Skip to content

Commit

Permalink
finished basic workflow results parsing
Browse files Browse the repository at this point in the history
  • Loading branch information
jrudz committed Oct 30, 2023
1 parent 34f1cca commit 5e05420
Show file tree
Hide file tree
Showing 2 changed files with 59 additions and 122 deletions.
29 changes: 26 additions & 3 deletions atomisticparsers/h5md/parser.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,8 @@
BarostatParameters, ThermostatParameters, DiffusionConstantValues,
MeanSquaredDisplacement, MeanSquaredDisplacementValues, MolecularDynamicsResults,
RadialDistributionFunction, RadialDistributionFunctionValues,
MolecularDynamics, MolecularDynamicsMethod, EnsembleProperty, EnsemblePropertyValues
MolecularDynamics, MolecularDynamicsMethod, EnsembleProperty, EnsemblePropertyValues,
CorrelationFunction, CorrelationFunctionValues
)
from .metainfo.h5md import ParamEntry, CalcEntry, Author
# from nomad.atomutils import get_molecules_from_bond_list, is_same_molecule, get_composition
Expand Down Expand Up @@ -746,6 +747,8 @@ def parse_workflow(self):
for quant_name, val in observable.items():
if quant_name == 'val':
continue
if quant_name == 'bins':
continue
if quant_name in EnsembleProperty.__dict__.keys():
sec_ensemble.m_set(sec_ensemble.m_get_quantity_definition(quant_name), val)
if quant_name in EnsemblePropertyValues.__dict__.keys():
Expand All @@ -754,16 +757,36 @@ def parse_workflow(self):

val = observable.get('value')
if val is not None:
print(val)
sec_ensemble_vals.value_unit = str(val.units) if hasattr(val, 'units') else None
sec_ensemble_vals.value_magnitude = val.magnitude if hasattr(val, 'units') else val

bins = observable.get('bins')
if bins is not None:
print(val)
sec_ensemble_vals.bins_unit = str(bins.units) if hasattr(bins, 'units') else None
sec_ensemble_vals.bins_magnitude = bins.magnitude if hasattr(bins, 'units') else bins

correlation_function_observables = self.observable_info.get('correlation_function')
sec_results = workflow.results
for observable_type, observable_dict in correlation_function_observables.items():
sec_correlation = sec_results.m_create(CorrelationFunction)
sec_correlation.label = observable_type
for key, observable in observable_dict.items():
sec_correlation_vals = sec_correlation.m_create(CorrelationFunctionValues)
sec_correlation_vals.label = key
for quant_name, val in observable.items():
if quant_name == 'val':
continue
if quant_name in CorrelationFunction.__dict__.keys():
sec_correlation.m_set(sec_correlation.m_get_quantity_definition(quant_name), val)
if quant_name in CorrelationFunctionValues.__dict__.keys():
sec_correlation_vals.m_set(sec_correlation_vals.m_get_quantity_definition(quant_name), val)
## TODO Still need to add custom values here.

val = observable.get('value')
if val is not None:
sec_correlation_vals.value_unit = str(val.units) if hasattr(val, 'units') else None
sec_correlation_vals.value_magnitude = val.magnitude if hasattr(val, 'units') else val

# map_key = observable_type + '-' + key if key else observable_type
# print(map_key)
# print(key)
Expand Down
152 changes: 33 additions & 119 deletions tests/test_h5md.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -155,122 +155,36 @@ def test_md(parser):
assert sec_method[0].force_field.force_calculations.neighbor_searching.neighbor_update_cutoff.magnitude == approx(1.2e-09)
assert sec_method[0].force_field.force_calculations.neighbor_searching.neighbor_update_cutoff.units == 'meter'


# def test_md_edr(parser):
# archive = EntryArchive()
# parser.parse('tests/data/gromacs/fe_test/mdrun.out', archive, None)

# assert len(archive.run[0].calculation) == 5


# def test_md_atomsgroup(parser):
# archive = EntryArchive()
# parser.parse('tests/data/gromacs/polymer_melt/step4.0_minimization.log', archive, None)

# sec_run = archive.run[0]
# sec_systems = sec_run.system

# assert len(sec_systems[0].atoms_group) == 1
# assert len(sec_systems[0].atoms_group[0].atoms_group) == 100

# assert sec_systems[0].atoms_group[0].label == 'group_S1P1'
# assert sec_systems[0].atoms_group[0].type == 'molecule_group'
# assert sec_systems[0].atoms_group[0].index == 0
# assert sec_systems[0].atoms_group[0].composition_formula == 'S1P1(100)'
# assert sec_systems[0].atoms_group[0].n_atoms == 7200
# assert sec_systems[0].atoms_group[0].atom_indices[5] == 5
# assert sec_systems[0].atoms_group[0].is_molecule is False

# assert sec_systems[0].atoms_group[0].atoms_group[52].label == 'S1P1'
# assert sec_systems[0].atoms_group[0].atoms_group[52].type == 'molecule'
# assert sec_systems[0].atoms_group[0].atoms_group[52].index == 52
# assert sec_systems[0].atoms_group[0].atoms_group[52].composition_formula == 'ETHOX(10)'
# assert sec_systems[0].atoms_group[0].atoms_group[52].n_atoms == 72
# assert sec_systems[0].atoms_group[0].atoms_group[52].atom_indices[8] == 3752
# assert sec_systems[0].atoms_group[0].atoms_group[52].is_molecule is True

# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].label == 'group_ETHOX'
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].type == 'monomer_group'
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].index == 0
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].composition_formula == 'ETHOX(10)'
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].n_atoms == 72
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atom_indices[5] == 5477
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].is_molecule is False

# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].label == 'ETHOX'
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].type == 'monomer'
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].index == 7
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].composition_formula == 'C(2)H(4)O(1)'
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].n_atoms == 7
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].atom_indices[5] == 5527
# assert sec_systems[0].atoms_group[0].atoms_group[76].atoms_group[0].atoms_group[7].is_molecule is False


# def test_rdf(parser):
# archive = EntryArchive()
# parser.parse('tests/data/gromacs/fe_test/mdrun.out', archive, None)

# sec_workflow = archive.workflow2
# section_md = sec_workflow.results

# assert section_md.radial_distribution_functions[0].type == 'molecular'
# assert section_md.radial_distribution_functions[0].n_smooth == 2
# assert section_md.radial_distribution_functions[0].variables_name[0] == 'distance'

# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[0].label == 'SOL-Protein'
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[0].n_bins == 198
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[0].bins[122].magnitude == approx(7.624056451320648 * 10**(-10))
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[0].bins[122].units == 'meter'
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[0].value[96] == approx(1.093694948374587)
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[0].frame_start == 0
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[0].frame_end == 2

# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[1].label == 'SOL-SOL'
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[1].n_bins == 198
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[1].bins[102].magnitude == approx(6.389391438961029 * 10**(-10))
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[1].bins[102].units == 'meter'
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[1].value[55] == approx(0.8368052672121375)
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[1].frame_start == 0
# assert section_md.radial_distribution_functions[0].radial_distribution_function_values[1].frame_end == 2


# def test_msd(parser):
# archive = EntryArchive()
# parser.parse('tests/data/gromacs/cgwater/mdrun.log', archive, None)

# sec_workflow = archive.workflow2
# section_md = sec_workflow.results

# assert section_md.mean_squared_displacements[0].type == 'molecular'
# assert section_md.mean_squared_displacements[0].direction == 'xyz'
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].label == 'LJ'
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].n_times == 54
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].times[52].magnitude == approx(95.0 * 10**(-12))
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].times[52].units == 'second'
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].value[32].magnitude == approx(250.15309179080856 * 10**(-20))
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].value[32].units == 'meter^2'
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].diffusion_constant.value.magnitude == approx(1.1311880364159048 * 10**(-8))
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].diffusion_constant.value.units == 'meter^2/second'
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].diffusion_constant.error_type == 'Pearson correlation coefficient'
# assert section_md.mean_squared_displacements[0].mean_squared_displacement_values[0].diffusion_constant.errors == 0.9999312519176002


# def test_geometry_optimization(parser):
# archive = EntryArchive()
# parser.parse('tests/data/gromacs/polymer_melt/step4.0_minimization.log', archive, None)

# sec_workflow = archive.workflow2

# assert sec_workflow.method.type == 'atomic'
# assert sec_workflow.method.method == 'steepest_descent'
# assert sec_workflow.method.convergence_tolerance_force_maximum.magnitude == approx(6.02214076e+38)
# assert sec_workflow.method.convergence_tolerance_force_maximum.units == 'newton'
# assert sec_workflow.results.final_force_maximum.magnitude == approx(1.303670442204273e+38)
# assert sec_workflow.results.final_force_maximum.units == 'newton'
# assert sec_workflow.results.optimization_steps == 12
# assert sec_workflow.method.optimization_steps_maximum == 5000
# assert len(sec_workflow.results.energies) == 11
# assert sec_workflow.results.energies[2].magnitude == approx(8.244726173423345e-17)
# assert sec_workflow.results.energies[2].units == 'joule'
# assert len(sec_workflow.results.steps) == 11
# assert sec_workflow.results.steps[4] == 5000
sec_workflow_results = sec_workflow.results
assert len(sec_workflow_results.ensemble_properties) == 2
ensemble_property_0 = sec_workflow_results.ensemble_properties[0]
assert ensemble_property_0.label == 'diffusion_constants'
assert ensemble_property_0.error_type == 'Pearson_correlation_coefficient'
assert len(ensemble_property_0.ensemble_property_values) == 2
assert ensemble_property_0.ensemble_property_values[1].label == 'MOL2'
assert ensemble_property_0.ensemble_property_values[1].errors == 0.95
assert ensemble_property_0.ensemble_property_values[1].value_magnitude == 2.
assert ensemble_property_0.ensemble_property_values[1].value_unit == 'angstrom ** 2 / picosecond'
ensemble_property_1 = sec_workflow_results.ensemble_properties[1]
assert ensemble_property_1.label == 'radial_distribution_functions'
assert ensemble_property_1.type == 'molecular'
assert len(ensemble_property_1.ensemble_property_values) == 3
assert ensemble_property_1.ensemble_property_values[1].label == 'MOL1-MOL2'
assert ensemble_property_1.ensemble_property_values[1].n_bins == 651
assert ensemble_property_1.ensemble_property_values[1].frame_start == 0
assert ensemble_property_1.ensemble_property_values[1].frame_end == 4
assert ensemble_property_1.ensemble_property_values[1].bins_magnitude[51] == approx(0.255)
assert ensemble_property_1.ensemble_property_values[1].bins_unit == 'angstrom'
assert ensemble_property_1.ensemble_property_values[1].value_magnitude[51] == approx(0.284764)
correlation_function_0 = sec_workflow_results.correlation_functions[0]
assert correlation_function_0.type == 'molecular'
assert correlation_function_0.label == 'mean_squared_displacements'
assert correlation_function_0.direction == 'xyz'
assert correlation_function_0.error_type == 'standard_deviation'
assert len(correlation_function_0.correlation_function_values) == 2
assert correlation_function_0.correlation_function_values[0].label == 'MOL1'
assert correlation_function_0.correlation_function_values[0].n_times == 51
assert correlation_function_0.correlation_function_values[0].times[10].magnitude == approx(2.e-11)
assert correlation_function_0.correlation_function_values[0].value_magnitude[10] == approx(0.679723)
assert correlation_function_0.correlation_function_values[0].value_unit == 'angstrom ** 2'
assert correlation_function_0.correlation_function_values[0].errors[10] == approx(0.0)

0 comments on commit 5e05420

Please sign in to comment.