inputparsing.py 11.2 KB
Newer Older
1
import numpy as np
2
3
import logging
from collections import defaultdict
4
logger = logging.getLogger("nomad")
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42


#===============================================================================
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)
43
44
45
46
47
48
49
50
        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
51
52
53

    def set_keyword(self, path, value):
        keyword, section = self.get_keyword_and_section(path)
54
        # If keyword found, put data in there
55
56
        if keyword and section:
            keyword.value = value
57
        # Keyword not found in the input tree, assuming it is a default keyword
58
59
60
        elif section is not None:
            split_path = path.rsplit("/", 1)
            keyword = split_path[1]
61
62
63
64
65
66
            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)
67
68
69
70
71
72
73

    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:
74
75
                message = "The CP2K input does not contain the section {}".format(path)
                logger.warning(message)
76
77
78
79
80
81
82
83
                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)
84
85
86
87
88
89

        if section is None:
            message = "The CP2K input does not contain the section {}".format(path)
            logger.warning(message)
            return (None, None)

90
91
92
        keyword = section.get_keyword(keyword)
        if keyword and section:
            return (keyword, section)
93
        else:
94
95
96
97
98
99
100
101
102
103
104
105
            return (None, section)

    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:
106
                return keyword.default_value
107
108

    def get_default_keyword(self, path):
109
        return self.get_section(path).default_keyword.value
110
111
112

    def set_section_accessed(self, path):
        section = self.get_section(path)
113
114
115
116
117
        if section:
            section.accessed = True
        else:
            message = "The CP2K input does not contain the section {}".format(path)
            logger.warning(message)
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135

    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)
136
137
138
139
140
141
142
        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)
143
144
145
146
147
148
149
150
151
152
153

    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


#===============================================================================
154
155
class InputObject(object):
    """Base class for all kind of data elements in the CP2K input.
156
    """
157
    __slots__ = ['name', 'value', 'default_value', 'description', 'data_type', 'data_dimension']
158

159
160
    def __init__(self, name):
        self.name = name
161
        self.value = None
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
        self.description = None
        self.data_type = None
        self.data_dimension = None
        self.default_value = None

    def get_formatted_value(self):
        """ Used to set the value of the keyword. The data will be transformed
        into the correct data type and dimension from a simple string.
        """
        returned = None
        dim = int(self.data_dimension)
        splitted = self.value.split()
        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))

        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(splitted)
            elif self.data_type == "keyword":
                returned = np.array(splitted)
            elif self.data_type == "string":
                returned = np.array(splitted)
            elif self.data_type == "logical":
                returned = np.array([True if x.upper() == "T" else False 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))
            return

        if len(returned) == 1:
            return returned[0]

        return returned
201

202
203
204
205
206
207
208
209
210
211
212
213
214
215
216

#===============================================================================
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

217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
    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


#===============================================================================
255
class Section(object):
256
257
    """An input section in a CP2K calculation.
    """
258
    __slots__ = ['accessed', 'name', 'keywords', 'default_keyword_names', 'default_keyword', 'section_parameter', 'sections', 'description']
259
260
261
262
263

    def __init__(self, name):
        self.accessed = False
        self.name = name
        self.keywords = defaultdict(list)
264
265
        self.default_keyword_names = []
        self.default_keyword = None
266
267
        self.section_parameter = None
        self.sections = defaultdict(list)
268
        self.description = None
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289

    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))


#===============================================================================
290
class SectionParameters(InputObject):
291
292
293
294
295
    """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.
    """
296
    __slots__ = ['lone_keyword_value']
297

298
299
    def __init__(self, default_value, lone_keyword_value):
        super(SectionParameters, self).__init__("SECTION_PARAMETERS")
300
        self.default_value = default_value
301
302
303
304
305
306
307
        self.lone_keyword_value = lone_keyword_value


#===============================================================================
class DefaultKeyword(InputObject):
    """Default keyword in the CP2K input.
    """
308
309
    __slots__ = ['lone_value']

310
311
312
313
    def __init__(self):
        super(DefaultKeyword, self).__init__("DEFAULT_KEYWORD")
        self.lone_value = None
        self.value = ""