diff --git a/lammpsparser/lammps_parser.py b/lammpsparser/lammps_parser.py
index 9e782e7fa6142d4b9e64bc169a0884badbd2dbb7..59e7a758ba6bfb34fca0bb15682908f400ff17e7 100644
--- a/lammpsparser/lammps_parser.py
+++ b/lammpsparser/lammps_parser.py
@@ -7,10 +7,9 @@ import pint
from .metainfo import m_env
from nomad.parsing.parser import FairdiParser
-from nomad.parsing.file_parser import Quantity, UnstructuredTextFileParser
-from nomad.datamodel.metainfo.public import section_run, section_sampling_method,\
- section_system, section_single_configuration_calculation, section_energy_contribution,\
- Workflow, MolecularDynamics
+from nomad.parsing.file_parser import Quantity, TextParser
+from nomad.datamodel.metainfo.common_dft import Run, SamplingMethod, System,\
+ SingleConfigurationCalculation, EnergyContribution, Workflow, MolecularDynamics
from nomad.datamodel.metainfo.common import section_topology, section_interaction
from .metainfo.lammps import x_lammps_section_input_output_files, x_lammps_section_control_parameters
@@ -85,7 +84,7 @@ def get_unit(units_type, property_type=None, dimension=3):
return units
-class DataParser(UnstructuredTextFileParser):
+class DataParser(TextParser):
def __init__(self):
self._headers = [
'atoms', 'bonds', 'angles', 'dihedrals', 'impropers', 'atom types', 'bond types',
@@ -109,8 +108,8 @@ class DataParser(UnstructuredTextFileParser):
def init_quantities(self):
self._quantities = []
for header in self._headers:
- self._quantities.append(
- Quantity(header, r'\s*([\+\-eE\d\. ]+)\s*%s\s*\n' % header, comment='#'))
+ self._quantities.append(Quantity(
+ header, r'\s*([\+\-eE\d\. ]+)\s*%s\s*\n' % header, comment='#', repeats=True))
def get_section_value(val):
val = val.split('\n')
@@ -137,7 +136,7 @@ class DataParser(UnstructuredTextFileParser):
self._quantities.append(
Quantity(
section, r'\s*%s\s*(#*\s*[\s\S]*?\n)\n*([\deE\-\+\.\s]+)\n' % section,
- str_operation=get_section_value))
+ str_operation=get_section_value, repeats=True))
def get_interactions(self):
styles_coeffs = []
@@ -153,7 +152,7 @@ class DataParser(UnstructuredTextFileParser):
return styles_coeffs
-class TrajParser(UnstructuredTextFileParser):
+class TrajParser(TextParser):
def __init__(self):
self._masses = None
self._reference_masses = dict(
@@ -183,15 +182,17 @@ class TrajParser(UnstructuredTextFileParser):
self._quantities = [
Quantity(
- 'time_step', r'\s*ITEM:\s*TIMESTEP\s*\n\s*(\d+)\s*\n', comment='#'),
+ 'time_step', r'\s*ITEM:\s*TIMESTEP\s*\n\s*(\d+)\s*\n', comment='#',
+ repeats=True),
Quantity(
- 'n_atoms', r'\s*ITEM:\s*NUMBER OF ATOMS\s*\n\s*(\d+)\s*\n', comment='#'),
+ 'n_atoms', r'\s*ITEM:\s*NUMBER OF ATOMS\s*\n\s*(\d+)\s*\n', comment='#',
+ repeats=True),
Quantity(
'pbc_cell', r'\s*ITEM: BOX BOUNDS\s*([\s\w]+)([\+\-\d\.eE\s]+)\n',
- str_operation=get_pbc_cell, comment='#'),
+ str_operation=get_pbc_cell, comment='#', repeats=True),
Quantity(
'atoms_info', r's*ITEM:\s*ATOMS\s*([ \w]+\n)*?([\+\-eE\d\.\n ]+)\n*I*',
- str_operation=get_atoms_info, comment='#')
+ str_operation=get_atoms_info, comment='#', repeats=True)
]
def with_trajectory(self):
@@ -291,7 +292,7 @@ class TrajParser(UnstructuredTextFileParser):
return pint.Quantity(forces, self._units.get('force', None))
-class LogParser(UnstructuredTextFileParser):
+class LogParser(TextParser):
def __init__(self):
self._commands = [
'angle_coeff', 'angle_style', 'atom_modify', 'atom_style', 'balance',
@@ -329,25 +330,18 @@ class LogParser(UnstructuredTextFileParser):
self._quantities = [
Quantity(
name, r'\n\s*%s\s+([\w\. \/\#\-]+)(\&\n[\w\. \/\#\-]*)*' % name,
- str_operation=str_op, comment='#') for name in self._commands]
+ str_operation=str_op, comment='#', repeats=True) for name in self._commands]
- self._quantities.append(
- Quantity('program_version', r'\s*LAMMPS\s*\(([\w ]+)\)\n', dtype=str)
+ self._quantities.append(Quantity(
+ 'program_version', r'\s*LAMMPS\s*\(([\w ]+)\)\n', dtype=str, repeats=False,
+ flatten=False)
)
- self._quantities.append(
- Quantity('finished', r'\s*Dangerous builds\s*=\s*(\d+)')
+ self._quantities.append(Quantity(
+ 'finished', r'\s*Dangerous builds\s*=\s*(\d+)', repeats=False)
)
- @property
- def units(self):
- if self._file_handler is None or self._units is None:
- units_type = self.get('units', ['lj'])[0]
- self._units = get_unit(units_type)
- return self._units
-
- def get_thermodynamic_data(self):
- def str_operation(val):
+ def str_to_thermo(val):
res = {}
if val.count('Step') > 1:
val = val.replace('-', '').replace('=', '').replace('(sec)', '').split()
@@ -369,14 +363,23 @@ class LogParser(UnstructuredTextFileParser):
return res
- pattern = r'\s*\-*(\s*Step\s*[\-\s\w\.\=\(\)]*[ \-\.\d\n]+)Loop'
+ self._quantities.append(Quantity(
+ 'thermo_data', r'\s*\-*(\s*Step\s*[\-\s\w\.\=\(\)]*[ \-\.\d\n]+)Loop',
+ str_operation=str_to_thermo, repeats=False, convert=False)
+ )
- parser = UnstructuredTextFileParser(
- self.mainfile, [Quantity('thermo_data', pattern, str_operation=str_operation)])
+ @property
+ def units(self):
+ if self._file_handler is None or self._units is None:
+ units_type = self.get('units', ['lj'])[0]
+ self._units = get_unit(units_type)
+ return self._units
- thermo_data = parser['thermo_data']
+ def get_thermodynamic_data(self):
+ self._thermo_data = self.get('thermo_data')
- self._thermo_data = list(thermo_data)[0] if thermo_data is not None else thermo_data
+ if self._thermo_data is None:
+ return
for key, val in self._thermo_data.items():
low_key = key.lower()
@@ -422,10 +425,6 @@ class LogParser(UnstructuredTextFileParser):
pbc = self.get('boundary', ['p', 'p', 'p'])
return [v == 'p' for v in pbc]
- def get_program_version(self):
- version = self.get('program_version', [''])[0]
- return ' '.join(version)
-
def get_sampling_method(self):
fix_style = self.get('fix', [[''] * 3])[0][2]
@@ -505,12 +504,6 @@ class LogParser(UnstructuredTextFileParser):
return styles_coeffs
- def finished_normally(self):
- return self.get('finished') is not None
-
- def with_thermodynamics(self):
- return self._thermo_data is not None
-
class LammpsParser(FairdiParser):
def __init__(self):
@@ -553,14 +546,14 @@ class LammpsParser(FairdiParser):
for n in range(n_evaluations):
if create_scc:
- sec_scc = sec_run.m_create(section_single_configuration_calculation)
+ sec_scc = sec_run.m_create(SingleConfigurationCalculation)
else:
sec_scc = sec_sccs[n]
for key, val in thermo_data.items():
key = key.lower()
if key in energy_keys_mapping:
- sec_energy = sec_scc.m_create(section_energy_contribution)
+ sec_energy = sec_scc.m_create(EnergyContribution)
sec_energy.energy_contibution_kind = energy_keys_mapping[key]
sec_energy.energy_contribution_value = val[n]
@@ -586,7 +579,7 @@ class LammpsParser(FairdiParser):
def parse_sampling_method(self):
sec_run = self.archive.section_run[-1]
- sec_sampling_method = sec_run.m_create(section_sampling_method)
+ sec_sampling_method = sec_run.m_create(SamplingMethod)
run_style = self.log_parser.get('run_style', ['verlet'])[0]
run = self.log_parser.get('run', [0])[0]
@@ -641,7 +634,7 @@ class LammpsParser(FairdiParser):
self.traj_parser._units = self.log_parser.units
for i in range(len(pbc_cell)):
- sec_system = sec_run.m_create(section_system)
+ sec_system = sec_run.m_create(System)
sec_system.number_of_atoms = n_atoms[i]
sec_system.configuration_periodic_dimensions = pbc_cell[i][0]
sec_system.simulation_cell = pbc_cell[i][1] * distance_unit
@@ -658,7 +651,7 @@ class LammpsParser(FairdiParser):
forces = self.traj_parser.get_forces(i)
if forces is not None:
if create_scc:
- sec_scc = sec_run.m_create(section_single_configuration_calculation)
+ sec_scc = sec_run.m_create(SingleConfigurationCalculation)
else:
sec_scc = sec_sccs[i]
@@ -723,11 +716,11 @@ class LammpsParser(FairdiParser):
self._init_parsers()
- sec_run = self.archive.m_create(section_run)
+ sec_run = self.archive.m_create(Run)
# parse basic
sec_run.program_name = 'LAMMPS'
- sec_run.program_version = self.log_parser.get_program_version()
+ sec_run.program_version = self.log_parser.get('program_version', '')
# parse method-related
self.parse_sampling_method()
@@ -760,6 +753,6 @@ class LammpsParser(FairdiParser):
if sec_workflow.workflow_type == 'molecular_dynamics':
sec_md = sec_workflow.m_create(MolecularDynamics)
- sec_md.finished_normally = self.log_parser.finished_normally()
+ sec_md.finished_normally = self.log_parser.get('finished') is not None
sec_md.with_trajectory = self.traj_parser.with_trajectory()
- sec_md.with_thermodynamics = self.log_parser.with_thermodynamics()
+ sec_md.with_thermodynamics = self.log_parser.get('thermo_data') is not None