bugfix (#21)

* bugfix * adding list * moving paramters out of protocolls * remove parameters from protocol module --------- Co-authored-by: wiederm <[email protected]>
Exscientia · Nov 7, 2023 · 6ad91f5 · 6ad91f5
1 parent c02f78e
commit 6ad91f5
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Showing 4 changed files with 112 additions and 82 deletions.
diff --git a/guardowl/parameters.py b/guardowl/parameters.py
@@ -0,0 +1,79 @@
+from dataclasses import dataclass, field
+from openmm import Platform, System, unit
+from openmm.app import StateDataReporter
+from openmmtools.testsystems import TestSystem
+from typing import List, Union, Optional
+
+
+@dataclass
+class BaseParameters:
+    system: System
+    platform: Platform
+    testsystem: TestSystem
+    output_folder: str
+    log_file_name: str
+
+
+@dataclass
+class MinimizationTestParameters(BaseParameters):
+    convergence_criteria: unit.Quantity = field(default_factory=1.0 * unit.kilojoule_per_mole / unit.nanometer)
+
+
+@dataclass
+class StabilityTestParameters(BaseParameters):
+    """Parameters for a stability test.
+
+    Parameters are stored as attributes.
+
+    Attributes
+    ----------
+    protocol_length : int
+        Length of the protocol in time units.
+    temperature : unit.Quantity
+        Temperature of the simulation.
+    ensemble : str
+        Ensemble type ('NVT', 'NPT', etc.).
+    simulated_annealing : bool
+        Whether simulated annealing is to be used.
+    system : System
+        The OpenMM System object.
+    platform : Platform
+        The OpenMM Platform object.
+    testsystem : TestSystem
+        The test system for the simulation.
+    output_folder : str
+        Path to the output folder.
+    log_file_name : str
+        Name of the log file.
+    state_data_reporter : StateDataReporter
+        The OpenMM StateDataReporter object.
+    """
+
+    protocol_length: int
+    temperature: Union[int, List[int]]
+    env: str
+    simulated_annealing: bool
+    state_data_reporter: StateDataReporter
+    device_index: int = 0
+    ensemble: Optional[str] = None
+
+
+@dataclass
+class DOFTestParameters(BaseParameters):
+    """Parameters for a degree of freedom (DOF) test.
+
+    In addition to attributes in StabilityTestParameters, extra attributes for DOF tests are included.
+
+    Attributes
+    ----------
+    bond : List
+        List of atom pairs to be considered as bonds.
+    angle : List
+        List of atom triplets to be considered as angles.
+    torsion : List
+        List of atom quartets to be considered as torsions.
+    """
+
+    bond: List = field(default_factory=lambda: [])
+    angle: List = field(default_factory=lambda: [])
+    torsion: List = field(default_factory=lambda: [])
diff --git a/guardowl/protocols.py b/guardowl/protocols.py
@@ -14,6 +14,11 @@
 from openmmtools.testsystems import TestSystem
 
 from .simulation import SimulationFactory
+from .parameters import (
+    StabilityTestParameters,
+    DOFTestParameters,
+    MinimizationTestParameters,
+)
 
 
 def initialize_ml_system(nnp: str, topology: Topology, implementation: str) -> System:
@@ -89,75 +94,6 @@ def report(self, simulation: Simulation, state: State) -> None:
         self._out.flush()
 
 
-@dataclass
-class BaseParameters:
-    system: System
-    platform: Platform
-    testsystem: TestSystem
-    output_folder: str
-    log_file_name: str
-
-
-@dataclass
-class StabilityTestParameters(BaseParameters):
-    """Parameters for a stability test.
-
-    Parameters are stored as attributes.
-
-    Attributes
-    ----------
-    protocol_length : int
-        Length of the protocol in time units.
-    temperature : unit.Quantity
-        Temperature of the simulation.
-    ensemble : str
-        Ensemble type ('NVT', 'NPT', etc.).
-    simulated_annealing : bool
-        Whether simulated annealing is to be used.
-    system : System
-        The OpenMM System object.
-    platform : Platform
-        The OpenMM Platform object.
-    testsystem : TestSystem
-        The test system for the simulation.
-    output_folder : str
-        Path to the output folder.
-    log_file_name : str
-        Name of the log file.
-    state_data_reporter : StateDataReporter
-        The OpenMM StateDataReporter object.
-    """
-
-    protocol_length: int
-    temperature: Union[int, List[int]]
-    env: str
-    simulated_annealing: bool
-    state_data_reporter: StateDataReporter
-    device_index: int = 0
-    ensemble: Optional[str] = None
-
-
-@dataclass
-class DOFTestParameters(BaseParameters):
-    """Parameters for a degree of freedom (DOF) test.
-
-    In addition to attributes in StabilityTestParameters, extra attributes for DOF tests are included.
-
-    Attributes
-    ----------
-    bond : List
-        List of atom pairs to be considered as bonds.
-    angle : List
-        List of atom triplets to be considered as angles.
-    torsion : List
-        List of atom quartets to be considered as torsions.
-    """
-
-    bond: List = field(default_factory=lambda: [])
-    angle: List = field(default_factory=lambda: [])
-    torsion: List = field(default_factory=lambda: [])
-
-
 class DOFTest(ABC):
     """Abstract base class for DOF tests.
 
@@ -609,7 +545,7 @@ def perform_stability_test(self, parms: StabilityTestParameters) -> None:
             )
         for temperature in parms.temperature:
             parms.log_file_name = f"{log_file_name_}_{temperature}"
-            log.info('Running simulation at temperature: {temperature} K')
+            log.info("Running simulation at temperature: {temperature} K")
             self._run_simulation(
                 parms,
                 temperature * unit.kelvin,
@@ -637,7 +573,7 @@ def run_hipen_protocol(
     """
     from guardowl.testsystems import HipenTestsystemFactory, hipen_systems
 
-    def _run_protocol(idx: int):
+    def _run_protocol(hipen_idx: int):
         name = list(hipen_systems.keys())[hipen_idx]
 
         print(

diff --git 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
+    hipen_idx: [0,1]
     nnp: "ani2x"
     implementation: "torchani"
     temperature: 300

diff --git a/scripts/test_config.yaml b/scripts/test_config.yaml
@@ -1,7 +1,16 @@
 # config.yaml
 tests:
   - protocol: "perform_alanine_dipeptide_protocol"
-    env: "solvent"
+    env: "solution"
+    ensemble: "npt"
+    nnp: "ani2x"
+    implementation: "torchani"
+    annealing: false
+    nr_of_simulation_steps: 50_000
+    temperature: 300
+
+  - protocol: "perform_alanine_dipeptide_protocol"
+    env: "vacuum"
     ensemble: "npt"
     nnp: "ani2x"
     implementation: "torchani"
@@ -10,7 +19,8 @@ tests:
     temperature: 300
 
   - protocol: "hipen_protocol"
-    hipen_idx: [0,1,2,3,4,5,6,7,8,9]
+    hipen_idx:
+      [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]
     nnp: "ani2x"
     implementation: "torchani"
     temperature: 300
@@ -21,28 +31,33 @@ tests:
     nnp: "ani2x"
     implementation: "nnpops"
     temperature: [300, 400, 500]
-    nr_of_simulation_steps: 100_000
+    nr_of_simulation_steps: 1_000_000
 
   - protocol: "waterbox_protocol"
-    edge_length: 15
+    edge_length: 30
     ensemble: "NVT"
     nnp: "ani2x"
     implementation: "nnpops"
     annealing: false
-    nr_of_simulation_steps: 50_000
+    nr_of_simulation_steps: 500_000
     temperature: 300
 
   - protocol: "waterbox_protocol"
-    edge_length: 15
+    edge_length: 30
     ensemble: "npt"
     nnp: "ani2x"
     implementation: "nnpops"
     annealing: false
-    nr_of_simulation_steps: 50_000
+    nr_of_simulation_steps: 500_000
     temperature: 300
 
-  - protocol: "perform_DOF_scan"
+  - protocol: "perform_pure_liquid_protocol"
+    molecule_name: ["ethane", "butane"]
+    nr_of_molecule: [100, 200]
+    ensemble: "npt"
     nnp: "ani2x"
     implementation: "torchani"
-    DOF_definition: { "bond": [0, 2] }
-    molecule_name: "ethanol"
+    annealing: false
+    nr_of_simulation_steps: 500_000
+    nr_of_equilibration_steps: 5_000
+    temperature: 300