From 7a0be530346a74295eb75ab31faad0b219e21b1b Mon Sep 17 00:00:00 2001 From: wiederm Date: Thu, 18 Apr 2024 11:53:36 +0200 Subject: [PATCH] adopt names --- README.md | 2 +- guardowl/protocols.py | 36 +++++++------------ .../stability_test_alanine_dipeptide.yaml | 2 +- guardowl/tests/stability_test_hipen.yaml | 4 +-- .../tests/stability_test_pure_liquid.yaml | 2 +- guardowl/tests/stability_test_waterbox.yaml | 2 +- guardowl/tests/test_stability_protocol.py | 25 +++++++------ scripts/alanine.yaml | 2 +- scripts/perform_stability_tests.py | 16 ++++----- scripts/test_config.yaml | 14 ++++---- 10 files changed, 47 insertions(+), 58 deletions(-) diff --git a/README.md b/README.md index 9af80dd..d4562f2 100644 --- a/README.md +++ b/README.md @@ -67,7 +67,7 @@ There is an example `test_config.yaml` file provided in the `scripts` directory For a stability test using a pure 15 Angstrom waterbox the `config.yaml` file may look like this ``` tests: - - protocol: "waterbox_protocol" # which protocol is performed + - protocol: "waterbox_test" # which protocol is performed edge_length: 15 # waterbox edge length in Angstrom ensemble: "NVT" # thermodynamic esamble that is used. Oter options are 'NpT' and 'NVE'. nnp: "ani2x" # the NNP used diff --git a/guardowl/protocols.py b/guardowl/protocols.py index 3758975..2dcdfa5 100644 --- a/guardowl/protocols.py +++ b/guardowl/protocols.py @@ -398,7 +398,7 @@ def perform_stability_test(self, parms: StabilityTestParameters) -> None: self._run_simulation(_parms, qsim) -def run_hipen_protocol( +def run_hipen_test( hipen_idx: Union[int, List[int]], nnp: str, temperature: Union[int, List[int]], @@ -438,15 +438,11 @@ def run_hipen_protocol( def _run_protocol(hipen_idx: int): name = list(TestsystemFactory._HIPEN_SYSTEMS.keys())[hipen_idx] - log.info( - f"Performing vacuum stability test for {name} using {nnp}." - ) + log.info(f"Performing vacuum stability test for {name} using {nnp}.") opt = SmallMoleculeVacuumOption(name) testsystem = TestsystemFactory().generate_testsystem(opt) - system = SystemFactory.initialize_system( - nnp, testsystem.topology - ) + system = SystemFactory.initialize_system(nnp, testsystem.topology) log_file_name = f"vacuum_{name}_{nnp}" # Select protocol based on whether temperature is a list or a single value @@ -482,7 +478,7 @@ def _run_protocol(hipen_idx: int): _run_protocol(idx) -def run_waterbox_protocol( +def run_waterbox_test( edge_length: int, ensemble: str, nnp: str, @@ -565,7 +561,7 @@ def run_waterbox_protocol( log.info(f"Simulation files saved to {output_folder}") -def run_pure_liquid_protocol( +def run_organic_liquid_test( molecule_name: Union[str, List[str]], nr_of_molecule: Union[int, List[int]], ensemble: str, @@ -627,14 +623,14 @@ def run_pure_liquid_protocol( opt = LiquidOption(name, nr_of_molecules) testsystem = TestsystemFactory().generate_testsystem(opt) - system = SystemFactory.initialize_system( - nnp, testsystem.topology - ) + system = SystemFactory.initialize_system(nnp, testsystem.topology) temperature_str = ( f"{temperature}K" if isinstance(temperature, int) else "multi-temp" ) - log_file_name = f"pure_liquid_{name}_{nr_of_molecules}_{nnp}_{ensemble}_{temperature_str}" + log_file_name = ( + f"pure_liquid_{name}_{nr_of_molecules}_{nnp}_{ensemble}_{temperature_str}" + ) log.info(f"Simulation output will be written to {log_file_name}") @@ -662,7 +658,7 @@ def run_pure_liquid_protocol( from typing import Literal -def run_alanine_dipeptide_protocol( +def run_alanine_dipeptide_test( nnp: str, temperature: int, reporter: StateDataReporter, @@ -769,9 +765,7 @@ def run_DOF_scan( The name of the molecule for simulation, defaults to 'ethanol'. """ - log.info( - f"Initiating DOF scan for {name} using {nnp}." - ) + log.info(f"Initiating DOF scan for {name} using {nnp}.") from guardowl.protocols import BondProfileProtocol, DOFTestParameters from guardowl.testsystems import TestsystemFactory, SmallMoleculeVacuumOption @@ -926,9 +920,7 @@ def _above_threshold(mol: Chem.Mol) -> bool: continue # set the minimized positions reference_testsystem.positions = minimized_position - system = SystemFactory.initialize_system( - nnp, reference_testsystem.topology - ) + system = SystemFactory.initialize_system(nnp, reference_testsystem.topology) log_file_name = f"ref_{name}_{nnp}" params = MinimizationTestParameters( @@ -952,9 +944,7 @@ def _above_threshold(mol: Chem.Mol) -> bool: minimize_testsystem = reference_testsystem minimize_testsystem.positions = start_position - system = SystemFactory.initialize_system( - nnp, minimize_testsystem.topology - ) + system = SystemFactory.initialize_system(nnp, minimize_testsystem.topology) log_file_name = f"minimize_{name}_{nnp}" params = MinimizationTestParameters( diff --git a/guardowl/tests/stability_test_alanine_dipeptide.yaml b/guardowl/tests/stability_test_alanine_dipeptide.yaml index 1f8e391..a87d9d4 100644 --- a/guardowl/tests/stability_test_alanine_dipeptide.yaml +++ b/guardowl/tests/stability_test_alanine_dipeptide.yaml @@ -1,6 +1,6 @@ # config.yaml tests: - - protocol: "alanine_dipeptide_protocol" + - protocol: "alanine_dipeptide_test" env: "vacuum" ensemble: "npt" nnp: "ani2x" diff --git a/guardowl/tests/stability_test_hipen.yaml b/guardowl/tests/stability_test_hipen.yaml index 91dea8c..c2cc4f2 100644 --- a/guardowl/tests/stability_test_hipen.yaml +++ b/guardowl/tests/stability_test_hipen.yaml @@ -1,7 +1,7 @@ # config.yaml tests: - - protocol: "hipen_protocol" - hipen_idx: [0,1] + - protocol: "hipen_test" + hipen_idx: [0, 1] nnp: "ani2x" temperature: 300 nr_of_simulation_steps: 5 diff --git a/guardowl/tests/stability_test_pure_liquid.yaml b/guardowl/tests/stability_test_pure_liquid.yaml index b9154a1..b5f1bfe 100644 --- a/guardowl/tests/stability_test_pure_liquid.yaml +++ b/guardowl/tests/stability_test_pure_liquid.yaml @@ -1,6 +1,6 @@ # config.yaml tests: - - protocol: "pure_liquid_protocol" + - protocol: "organic_liquid_test" molecule_name: ["ethane", "butane"] nr_of_molecule: [10, 20] ensemble: "npt" diff --git a/guardowl/tests/stability_test_waterbox.yaml b/guardowl/tests/stability_test_waterbox.yaml index 5273161..e7f4d87 100644 --- a/guardowl/tests/stability_test_waterbox.yaml +++ b/guardowl/tests/stability_test_waterbox.yaml @@ -1,6 +1,6 @@ # config.yaml tests: - - protocol: "waterbox_protocol" + - protocol: "waterbox_test" edge_length: 5 ensemble: "npt" nnp: "ani2x" diff --git a/guardowl/tests/test_stability_protocol.py b/guardowl/tests/test_stability_protocol.py index 8c37578..1722974 100644 --- a/guardowl/tests/test_stability_protocol.py +++ b/guardowl/tests/test_stability_protocol.py @@ -78,7 +78,7 @@ def test_setup_vacuum_protocol_individual_parts( @pytest.mark.parametrize("params", get_available_nnps()) def test_run_vacuum_protocol(params: Dict[str, Tuple[str, int, float]]) -> None: - from guardowl.protocols import run_hipen_protocol + from guardowl.protocols import run_hipen_test reporter = StateDataReporter( file=None, # it is necessary to set this to None since it otherwise can't be passed to mp @@ -95,7 +95,7 @@ def test_run_vacuum_protocol(params: Dict[str, Tuple[str, int, float]]) -> None: output_folder = "test_stability_protocol" nnp_instance = PotentialFactory().initialize_potential(params) - run_hipen_protocol( + run_hipen_test( 1, nnp_instance, 300, @@ -108,7 +108,7 @@ def test_run_vacuum_protocol(params: Dict[str, Tuple[str, int, float]]) -> None: @pytest.mark.parametrize("ensemble", ["NVE", "NVT", "NpT"]) @pytest.mark.parametrize("params", get_available_nnps()) -def test_setup_waterbox_protocol_individual_parts( +def test_setup_waterbox_test_individual_parts( ensemble: str, params: Dict[str, Tuple[str, int, float]], temperature: int = 300 ) -> None: """Test if we can run a simulation for a number of steps""" @@ -120,7 +120,6 @@ def test_setup_waterbox_protocol_individual_parts( testsystem = TestsystemFactory().generate_testsystem(opt) nnp_instance = PotentialFactory().initialize_potential(params) - system = SystemFactory().initialize_system( nnp_instance, testsystem.topology, @@ -168,10 +167,10 @@ def test_setup_waterbox_protocol_individual_parts( @pytest.mark.parametrize("ensemble", ["NVE", "NVT", "NpT"]) @pytest.mark.parametrize("params", get_available_nnps()) -def test_run_waterbox_protocol( +def test_run_waterbox_test( ensemble: str, params: Dict[str, Tuple[str, int, float]] ) -> None: - from guardowl.protocols import run_waterbox_protocol + from guardowl.protocols import run_waterbox_test reporter = StateDataReporter( file=None, # it is necessary to set this to None since it otherwise can't be passed to mp @@ -188,7 +187,7 @@ def test_run_waterbox_protocol( output_folder = "test_stability_protocol" nnp_instance = PotentialFactory().initialize_potential(params) - run_waterbox_protocol( + run_waterbox_test( 5, ensemble, nnp_instance, @@ -204,10 +203,10 @@ def test_run_waterbox_protocol( @pytest.mark.parametrize("environment", ["vacuum", "solution"]) @pytest.mark.parametrize("ensemble", ["NVE", "NVT", "NpT"]) @pytest.mark.parametrize("params", get_available_nnps()) -def test_run_alanine_dipeptide_protocol( +def test_run_alanine_dipeptide_test( environment: str, ensemble: str, params: Dict[str, Tuple[str, int, float]] ) -> None: - from guardowl.protocols import run_alanine_dipeptide_protocol + from guardowl.protocols import run_alanine_dipeptide_test reporter = StateDataReporter( file=None, # it is necessary to set this to None since it otherwise can't be passed to mp @@ -223,7 +222,7 @@ def test_run_alanine_dipeptide_protocol( platform = get_fastest_platform() output_folder = "test_stability_protocol" nnp_instance = PotentialFactory().initialize_potential(params) - run_alanine_dipeptide_protocol( + run_alanine_dipeptide_test( nnp_instance, 300, reporter, @@ -237,10 +236,10 @@ def test_run_alanine_dipeptide_protocol( @pytest.mark.parametrize("ensemble", ["NVE", "NVT", "NpT"]) @pytest.mark.parametrize("params", get_available_nnps()) -def test_run_pure_liquid_protocol( +def test_run_organic_liquid_test( ensemble: str, params: Dict[str, Tuple[str, int, float]] ) -> None: - from guardowl.protocols import run_pure_liquid_protocol + from guardowl.protocols import run_organic_liquid_test reporter = StateDataReporter( file=None, # it is necessary to set this to None since it otherwise can't be passed to mp @@ -258,7 +257,7 @@ def test_run_pure_liquid_protocol( output_folder = "test_stability_protocol" nnp_instance = PotentialFactory().initialize_potential(params) - run_pure_liquid_protocol( + run_organic_liquid_test( nnp=nnp_instance, temperature=300, reporter=reporter, diff --git a/scripts/alanine.yaml b/scripts/alanine.yaml index 0aef60e..a059180 100644 --- a/scripts/alanine.yaml +++ b/scripts/alanine.yaml @@ -1,6 +1,6 @@ # config.yaml tests: - - protocol: "perform_alanine_dipeptide_protocol" + - protocol: "perform_alanine_dipeptide_test" env: "solution" ensemble: "npt" nnp: "ani2x" diff --git a/scripts/perform_stability_tests.py b/scripts/perform_stability_tests.py index e4d5f56..d433e0c 100644 --- a/scripts/perform_stability_tests.py +++ b/scripts/perform_stability_tests.py @@ -139,17 +139,17 @@ def process_test(test: Dict[str, Any], platform: Platform, output: str) -> None: """ from guardowl.protocols import ( run_DOF_scan, - run_hipen_protocol, - run_waterbox_protocol, - run_alanine_dipeptide_protocol, - run_pure_liquid_protocol, + run_hipen_test, + run_waterbox_test, + run_alanine_dipeptide_test, + run_organic_liquid_test, ) protocol_function = { - "hipen_protocol": run_hipen_protocol, - "waterbox_protocol": run_waterbox_protocol, - "alanine_dipeptide_protocol": run_alanine_dipeptide_protocol, - "pure_liquid_protocol": run_pure_liquid_protocol, + "hipen_test": run_hipen_test, + "waterbox_test": run_waterbox_test, + "alanine_dipeptide_test": run_alanine_dipeptide_test, + "organic_liquid_test": run_organic_liquid_test, "DOF_scan": run_DOF_scan, }.get(test.get("protocol")) diff --git a/scripts/test_config.yaml b/scripts/test_config.yaml index daf1ca1..f2e3c49 100644 --- a/scripts/test_config.yaml +++ b/scripts/test_config.yaml @@ -1,7 +1,7 @@ # config.yaml potentials: - physicsml-model: - - model_name: 'MACE' + - model_name: "MACE" - precision: 64 - position_scaling: 10.0 - output_scaling: 4.184 * 627 @@ -11,7 +11,7 @@ potentials: - model_name: "ANI2x" tests: - - protocol: "alanine_dipeptide_protocol" + - protocol: "alanine_dipeptide_test" env: "solution" ensemble: "npt" nnp: "ani2x" @@ -19,7 +19,7 @@ tests: nr_of_simulation_steps: 50 temperature: 300 - - protocol: "alanine_dipeptide_protocol" + - protocol: "alanine_dipeptide_test" env: "vacuum" ensemble: "npt" nnp: "ani2x" @@ -27,13 +27,13 @@ tests: nr_of_simulation_steps: 500 temperature: 300 - - protocol: "hipen_protocol" + - protocol: "hipen_test" hipen_idx: [0, 1, 15] nnp: "ani2x" temperature: [300, 400, 500] nr_of_simulation_steps: 500 - - protocol: "waterbox_protocol" + - protocol: "waterbox_test" edge_length: 25 ensemble: "npt" nnp: "ani2x" @@ -41,7 +41,7 @@ tests: nr_of_simulation_steps: 50 temperature: 300 - - protocol: "waterbox_protocol" + - protocol: "waterbox_test" edge_length: 25 ensemble: "npt" nnp: "ani2x" @@ -49,7 +49,7 @@ tests: nr_of_simulation_steps: 50 temperature: 500 - - protocol: "pure_liquid_protocol" + - protocol: "organic_liquid_test" molecule_name: ["ethane", "butane", "methanol"] nr_of_molecule: [100, 200, 300] ensemble: "npt"