115 problematic parsing of traj files from ase

atomisticparsers/__init__.py

@@ -74,7 +74,7 @@ def load(self):
     python_package='atomisticparsers.asap',
     mainfile_binary_header_re=b'AFFormatASE\\-Trajectory',
     mainfile_mime_re='application/octet-stream',
-    mainfile_name_re=r'.*.traj$',
+    mainfile_name_re=r'.*.traj$',  # can this be specified here? to directly check for the emt calculator maybe? somehow we need to seperate the general ase/traj parser from the asap parser
     parser_class_name='atomisticparsers.asap.AsapParser',
     code_name='ASAP',
     code_homepage='https://wiki.fysik.dtu.dk/asap',
@@ -94,6 +94,33 @@ def load(self):
     },
 )
 
+ase_parser_entry_point = EntryPoint(
+    name='parsers/ase',
+    aliases=['parsers/ase'],
+    description='NOMAD parser for ASE.',
+    python_package='atomisticparsers.ase',
+    mainfile_binary_header_re=b'.+?ASE\\-Trajectory',
+    mainfile_mime_re='application/octet-stream',
+    mainfile_name_re=r'.*.traj$',
+    parser_class_name='atomisticparsers.ase.AseParser',
+    code_name='ASE',
+    code_homepage='https://wiki.fysik.dtu.dk/ase',
+    code_category='Atomistic code',
+    metadata={
+        'codeCategory': 'Atomistic code',
+        'codeLabel': 'ASE',
+        'codeLabelStyle': 'all in capitals',
+        'codeName': 'ase',
+        'codeUrl': 'https://wiki.fysik.dtu.dk/ase',
+        'parserDirName': 'dependencies/parsers/atomistic/atomisticparsers/ase/',
+        'parserGitUrl': 'https://github.com/nomad-coe/atomistic-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
+
 bopfox_parser_entry_point = EntryPoint(
     name='parsers/bopfox',
     aliases=['parsers/bopfox'],

atomisticparsers/asap/parser.py

@@ -16,182 +16,41 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+from simulationworkflowschema.geometry_optimization import GeometryOptimization
+from simulationworkflowschema.molecular_dynamics import MolecularDynamics
+from atomisticparsers.utils import ASETrajParser
+from .metainfo import asap  # pylint: disable=unused-import
 
-import os
-import logging
-import numpy as np
-from ase.io.trajectory import Trajectory
-
-from nomad.units import ureg
-from nomad.parsing.file_parser import FileParser
-from runschema.run import Run, Program
-from runschema.method import Method, ForceField, Model
-from simulationworkflowschema import GeometryOptimization, GeometryOptimizationMethod
-from atomisticparsers.utils import MDParser
-from .metainfo.asap import MolecularDynamics  # pylint: disable=unused-import
-
-
-class TrajParser(FileParser):
-    def __init__(self):
-        super().__init__()
-
-    @property
-    def traj(self):
-        if self._file_handler is None:
-            try:
-                self._file_handler = Trajectory(self.mainfile, 'r')
-                # check if traj file is really asap
-                if 'calculator' in self._file_handler.backend.keys():
-                    if self._file_handler.backend.calculator.name != 'emt':  # pylint: disable=E1101
-                        self.logger.error('Trajectory is not ASAP.')
-                        self._file_handler = None
-            except Exception:
-                self.logger.error('Error reading trajectory file.')
-        return self._file_handler
-
-    def get_version(self):
-        if hasattr(self.traj, 'ase_version') and self.traj.ase_version:
-            return self.traj.ase_version
-        else:
-            return '3.x.x'
-
-    def parse(self):
-        pass
-
-
-class AsapParser(MDParser):
-    def __init__(self):
-        self.traj_parser = TrajParser()
-        super().__init__()
 
+class AsapParser(ASETrajParser):
     def parse_method(self):
+        super().parse_method()
         traj = self.traj_parser.traj
-        sec_method = Method()
-        self.archive.run[0].method.append(sec_method)
-
-        if traj[0].calc is not None:
-            sec_method.force_field = ForceField(model=[Model(name=traj[0].calc.name)])
 
         description = traj.description if hasattr(traj, 'description') else dict()
         if not description:
             return
 
-        calc_type = description.get('type')
-        if calc_type == 'optimization':
-            workflow = GeometryOptimization(method=GeometryOptimizationMethod())
+        workflow = self.archive.workflow2
+        if isinstance(workflow, GeometryOptimization):
             workflow.x_asap_maxstep = description.get('maxstep', 0)
-            workflow.method.method = description.get('optimizer', '').lower()
-            self.archive.workflow2 = workflow
-        elif calc_type == 'molecular-dynamics':
-            data = {}
-            data['x_asap_timestep'] = description.get('timestep', 0)
-            data['x_asap_temperature'] = description.get('temperature', 0)
+        elif isinstance(workflow, MolecularDynamics):
+            workflow.x_asap_timestep = description.get('timestep', 0)
+            workflow.x_asap_temperature = description.get('temperature', 0)
             md_type = description.get('md-type', '')
-            thermodynamic_ensemble = None
             if 'Langevin' in md_type:
-                data['x_asap_langevin_friction'] = description.get('friction', 0)
-                thermodynamic_ensemble = 'NVT'
-            elif 'NVT' in md_type:
-                thermodynamic_ensemble = 'NVT'
-            elif 'Verlet' in md_type:
-                thermodynamic_ensemble = 'NVE'
-            elif 'NPT' in md_type:
-                thermodynamic_ensemble = 'NPT'
-            data['method'] = {'thermodynamic_ensemble': thermodynamic_ensemble}
-            self.parse_md_workflow(data)
+                workflow.x_asap_langevin_friction = description.get('friction', 0)
 
     def write_to_archive(self) -> None:
         self.traj_parser.mainfile = self.mainfile
-        if self.traj_parser.traj is None:
-            return
-
-        sec_run = Run()
-        self.archive.run.append(sec_run)
-        sec_run.program = Program(name='ASAP', version=self.traj_parser.get_version())
-
-        # TODO do we build the topology and method for each frame
-        self.parse_method()
-
-        # set up md parser
-        self.n_atoms = max(
-            [traj.get_global_number_of_atoms() for traj in self.traj_parser.traj]
-        )
-        steps = [
-            (traj.description if hasattr(traj, 'description') else dict()).get(
-                'interval', 1
-            )
-            * n
-            for n, traj in enumerate(self.traj_parser.traj)
-        ]
-        self.trajectory_steps = steps
-        self.thermodynamics_steps = steps
-
-        def get_constraint_name(constraint):
-            def index():
-                d = constraint['kwargs'].get('direction')
-                return ((d / np.linalg.norm(d)) ** 2).argsort()[2]
-
-            name = constraint.get('name')
-            if name == 'FixedPlane':
-                return ['fix_yz', 'fix_xz', 'fix_xy'][index()]
-            elif name == 'FixedLine':
-                return ['fix_x', 'fix_y', 'fix_z'][index()]
-            elif name == 'FixAtoms':
-                return 'fix_xyz'
-            else:
-                return name
 
-        for step in self.trajectory_steps:
-            traj = self.traj_parser.traj[steps.index(step)]
-            lattice_vectors = traj.get_cell() * ureg.angstrom
-            labels = traj.get_chemical_symbols()
-            positions = traj.get_positions() * ureg.angstrom
-            periodic = traj.get_pbc()
-            if (velocities := traj.get_velocities()) is not None:
-                velocities = velocities * (ureg.angstrom / ureg.fs)
+        # check if traj file is really asap
+        if 'calculator' in self.traj_parser.traj.backend.keys():
+            if self.traj_parser.traj.backend.calculator.name != 'emt':  # pylint: disable=E1101
+                self.logger.error('Trajectory is not ASAP.')
+                return
 
-            constraints = []
-            for constraint in traj.constraints:
-                as_dict = constraint.todict()
-                indices = as_dict['kwargs'].get('a', as_dict['kwargs'].get('indices'))
-                indices = (
-                    indices
-                    if isinstance(indices, (np.ndarray, list))
-                    else [int(indices)]
-                )
-                constraints.append(
-                    dict(
-                        atom_indices=[np.asarray(indices)],
-                        kind=get_constraint_name(as_dict),
-                    )
-                )
-            self.parse_trajectory_step(
-                dict(
-                    atoms=dict(
-                        lattice_vectors=lattice_vectors,
-                        labels=labels,
-                        positions=positions,
-                        periodic=periodic,
-                        velocities=velocities,
-                    ),
-                    constraint=constraints,
-                )
-            )
+        super().write_to_archive()
 
-        for step in self.thermodynamics_steps:
-            try:
-                traj = self.traj_parser.traj[steps.index(step)]
-                if (total_energy := traj.get_total_energy()) is not None:
-                    total_energy = total_energy * ureg.eV
-                if (forces := traj.get_forces()) is not None:
-                    forces = forces * ureg.eV / ureg.angstrom
-                if (forces_raw := traj.get_forces(apply_constraint=False)) is not None:
-                    forces_raw * ureg.eV / ureg.angstrom
-                self.parse_thermodynamics_step(
-                    dict(
-                        energy=dict(total=dict(value=total_energy)),
-                        forces=dict(total=dict(value=forces, value_raw=forces_raw)),
-                    )
-                )
-            except Exception:
-                pass
+        if self.archive.run:
+            self.archive.run[0].program.name = 'ASAP'

atomisticparsers/ase/__init__.py

@@ -0,0 +1,19 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# 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.
+#
+from .parser import AseParser

atomisticparsers/ase/__main__.py

@@ -0,0 +1,31 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# 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 sys
+import json
+import logging
+
+from nomad.utils import configure_logging
+from nomad.datamodel import EntryArchive
+from atomisticparsers.ase import AseParser
+
+if __name__ == '__main__':
+    configure_logging(console_log_level=logging.DEBUG)
+    archive = EntryArchive()
+    AseParser().parse(sys.argv[1], archive, logging)
+    json.dump(archive.m_to_dict(), sys.stdout, indent=2)

atomisticparsers/ase/parser.py

@@ -0,0 +1,30 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# 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.
+#
+
+from atomisticparsers.utils import ASETrajParser
+
+
+class AseParser(ASETrajParser):
+    def write_to_archive(self) -> None:
+        super().write_to_archive()
+
+        if self.archive.run:
+            self.archive.run[0].program.name = 'ASE'
+
+    # TODO add tests

atomisticparsers/gromacs/parser.py

@@ -53,7 +53,9 @@
     x_gromacs_section_input_output_files,
 )
 from atomisticparsers.utils import MDAnalysisParser, MDParser
-from simulationworkflowschema.molecular_dynamics import get_bond_list_from_model_contributions
+from simulationworkflowschema.molecular_dynamics import (
+    get_bond_list_from_model_contributions,
+)
 
 re_float = r'[-+]?\d+\.*\d*(?:[Ee][-+]\d+)?'
 re_n = r'[\n\r]'

atomisticparsers/lammps/parser.py

@@ -44,7 +44,9 @@
     x_lammps_section_control_parameters,
 )
 from atomisticparsers.utils import MDAnalysisParser, MDParser
-from simulationworkflowschema.molecular_dynamics import get_bond_list_from_model_contributions
+from simulationworkflowschema.molecular_dynamics import (
+    get_bond_list_from_model_contributions,
+)
 
 
 re_float = r'[-+]?\d+\.*\d*(?:[Ee][-+]\d+)?'

atomisticparsers/utils/__init__.py

@@ -17,6 +17,6 @@
 # limitations under the License.
 
 from .mdanalysis import MDAnalysisParser
-from .parsers import MDParser
+from .parsers import MDParser, ASETrajParser
 
 MOL = 6.022140857e23

atomisticparsers/utils/mdanalysis.py

@@ -35,7 +35,10 @@
 
 from nomad.units import ureg
 from nomad.parsing.file_parser import FileParser
-from simulationworkflowschema.molecular_dynamics import BeadGroup, shifted_correlation_average
+from simulationworkflowschema.molecular_dynamics import (
+    BeadGroup,
+    shifted_correlation_average,
+)
 
 
 MOL = 6.022140857e23