Added parsing of input file if found, added support for more functionals,...

Added parsing of input file if found, added support for more functionals, corrected the formatting of functionals, restructured the package a bit.

.gitignore

@@ -56,6 +56,7 @@ env/
 # CP2K files
 *.inp
 *.wfn
+*.cube
 test/unittests/BASIS_SET
 test/unittests/GTH_POTENTIALS
 

parser/parser-cp2k/cp2kparser/generic/inputparsing.py

+import logging
+from collections import defaultdict
+logger = logging.getLogger(__name__)
+
+
+#===============================================================================
+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)
+        parameter.value = value
+
+    def set_keyword(self, path, value):
+        keyword, section = self.get_keyword_and_section(path)
+        if keyword and section:
+            keyword.value = value
+        elif section is not None:
+            # print "Saving default keyword at path '{}'".format(path)
+            split_path = path.rsplit("/", 1)
+            keyword = split_path[1]
+            section.default_keyword += keyword + " " + value + "\n"
+
+    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:
+                print "Error in getting section at path '{}'.".format(path)
+                return None
+        return section
+
+    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)
+        keyword = section.get_keyword(keyword)
+        if keyword and section:
+            return (keyword, section)
+        elif section:
+            return (None, section)
+        return (None, None)
+
+    def get_keyword(self, path):
+        """Returns the keyword that is specified by the given path.
+        If the keyword has no value set, returns the default value defined in
+        the XML.
+        """
+        keyword, section = self.get_keyword_and_section(path)
+        if keyword:
+            if keyword.value is not None:
+                return keyword.get_value()
+            else:
+                if section.accessed:
+                    return keyword.default_value
+
+    def get_default_keyword(self, path):
+        return self.get_section(path).default_keyword
+
+    def set_section_accessed(self, path):
+        section = self.get_section(path)
+        section.accessed = True
+
+    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)
+        parameter = section.section_parameter
+        return (parameter, section)
+
+    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
+
+
+#===============================================================================
+class Keyword(object):
+    """Information about a keyword in a CP2K calculation.
+    """
+    __slots__ = ['value', 'unit', 'value_no_unit', 'default_name', 'default_value', 'default_unit']
+
+    def __init__(self, default_name, default_value, default_unit_value):
+        self.value = None
+        self.unit = None
+        self.value_no_unit = None
+        self.default_name = default_name
+        self.default_value = default_value
+        self.default_unit = default_unit_value
+
+    def get_value(self):
+        """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):
+        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))
+
+    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
+
+
+#===============================================================================
+class Section(object):
+    """An input section in a CP2K calculation.
+    """
+    __slots__ = ['accessed', 'name', 'keywords', 'default_keyword', 'section_parameter', 'sections']
+
+    def __init__(self, name):
+        self.accessed = False
+        self.name = name
+        self.keywords = defaultdict(list)
+        self.default_keyword = ""
+        self.section_parameter = None
+        self.sections = defaultdict(list)
+
+    def get_keyword(self, name):
+        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))
+
+    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))
+
+
+#===============================================================================
+class SectionParameters(object):
+    """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.
+    """
+    __slots__ = ['value', 'default_value', 'lone_value']
+
+    def __init__(self, default_value, lone_value):
+        self.value = None
+        self.default_value = default_value
+        self.lone_value = lone_value

parser/parser-cp2k/cp2kparser/parser.py

+import os
+import re
+import logging
+from cp2kparser.generic.baseclasses import ParserInterface
+from cp2kparser.versions.versionsetup import get_main_parser
+logger = logging.getLogger(__name__)
+
+
+#===============================================================================
+class CP2KParser(ParserInterface):
+    """This class handles the initial setup before any parsing can happen. It
+    determines which version of CP2K was used to generate the output and then
+    sets up a correct implementation.
+
+    After the implementation has been setup, you can parse the files with
+    parse().
+    """
+    def __init__(self, main_file, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None):
+        super(CP2KParser, self).__init__(main_file, metainfo_to_keep, backend, default_units, metainfo_units)
+
+    def setup_version(self):
+        """Setups the version by looking at the output file and the version
+        specified in it.
+        """
+        # Search for the version specification and initialize a correct
+        # main parser for this version.
+        regex = re.compile(r" CP2K\| version string:\s+CP2K version ([\d\.]+)")
+        n_lines = 30
+        with open(self.parser_context.main_file, 'r') as outputfile:
+            for i_line in xrange(n_lines):
+                line = next(outputfile)
+                result = regex.match(line)
+                if result:
+                    version_id = result.group(1).replace('.', '')
+                    break
+        if not result:
+            logger.error("Could not find a version specification from the given main file.")
+
+        # Setup the root folder to the fileservice that is used to access files
+        dirpath, filename = os.path.split(self.parser_context.main_file)
+        self.parser_context.file_service.setup_root_folder(dirpath)
+        self.parser_context.file_service.set_file_id(filename, "output")
+
+        # Setup the correct main parser based on the version id. If no match
+        # for the version is found, use the main parser for CP2K 2.6.2
+        self.main_parser = get_main_parser(version_id)(self.parser_context.main_file, self.parser_context)
+
+    def get_metainfo_filename(self):
+        return "cp2k.nomadmetainfo.json"
+
+    def get_parser_info(self):
+        return {'name': 'cp2k-parser', 'version': '1.0'}

parser/parser-cp2k/cp2kparser/tools/xmlpreparser.py

+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""Provides functions for creating a python object representing a CP2K input
+structure.
+
+Creates preparsed versions of the cp2k_input.xmls and pickles them (python
+version of serialization). The pickle files can then be easily reused without
+doing the xml parsing again.
+
+The actual calculation input contents can later be added to this object. Then
+the object can be queried for the results, or the default values defined by the
+cp2k_input.xml.
+"""
+
+import xml.etree.cElementTree as ET
+import logging
+import cPickle as pickle
+from cp2kparser.generic.inputparsing import *
+logger = logging
+
+
+#===============================================================================
+def generate_object_tree(xml_file):
+
+    xml_element = ET.parse(xml_file)
+    object_tree = recursive_tree_generation(xml_element)
+    return object_tree
+
+
+#===============================================================================
+def recursive_tree_generation(xml_element):
+
+    # Make new section object for the root
+    section_name_element = xml_element.find("NAME")
+    if section_name_element is not None:
+        section_name = section_name_element.text
+    else:
+        section_name = "CP2K_INPUT"
+    section = Section(section_name)
+
+    # Section parameters
+    parameter = xml_element.find("SECTION_PARAMETERS")
+    if parameter:
+        sp_default_element = parameter.find("DEFAULT_VALUE")
+        sp_default_value = None
+        if sp_default_element is not None:
+            sp_default_value = sp_default_element.text
+        sp_lone_element = parameter.find("LONE_KEYWORD_VALUE")
+        sp_lone_value = None
+        if sp_lone_element is not None:
+            sp_lone_value = sp_lone_element.text
+        parameter_object = SectionParameters(sp_default_value, sp_lone_value)
+        section.section_parameter = parameter_object
+
+    # Keywords
+    for keyword in xml_element.findall("KEYWORD"):
+        keyword_names = keyword.findall("NAME")
+        default_name = None
+        aliases = []
+        for name in keyword_names:
+            keytype = name.get("type")
+            if keytype == "default":
+                default_name = name.text
+            else:
+                aliases.append(name.text)
+        default_keyword_element = keyword.find("DEFAULT_VALUE")
+        default_keyword_value = None
+        if default_keyword_element is not None:
+            default_keyword_value = default_keyword_element.text
+
+        default_unit_element = keyword.find("DEFAULT_UNIT")
+        default_unit_value = None
+        if default_unit_element is not None:
+            default_unit_value = default_unit_element.text
+
+        keyword_object = Keyword(default_name, default_keyword_value, default_unit_value)
+        section.keywords[default_name].append(keyword_object)
+        for alias in aliases:
+            section.keywords[alias].append(keyword_object)
+
+    # Sections
+    for sub_section_element in xml_element.findall("SECTION"):
+        sub_section = recursive_tree_generation(sub_section_element)
+        section.sections[sub_section.name].append(sub_section)
+
+    # Return section
+    return section
+
+#===============================================================================
+# Run main function by default
+if __name__ == "__main__":
+    xml_file = open("../versions/cp2k262/input_data/cp2k_input.xml", 'r')
+    object_tree = CP2KInput(generate_object_tree(xml_file))
+    file_name = "../versions/cp2k262/input_data/cp2k_input_tree.pickle"
+    fh = open(file_name, "wb")
+    pickle.dump(object_tree, fh, protocol=2)

parser/parser-cp2k/cp2kparser/versions/cp2k262/input_data/units.html

+<HTML><BODY><HEAD><TITLE>The cp2k units list</TITLE>
+<H1>CP2K Available Units of Measurement</H1>
+<H2>Undefined</H2>
+If the default unit of a keyword is explicitly undefined, all possible units of measurement can be used to define a proper value.<BR><DL>
+<DD><B>internal_cp2k</B></DD>
+</DL><P>
+<H2>Energy</H2>
+Possible units of measurement for Energies. The [energy] entry acts like a dummy flag (assumes the unit of measurement of energy is in internal units), useful for dimensional analysis.<BR><DL>
+<DD><B>hartree</B></DD>
+<DD><B>wavenumber_e</B></DD>
+<DD><B>joule</B></DD>
+<DD><B>kcalmol</B></DD>
+<DD><B>kjmol</B></DD>
+<DD><B>Ry</B></DD>
+<DD><B>eV</B></DD>
+<DD><B>K_e</B></DD>
+<DD><B>energy</B></DD>
+</DL><P>
+<H2>Length</H2>
+Possible units of measurement for Lengths. The [length] entry acts like a dummy flag (assumes the unit of measurement of length is in internal units), useful for dimensional analysis.<BR><DL>
+<DD><B>bohr</B></DD>
+<DD><B>m</B></DD>
+<DD><B>pm</B></DD>
+<DD><B>nm</B></DD>
+<DD><B>angstrom</B></DD>
+<DD><B>length</B></DD>
+</DL><P>
+<H2>Temperature</H2>
+Possible units of measurement for Temperature. The [temperature] entry acts like a dummy flag (assumes the unit of measurement of temperature is in internal units), useful for dimensional analysis.<BR><DL>
+<DD><B>K</B></DD>
+<DD><B>au_temp</B></DD>
+<DD><B>temperature</B></DD>
+</DL><P>
+<H2>Pressure</H2>
+Possible units of measurement for Pressure. The [pressure] entry acts like a dummy flag (assumes the unit of measurement of pressure is in internal units), useful for dimensional analysis.<BR><DL>
+<DD><B>bar</B></DD>
+<DD><B>atm</B></DD>
+<DD><B>kbar</B></DD>
+<DD><B>Pa</B></DD>
+<DD><B>MPa</B></DD>
+<DD><B>GPa</B></DD>
+<DD><B>au_p</B></DD>
+<DD><B>pressure</B></DD>
+</DL><P>
+<H2>Angle</H2>
+Possible units of measurement for Angles. The [angle] entry acts like a dummy flag (assumes the unit of measurement of angle is in internal units), useful for dimensional analysis.<BR><DL>
+<DD><B>rad</B></DD>
+<DD><B>deg</B></DD>
+<DD><B>angle</B></DD>
+</DL><P>
+<H2>Time</H2>
+Possible units of measurement for Time. The [time] entry acts like a dummy flag (assumes the unit of measurement of time is in internal units), useful for dimensional analysis.<BR><DL>
+<DD><B>s</B></DD>
+<DD><B>fs</B></DD>
+<DD><B>ps</B></DD>
+<DD><B>au_t</B></DD>
+<DD><B>wavenumber_t</B></DD>
+<DD><B>time</B></DD>
+</DL><P>
+<H2>Mass</H2>
+Possible units of measurement for Masses. The [mass] entry acts like a dummy flag (assumes the unit of measurement of mass is in internal units), useful for dimensional analysis.<BR><DL>
+<DD><B>kg</B></DD>
+<DD><B>amu</B></DD>
+<DD><B>m_e</B></DD>
+<DD><B>mass</B></DD>
+</DL><P>
+<H2>Potential</H2>
+Possible units of measurement for potentials. The [potential] entry acts like a dummy flag (assumes the unit of measurement of potential is in internal units), useful for dimensional analysis.<BR><DL>
+<DD><B>volt</B></DD>
+<DD><B>au_pot</B></DD>
+<DD><B>potential</B></DD>
+</DL><P>
+<H2>Force</H2>
+Possible units of measurement for forces. The [force] entry acts like a dummy flag (assumes the unit of measurement of force is in internal units), useful for dimensional analysis.<BR><DL>
+<DD><B>N</B></DD>
+<DD><B>Newton</B></DD>
+<DD><B>mN</B></DD>
+<DD><B>mNewton</B></DD>
+<DD><B>au_f</B></DD>
+<DD><B>force</B></DD>
+</DL><P>
+</BODY></HTML>

parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py

+import os
+import logging
+import cPickle as pickle
+from cp2kparser.generic.baseclasses import BasicParser
+from cp2kparser.generic.inputparsing import *
+logger = logging.getLogger(__name__)
+
+
+#===============================================================================
+class CP2KInputParser(BasicParser):
+    """Used to parse out a CP2K input file.
+
+    When given a filepath to a CP2K input file, this class attemts to parse
+    it's contents.
+    """
+    def __init__(self, file_path, parser_context):
+        super(CP2KInputParser, self).__init__(file_path, parser_context)
+        self.root_section = None
+        self.input_tree = None
+
+    def parse(self):
+
+        # Gather the information from the input file
+        self.fill_input_tree(self.file_path)
+
+        # Parse the used XC_functionals and their parameters
+        xc = self.input_tree.get_section("FORCE_EVAL/DFT/XC/XC_FUNCTIONAL")
+        if xc is not None:
+            xc_list = []
+
+            class XCFunctional(object):
+                def __init__(self, name, weight=1, parameters=None):
+                    self.name = name
+                    self.weight = weight
+                    self.parameters = parameters
+
+            # First see if a functional has been specified in the section parameter
+            section_parameter = xc.section_parameter.value
+            if section_parameter is not None:
+
+                if section_parameter == "BLYP":
+                    xc_list.append(XCFunctional("GGA_X_B88"))
+                    xc_list.append(XCFunctional("GGA_C_LYP"))
+
+                elif section_parameter == "LDA" or section_parameter == "PADE":
+                    xc_list.append(XCFunctional("LDA_XC_TETER93"))
+
+                elif section_parameter == "PBE":
+                    xc_list.append(XCFunctional("GGA_X_PBE"))
+                    xc_list.append(XCFunctional("GGA_C_PBE"))
+
+                elif section_parameter == "OLYP":
+                    xc_list.append(XCFunctional("GGA_X_OPTX"))
+                    xc_list.append(XCFunctional("GGA_C_LYP"))
+
+                elif section_parameter == "HCTH120":
+                    xc_list.append(XCFunctional("GGA_XC_HCTH_120"))
+
+                elif section_parameter == "PBE0":
+                    xc_list.append(XCFunctional("HYB_GGA_XC_PBEH"))
+
+                elif section_parameter == "B3LYP":
+                    xc_list.append(XCFunctional("HYB_GGA_XC_B3LYP"))
+
+                else:
+                    logger.warning("Unknown XC functional given in XC_FUNCTIONAL section parameter.")
+
+            # Otherwise one has to look at the individual functional settings
+            else:
+                pass
+
+            # Sort the functionals alphabetically by name
+            xc_list.sort(key=lambda x: x.name)
+            xc_summary = ""
+
+            # For every defined functional, stream the information to the
+            # backend and construct the summary string
+            for i, functional in enumerate(xc_list):
+
+                gId = self.backend.openSection("section_XC_functionals")
+                self.backend.addValue("XC_functional_name", functional.name)
+                self.backend.addValue("XC_functional_weight", functional.weight)
+                if functional.parameters is not None:
+                    pass
+                self.backend.closeSection("section_XC_functionals", gId)
+
+                if i != 0:
+                    xc_summary += "+"
+                xc_summary += "{}*{}".format(functional.weight, functional.name)
+                if functional.parameters is not None:
+                    xc_summary += ":{}".format()
+
+            # Stream summary
+            if xc_summary is not "":
+                self.backend.addValue("XC_functional", xc_summary)
+
+    def fill_input_tree(self, file_path):
+        """Parses a CP2K input file into an object tree.
+
+        Return an object tree represenation of the input augmented with the
+        default values and lone keyword values from the cp2k_input.xml file
+        which is version specific. Keyword aliases are also mapped to the same
+        data.
+
+        The cp2k input is largely case-insensitive. In the input tree, we wan't
+        only one standard way to name things, so all section names and section
+        parameters will be transformed into upper case.
+
+        To query the returned tree use the following functions:
+            get_keyword("GLOBAL/PROJECT_NAME")
+            get_parameter("GLOBAL/PRINT")
+            get_default_keyword("FORCE_EVAL/SUBSYS/COORD")
+
+        Args:
+            : A string containing the contents of a CP2K input file. The