Implemented new lammps parser

elastic @ 2b9ee49d

-Subproject commit 1c1dacfde7328e8ec9ca49419fae7d56157d9479
+Subproject commit 2b9ee49d74cf89bb07e2b798e6e391fd5ac724c6

lammps @ 84602c2c

-Subproject commit 3e4eb8aac2cf46882569e3823669f894c6890885
+Subproject commit 84602c2c62462b93274dab91fce38a72b249cb49

nomad/datamodel/metainfo/public.py

@@ -1607,6 +1607,32 @@ class section_energy_van_der_Waals(MSection):
         a_legacy=LegacyDefinition(name='energy_van_der_Waals'))
 
 
+class section_energy_contribution(MSection):
+    '''
+    Section describing the contributions to the total energy.
+    '''
+
+    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_energy_contribution'))
+
+    energy_contibution_kind = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        The kind of the energy contribution. Can be one of bond, pair, coulomb, etc.
+        ''',
+        a_legacy=LegacyDefinition(name='energy_contibution_kind'))
+
+    energy_contribution_value = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='joule',
+        description='''
+        Value of the energy contribution.
+        ''',
+        categories=[energy_component, energy_value],
+        a_legacy=LegacyDefinition(name='energy_contribution_value'))
+
+
 class section_frame_sequence_user_quantity(MSection):
     '''
     Section collecting some user-defined quantities evaluated along a sequence of frame.
@@ -4460,6 +4486,42 @@ class section_single_configuration_calculation(MSection):
         ''',
         a_legacy=LegacyDefinition(name='zero_point_method'))
 
+    enthalpy = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='joule',
+        description='''
+        Value of the calculated enthalpy i.e. energy_total + pressure * volume.
+        ''',
+        categories=[energy_component, energy_value],
+        a_legacy=LegacyDefinition(name='energy_enthalpy'))
+
+    pressure = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='pascal',
+        description='''
+        Value of the pressure of the system.
+        ''',
+        a_legacy=LegacyDefinition(name='pressure'))
+
+    temperature = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='kelvin',
+        description='''
+        Value of the temperature of the system.
+        ''',
+        a_legacy=LegacyDefinition(name='temperature'))
+
+    time_step = Quantity(
+        type=int,
+        shape=[],
+        description='''
+        The number of time steps with respect to the start of the calculation.
+        ''',
+        a_legacy=LegacyDefinition(name='time_step'))
+
     section_atom_projected_dos = SubSection(
         sub_section=SectionProxy('section_atom_projected_dos'),
         repeats=True,
@@ -4505,6 +4567,11 @@ class section_single_configuration_calculation(MSection):
         repeats=True,
         a_legacy=LegacyDefinition(name='section_energy_van_der_Waals'))
 
+    section_energy_contribution = SubSection(
+        sub_section=SectionProxy('section_energy_contribution'),
+        repeats=True,
+        a_legacy=LegacyDefinition(name='section_energy_contribution'))
+
     section_k_band_normalized = SubSection(
         sub_section=SectionProxy('section_k_band_normalized'),
         repeats=True,
@@ -5771,6 +5838,41 @@ class Elastic(MSection):
         a_legacy=LegacyDefinition(name='strain_maximum'))
 
 
+class MolecularDynamics(MSection):
+    '''
+    Section containing results of molecular dynamics workflow.
+    '''
+
+    m_def = Section(
+        validate=False, a_legacy=LegacyDefinition(name='section_molecular_dynamics'))
+
+    finished_normally = Quantity(
+        type=bool,
+        shape=[],
+        description='''
+        Indicates if calculation terminated normally.
+        ''',
+        a_legacy=LegacyDefinition(name='finished_normally'))
+
+    with_trajectory = Quantity(
+        type=bool,
+        shape=[],
+        description='''
+        Indicates if calculation includes trajectory data.
+        ''',
+        a_legacy=LegacyDefinition(name='with_trajectory'),
+        a_search=Search())
+
+    with_thermodynamics = Quantity(
+        type=bool,
+        shape=[],
+        description='''
+        Indicates if calculation contains thermodynamic data.
+        ''',
+        a_legacy=LegacyDefinition(name='with_thermodynamics'),
+        a_search=Search())
+
+
 class Workflow(MSection):
     '''
     Section containing the  results of a workflow.
@@ -5802,5 +5904,9 @@ class Workflow(MSection):
         sub_section=SectionProxy('Elastic'),
         a_legacy=LegacyDefinition(name='section_elastic'))
 
+    section_molecular_dynamics = SubSection(
+        sub_section=SectionProxy('MolecularDynamics'),
+        a_legacy=LegacyDefinition(name='section_molecular_dynamics'))
+
 
 m_package.__init_metainfo__()

nomad/parsing/parsers.py

@@ -27,6 +27,7 @@ from aptfimparser import APTFIMParser
 from vaspparser import VASPParser
 from phonopyparser import PhonopyParser
 from elasticparser import ElasticParser
+from lammpsparser import LammpsParser
 
 try:
     # these packages are not available without parsing extra, which is ok, if the
@@ -378,11 +379,7 @@ parsers = [
         parser_class_name='tinkerparser.TinkerParser',
         mainfile_contents_re=r'TINKER  ---  Software Tools for Molecular Design'
     ),
-    LegacyParser(
-        name='parsers/lammps', code_name='lammps', domain='dft',
-        parser_class_name='lammpsparser.LammpsParser',
-        mainfile_contents_re=r'^LAMMPS'
-    ),
+    LammpsParser(),
     LegacyParser(
         name='parsers/amber', code_name='Amber', domain='dft',
         parser_class_name='amberparser.AMBERParser',

nomad/parsing/text_parser.py

@@ -20,7 +20,7 @@ import logging
 
 
 class Quantity:
-    def __init__(self, name, re_pattern, str_operation=None, unit=None, dtype=None):
+    def __init__(self, name, re_pattern, str_operation=None, unit=None, dtype=None, comment=None):
         self.name = name
         self.re_pattern = re.compile(re_pattern.encode())
         self.unit = unit
@@ -28,6 +28,7 @@ class Quantity:
         self.dtype = dtype
         self._value = None
         self._str_operation = str_operation
+        self._comment = comment
 
     @property
     def value(self):
@@ -37,6 +38,10 @@ class Quantity:
     def value(self, val_in):
 
         def convert_value(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)
 
@@ -44,36 +49,44 @@ class Quantity:
                 val = val.strip().split() if isinstance(val, str) else val
                 val = val[0] if len(val) == 1 else val
 
-            def _get_dtype(val):
-                dtype = type(val)
-
+            def _convert(val):
                 if isinstance(val, str):
                     if self.dtype is None:
                         if val.isdecimal():
-                            self.dtype = int
+                            val = int(val)
                         else:
                             try:
-                                float(val)
-                                self.dtype = float
+                                val = float(val)
                             except Exception:
-                                self.dtype = str
+                                pass
 
                     self.shape = []
-                    return self.dtype
+                    return val
+
+                elif type(val) in [np.ndarray, list]:
+                    try:
+                        dtype = float if self.dtype is None else self.dtype
+                        val = np.array(val, dtype=dtype)
+                        self.dtype = dtype
+                        if np.all(np.mod(val, 1) == 0):
+                            val = np.array(val, dtype=int)
+                            self.dtype = int
+                        self.shape = list(np.shape(val))
+
+                    except Exception:
+                        val = [_convert(v) for v in val]
+                        self.dtype = None
 
-                elif dtype in (np.ndarray, list, tuple):
-                    if len(val) > 0:
-                        _get_dtype(val[-1])
-                    self.shape = list(np.shape(val))
-                    return lambda x: np.array(x, dtype=self.dtype)
+                    return val
 
                 else:
                     self.dtype = type(val)
                     self.shape = []
-                    return self.dtype
+                    return val
+
+            val = _convert(val)
 
-            dtype = _get_dtype(val)
-            return dtype(val)
+            return val
 
         self._value = None if val_in is None else [convert_value(val) for val in val_in]
 
@@ -149,7 +162,7 @@ class UnstructuredTextFileParser:
             if key is None or quantity.name in key:
                 value = []
                 for res in quantity.re_pattern.finditer(self.file_mmap):
-                    value.append(''.join([group.decode() for group in res.groups()]))
+                    value.append(''.join([group.decode() for group in res.groups() if group]))
                 if not value:
                     continue