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full implementation of parse() with old code commented
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jrudz committed Jan 15, 2024
1 parent 869266f commit 1fa25cf
Showing 1 changed file with 64 additions and 25 deletions.
89 changes: 64 additions & 25 deletions atomisticparsers/h5md/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,13 +21,13 @@
import logging
import h5py

from typing import List, Dict, Tuple, Any, Union, Iterable, cast, Callable, TYPE_CHECKING
from typing import List, Dict
from h5py import Group

from nomad.datamodel import EntryArchive
from nomad.metainfo.util import MEnum
from nomad.parsing.file_parser import FileParser
from nomad.datamodel.metainfo.simulation.run import Run, Program # TimeRun
from nomad.datamodel.metainfo.simulation.run import Run, Program
from nomad.datamodel.metainfo.simulation.method import (
Method, ForceField, Model, AtomParameters, ForceCalculations, NeighborSearching
)
Expand Down Expand Up @@ -192,7 +192,7 @@ def format_times(self, times):
return np.around(times.magnitude * ureg.convert(1.0, times.units, self._time_unit), 5)

@property
def frame_rate(self): # TODO extend to non-fixed n_atoms
def frame_rate(self): # TODO extend to non-fixed n_atoms, check integration of MDParser class here
if self._frame_rate is None:
if self._n_atoms == 0 or self._n_frames == 0:
self._frame_rate = 1
Expand Down Expand Up @@ -228,7 +228,7 @@ def parse_atom_parameters(self):
def parse_system_info(self):
self._system_info = {'system': {}, 'calculation': {}}
particles_group = self._h5md_particle_group_all
positions_group = self._h5md_positions_group_all
# positions_group = self._h5md_positions_group_all
positions_value = self._h5md_positions_value_all
n_frames = self._n_frames
if particles_group is None or positions_value is None or positions_value is None: # For now we require that positions are present in the H5MD file to store other particle attributes
Expand Down Expand Up @@ -300,7 +300,8 @@ def get_value(value, steps, path=''):
values_dict[sec_key][key] = get_value(value, steps, path=path)

# get the box quantities
box = self._data_parser.get_value(particles_group, 'box')
# box = self._data_parser.get_value(particles_group, 'box')
box = self._data_parser.get(f'{self._path_group_particles_all}.box')
if box is not None:
box_attributes = {'dimension': 'system', 'periodic': 'system'}
for box_key, sec_key in box_attributes.items():
Expand Down Expand Up @@ -360,7 +361,7 @@ def get_observable_paths(observable_group: Dict, current_path: str) -> List:
thermodynamics_steps = list(set(steps) | set(thermodynamics_steps))
# times = self._data_parser.get_value(observable, 'time')
times = self._data_parser.get(f'{full_path}.time')
values = self._data_parser.get_value(observable, 'value')
# values = self._data_parser.get_value(observable, 'value')
values = self._data_parser.get(f'{full_path}.value')
if isinstance(values, h5py.Group):
self.logger.warning('Group structures within individual observables not supported. These will not be stored.')
Expand All @@ -385,9 +386,34 @@ def get_observable_paths(observable_group: Dict, current_path: str) -> List:

self.thermodynamics_steps = thermodynamics_steps

def parse_atomsgroup(self, nomad_sec, h5md_sec_particlesgroup: Group):
# def parse_atomsgroup(self, nomad_sec, h5md_sec_particlesgroup: Group):
# for i_key, key in enumerate(h5md_sec_particlesgroup.keys()):
# particles_group = {group_key: self._data_parser.get_value(h5md_sec_particlesgroup[key], group_key) for group_key in h5md_sec_particlesgroup[key].keys()}
# sec_atomsgroup = AtomsGroup()
# nomad_sec.atoms_group.append(sec_atomsgroup)
# sec_atomsgroup.type = particles_group.pop('type', None)
# sec_atomsgroup.index = i_key
# sec_atomsgroup.atom_indices = particles_group.pop('indices', None)
# sec_atomsgroup.n_atoms = len(sec_atomsgroup.atom_indices) if sec_atomsgroup.atom_indices is not None else None
# sec_atomsgroup.is_molecule = particles_group.pop('is_molecule', None)
# sec_atomsgroup.label = particles_group.pop('label', None)
# sec_atomsgroup.composition_formula = particles_group.pop('formula', None)
# particles_subgroup = particles_group.pop('particles_group', None)
# # set the remaining attributes
# for particles_group_key in particles_group.keys():
# val = particles_group.get(particles_group_key)
# units = val.units if hasattr(val, 'units') else None
# val = val.magnitude if units is not None else val
# sec_atomsgroup.x_h5md_parameters.append(ParamEntry(kind=particles_group_key, value=val, unit=units))
# # get the next atomsgroup
# if particles_subgroup:
# self.parse_atomsgroup(sec_atomsgroup, particles_subgroup)

def parse_atomsgroup(self, nomad_sec, h5md_sec_particlesgroup: Group, path_particlesgroup: str):
for i_key, key in enumerate(h5md_sec_particlesgroup.keys()):
particles_group = {group_key: self._data_parser.get_value(h5md_sec_particlesgroup[key], group_key) for group_key in h5md_sec_particlesgroup[key].keys()}
path_particlesgroup_key = f'{path_particlesgroup}.{key}'
# particles_group = {group_key: self._data_parser.get_value(h5md_sec_particlesgroup[key], group_key) for group_key in h5md_sec_particlesgroup[key].keys()}
particles_group = {group_key: self._data_parser.get(f'{path_particlesgroup_key}.{group_key}') for group_key in h5md_sec_particlesgroup[key].keys()}
sec_atomsgroup = AtomsGroup()
nomad_sec.atoms_group.append(sec_atomsgroup)
sec_atomsgroup.type = particles_group.pop('type', None)
Expand All @@ -406,7 +432,7 @@ def parse_atomsgroup(self, nomad_sec, h5md_sec_particlesgroup: Group):
sec_atomsgroup.x_h5md_parameters.append(ParamEntry(kind=particles_group_key, value=val, unit=units))
# get the next atomsgroup
if particles_subgroup:
self.parse_atomsgroup(sec_atomsgroup, particles_subgroup)
self.parse_atomsgroup(sec_atomsgroup, particles_subgroup, f'{path_particlesgroup_key}.particles_group')

def is_valid_key_val(self, metainfo_class, key: str, val) -> bool:
if hasattr(metainfo_class, key):
Expand Down Expand Up @@ -446,16 +472,12 @@ def parameter_info(self):
def get_parameters(parameter_group: Group, path: str) -> Dict:
param_dict = {}
for key, val in parameter_group.items():
print(key)
path_key = f'{path}.{key}'
print(path)
if isinstance(val, h5py.Group):
param_dict[key] = get_parameters(val, path_key)
print(param_dict[key])
else:
# param_dict[key] = self._data_parser.get_value(parameter_group, key)
param_dict[key] = self._data_parser.get(path_key)
print(param_dict[key])
if isinstance(param_dict[key], str):
if key == 'thermodynamic_ensemble':
param_dict[key] = param_dict[key].upper() # TODO change enums to lower case and adjust Gromacs and Lammps code accordingly
Expand All @@ -467,11 +489,13 @@ def get_parameters(parameter_group: Group, path: str) -> Dict:
return param_dict

path_force_calculations = 'parameters.force_calculations'
force_calculations_group = self._data_parser.get_value(self._data_parser.filehdf5, path_force_calculations)
# force_calculations_group = self._data_parser.get_value(self._data_parser.filehdf5, path_force_calculations)
force_calculations_group = self._data_parser.get(path_force_calculations)
if force_calculations_group is not None:
self._parameter_info['force_calculations'] = get_parameters(force_calculations_group, path_force_calculations)
path_workflow = 'parameters.workflow'
workflow_group = self._data_parser.get_value(self._data_parser.filehdf5, path_workflow)
# workflow_group = self._data_parser.get_value(self._data_parser.filehdf5, path_workflow)
workflow_group = self._data_parser.get(path_workflow)
if workflow_group is not None:
self._parameter_info['workflow'] = get_parameters(workflow_group, path_workflow)

Expand Down Expand Up @@ -564,14 +588,17 @@ def parse_system(self):
if i_step == 0 and self._connectivity_group: # TODO extend to time-dependent bond lists and topologies
# atoms_dict['bond_list'] = self._data_parser.get_value(self._connectivity_group, 'bonds')
atoms_dict['bond_list'] = self._data_parser.get('connectivity.bonds')
topology = self._data_parser.get_value(self._connectivity_group, 'particles_group', None) # JFR - come back to this to consider the new get() functionality
path_topology = 'connectivity.particles_group'
# topology = self._data_parser.get_value(self._connectivity_group, 'particles_group', None)
topology = self._data_parser.get(path_topology)

self.parse_trajectory_step({
'atoms': atoms_dict
})

if topology:
self.parse_atomsgroup(sec_run.system[i_step], topology)
# self.parse_atomsgroup(sec_run.system[i_step], topology)
self.parse_atomsgroup(sec_run.system[i_step], topology, path_topology)

def parse_method(self):

Expand Down Expand Up @@ -751,25 +778,37 @@ def parse(self, filepath, archive: EntryArchive, logger):
self._n_frames = len(positions) if positions is not None else None
self._n_atoms = [len(pos) for pos in positions] if positions is not None else None

self._particles_group = self._data_parser.get_value(self._data_parser.filehdf5, 'particles')
# self._particles_group = self._data_parser.get_value(self._data_parser.filehdf5, 'particles')
path = 'particles'
self._particles_group = self._data_parser.get(path)
if self._particles_group:
self._h5md_particle_group_all = self._data_parser.get_value(self._particles_group, 'all')
# self._h5md_particle_group_all = self._data_parser.get_value(self._particles_group, 'all')
path = f'{path}.all'
self._h5md_particle_group_all = self._data_parser.get(path)
if self._h5md_particle_group_all:
self._h5md_positions_group_all = self._data_parser.get_value(self._h5md_particle_group_all, 'position')
# self._h5md_positions_group_all = self._data_parser.get_value(self._h5md_particle_group_all, 'position')
path = f'{path}.position'
self._h5md_positions_group_all = self._data_parser.get(path)
if self._h5md_positions_group_all:
self._h5md_positions_value_all = self._data_parser.get_value(self._h5md_positions_group_all, 'value')
# self._h5md_positions_value_all = self._data_parser.get_value(self._h5md_positions_group_all, 'value')
path = f'{path}.value'
self._h5md_positions_value_all = self._data_parser.get(path)
# if self._h5md_positions_value_all is not None:
# self._n_frames = len(self._h5md_positions_value_all) if self._h5md_positions_value_all is not None else None
# self._n_atoms = [len(pos) for pos in self._h5md_positions_value_all] if self._h5md_positions_value_all is not None else None
self._observables_group = self._data_parser.get_value(self._data_parser.filehdf5, 'observables')
self._connectivity_group = self._data_parser.get_value(self._data_parser.filehdf5, 'connectivity')
self._parameters_group = self._data_parser.get_value(self._data_parser.filehdf5, 'parameters')
# self._observables_group = self._data_parser.get_value(self._data_parser.filehdf5, 'observables')
# self._connectivity_group = self._data_parser.get_value(self._data_parser.filehdf5, 'connectivity')
# self._parameters_group = self._data_parser.get_value(self._data_parser.filehdf5, 'parameters')
self._observables_group = self._data_parser.get('observables')
self._connectivity_group = self._data_parser.get('connectivity')
self._parameters_group = self._data_parser.get('parameters')

# Parse the hdf5 groups
sec_run = Run()
self.archive.run.append(sec_run)

group_h5md = self._data_parser.get_value(self._data_parser.filehdf5, 'h5md')
# group_h5md = self._data_parser.get_value(self._data_parser.filehdf5, 'h5md')
group_h5md = self._data_parser.get('h5md')
if group_h5md:
# program_name = self._data_parser.get_attribute(group_h5md, 'name', path='program')
program_name = self._data_parser.get('h5md.program.name', isattr=True)
Expand Down

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