diff --git a/README.md b/README.md index a38045d..7f0b39d 100644 --- a/README.md +++ b/README.md @@ -144,7 +144,7 @@ result, calc_node = run_get_node(builder) $ verdi process list -D desc -a -l 1 PK Created Process label Process State Process status ---- --------- ---------------- --------------- ---------------- -2480 32s ago ForceCalculation Finished [0] +2480 32s ago LammpsForceCalculation Finished [0] Total results: 1 @@ -168,7 +168,7 @@ Inputs PK Type ---------- ---- ------------------ code 1351 Code parameters 2479 Dict -potential 2478 EmpiricalPotential +potential 2478 LammpsEmpiricalPotential structure 2477 StructureData Outputs PK Type @@ -185,7 +185,7 @@ calc_node.outputs.results.attributes ```python {'parser_version': '0.4.0b3', - 'parser_class': 'ForceParser', + 'parser_class': 'LammpsForceParser', 'errors': [], 'warnings': '', 'distance_units': 'Angstroms', @@ -264,7 +264,7 @@ Inputs PK Type ---------- ---- ------------------ code 1344 Code parameters 2485 Dict -potential 2478 EmpiricalPotential +potential 2478 LammpsEmpiricalPotential structure 2477 StructureData Outputs PK Type @@ -282,7 +282,7 @@ calc_node.outputs.results.attributes ```python {'parser_version': '0.4.0b3', - 'parser_class': 'OptimizeParser', + 'parser_class': 'LammpsOptimizeParser', 'errors': [], 'warnings': '', 'stress_units': 'bars', @@ -342,7 +342,7 @@ result, calc_node = run_get_node(builder) $ verdi process list -D desc -a -l 1 PK Created Process label Process State Process status ---- --------- --------------- --------------- ---------------- -2493 12s ago MdCalculation ⏹ Finished [0] +2493 12s ago LammpsMdCalculation ⏹ Finished [0] Total results: 1 @@ -366,7 +366,7 @@ Inputs PK Type ---------- ---- ------------------ code 1540 Code parameters 2492 Dict -potential 2478 EmpiricalPotential +potential 2478 LammpsEmpiricalPotential structure 2477 StructureData Outputs PK Type @@ -384,7 +384,7 @@ calc_node.outputs.results.attributes ```python {'parser_version': '0.4.0b3', - 'parser_class': 'MdParser', + 'parser_class': 'LammpsMdParser', 'errors': [], 'warnings': '', 'time_units': 'picoseconds', diff --git a/aiida_lammps/calculations/lammps/__init__.py b/aiida_lammps/calculations/lammps/__init__.py index 15e5213..10476b9 100644 --- a/aiida_lammps/calculations/lammps/__init__.py +++ b/aiida_lammps/calculations/lammps/__init__.py @@ -9,7 +9,7 @@ import numpy as np from aiida_lammps.common.generate_structure import generate_lammps_structure -from aiida_lammps.data.potential import EmpiricalPotential +from aiida_lammps.data.potential import LammpsEmpiricalPotential class BaseLammpsCalculation(CalcJob): @@ -40,7 +40,7 @@ def define(cls, spec): ) spec.input( "potential", - valid_type=EmpiricalPotential, + valid_type=LammpsEmpiricalPotential, help="lammps potential", ) spec.input( diff --git a/aiida_lammps/calculations/lammps/base.py b/aiida_lammps/calculations/lammps/base.py index bf84d89..f44a58c 100644 --- a/aiida_lammps/calculations/lammps/base.py +++ b/aiida_lammps/calculations/lammps/base.py @@ -18,7 +18,7 @@ from aiida_lammps.data.trajectory import LammpsTrajectory -class BaseLammpsCalculation(CalcJob): +class LammpsBaseCalculation(CalcJob): """ A basic plugin for performing calculations in ``LAMMPS`` using aiida. diff --git a/aiida_lammps/calculations/lammps/force.py b/aiida_lammps/calculations/lammps/force.py index 6d4885a..f804e4e 100644 --- a/aiida_lammps/calculations/lammps/force.py +++ b/aiida_lammps/calculations/lammps/force.py @@ -7,7 +7,7 @@ from aiida_lammps.validation import validate_against_schema -class ForceCalculation(BaseLammpsCalculation): +class LammpsForceCalculation(BaseLammpsCalculation): """Calculation of a single point in LAMMPS, to obtain the energy of the system.""" @classmethod diff --git a/aiida_lammps/calculations/lammps/md.py b/aiida_lammps/calculations/lammps/md.py index d599f9b..c41afb1 100644 --- a/aiida_lammps/calculations/lammps/md.py +++ b/aiida_lammps/calculations/lammps/md.py @@ -10,7 +10,7 @@ from aiida_lammps.validation import validate_against_schema -class MdCalculation(BaseLammpsCalculation): +class LammpsMdCalculation(BaseLammpsCalculation): """Calculation of a single MD stage in LAMMPS.""" @classmethod diff --git a/aiida_lammps/calculations/lammps/md_multi.py b/aiida_lammps/calculations/lammps/md_multi.py index 1224b4e..cfa0178 100644 --- a/aiida_lammps/calculations/lammps/md_multi.py +++ b/aiida_lammps/calculations/lammps/md_multi.py @@ -9,7 +9,7 @@ from aiida_lammps.validation import validate_against_schema -class MdMultiCalculation(BaseLammpsCalculation): +class LammpsMdMultiCalculation(BaseLammpsCalculation): """Run a multi-stage molecular dynamic simulation.""" @classmethod diff --git a/aiida_lammps/calculations/lammps/optimize.py b/aiida_lammps/calculations/lammps/optimize.py index 9edf68a..5c08d0d 100644 --- a/aiida_lammps/calculations/lammps/optimize.py +++ b/aiida_lammps/calculations/lammps/optimize.py @@ -12,7 +12,7 @@ from aiida_lammps.validation import validate_against_schema -class OptimizeCalculation(BaseLammpsCalculation): +class LammpsOptimizeCalculation(BaseLammpsCalculation): """Calculation for the optimization of the structure in LAMMPS.""" @classmethod @@ -147,7 +147,7 @@ def validate_parameters(param_data, potential_object) -> bool: :param param_data: input parameters for the optimization calculations :type param_data: orm.Dict :param potential_object: LAMMPS potential - :type potential_object: EmpiricalPotential + :type potential_object: LammpsEmpiricalPotential :raises InputValidationError: if there is no parameters data passed :raises InputValidationError: if the units of the parameters and the potential are different. diff --git a/aiida_lammps/common/raw_parsers.py b/aiida_lammps/common/raw_parsers.py index a8f4333..c295711 100644 --- a/aiida_lammps/common/raw_parsers.py +++ b/aiida_lammps/common/raw_parsers.py @@ -146,7 +146,7 @@ def read_log_file(logdata_txt, compute_stress=False): found_end = True elif "Total wall time:" in line: data_dict["total_wall_time"] = line.split()[-1] - # These are handled in LAMMPSBaseParser.add_warnings_and_errors + # These are handled in LammpsBaseParser.add_warnings_and_errors # if line.strip().startswith("WARNING"): # data_dict.setdefault("warnings", []).append(line.strip()) # if line.strip().startswith("ERROR"): diff --git a/aiida_lammps/data/potential.py b/aiida_lammps/data/potential.py index 9d73c24..b8f7172 100644 --- a/aiida_lammps/data/potential.py +++ b/aiida_lammps/data/potential.py @@ -7,7 +7,7 @@ from aiida.plugins.entry_point import get_entry_point_names, load_entry_point -class EmpiricalPotential(Data): +class LammpsEmpiricalPotential(Data): """ Store the empirical potential data """ diff --git a/aiida_lammps/parsers/lammps/base.py b/aiida_lammps/parsers/lammps/base.py index 1ac69ce..829543b 100644 --- a/aiida_lammps/parsers/lammps/base.py +++ b/aiida_lammps/parsers/lammps/base.py @@ -16,7 +16,7 @@ ) -class LAMMPSBaseParser(Parser): +class LammpsBaseParser(Parser): """Abstract Base Parser for LAMMPS, supplying common methods.""" def __init__(self, node): diff --git a/aiida_lammps/parsers/lammps/force.py b/aiida_lammps/parsers/lammps/force.py index fc3a087..2b8b8e4 100644 --- a/aiida_lammps/parsers/lammps/force.py +++ b/aiida_lammps/parsers/lammps/force.py @@ -4,10 +4,10 @@ from aiida_lammps.common.parse_trajectory import iter_trajectories from aiida_lammps.common.raw_parsers import get_units_dict -from aiida_lammps.parsers.lammps.base import LAMMPSBaseParser +from aiida_lammps.parsers.lammps.base import LammpsBaseParser -class ForceParser(LAMMPSBaseParser): +class LammpsForceParser(LammpsBaseParser): """Parser for LAMMPS single point energy calculation.""" def __init__(self, node): diff --git a/aiida_lammps/parsers/lammps/lammps_parser.py b/aiida_lammps/parsers/lammps/lammps_parser.py index 1d45ea6..58df912 100644 --- a/aiida_lammps/parsers/lammps/lammps_parser.py +++ b/aiida_lammps/parsers/lammps/lammps_parser.py @@ -18,7 +18,7 @@ from aiida_lammps.data.trajectory import LammpsTrajectory -class LAMMPSBaseParser(Parser): +class LammpsBaseParser(Parser): """ Base parser for LAMMPS calculations. diff --git a/aiida_lammps/parsers/lammps/md.py b/aiida_lammps/parsers/lammps/md.py index ae754e5..9d74a4d 100644 --- a/aiida_lammps/parsers/lammps/md.py +++ b/aiida_lammps/parsers/lammps/md.py @@ -6,10 +6,10 @@ from aiida_lammps.common.raw_parsers import convert_units, get_units_dict from aiida_lammps.data.trajectory import LammpsTrajectory -from aiida_lammps.parsers.lammps.base import LAMMPSBaseParser +from aiida_lammps.parsers.lammps.base import LammpsBaseParser -class MdParser(LAMMPSBaseParser): +class LammpsMdParser(LammpsBaseParser): """Parser for LAMMPS MD calculations.""" def __init__(self, node): diff --git a/aiida_lammps/parsers/lammps/md_multi.py b/aiida_lammps/parsers/lammps/md_multi.py index 11266cb..3cfbf41 100644 --- a/aiida_lammps/parsers/lammps/md_multi.py +++ b/aiida_lammps/parsers/lammps/md_multi.py @@ -7,10 +7,10 @@ from aiida_lammps.common.raw_parsers import convert_units, get_units_dict from aiida_lammps.data.trajectory import LammpsTrajectory -from aiida_lammps.parsers.lammps.base import LAMMPSBaseParser +from aiida_lammps.parsers.lammps.base import LammpsBaseParser -class MdMultiParser(LAMMPSBaseParser): +class LammpsMdMultiParser(LammpsBaseParser): """Parser for LAMMPS MDMulti calculations.""" def __init__(self, node): diff --git a/aiida_lammps/parsers/lammps/optimize.py b/aiida_lammps/parsers/lammps/optimize.py index 913af07..e6aeb3d 100644 --- a/aiida_lammps/parsers/lammps/optimize.py +++ b/aiida_lammps/parsers/lammps/optimize.py @@ -9,10 +9,10 @@ from aiida_lammps.common.raw_parsers import get_units_dict from aiida_lammps.data.trajectory import LammpsTrajectory -from aiida_lammps.parsers.lammps.base import LAMMPSBaseParser +from aiida_lammps.parsers.lammps.base import LammpsBaseParser -class OptimizeParser(LAMMPSBaseParser): +class LammpsOptimizeParser(LammpsBaseParser): """Parser for LAMMPS optimization calculation.""" def __init__(self, node): diff --git a/examples/launch_lammps_force_gan.py b/examples/launch_lammps_force_gan.py index 7d9b53a..938e29e 100644 --- a/examples/launch_lammps_force_gan.py +++ b/examples/launch_lammps_force_gan.py @@ -4,7 +4,7 @@ from aiida.plugins import CalculationFactory import numpy as np -from aiida_lammps.data.potential import EmpiricalPotential +from aiida_lammps.data.potential import LammpsEmpiricalPotential if __name__ == "__main__": @@ -81,7 +81,7 @@ # setup nodes inputs.structure = structure - inputs.potential = EmpiricalPotential( + inputs.potential = LammpsEmpiricalPotential( type=potential["pair_style"], data=potential["data"] ) diff --git a/examples/launch_lammps_md_si.py b/examples/launch_lammps_md_si.py index 20bbaf0..91fe1c4 100644 --- a/examples/launch_lammps_md_si.py +++ b/examples/launch_lammps_md_si.py @@ -4,7 +4,7 @@ from aiida.plugins import CalculationFactory import numpy as np -from aiida_lammps.data.potential import EmpiricalPotential +from aiida_lammps.data.potential import LammpsEmpiricalPotential if __name__ == "__main__": @@ -83,7 +83,7 @@ # setup nodes inputs.structure = structure - inputs.potential = EmpiricalPotential( + inputs.potential = LammpsEmpiricalPotential( type=potential["pair_style"], data=potential["data"] ) diff --git a/examples/launch_lammps_optimization_fe.py b/examples/launch_lammps_optimization_fe.py index 65dccfc..ea94ab5 100644 --- a/examples/launch_lammps_optimization_fe.py +++ b/examples/launch_lammps_optimization_fe.py @@ -4,7 +4,7 @@ from aiida.plugins import CalculationFactory import numpy as np -from aiida_lammps.data.potential import EmpiricalPotential +from aiida_lammps.data.potential import LammpsEmpiricalPotential if __name__ == "__main__": @@ -87,7 +87,7 @@ # setup nodes inputs.structure = structure - inputs.potential = EmpiricalPotential( + inputs.potential = LammpsEmpiricalPotential( type=potential["pair_style"], data=potential["data"] ) diff --git a/examples/launch_lammps_optimization_gan.py b/examples/launch_lammps_optimization_gan.py index a71752d..5c62447 100644 --- a/examples/launch_lammps_optimization_gan.py +++ b/examples/launch_lammps_optimization_gan.py @@ -4,7 +4,7 @@ from aiida.plugins import CalculationFactory import numpy as np -from aiida_lammps.data.potential import EmpiricalPotential +from aiida_lammps.data.potential import LammpsEmpiricalPotential if __name__ == "__main__": @@ -101,7 +101,7 @@ # setup nodes inputs.structure = structure - inputs.potential = EmpiricalPotential( + inputs.potential = LammpsEmpiricalPotential( type=potential["pair_style"], data=potential["data"] ) diff --git a/examples/launch_lammps_optimization_lj.py b/examples/launch_lammps_optimization_lj.py index 5641a00..ce9f07f 100644 --- a/examples/launch_lammps_optimization_lj.py +++ b/examples/launch_lammps_optimization_lj.py @@ -4,7 +4,7 @@ from aiida.plugins import CalculationFactory import numpy as np -from aiida_lammps.data.potential import EmpiricalPotential +from aiida_lammps.data.potential import LammpsEmpiricalPotential if __name__ == "__main__": @@ -88,7 +88,7 @@ # setup nodes inputs.structure = structure - inputs.potential = EmpiricalPotential( + inputs.potential = LammpsEmpiricalPotential( type=potential["pair_style"], data=potential["data"] ) diff --git a/pyproject.toml b/pyproject.toml index 9de8629..efaab55 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,22 +60,22 @@ docs = [ ] [project.entry-points."aiida.calculations"] -"lammps.base" = "aiida_lammps.calculations.lammps.base:BaseLammpsCalculation" -"lammps.combinate" = "aiida_lammps.calculations.lammps.combinate:CombinateCalculation" -"lammps.force" = "aiida_lammps.calculations.lammps.force:ForceCalculation" -"lammps.md" = "aiida_lammps.calculations.lammps.md:MdCalculation" -"lammps.md.multi" = "aiida_lammps.calculations.lammps.md_multi:MdMultiCalculation" -"lammps.optimize" = "aiida_lammps.calculations.lammps.optimize:OptimizeCalculation" +"lammps.base" = "aiida_lammps.calculations.lammps.base:LammpsBaseCalculation" +"lammps.combinate" = "aiida_lammps.calculations.lammps.combinate:LammpsCombinateCalculation" +"lammps.force" = "aiida_lammps.calculations.lammps.force:LammpsForceCalculation" +"lammps.md" = "aiida_lammps.calculations.lammps.md:LammpsMdCalculation" +"lammps.md.multi" = "aiida_lammps.calculations.lammps.md_multi:LammpsMdMultiCalculation" +"lammps.optimize" = "aiida_lammps.calculations.lammps.optimize:LammpsOptimizeCalculation" [project.entry-points."aiida.parsers"] -"lammps.base" = "aiida_lammps.parsers.lammps.lammps_parser:LAMMPSBaseParser" -"lammps.force" = "aiida_lammps.parsers.lammps.force:ForceParser" -"lammps.md" = "aiida_lammps.parsers.lammps.md:MdParser" -"lammps.md.multi" = "aiida_lammps.parsers.lammps.md_multi:MdMultiParser" -"lammps.optimize" = "aiida_lammps.parsers.lammps.optimize:OptimizeParser" +"lammps.base" = "aiida_lammps.parsers.lammps.lammps_parser:LammpsBaseParser" +"lammps.force" = "aiida_lammps.parsers.lammps.force:LammpsForceParser" +"lammps.md" = "aiida_lammps.parsers.lammps.md:LammpsMdParser" +"lammps.md.multi" = "aiida_lammps.parsers.lammps.md_multi:LammpsMdMultiParser" +"lammps.optimize" = "aiida_lammps.parsers.lammps.optimize:LammpsOptimizeParser" [project.entry-points."aiida.data"] -"lammps.potential" = "aiida_lammps.data.potential:EmpiricalPotential" +"lammps.potential" = "aiida_lammps.data.potential:LammpsEmpiricalPotential" "lammps.lammps_potential" = "aiida_lammps.data.lammps_potential:LammpsPotentialData" "lammps.trajectory" = "aiida_lammps.data.trajectory:LammpsTrajectory" diff --git a/tests/test_calculations.py b/tests/test_calculations.py index 2e464cb..543aba9 100644 --- a/tests/test_calculations.py +++ b/tests/test_calculations.py @@ -692,8 +692,8 @@ def test_lammps_base( def test_lammps_base_script(generate_calc_job, aiida_local_code_factory): - """Test the ``BaseLammpsCalculation`` with the ``script`` input.""" - from aiida_lammps.calculations.lammps.base import BaseLammpsCalculation + """Test the ``LammpsBaseCalculation`` with the ``script`` input.""" + from aiida_lammps.calculations.lammps.base import LammpsBaseCalculation inputs = { "code": aiida_local_code_factory("lammps.base", "bash"), @@ -722,7 +722,7 @@ def test_lammps_base_script(generate_calc_job, aiida_local_code_factory): inputs["script"] = script tmp_path, calc_info = generate_calc_job("lammps.base", inputs) - assert (tmp_path / BaseLammpsCalculation._INPUT_FILENAME).read_text() == content + assert (tmp_path / LammpsBaseCalculation._INPUT_FILENAME).read_text() == content @pytest.mark.lammps_call @@ -897,8 +897,8 @@ def test_lammps_base_settings_invalid(generate_calc_job, aiida_local_code_factor def test_lammps_base_settings(generate_calc_job, aiida_local_code_factory): - """Test the ``BaseLammpsCalculation`` with the ``settings`` input.""" - from aiida_lammps.calculations.lammps.base import BaseLammpsCalculation + """Test the ``LammpsBaseCalculation`` with the ``settings`` input.""" + from aiida_lammps.calculations.lammps.base import LammpsBaseCalculation inputs = { "code": aiida_local_code_factory("lammps.base", "bash"), diff --git a/tests/test_calculations/test_force_process_eam_.yml b/tests/test_calculations/test_force_process_eam_.yml index 9c349f8..888557b 100644 --- a/tests/test_calculations/test_force_process_eam_.yml +++ b/tests/test_calculations/test_force_process_eam_.yml @@ -11,5 +11,5 @@ results: etotal: -8.2 temp: 0.0 force_units: eV/Angstrom - parser_class: ForceParser + parser_class: LammpsForceParser units_style: metal diff --git a/tests/test_calculations/test_force_process_lennard_jones_.yml b/tests/test_calculations/test_force_process_lennard_jones_.yml index 3e4bd60..24884ca 100644 --- a/tests/test_calculations/test_force_process_lennard_jones_.yml +++ b/tests/test_calculations/test_force_process_lennard_jones_.yml @@ -11,5 +11,5 @@ results: etotal: 0.0 temp: 0.0 force_units: eV/Angstrom - parser_class: ForceParser + parser_class: LammpsForceParser units_style: metal diff --git a/tests/test_calculations/test_force_process_reaxff_.yml b/tests/test_calculations/test_force_process_reaxff_.yml index 7a7fd79..c9f7a6f 100644 --- a/tests/test_calculations/test_force_process_reaxff_.yml +++ b/tests/test_calculations/test_force_process_reaxff_.yml @@ -14,5 +14,5 @@ results: etotal: -1028.0 temp: 0.0 force_units: Kcal/mole-Angstrom - parser_class: ForceParser + parser_class: LammpsForceParser units_style: real diff --git a/tests/test_calculations/test_force_process_tersoff_.yml b/tests/test_calculations/test_force_process_tersoff_.yml index a0c3b7c..10548c5 100644 --- a/tests/test_calculations/test_force_process_tersoff_.yml +++ b/tests/test_calculations/test_force_process_tersoff_.yml @@ -11,5 +11,5 @@ results: etotal: -18.1 temp: 0.0 force_units: eV/Angstrom - parser_class: ForceParser + parser_class: LammpsForceParser units_style: metal diff --git a/tests/test_calculations/test_md_multi_process_eam_.yml b/tests/test_calculations/test_md_multi_process_eam_.yml index 57b8c97..34850a0 100644 --- a/tests/test_calculations/test_md_multi_process_eam_.yml +++ b/tests/test_calculations/test_md_multi_process_eam_.yml @@ -3,7 +3,7 @@ results: energy: -8.2 energy_units: eV errors: [] - parser_class: MdMultiParser + parser_class: LammpsMdMultiParser stage_names: - thermalise - equilibrate diff --git a/tests/test_calculations/test_md_multi_process_lennard_jones_.yml b/tests/test_calculations/test_md_multi_process_lennard_jones_.yml index f2f0de3..132d27d 100644 --- a/tests/test_calculations/test_md_multi_process_lennard_jones_.yml +++ b/tests/test_calculations/test_md_multi_process_lennard_jones_.yml @@ -3,7 +3,7 @@ results: energy: 0.0 energy_units: eV errors: [] - parser_class: MdMultiParser + parser_class: LammpsMdMultiParser stage_names: - thermalise - equilibrate diff --git a/tests/test_calculations/test_md_multi_process_reaxff_.yml b/tests/test_calculations/test_md_multi_process_reaxff_.yml index f32913e..d14bd0d 100644 --- a/tests/test_calculations/test_md_multi_process_reaxff_.yml +++ b/tests/test_calculations/test_md_multi_process_reaxff_.yml @@ -3,7 +3,7 @@ results: energy: -1018.1 energy_units: Kcal/mole errors: [] - parser_class: MdMultiParser + parser_class: LammpsMdMultiParser stage_names: - thermalise - equilibrate diff --git a/tests/test_calculations/test_md_multi_process_tersoff_.yml b/tests/test_calculations/test_md_multi_process_tersoff_.yml index 26e2c57..35ac004 100644 --- a/tests/test_calculations/test_md_multi_process_tersoff_.yml +++ b/tests/test_calculations/test_md_multi_process_tersoff_.yml @@ -3,7 +3,7 @@ results: energy: -18.0 energy_units: eV errors: [] - parser_class: MdMultiParser + parser_class: LammpsMdMultiParser stage_names: - thermalise - equilibrate diff --git a/tests/test_calculations/test_md_process-eam-2019.yml b/tests/test_calculations/test_md_process-eam-2019.yml index d84d37b..f93d333 100644 --- a/tests/test_calculations/test_md_process-eam-2019.yml +++ b/tests/test_calculations/test_md_process-eam-2019.yml @@ -3,7 +3,7 @@ results: energy: -8.1 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-eam-2020.yml b/tests/test_calculations/test_md_process-eam-2020.yml index 8ee9b9c..a8cc50a 100644 --- a/tests/test_calculations/test_md_process-eam-2020.yml +++ b/tests/test_calculations/test_md_process-eam-2020.yml @@ -3,7 +3,7 @@ results: energy: -8.1 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-eam-2021.yml b/tests/test_calculations/test_md_process-eam-2021.yml index 8ee9b9c..a8cc50a 100644 --- a/tests/test_calculations/test_md_process-eam-2021.yml +++ b/tests/test_calculations/test_md_process-eam-2021.yml @@ -3,7 +3,7 @@ results: energy: -8.1 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-eam-2022.yml b/tests/test_calculations/test_md_process-eam-2022.yml index 8ee9b9c..a8cc50a 100644 --- a/tests/test_calculations/test_md_process-eam-2022.yml +++ b/tests/test_calculations/test_md_process-eam-2022.yml @@ -3,7 +3,7 @@ results: energy: -8.1 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-lennard-jones-2019.yml b/tests/test_calculations/test_md_process-lennard-jones-2019.yml index 0d4e2af..a2802ef 100644 --- a/tests/test_calculations/test_md_process-lennard-jones-2019.yml +++ b/tests/test_calculations/test_md_process-lennard-jones-2019.yml @@ -3,7 +3,7 @@ results: energy: 0.1 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-lennard-jones-2020.yml b/tests/test_calculations/test_md_process-lennard-jones-2020.yml index d84dfc4..28a155c 100644 --- a/tests/test_calculations/test_md_process-lennard-jones-2020.yml +++ b/tests/test_calculations/test_md_process-lennard-jones-2020.yml @@ -3,7 +3,7 @@ results: energy: 0.1 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-lennard-jones-2021.yml b/tests/test_calculations/test_md_process-lennard-jones-2021.yml index d84dfc4..28a155c 100644 --- a/tests/test_calculations/test_md_process-lennard-jones-2021.yml +++ b/tests/test_calculations/test_md_process-lennard-jones-2021.yml @@ -3,7 +3,7 @@ results: energy: 0.1 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-lennard-jones-2022.yml b/tests/test_calculations/test_md_process-lennard-jones-2022.yml index d84dfc4..28a155c 100644 --- a/tests/test_calculations/test_md_process-lennard-jones-2022.yml +++ b/tests/test_calculations/test_md_process-lennard-jones-2022.yml @@ -3,7 +3,7 @@ results: energy: 0.1 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-tersoff-2019.yml b/tests/test_calculations/test_md_process-tersoff-2019.yml index 7a7b829..e3b11f0 100644 --- a/tests/test_calculations/test_md_process-tersoff-2019.yml +++ b/tests/test_calculations/test_md_process-tersoff-2019.yml @@ -3,7 +3,7 @@ results: energy: -17.8 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-tersoff-2020.yml b/tests/test_calculations/test_md_process-tersoff-2020.yml index e1abc5e..d326c75 100644 --- a/tests/test_calculations/test_md_process-tersoff-2020.yml +++ b/tests/test_calculations/test_md_process-tersoff-2020.yml @@ -3,7 +3,7 @@ results: energy: -17.8 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-tersoff-2021.yml b/tests/test_calculations/test_md_process-tersoff-2021.yml index e1abc5e..d326c75 100644 --- a/tests/test_calculations/test_md_process-tersoff-2021.yml +++ b/tests/test_calculations/test_md_process-tersoff-2021.yml @@ -3,7 +3,7 @@ results: energy: -17.8 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_md_process-tersoff-2022.yml b/tests/test_calculations/test_md_process-tersoff-2022.yml index e1abc5e..d326c75 100644 --- a/tests/test_calculations/test_md_process-tersoff-2022.yml +++ b/tests/test_calculations/test_md_process-tersoff-2022.yml @@ -3,7 +3,7 @@ results: energy: -17.8 energy_units: eV errors: [] - parser_class: MdParser + parser_class: LammpsMdParser time_units: picoseconds timestep_picoseconds: 0.001 units_style: metal diff --git a/tests/test_calculations/test_optimize_process_eam_.yml b/tests/test_calculations/test_optimize_process_eam_.yml index 0cfed69..784dc73 100644 --- a/tests/test_calculations/test_optimize_process_eam_.yml +++ b/tests/test_calculations/test_optimize_process_eam_.yml @@ -7,7 +7,7 @@ results: etotal: -8.2 temp: 0.0 force_units: eV/Angstrom - parser_class: OptimizeParser + parser_class: LammpsOptimizeParser stress_units: bars units_style: metal structure: diff --git a/tests/test_calculations/test_optimize_process_lennard_jones_.yml b/tests/test_calculations/test_optimize_process_lennard_jones_.yml index aa106ca..df96331 100644 --- a/tests/test_calculations/test_optimize_process_lennard_jones_.yml +++ b/tests/test_calculations/test_optimize_process_lennard_jones_.yml @@ -7,7 +7,7 @@ results: etotal: 0.0 temp: 0.0 force_units: eV/Angstrom - parser_class: OptimizeParser + parser_class: LammpsOptimizeParser stress_units: bars units_style: metal structure: diff --git a/tests/test_calculations/test_optimize_process_reaxff_.yml b/tests/test_calculations/test_optimize_process_reaxff_.yml index 5c3d698..e896a2e 100644 --- a/tests/test_calculations/test_optimize_process_reaxff_.yml +++ b/tests/test_calculations/test_optimize_process_reaxff_.yml @@ -8,7 +8,7 @@ results: etotal: -1030.4 temp: 0.0 force_units: Kcal/mole-Angstrom - parser_class: OptimizeParser + parser_class: LammpsOptimizeParser stress_units: atmospheres units_style: real structure: diff --git a/tests/test_calculations/test_optimize_process_tersoff_.yml b/tests/test_calculations/test_optimize_process_tersoff_.yml index c940d6e..d62d40f 100644 --- a/tests/test_calculations/test_optimize_process_tersoff_.yml +++ b/tests/test_calculations/test_optimize_process_tersoff_.yml @@ -7,7 +7,7 @@ results: etotal: -18.1 temp: 0.0 force_units: eV/Angstrom - parser_class: OptimizeParser + parser_class: LammpsOptimizeParser stress_units: bars units_style: metal structure: diff --git a/tests/test_potential_data.py b/tests/test_potential_data.py index 031875b..b126bec 100644 --- a/tests/test_potential_data.py +++ b/tests/test_potential_data.py @@ -6,20 +6,20 @@ from aiida_lammps.common import input_generator from aiida_lammps.data.lammps_potential import LammpsPotentialData -from aiida_lammps.data.potential import EmpiricalPotential +from aiida_lammps.data.potential import LammpsEmpiricalPotential from .utils import TEST_DIR def test_list_potentials(): """Test that all the supported potential types are recognized.""" - assert set(EmpiricalPotential.list_types()).issuperset( + assert set(LammpsEmpiricalPotential.list_types()).issuperset( ["eam", "lennard_jones", "reaxff", "tersoff"] ) def test_load_type(): """Test that an specific potential can be loaded""" - EmpiricalPotential.load_type("eam") + LammpsEmpiricalPotential.load_type("eam") @pytest.mark.parametrize( @@ -34,7 +34,7 @@ def test_init( ): """Test that the potential can be generated""" potential = get_potential_data(potential_type) - node = EmpiricalPotential( + node = LammpsEmpiricalPotential( potential_type=potential.type, data=potential.data, ) @@ -50,7 +50,7 @@ def test_potential_files( ): """Test that one can read the potential content.""" potential = get_potential_data(potential_type) - node = EmpiricalPotential( + node = LammpsEmpiricalPotential( potential_type=potential.type, data=potential.data, ) @@ -69,7 +69,7 @@ def test_input_lines( ): """Test that one can get the potential lines for a given aiida-lammps potential""" potential = get_potential_data(potential_type) - node = EmpiricalPotential( + node = LammpsEmpiricalPotential( potential_type=potential.type, data=potential.data, )