diff --git a/atomisticparsers/amber/metainfo/amber.py b/atomisticparsers/amber/metainfo/amber.py index 8559e666..1bcc3aa9 100644 --- a/atomisticparsers/amber/metainfo/amber.py +++ b/atomisticparsers/amber/metainfo/amber.py @@ -23,6 +23,7 @@ Reference ) from nomad.datamodel.metainfo import simulation +import simulationworkflowschema m_package = Package() @@ -169,7 +170,7 @@ class System(simulation.system.System): ''') -class MolecularDynamics(simulation.workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True) diff --git a/atomisticparsers/asap/metainfo/asap.py b/atomisticparsers/asap/metainfo/asap.py index ca0f9470..dbe3369f 100644 --- a/atomisticparsers/asap/metainfo/asap.py +++ b/atomisticparsers/asap/metainfo/asap.py @@ -22,13 +22,13 @@ MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy, Reference ) -from nomad.datamodel.metainfo.simulation import workflow +import simulationworkflowschema m_package = Package() -class MolecularDynamics(workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True) @@ -54,7 +54,7 @@ class MolecularDynamics(workflow.MolecularDynamics): ''') -class GeometryOptimization(workflow.GeometryOptimization): +class GeometryOptimization(simulationworkflowschema.GeometryOptimization): m_def = Section(validate=False, extends_base_section=True) diff --git a/atomisticparsers/asap/parser.py b/atomisticparsers/asap/parser.py index 7e0de91c..71c72923 100644 --- a/atomisticparsers/asap/parser.py +++ b/atomisticparsers/asap/parser.py @@ -27,8 +27,8 @@ from nomad.datamodel.metainfo.simulation.run import Run, Program from nomad.datamodel.metainfo.simulation.method import ( Method, ForceField, Model) -from nomad.datamodel.metainfo.simulation.workflow import ( - GeometryOptimization, GeometryOptimizationMethod, +from simulationworkflowschema import ( + GeometryOptimization, GeometryOptimizationMethod ) from atomisticparsers.utils import MDParser from .metainfo.asap import MolecularDynamics # pylint: disable=unused-import diff --git a/atomisticparsers/bopfox/parser.py b/atomisticparsers/bopfox/parser.py index d6a97459..6bd62a46 100644 --- a/atomisticparsers/bopfox/parser.py +++ b/atomisticparsers/bopfox/parser.py @@ -31,7 +31,7 @@ Calculation, Energy, EnergyEntry, Forces, ForcesEntry, Stress, StressEntry, Charges, ChargesValue ) -from nomad.datamodel.metainfo.simulation.workflow import ( +from simulationworkflowschema import ( GeometryOptimization, GeometryOptimizationMethod, SinglePoint ) from atomisticparsers.utils import MDParser diff --git a/atomisticparsers/dlpoly/metainfo/dl_poly.py b/atomisticparsers/dlpoly/metainfo/dl_poly.py index d452e2ee..683380d2 100644 --- a/atomisticparsers/dlpoly/metainfo/dl_poly.py +++ b/atomisticparsers/dlpoly/metainfo/dl_poly.py @@ -23,6 +23,7 @@ Reference, JSON ) from nomad.datamodel.metainfo import simulation +import simulationworkflowschema m_package = Package() @@ -69,7 +70,7 @@ class x_dl_poly_section_md_topology(MSection): repeats=True) -class MolecularDynamics(simulation.workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True) diff --git a/atomisticparsers/gromacs/metainfo/gromacs.py b/atomisticparsers/gromacs/metainfo/gromacs.py index 780632a6..113a41f4 100644 --- a/atomisticparsers/gromacs/metainfo/gromacs.py +++ b/atomisticparsers/gromacs/metainfo/gromacs.py @@ -22,6 +22,7 @@ MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy ) from nomad.datamodel.metainfo import simulation +import simulationworkflowschema m_package = Package() @@ -1572,7 +1573,7 @@ class System(simulation.system.System): ''',) -class MolecularDynamics(simulation.workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True,) diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py index d04a879f..092630e5 100644 --- a/atomisticparsers/gromacs/parser.py +++ b/atomisticparsers/gromacs/parser.py @@ -39,7 +39,7 @@ from nomad.datamodel.metainfo.simulation.system import ( AtomsGroup ) -from nomad.datamodel.metainfo.simulation.workflow import ( +from simulationworkflowschema import ( GeometryOptimization, GeometryOptimizationMethod, GeometryOptimizationResults ) from .metainfo.gromacs import x_gromacs_section_control_parameters, x_gromacs_section_input_output_files diff --git a/atomisticparsers/gromos/metainfo/gromos.py b/atomisticparsers/gromos/metainfo/gromos.py index c5722564..1ccc8d54 100644 --- a/atomisticparsers/gromos/metainfo/gromos.py +++ b/atomisticparsers/gromos/metainfo/gromos.py @@ -23,6 +23,7 @@ Reference ) from nomad.datamodel.metainfo import simulation +import simulationworkflowschema m_package = Package() @@ -1388,7 +1389,7 @@ class System(simulation.system.System): ''') -class MolecularDynamics(simulation.workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True) diff --git a/atomisticparsers/gulp/metainfo/gulp.py b/atomisticparsers/gulp/metainfo/gulp.py index 1407634f..94319514 100644 --- a/atomisticparsers/gulp/metainfo/gulp.py +++ b/atomisticparsers/gulp/metainfo/gulp.py @@ -24,6 +24,7 @@ Reference ) from nomad.datamodel.metainfo import simulation +import simulationworkflowschema m_package = Package() @@ -827,7 +828,7 @@ class Calculation(simulation.calculation.Calculation): x_gulp_bulk_optimisation = SubSection(sub_section=x_gulp_bulk_optimisation.m_def) -class ElasticResults(simulation.workflow.ElasticResults): +class ElasticResults(simulationworkflowschema.ElasticResults): m_def = Section(validate=False, extends_base_section=True) @@ -909,7 +910,7 @@ class ElasticResults(simulation.workflow.ElasticResults): ''') -class MolecularDynamics(simulation.workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True) diff --git a/atomisticparsers/gulp/parser.py b/atomisticparsers/gulp/parser.py index 810a4a9b..f1e55c91 100644 --- a/atomisticparsers/gulp/parser.py +++ b/atomisticparsers/gulp/parser.py @@ -35,7 +35,7 @@ from nomad.datamodel.metainfo.simulation.calculation import ( Calculation, Energy, EnergyEntry ) -from nomad.datamodel.metainfo.simulation.workflow import ( +from simulationworkflowschema import ( Elastic, ElasticMethod, ElasticResults, MolecularDynamics, MolecularDynamicsMethod ) from atomisticparsers.gulp.metainfo.gulp import x_gulp_bulk_optimisation, x_gulp_bulk_optimisation_cycle diff --git a/atomisticparsers/lammps/metainfo/lammps.py b/atomisticparsers/lammps/metainfo/lammps.py index 6e280bc8..1ed63a95 100644 --- a/atomisticparsers/lammps/metainfo/lammps.py +++ b/atomisticparsers/lammps/metainfo/lammps.py @@ -23,6 +23,7 @@ Reference ) from nomad.datamodel.metainfo import simulation +import simulationworkflowschema m_package = Package() @@ -99,7 +100,7 @@ class System(simulation.system.System): ''') -class MolecularDynamics(simulation.workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True) diff --git a/atomisticparsers/lammps/parser.py b/atomisticparsers/lammps/parser.py index 44cb7446..ad47346f 100644 --- a/atomisticparsers/lammps/parser.py +++ b/atomisticparsers/lammps/parser.py @@ -31,7 +31,7 @@ from nomad.datamodel.metainfo.simulation.system import ( AtomsGroup ) -from nomad.datamodel.metainfo.simulation.workflow import ( +from simulationworkflowschema import ( GeometryOptimization, GeometryOptimizationMethod, GeometryOptimizationResults ) from .metainfo.lammps import x_lammps_section_input_output_files, x_lammps_section_control_parameters diff --git a/atomisticparsers/namd/metainfo/namd.py b/atomisticparsers/namd/metainfo/namd.py index 66fa6f07..a782a958 100644 --- a/atomisticparsers/namd/metainfo/namd.py +++ b/atomisticparsers/namd/metainfo/namd.py @@ -23,6 +23,7 @@ Reference, JSON ) from nomad.datamodel.metainfo import simulation +import simulationworkflowschema m_package = Package() @@ -1006,7 +1007,7 @@ class System(simulation.system.System): ''') -class MolecularDynamics(simulation.workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True) diff --git a/atomisticparsers/namd/parser.py b/atomisticparsers/namd/parser.py index 4c565798..a9147ad3 100644 --- a/atomisticparsers/namd/parser.py +++ b/atomisticparsers/namd/parser.py @@ -27,7 +27,7 @@ from nomad.parsing.file_parser import TextParser, Quantity from nomad.datamodel.metainfo.simulation.run import Run, Program from nomad.datamodel.metainfo.simulation.method import Method -from nomad.datamodel.metainfo.simulation.workflow import MolecularDynamics +from simulationworkflowschema import MolecularDynamics from atomisticparsers.utils import MDAnalysisParser, MDParser from .metainfo import m_env # pylint: disable=unused-import diff --git a/atomisticparsers/tinker/metainfo/tinker.py b/atomisticparsers/tinker/metainfo/tinker.py index b4640ac3..ef1e377d 100644 --- a/atomisticparsers/tinker/metainfo/tinker.py +++ b/atomisticparsers/tinker/metainfo/tinker.py @@ -22,6 +22,7 @@ Reference, JSON ) from nomad.datamodel.metainfo import simulation +import simulationworkflowschema m_package = Package() @@ -778,7 +779,7 @@ class System(simulation.system.System): ''') -class MolecularDynamics(simulation.workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True) @@ -872,7 +873,7 @@ class MolecularDynamics(simulation.workflow.MolecularDynamics): ''') -class GeometryOptimization(simulation.workflow.GeometryOptimization): +class GeometryOptimization(simulationworkflowschema.GeometryOptimization): m_def = Section(validate=False, extends_base_section=True) diff --git a/atomisticparsers/tinker/parser.py b/atomisticparsers/tinker/parser.py index ea4876e2..1b46eead 100644 --- a/atomisticparsers/tinker/parser.py +++ b/atomisticparsers/tinker/parser.py @@ -34,7 +34,7 @@ from nomad.datamodel.metainfo.simulation.calculation import ( Calculation, Energy, EnergyEntry, VibrationalFrequencies ) -from nomad.datamodel.metainfo.simulation.workflow import ( +from simulationworkflowschema import ( GeometryOptimization, GeometryOptimizationMethod ) from atomisticparsers.utils import MDAnalysisParser, MDParser diff --git a/atomisticparsers/utils/parsers.py b/atomisticparsers/utils/parsers.py index ec000e55..75c95808 100644 --- a/atomisticparsers/utils/parsers.py +++ b/atomisticparsers/utils/parsers.py @@ -28,7 +28,7 @@ from nomad.datamodel.metainfo.simulation.run import Run from nomad.datamodel.metainfo.simulation.system import System from nomad.datamodel.metainfo.simulation.calculation import Calculation -from nomad.datamodel.metainfo.simulation.workflow import MolecularDynamics +from simulationworkflowschema import MolecularDynamics from nomad.datamodel.metainfo.simulation.method import Interaction diff --git a/atomisticparsers/xtb/metainfo/xtb.py b/atomisticparsers/xtb/metainfo/xtb.py index caa280e2..e4b370a0 100644 --- a/atomisticparsers/xtb/metainfo/xtb.py +++ b/atomisticparsers/xtb/metainfo/xtb.py @@ -22,6 +22,7 @@ Package, Quantity, Section, SubSection, JSON ) from nomad.datamodel.metainfo import simulation +import simulationworkflowschema m_package = Package() @@ -87,7 +88,7 @@ class MultipolesEntry(simulation.calculation.MultipolesEntry): ''') -class GeometryOptimization(simulation.workflow.GeometryOptimization): +class GeometryOptimization(simulationworkflowschema.GeometryOptimization): m_def = Section(validate=False, extends_base_section=True) @@ -146,7 +147,7 @@ class GeometryOptimization(simulation.workflow.GeometryOptimization): ''') -class MolecularDynamics(simulation.workflow.MolecularDynamics): +class MolecularDynamics(simulationworkflowschema.MolecularDynamics): m_def = Section(validate=False, extends_base_section=True) diff --git a/atomisticparsers/xtb/parser.py b/atomisticparsers/xtb/parser.py index c1d9968c..a10cf61c 100644 --- a/atomisticparsers/xtb/parser.py +++ b/atomisticparsers/xtb/parser.py @@ -31,7 +31,7 @@ from nomad.datamodel.metainfo.simulation.calculation import ( Calculation, ScfIteration, Energy, EnergyEntry, BandEnergies, Multipoles, MultipolesEntry ) -from nomad.datamodel.metainfo.simulation.workflow import ( +from simulationworkflowschema import ( SinglePoint, GeometryOptimization, GeometryOptimizationMethod ) from atomisticparsers.utils import MDParser diff --git a/pyproject.toml b/pyproject.toml index 8ed2db95..66ef7565 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,6 +11,7 @@ authors = [{ name = "The NOMAD Authors" }] license = { file = "LICENSE" } dependencies = [ 'nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop', + "nomad-schema-plugin-simulation-workflow@git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@develop", 'lxml==4.7.1', 'MDAnalysis', 'panedr==0.2',