diff --git a/dependencies/parsers/elastic b/dependencies/parsers/elastic
index 1c1dacfde7328e8ec9ca49419fae7d56157d9479..2b9ee49d74cf89bb07e2b798e6e391fd5ac724c6 160000
--- a/dependencies/parsers/elastic
+++ b/dependencies/parsers/elastic
@@ -1 +1 @@
-Subproject commit 1c1dacfde7328e8ec9ca49419fae7d56157d9479
+Subproject commit 2b9ee49d74cf89bb07e2b798e6e391fd5ac724c6
diff --git a/dependencies/parsers/lammps b/dependencies/parsers/lammps
index 3e4eb8aac2cf46882569e3823669f894c6890885..84602c2c62462b93274dab91fce38a72b249cb49 160000
--- a/dependencies/parsers/lammps
+++ b/dependencies/parsers/lammps
@@ -1 +1 @@
-Subproject commit 3e4eb8aac2cf46882569e3823669f894c6890885
+Subproject commit 84602c2c62462b93274dab91fce38a72b249cb49
diff --git a/nomad/datamodel/metainfo/public.py b/nomad/datamodel/metainfo/public.py
index ee6eeb157452f17f198f64d8c58538a17413f839..e24adfbab979e13a93ff3b1351bb8194e621158e 100644
--- a/nomad/datamodel/metainfo/public.py
+++ b/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__()
diff --git a/nomad/parsing/parsers.py b/nomad/parsing/parsers.py
index 04f843b685e97f24829f97f0001684d2d4260565..cb34990c95bb969c74fe9db1cfd6ed8a8b3e3050 100644
--- a/nomad/parsing/parsers.py
+++ b/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',
diff --git a/nomad/parsing/text_parser.py b/nomad/parsing/text_parser.py
index 47d0dbe9d66dcf5b37851e347433bd3d8685e79e..c1caabd37467234775d9226e298bf4b9db3f2903 100644
--- a/nomad/parsing/text_parser.py
+++ b/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