Merged file-parser into v0.9.8.

README.md

@@ -46,6 +46,9 @@ contributing, and API reference.
 
 Omitted versions are plain bugfix releases with only minor changes and fixes.
 
+### v0.9.8
+- A new library for parsing text-based raw files.
+
 ### v0.9.3
 - Encyclopedia with dedicated materials search index.
 

elastic @ 9d4518fe

-Subproject commit c17dbecac0f395b48fc65b0c7dcc2ba4de1be271
+Subproject commit 9d4518fefb1f1146b7fa7ed95547822683020533

gromacs @ 3b5866bc

-Subproject commit 3f78e35b56714fe8c79b010ed52d97def19cb2dc
+Subproject commit 3b5866bc8dff77d398eddc6baceb19e1c30180c1

lammps @ 8944d5ff

-Subproject commit 7ed44cab4410099208f5e399bfa4c1dc2e9c29fe
+Subproject commit 8944d5ffd4cac01e43aaac5c5687b0a8831f2bc7

python_common @ c1aca042

-Subproject commit afdd0937aab2681ca3912cfd9d95c7633fdcd7b9
+Subproject commit c1aca04237d69097bbeb17d3a397be66e9c6797f

nomad/datamodel/metainfo/common.py

@@ -963,7 +963,7 @@ class section_method(public.section_method):
 
     gw_frequency_number = Quantity(
         type=np.dtype(np.int32),
-        shape=[],
+        shape=['gw_number_of_frequencies'],
         description='''
         Number referring to the frequency used in the calculation of the self energy.
         ''',
@@ -971,7 +971,7 @@ class section_method(public.section_method):
 
     gw_frequency_values = Quantity(
         type=np.dtype(np.float64),
-        shape=[],
+        shape=['gw_number_of_frequencies'],
         unit='joule',
         description='''
         Values of the frequency used in the calculation of the self energy.
@@ -980,7 +980,7 @@ class section_method(public.section_method):
 
     gw_frequency_weights = Quantity(
         type=np.dtype(np.float64),
-        shape=[],
+        shape=['gw_number_of_frequencies'],
         description='''
         Weights of the frequency used in the calculation of the self energy.
         ''',

nomad/datamodel/metainfo/public.py

@@ -3614,6 +3614,16 @@ class section_scf_iteration(MSection):
 
     m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_scf_iteration'))
 
+    charge_total_scf_iteration = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='coulomb',
+        description='''
+        Value of the total charge, calculated with the method described in XC_method
+        during each self-consistent field (SCF) iteration.
+        ''',
+        a_legacy=LegacyDefinition(name='charge_total_scf_iteration'))
+
     electronic_kinetic_energy_scf_iteration = Quantity(
         type=np.dtype(np.float64),
         shape=[],
@@ -3867,6 +3877,16 @@ class section_scf_iteration(MSection):
         categories=[time_info, accessory_info],
         a_legacy=LegacyDefinition(name='time_scf_iteration_wall_start'))
 
+    time_scf_iteration = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='second',
+        description='''
+        Total time of the self-consistent field (SCF) iteration.
+        ''',
+        categories=[time_info, accessory_info],
+        a_legacy=LegacyDefinition(name='time_scf_iteration'))
+
 
 class section_single_configuration_calculation(MSection):
     '''
@@ -3995,6 +4015,15 @@ class section_single_configuration_calculation(MSection):
         categories=[atom_forces_type],
         a_legacy=LegacyDefinition(name='atom_forces'))
 
+    charge_total = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='coulomb',
+        description='''
+        Value of the total charge, calculated with the method described in XC_method.
+        ''',
+        a_legacy=LegacyDefinition(name='charge_total'))
+
     electronic_kinetic_energy = Quantity(
         type=np.dtype(np.float64),
         shape=[],
@@ -5211,6 +5240,18 @@ class section_system(MSection):
         categories=[configuration_core],
         a_legacy=LegacyDefinition(name='lattice_vectors'))
 
+    lattice_vectors_reciprocal = Quantity(
+        type=np.dtype(np.float64),
+        shape=[3, 3],
+        unit='1/meter',
+        description='''
+        Reciprocal lattice vectors (in Cartesian coordinates) of the simulation cell. The
+        first index runs over the $x,y,z$ Cartesian coordinates, and the second index runs
+        over the 3 lattice vectors.
+        ''',
+        categories=[configuration_core],
+        a_legacy=LegacyDefinition(name='lattice_vectors_reciprocal'))
+
     local_rotations = Quantity(
         type=np.dtype(np.float64),
         shape=['number_of_atoms', 3, 3],

nomad/parsing/file_parser/README.md

+# NOMAD file parsing module
+
+The parsing module consists of the `UnstructuredTextFileParser`, `DataTextFileParser`
+and `XMLParser` classes to enable the parsing of unstructured text, structured data text,
+and xml files, respectively. These classes are based on the FileParser class which
+provides the common methods for file handling, and querying the parsed results.
+
+## UnstructuredTextFileParser
+
+The most common type of file that are parsed in NOMAD are unstructured text files which
+can be handled using the UnstructuredTextFileParser. The parser uses the `re` module to
+match a given pattern for a quantity in the text file. To illustrate the use of this parser,
+let us consider a file `super_code.out` with the following contents:
+
+```
+2020/05/15
+               *** super_code v2 ***
+
+system 1
+--------
+sites: H(1.23, 0, 0), H(-1.23, 0, 0), O(0, 0.33, 0)
+latice: (0, 0, 0), (1, 0, 0), (1, 1, 0)
+energy: 1.29372
+
+*** This was done with magic source                                ***
+***                                x°42                            ***
+
+
+system 2
+--------
+sites: H(1.23, 0, 0), H(-1.23, 0, 0), O(0, 0.33, 0)
+cell: (0, 0, 0), (1, 0, 0), (1, 1, 0)
+energy: 1.29372
+```
+
+In order to create a nomad archive from this file, we first have to parse the necessary
+quantities which includes the date, system, energy, etc. The following python code
+illustrates how can this be achieved. Note that we will be using *parser* to refer to the
+file parser and to the code parser that writes the archive.
+
+```python
+import datetime
+import numpy as np
+
+from nomad.parsing.file_parser import UnstructuredTextFileParser, Quantity
+from nomad.datamodel import EntryArchive
+from nomad.datamodel.metainfo.public import section_run, section_system, section_single_configuration_calculation
+
+p = UnstructuredTextFileParser()
+
+def str_to_sites(string):
+    sym, pos = string.split('(')
+    pos = np.array(pos.split(')')[0].split(',')[:3], dtype=float)
+    return sym, pos
+
+q_system = Quantity(
+    'system', r'\s*system \d+([\s\S]+?energy: [\d\.]+)([\s\S]+\*\*\*)*',
+    sub_parser=UnstructuredTextFileParser(quantities=[
+        Quantity(
+            'sites', r'([A-Z]\([\d\.\, \-]+\))',
+            str_operation=str_to_sites),
+        Quantity(
+            section_system.lattice_vectors,
+            r'(?:latice|cell): \((\d)\, (\d), (\d)\)\,?\s*\((\d)\, (\d), (\d)\)\,?\s*\((\d)\, (\d), (\d)\)\,?\s*',
+            repeats=False),
+        Quantity(
+            'energy', r'energy: (\d\.\d+)'),
+        Quantity(
+            'magic_source', r'done with magic source\s*\*{3}\s*\*{3}\s*([\S]+)',
+            repeats=False)]),
+    repeats=True)
+
+quantities = [
+        Quantity('date', r'(\d\d\d\d\/\d\d\/\d\d)', repeats=False),
+        Quantity('program_version', r'super\_code\s*v(\d+)\s*', repeats=False),
+        q_system]
+
+p.quantities = quantities
+# this returns the energy for system 2
+p.system[1].get('energy', unit='hartree')
+```
+
+The quantities to be parsed can be specified as a list of `Quantity` objects with a name
+and a re pattern. The matched value should be enclosed in a group(s). By default,
+the parser uses the findall method of `re`, hence overlap
+between matches is not tolerated. If overlap cannot be avoided, one should switch to the
+finditer method by passing *findall=False* to the parser. Multiple
+matches for the quantity are returned if *repeats=True* (default). The name, data type,
+shape and unit for the quantity can also intialized by passing a metainfo Quantity.
+An external function *str_operation* can be also be passed to perform more specific
+string operations on the matched value. A local parsing on a matched block can be carried
+out by nesting a *sub_parser*. This is also an instance of the `UnstructuredTextFileParser`
+with a list of quantities to parse. To access a parsed quantity, one can use the *get*
+method.
+
+The creation of the archive is implemented in the parse method of the code parser which takes
+the mainfile, archive and logger as arguments. The file parser, *out_parser* is
+created only in the constructor and subsequent parsing on a different *mainfile* can be
+performed by assigning it to the file parser.
+
+```python
+class SupercodeParser:
+    def __init__(self):
+        self.out_parser = UnstructuredTextFileParser()
+        self.out_parser.quantities = quantities
+
+    def parse(self, mainfile, archive, logger):
+        self.out_parser.mainfile = mainfile
+        sec_run = archive.m_create(section_run)
+        sec_run.program_name = 'super_code'
+        sec_run.program_version = str(self.out_parser.get('program_version'))
+        date = datetime.datetime.strptime(
+            self.out_parser.get('date'), '%Y/%m/%d') - datetime.datetime(1970, 1, 1)
+        sec_run.program_compilation_datetime = date.total_seconds()
+        for system in self.out_parser.get('system'):
+            sec_system = sec_run.m_create(section_system)
+            sec_system.lattice_vectors = system.get('lattice_vectors')
+            sites = system.get('sites')
+            sec_system.atom_labels = [site[0]  for site in sites]
+            sec_system.atom_positions = [site[1] for site in sites]
+
+            sec_scc = sec_run.m_create(section_single_configuration_calculation)
+            sec_scc.energy_total = system.get('energy')
+            sec_scc.single_configuration_calculation_to_system_ref = sec_system
+            magic_source = system.get('magic_source')
+            if magic_source is not None:
+                sec_scc.message_info_evaluation = magic_source
+
+archive = EntryArchive()
+
+parser = SupercodeParser()
+parser.parse('temp.dat', archive, None)
+
+print(archive.m_to_json())
+```
+
+## DataTextFileParser
+The `DataTextFileParser` uses the numpy.loadtxt function to load an structured data file.
+The loaded data can be accessed from property *data*.
+
+## XMLParser
+The `XMLParser` uses the ElementTree module to parse an xml file. The parse method of the
+parser takes in an xpath style key to access individual quantities. By default, automatic
+data type conversion is performed, which can be switched off by setting *convert=False*.
+
+

nomad/parsing/file_parser/__init__.py

+from .file_parser import FileParser
+from .text_parser import UnstructuredTextFileParser, DataTextFileParser, Quantity, ParsePattern
+from .xml_parser import XMLParser

nomad/parsing/file_parser/file_parser.py

+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+import os
+import logging
+import pint
+from typing import Any, Dict
+
+
+class FileParser:
+    '''
+    Base class for parsers. The parse method implemented here simply sets the parsed
+    quantities as attributes of the class. The parse method specific to a file type
+    should be implemented in the corresponding child class. The parsed quantities are
+    stored in results. One can access a quantity by using the get method.
+
+    Arguments:
+        mainfile: the file to be parsed
+        logger: optional logger
+    '''
+    def __init__(self, mainfile: str, logger=None):
+        self._mainfile: str = os.path.abspath(mainfile) if mainfile else mainfile
+        self.logger = logger if logger else logging
+        self._results: Dict[str, Any] = None
+        # a key is necessary for xml parsers, where parsing is done dynamically
+        self._key: str = None
+        self._kwargs: Dict[str, Any] = None
+        self._file_handler: Any = None
+
+    @property
+    def results(self):
+        if self._results is None:
+            self._results = dict()
+        if self._key not in self._results:
+            self.parse(self._key, **self._kwargs)
+
+        return self._results
+
+    @property
+    def maindir(self):
+        return os.path.dirname(self._mainfile)
+
+    @property
+    def mainfile(self):
+        if self._mainfile is None:
+            return
+
+        if not os.path.isfile(self._mainfile):
+            return
+        return self._mainfile
+
+    @mainfile.setter
+    def mainfile(self, val):
+        self._results = None
+        self._file_handler = None
+        self._mainfile = os.path.abspath(val) if val is not None else val
+
+    def get(self, key: str, default: Any = None, unit: str = None, **kwargs):
+        '''
+        Returns the parsed result for quantity with name key. If quantity is not in
+        results default will be returned. A pint unit can be provided which is attached
+        to the returned value.
+        '''
+        self._key = key
+        self._kwargs = kwargs
+        val = self.results.get(key, None)
+        if val is None:
+            val = default
+
+        if val is None:
+            return
+
+        if unit is not None:
+            if isinstance(unit, pint.Quantity):
+                val = val * unit
+
+            elif isinstance(val, pint.Quantity):
+                val = val.to(unit)
+
+            else:
+                val = pint.Quantity(val, unit)
+
+        return val
+
+    def __getitem__(self, key):
+        if isinstance(key, str):
+            return self.get(key)
+        elif isinstance(key, int):
+            return self[int]
+
+    def parse(self, quantity_key: str = None):
+        '''
+        Sets quantities in result as class attributes.
+        '''
+        for key, val in self._results.items():
+            try:
+                setattr(self, key, val)
+            except Exception:
+                pass
+        return self

nomad/parsing/file_parser/text_parser.py

+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+import logging
+import mmap
+import re
+import numpy as np
+import pint
+from typing import List, Union, Callable, Type
+
+from nomad.parsing.file_parser import FileParser
+from nomad.metainfo import Quantity as mQuantity
+
+
+class ParsePattern:
+    def __init__(self, **kwargs):
+        self._head = kwargs.get('head', '')
+        self._key = kwargs.get('key', '')
+        value = kwargs.get('value', 're_float_array')
+        if value.startswith('re_'):
+            token = ''
+            if 'float' in value:
+                token += r'Ee\+\d\.\-'
+            if 'int' in value:
+                token += r'\d'
+            if 'string' in value:
+                token += r'\w'
+            if 'array' in value:
+                token += r' '
+            value = r'[%s]+' % token
+        self._value = value
+        self._tail = kwargs.get('tail', '\n')
+        self._re_pattern = None
+
+    @property
+    def re_pattern(self):
+        if self._re_pattern is None:
+            head = r'%s[\s\S]*?' % self._head if self._head else ''
+            key = r'%s\s*\:*\=*\s*' % self._key if self._key else ''
+            self._re_pattern = r'%s%s\s*\:*\=*\s*(%s)%s' % (
+                head, key, self._value, self._tail)
+        return self._re_pattern
+
+    def __call__(self, text, repeats=True):
+        values = []
+        units = []
+        if repeats:
+            for res in self.re_pattern.finditer(text):
+                unit = res.groupdict().get('__unit', None)
+                values.append(
+                    ''.join([group.decode() for group in res.groups() if group and group != unit]))
+                units.append(unit.decode() if unit is not None else None)
+        else:
+            res = self.re_pattern.search(text)
+            if res is not None:
+                unit = res.groupdict().get('__unit', None)
+                units.append(unit.decode() if unit is not None else None)
+                values.append(''.join(
+                    [group.decode() for group in res.groups() if group and group != unit]))
+
+
+class Quantity:
+    '''
+    Class to define a quantity to be parsed in the UnstructuredTextFileParser.
+
+    Arguments:
+        quantity: string to identify the name or a metainfo quantity to initialize the
+            quantity object.
+        re_pattern: pattern to be used by re for matching. Ideally, overlaps among
+            quantities for a given parser should be avoided.
+        sub_parser: instance of UnstructuredTextFileParser to perform local parsing
+            within a matched block
+        str_operation: external function to be performed on a matched block
+        dtype: data type of the quantity
+        unit: unit of the quantity
+        shape: shape of the quantity
+        repeats: denotes if multiple matches are expected
+        convert: switch automatic data type conversion
+        comment: character to denote a line to be ignored
+
+    '''
+    def __init__(self, quantity: Union[str, mQuantity], re_pattern: Union[str, ParsePattern], **kwargs):
+        self.name: str
+        self.dtype: str
+        self.unit: str
+        self.shape: List[int]
+        if isinstance(quantity, str):
+            self.name = quantity
+            self.dtype = None
+            self.unit = None
+            self.shape = None
+        elif isinstance(quantity, mQuantity):
+            self.name = quantity.name
+            self.dtype = quantity.type
+            self.unit = quantity.unit
+            # check if metainfo shape has dependencies
+            self.shape = quantity.shape
+            if False in [str(i).isdigit() for i in self.shape]:
+                self.shape = None
+        # override metainfo
+        self.dtype = kwargs.get('dtype', self.dtype)
+        self.unit = kwargs.get('unit', self.unit)
+        self.shape = kwargs.get('shape', self.shape)
+
+        self._re_pattern: str = re_pattern.re_pattern if isinstance(
+            re_pattern, ParsePattern) else re_pattern
+        self._str_operation: Callable = kwargs.get('str_operation', None)
+        self._sub_parser: UnstructuredTextFileParser = kwargs.get('sub_parser', None)
+        self.repeats: bool = kwargs.get('repeats', True)
+        self.convert: bool = kwargs.get('convert', True)
+        self.comment: str = kwargs.get('comment', None)
+
+    @property
+    def re_pattern(self):
+        '''
+        Returns a compiled re pattern.
+        '''
+        if isinstance(self._re_pattern, str):
+            re_pattern = self._re_pattern.replace('__unit', '__unit_%s' % self.name)
+            self._re_pattern = re.compile(re_pattern.encode())
+        return self._re_pattern
+
+    @re_pattern.setter
+    def re_pattern(self, val: str):
+        self._re_pattern = val
+
+    @property
+    def str_operation(self):
+        return self._str_operation
+
+    @str_operation.setter
+    def str_operation(self, val: Callable):
+        self._str_operation = val
+
+    def to_data(self, val_in: List[str]):
+        '''
+        Converts the parsed block into data.
+        '''
+        def process(val):
+            if self.comment is not None:
+                if val.strip()[0] == self.comment:
+                    return
+
+            if self.str_operation is not None:
+                val = self.str_operation(val)
+
+            else:
+                val = val.strip().split() if isinstance(val, str) else val
+                val = val[0] if len(val) == 1 else val
+
+            def _convert(val):
+                if isinstance(val, str):
+                    if self.dtype is None:
+                        if val.isdecimal():
+                            val = int(val)
+                        else:
+                            try:
+                                val = float(val)
+                            except Exception:
+                                pass
+
+                    self.shape = [] if self.shape is None else self.shape
+                    return val
+
+                elif type(val) in [np.ndarray, list]:
+                    try:
+                        dtype = float if self.dtype is None else self.dtype
+                        val_test = np.array(val, dtype=dtype)
+                        if self.dtype is None:
+                            if np.all(np.mod(val_test, 1) == 0):
+                                val_test = np.array(val_test, dtype=int)
+                        self.shape = list(np.shape(val)) if self.shape is None else self.shape
+                        val = val_test
+
+                    except Exception:
+                        val = [_convert(v) for v in val]
+
+                    return val
+
+                elif isinstance(val, dict):
+                    for k, v in val.items():
+                        self.dtype = None
+                        val[k] = _convert(v)
+                    return val
+
+                else:
+                    self.dtype = type(val)
+                    self.shape = [] if self.shape is None else self.shape
+                    return val
+
+            if self.convert:
+                val = _convert(val)
+
+            if isinstance(val, np.ndarray) and self.shape:
+                val = np.reshape(val, self.shape)
+
+            return val
+
+        val_out = [process(val) for val in val_in]
+
+        if isinstance(val_out[0], np.ndarray):