Merge pull request #23 from OpenFreeEnergy/remove_engine_settings

Remove OpenMMEngineSettings and create GromacsEngineSettings

openfe_gromacs/protocols/gromacs_md/md_methods.py

@@ -42,14 +42,14 @@
     EMOutputSettings,
     EMSimulationSettings,
     FFSettingsOpenMM,
+    GromacsEngineSettings,
     GromacsMDProtocolSettings,
     IntegratorSettings,
     NPTOutputSettings,
     NPTSimulationSettings,
     NVTOutputSettings,
     NVTSimulationSettings,
     OpenFFPartialChargeSettings,
-    OpenMMEngineSettings,
     OpenMMSolvationSettings,
 )
 
@@ -114,7 +114,6 @@ def _dict2mdp(settings_dict: dict, shared_basepath):
         "edr_file",
         "log_file",
         "cpt_file",
-        "ntomp",
     ]
     for setting in non_mdps:
         settings_dict.pop(setting)
@@ -483,7 +482,6 @@ def _default_settings(cls):
             ),
             partial_charge_settings=OpenFFPartialChargeSettings(),
             solvation_settings=OpenMMSolvationSettings(),
-            engine_settings=OpenMMEngineSettings(),
             integrator_settings=IntegratorSettings(),
             simulation_settings_em=EMSimulationSettings(
                 integrator="steep",
@@ -499,6 +497,7 @@ def _default_settings(cls):
                 pcoupl="C-rescale",
                 gen_vel="no",  # If continuation from NVT simulation
             ),
+            engine_settings=GromacsEngineSettings(),
             output_settings_em=EMOutputSettings(
                 mdp_file="em.mdp",
                 tpr_file="em.tpr",
@@ -990,7 +989,7 @@ def _run_gromacs(
         cpt: str,
         log: str,
         edr: str,
-        ntomp: int,
+        engine_settings: GromacsEngineSettings,
         shared_basebath: pathlib.Path,
     ):
         """
@@ -1009,6 +1008,7 @@ def _run_gromacs(
         :param cpt: str
         :param log: str
         :param edr: str
+        :param engine_settings: GromacsEngineSettings
         :param shared_basebath: Pathlike, optional
           Where to run the calculation, defaults to current working directory
         """
@@ -1053,7 +1053,17 @@ def _run_gromacs(
                 "-ntmpi",
                 "1",
                 "-ntomp",
-                str(ntomp),
+                str(engine_settings.ntomp),
+                "-pme",
+                str(engine_settings.pme),
+                "-pmefft",
+                str(engine_settings.pmefft),
+                "-bonded",
+                str(engine_settings.bonded),
+                "-nb",
+                str(engine_settings.nb),
+                "-update",
+                str(engine_settings.update),
             ],
             stdin=subprocess.PIPE,
             cwd=shared_basebath,
@@ -1105,6 +1115,7 @@ def _execute(
         sim_settings_npt: NPTSimulationSettings = (
             protocol_settings.simulation_settings_npt
         )
+        engine_settings: GromacsEngineSettings = protocol_settings.engine_settings
         output_settings_em: EMOutputSettings = protocol_settings.output_settings_em
         output_settings_nvt: NVTOutputSettings = protocol_settings.output_settings_nvt
         output_settings_npt: NPTOutputSettings = protocol_settings.output_settings_npt
@@ -1131,7 +1142,7 @@ def _execute(
                 output_settings_em.cpt_file,
                 output_settings_em.log_file,
                 output_settings_em.edr_file,
-                sim_settings_em.ntomp,
+                engine_settings,
                 ctx.shared,
             )
 
@@ -1159,7 +1170,7 @@ def _execute(
                 output_settings_nvt.cpt_file,
                 output_settings_nvt.log_file,
                 output_settings_nvt.edr_file,
-                sim_settings_nvt.ntomp,
+                engine_settings,
                 ctx.shared,
             )
 
@@ -1190,7 +1201,7 @@ def _execute(
                 output_settings_npt.cpt_file,
                 output_settings_npt.log_file,
                 output_settings_npt.edr_file,
-                sim_settings_npt.ntomp,
+                engine_settings,
                 ctx.shared,
             )
 

openfe_gromacs/protocols/gromacs_md/md_settings.py

@@ -9,12 +9,10 @@
 """
 from typing import Literal, Optional
 
-import pint
 from gufe.settings import OpenMMSystemGeneratorFFSettings, SettingsBaseModel
 from openfe.protocols.openmm_utils.omm_settings import (
     IntegratorSettings,
     OpenFFPartialChargeSettings,
-    OpenMMEngineSettings,
     OpenMMSolvationSettings,
     Settings,
 )
@@ -206,12 +204,6 @@ class Config:
     Number of iterations to correct for rotational lengthening in LINCS.
     Default 1.
     """
-    ntomp: int = 1
-    """
-    Number of threads to be used for OpenMP multithreading.
-    GROMACS must be compiled with OpenMP support if a value greater than 1 is
-    set here.
-    """
 
     @validator(
         "nsteps",
@@ -673,6 +665,46 @@ def has_no_constraints(cls, v):
         return v
 
 
+class GromacsEngineSettings(SettingsBaseModel):
+    """
+    MD engine settings for running simulations in Gromacs.
+    """
+
+    ntomp: int = 1
+    """
+    Number of threads to be used for OpenMP multithreading.
+    GROMACS must be compiled with OpenMP support if a value greater than 1 is
+    set here.
+    """
+    pme: Literal["auto", "cpu", "gpu"] = "auto"
+    """
+    Perform PME calculations on: auto, cpu, gpu. Default: "auto"
+    """
+    pmefft: Literal["auto", "cpu", "gpu"] = "auto"
+    """
+    Perform PME FFT calculations on: auto, cpu, gpu. Default: "auto"
+    """
+    bonded: Literal["auto", "cpu", "gpu"] = "auto"
+    """
+    Perform bonded calculations on: auto, cpu, gpu. Default: "auto"
+    """
+    nb: Literal["auto", "cpu", "gpu"] = "auto"
+    """
+    Calculate non-bonded interactions on: auto, cpu, gpu. Default: "auto"
+    """
+    update: Literal["auto", "cpu", "gpu"] = "auto"
+    """
+    Perform update and constraints on: auto, cpu, gpu. Default: "auto"
+    """
+
+    @validator("ntomp")
+    def must_be_positive(cls, v):
+        if v <= 0:
+            errmsg = f"ntomp must be positive values, " f"got {v}."
+            raise ValueError(errmsg)
+        return v
+
+
 class GromacsMDProtocolSettings(Settings):
     class Config:
         arbitrary_types_allowed = True
@@ -693,22 +725,20 @@ def must_be_positive(cls, v):
     gro: str
     top: str
 
-    # Things for creating the OpenMM systems
+    # Settings for creating the OpenMM systems
     forcefield_settings: FFSettingsOpenMM
     partial_charge_settings: OpenFFPartialChargeSettings
     solvation_settings: OpenMMSolvationSettings
-
-    # MD Engine things
-    engine_settings: OpenMMEngineSettings
-
-    # Sampling State defining things
     integrator_settings: IntegratorSettings
 
     # Simulation run settings
     simulation_settings_em: EMSimulationSettings
     simulation_settings_nvt: NVTSimulationSettings
     simulation_settings_npt: NPTSimulationSettings
 
+    # Gromacs run/engine settings
+    engine_settings: GromacsEngineSettings
+
     # Simulations output settings
     output_settings_em: EMOutputSettings
     output_settings_nvt: NVTOutputSettings

openfe_gromacs/tests/protocols/test_md_tokenization.py

@@ -41,7 +41,7 @@ def protocol_result(md_json):
 
 class TestGromacsMDProtocol(GufeTokenizableTestsMixin):
     cls = gromacs_md.GromacsMDProtocol
-    key = "GromacsMDProtocol-76fa290de019030035f2010e9155f57f"
+    key = "GromacsMDProtocol-dac6fd8b3fa26dcff42763515a67f557"
     repr = f"<{key}>"
 
     @pytest.fixture()
@@ -64,7 +64,7 @@ def test_key_stable(self):
 
 class TestGromacsMDProtocolResult(GufeTokenizableTestsMixin):
     cls = gromacs_md.GromacsMDProtocolResult
-    key = "GromacsMDProtocolResult-4739ae9a56f36a1e7c95c503601769f4"
+    key = "GromacsMDProtocolResult-d11eb101c28e59af5150ec45e1961e4d"
     repr = f"<{key}>"
 
     @pytest.fixture()