)
            if not section:
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                message = "The CP2K input does not contain the section {}".format(path)
                logger.warning(message)
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                return None
        return section

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    def get_section_list(self, path):
        split_path = path.split("/")
        last_section = split_path[-1]
        split_path.pop()
        section = self.root_section
        for part in split_path:
            section = section.get_subsection(part)
            if not section:
                message = "The CP2K input does not contain the section {}".format(path)
                logger.warning(message)
                return None
        return section.get_subsection_list(last_section)

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    def get_keyword_and_section(self, path):
        split_path = path.rsplit("/", 1)
        keyword = split_path[1]
        section_path = split_path[0]
        section = self.get_section(section_path)
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        if section is None:
            message = "The CP2K input does not contain the section {}".format(path)
            logger.warning(message)
            return (None, None)

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        keyword = section.get_keyword_object(keyword)
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        if keyword and section:
            return (keyword, section)
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        else:
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            return (None, section)

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    def get_keyword(self, path, format_value=True):
        if format_value:
            return self.get_keyword_value_formatted(path)
        else:
            return self.get_keyword_value_raw(path)

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    def get_keyword_value_formatted(self, path):
        """
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        """
        keyword, section = self.get_keyword_and_section(path)
        if keyword:
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            return keyword.get_value_formatted()

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    def get_keyword_value_raw(self, path):
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        """
        """
        keyword, section = self.get_keyword_and_section(path)
        if keyword:
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            return keyword.get_value_raw()
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    def get_default_keyword(self, path):
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        return self.get_section(path).default_keyword.value
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    def set_section_accessed(self, path):
        section = self.get_section(path)
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        if section:
            section.accessed = True
        else:
            message = "The CP2K input does not contain the section {}".format(path)
            logger.warning(message)
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    def get_keyword_default(self, path):
        keyword, section = self.get_keyword_and_section(path)
        if keyword:
            return keyword.default_value

    def get_default_unit(self, path):
        keyword, section = self.get_keyword_and_section(path)
        if keyword:
            return keyword.default_unit

    def get_unit(self, path):
        keyword, section = self.get_keyword_and_section(path)
        if keyword:
            return keyword.get_unit()

    def get_parameter_and_section(self, path):
        section = self.get_section(path)
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        if section is None:
            return (None, None)
        if section.section_parameter is not None:
            parameter = section.section_parameter
            return (parameter, section)
        else:
            return (None, section)
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    def get_parameter(self, path):
        parameter, section = self.get_parameter_and_section(path)
        if parameter:
            if parameter.value:
                return parameter.value
            elif section and section.accessed:
                return parameter.lone_value


#===============================================================================
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class InputObject(object):
    """Base class for all kind of data elements in the CP2K input.
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    """
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    __slots__ = ['name', 'value', 'default_value', 'description', 'data_type', 'data_dimension']
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    def __init__(self, name):
        self.name = name
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        self.value = None
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        self.description = None
        self.data_type = None
        self.data_dimension = None
        self.default_value = None

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#===============================================================================
class Keyword(InputObject):
    """Information about a keyword in a CP2K calculation.
    """
    __slots__ = ['unit', 'value_no_unit', 'default_unit', 'default_name']

    def __init__(self, name, default_value,  default_unit, default_name):
        super(Keyword, self).__init__(name)
        self.unit = None
        self.value_no_unit = None
        self.default_unit = default_unit
        self.default_value = default_value
        self.default_name = default_name

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    def get_value_raw(self):
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        """Returns the unformatted value of this keyword. This is exactly what
        was set by the used in the input as a string.
        """
        return self.value

    def get_value_formatted(self):
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        """Returns the value stored in this keyword by removing the possible
        unit definition and formatting the string into the correct data type.
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        """
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        # Decode the unit and the value if not done before
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        proper_value = None
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        if self.default_unit:
            if not self.value_no_unit:
                self.decode_cp2k_unit_and_value()
        if self.value_no_unit is not None:
            proper_value = self.value_no_unit
        else:
            proper_value = self.value
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        if proper_value is None:
            proper_value = self.default_value
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        if proper_value is None:
            return None
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        returned = None
        dim = int(self.data_dimension)
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        splitted = proper_value.split()
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        if len(splitted) != dim:
            logger.error("The dimensions of the CP2K input parameter {} do not match the specification in the XML file.".format(self.name))

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        if dim == 1:
            try:
                if self.data_type == "integer":
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                    returned = int(proper_value)
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                elif self.data_type == "real":
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                    returned = float(proper_value)
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                elif self.data_type == "word":
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                    returned = str(proper_value)
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                elif self.data_type == "keyword":
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                    returned = str(proper_value)
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                elif self.data_type == "string":
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                    returned = str(proper_value)
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                elif self.data_type == "logical":
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                    returned = str(proper_value)
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                else:
                    logger.error("Unknown data type '{}'".format(self.data_type))
                    return
            except TypeError:
                logger.error("The CP2K input parameter {} could not be converted to the type specified in the XML file.".format(self.name))
                return
        else:
            try:
                if self.data_type == "integer":
                    returned = np.array([int(x) for x in splitted])
                elif self.data_type == "real":
                    returned = np.array([float(x) for x in splitted])
                elif self.data_type == "word":
                    returned = np.array([str(x) for x in splitted])
                elif self.data_type == "keyword":
                    returned = np.array([str(x) for x in splitted])
                elif self.data_type == "string":
                    returned = np.array([str(x) for x in splitted])
                elif self.data_type == "logical":
                    returned = np.array([str(x) for x in splitted])
                else:
                    logger.error("Unknown data type '{}'".format(self.data_type))
                    return
            except TypeError:
                logger.error("The CP2K input parameter {} could not be converted to the type specified in the XML file.".format(self.name))
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                return

        return returned
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    def determine_value_and_unit(self):
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        """If the units of this value can be changed, return a value and the
        unit separately.
        """
        if self.default_unit:
            if not self.value_no_unit:
                self.decode_cp2k_unit_and_value()
            return self.value_no_unit
        else:
            return self.value

    def get_unit(self):
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        # Decode the unit and the value if not done before
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        if self.default_unit:
            if not self.unit:
                self.decode_cp2k_unit_and_value()
            return self.unit
        else:
            logger.error("The keyword '{}' does not have a unit.".format(self.default_name))
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            return None
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    def decode_cp2k_unit_and_value(self):
        """Given a CP2K unit name, decode it as Pint unit definition.
        """
        splitted = self.value.split(None, 1)
        unit_definition = splitted[0]
        if unit_definition.startswith('[') and unit_definition.endswith(']'):
            unit_definition = unit_definition[1:-1]
            self.unit = CP2KInput.decode_cp2k_unit(self.default_unit)
            self.value_no_unit = splitted[1]
        elif self.default_unit:
            logger.debug("No special unit definition found, returning default unit.")
            self.unit = CP2KInput.decode_cp2k_unit(self.default_unit)
            self.value_no_unit = self.value
        else:
            logger.debug("The value has no unit, returning bare value.")
            self.value_no_unit = self.value


#===============================================================================
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class Section(object):
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    """An input section in a CP2K calculation.
    """
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    __slots__ = ['accessed', 'name', 'keywords', 'default_keyword_names', 'default_keyword', 'section_parameter', 'sections', 'description']
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    def __init__(self, name):
        self.accessed = False
        self.name = name
        self.keywords = defaultdict(list)
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        self.default_keyword_names = []
        self.default_keyword = None
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        self.section_parameter = None
        self.sections = defaultdict(list)
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        self.description = None
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    def get_keyword_object(self, name):
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        keyword = self.keywords.get(name)
        if keyword:
            if len(keyword) == 1:
                return keyword[0]
            else:
                logger.error("The keyword '{}' in '{}' does not exist or has too many entries.".format(name, self.name))

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    def get_keyword_value_formatted(self, name):
        """Returns the keyword value formatted to the correct shape and type,
        and returns the default value if nothing was specified.
        """
        keyword_object = self.get_keyword_object(name)
        if keyword_object is not None:
            value = keyword_object.get_value_formatted()
            return value

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    def get_keyword_value_raw(self, name):
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        """Returns the keyword value as a raw string as specfied by the used.
        """
        keyword_object = self.get_keyword_object(name)
        if keyword_object is not None:
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            return keyword_object.get_value_raw()
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    def get_subsection(self, name):
        subsection = self.sections.get(name)
        if subsection:
            if len(subsection) == 1:
                return subsection[0]
            else:
                logger.error("The subsection '{}' in '{}' has too many entries.".format(name, self.name))
        else:
            logger.error("The subsection '{}' in '{}' does not exist.".format(name, self.name))

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    def get_subsection_list(self, name):
        subsection = self.sections.get(name)
        return subsection

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    def get_section_parameter(self):
        """Get the section parameter, or if not specified the lone keyword
        value.
        """
        if self.section_parameter is not None:
            value = self.section_parameter.value
            if value is None:
                value = self.section_parameter.lone_keyword_value
            return value.upper()

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#===============================================================================
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class SectionParameters(InputObject):
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    """Section parameters in a CP2K calculation.

    Section parameters are the short values that can be added right after a
    section name, e.g. &PRINT ON, where ON is the section parameter.
    """
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    __slots__ = ['lone_keyword_value']
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    def __init__(self, default_value, lone_keyword_value):
        super(SectionParameters, self).__init__("SECTION_PARAMETERS")
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        self.default_value = default_value
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        self.lone_keyword_value = lone_keyword_value


#===============================================================================
class DefaultKeyword(InputObject):
    """Default keyword in the CP2K input.
    """
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    __slots__ = ['lone_value']

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    def __init__(self):
        super(DefaultKeyword, self).__init__("DEFAULT_KEYWORD")
        self.lone_value = None
        self.value = ""