Add mdout file to output_settings

OpenFreeEnergy · Oct 1, 2024 · db009fe · db009fe
1 parent b546e01
commit db009fe
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Showing 7 changed files with 31 additions and 10 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -26,12 +26,7 @@ repos:
   hooks:
   - id: flake8
     files: ^openfe_gromacs
-    additional_dependencies: [
-        'flake8-bugbear',
-        'flake8-absolute-import',
-        'flake8-pytest-style==2',
-        'flake8-no-pep420',
-    ]
+    additional_dependencies: [Flake8-pyproject]
 - repo: https://github.com/asottile/pyupgrade
   rev: 'v3.17.0'
   hooks:

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -168,6 +168,7 @@ def get_filenames_em(self) -> dict[str, list[pathlib.Path]]:
         - "edr_em"
         - "log_em"
         - "cpt_em"
+        - "grompp_mdp_em"
 
         Returns
         -------
@@ -183,6 +184,7 @@ def get_filenames_em(self) -> dict[str, list[pathlib.Path]]:
             "edr_em",
             "log_em",
             "cpt_em",
+            "grompp_mdp_em",
         ]
         dict_npt = {}
         for file in file_keys:
@@ -231,6 +233,7 @@ def get_filenames_nvt(self) -> dict[str, list[pathlib.Path]]:
         - "edr_nvt"
         - "log_nvt"
         - "cpt_nvt"
+        - "grompp_mdp_nvt"
 
         Returns
         -------
@@ -246,6 +249,7 @@ def get_filenames_nvt(self) -> dict[str, list[pathlib.Path]]:
             "edr_nvt",
             "log_nvt",
             "cpt_nvt",
+            "grompp_mdp_nvt",
         ]
         dict_npt = {}
         for file in file_keys:
@@ -294,6 +298,7 @@ def get_filenames_npt(self) -> dict[str, list[pathlib.Path]]:
         - "edr_npt"
         - "log_npt"
         - "cpt_npt"
+        - "grompp_mdp_npt"
 
         Returns
         -------
@@ -309,6 +314,7 @@ def get_filenames_npt(self) -> dict[str, list[pathlib.Path]]:
             "edr_npt",
             "log_npt",
             "cpt_npt",
+            "grompp_mdp_em",
         ]
         dict_npt = {}
         for file in file_keys:
@@ -403,6 +409,7 @@ def _default_settings(cls):
             engine_settings=GromacsEngineSettings(),
             output_settings_em=EMOutputSettings(
                 mdp_file="em.mdp",
+                grompp_mdp_file="mdout_em.mdp",
                 tpr_file="em.tpr",
                 gro_file="em.gro",
                 trr_file="em.trr",
@@ -413,6 +420,7 @@ def _default_settings(cls):
             ),
             output_settings_nvt=NVTOutputSettings(
                 mdp_file="nvt.mdp",
+                grompp_mdp_file="mdout_nvt.mdp",
                 tpr_file="nvt.tpr",
                 gro_file="nvt.gro",
                 trr_file="nvt.trr",
@@ -423,6 +431,7 @@ def _default_settings(cls):
             ),
             output_settings_npt=NPTOutputSettings(
                 mdp_file="npt.mdp",
+                grompp_mdp_file="mdout_npt.mdp",
                 tpr_file="npt.tpr",
                 gro_file="npt.gro",
                 trr_file="npt.trr",
@@ -735,6 +744,7 @@ def _run_gromacs(
         cpt: str,
         log: str,
         edr: str,
+        out_mdp: str,
         engine_settings: GromacsEngineSettings,
         shared_basebath: pathlib.Path,
     ):
@@ -754,6 +764,7 @@ def _run_gromacs(
         cpt: str
         log: str
         edr: str
+        out_mdp: str
         engine_settings: GromacsEngineSettings
         shared_basebath: Pathlike, optional
           Where to run the calculation, defaults to current working directory
@@ -773,6 +784,8 @@ def _run_gromacs(
                 top,
                 "-o",
                 tpr,
+                "-po",
+                shared_basebath / out_mdp,
             ],
             stdin=subprocess.PIPE,
         )
@@ -894,6 +907,7 @@ def _execute(
                 output_settings_em.cpt_file,
                 output_settings_em.log_file,
                 output_settings_em.edr_file,
+                output_settings_em.grompp_mdp_file,
                 engine_settings,
                 ctx.shared,
             )
@@ -904,6 +918,7 @@ def _execute(
             output_dict["edr_em"] = shared_basepath / output_settings_em.edr_file
             output_dict["log_em"] = shared_basepath / output_settings_em.log_file
             output_dict["cpt_em"] = shared_basepath / output_settings_em.cpt_file
+            output_dict["grompp_mdp_em"] = shared_basepath / output_settings_em.grompp_mdp_file
 
         # ToDo: Should we disallow running MD without EM?
         # Run NVT
@@ -929,6 +944,7 @@ def _execute(
                 output_settings_nvt.cpt_file,
                 output_settings_nvt.log_file,
                 output_settings_nvt.edr_file,
+                output_settings_nvt.grompp_mdp_file,
                 engine_settings,
                 ctx.shared,
             )
@@ -939,6 +955,7 @@ def _execute(
             output_dict["edr_nvt"] = shared_basepath / output_settings_nvt.edr_file
             output_dict["log_nvt"] = shared_basepath / output_settings_nvt.log_file
             output_dict["cpt_nvt"] = shared_basepath / output_settings_nvt.cpt_file
+            output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file
 
         # Run NPT MD simulation
         if sim_settings_npt.nsteps > 0:
@@ -967,6 +984,7 @@ def _execute(
                 output_settings_npt.cpt_file,
                 output_settings_npt.log_file,
                 output_settings_npt.edr_file,
+                output_settings_npt.grompp_mdp_file,
                 engine_settings,
                 ctx.shared,
             )
@@ -977,5 +995,6 @@ def _execute(
             output_dict["edr_npt"] = shared_basepath / output_settings_npt.edr_file
             output_dict["log_npt"] = shared_basepath / output_settings_npt.log_file
             output_dict["cpt_npt"] = shared_basepath / output_settings_npt.cpt_file
+            output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file
 
         return output_dict
diff --git a/openfe_gromacs/protocols/gromacs_md/md_settings.py b/openfe_gromacs/protocols/gromacs_md/md_settings.py
@@ -265,6 +265,12 @@ class OutputSettings(SettingsBaseModel):
     Filename for the mdp file for running simulations in Gromacs.
     Default 'em.mdp'
     """
+    grompp_mdp_file: str = "mdout_em.mdp"
+    """
+    Filename for the mdp file that gmx grompp outputs. This file contains 
+    comment lines, as well as the input that gmx grompp has read.
+    Default 'mdout_em.mdp'
+    """
     tpr_file: str = "em.tpr"
     """
     Filename for the tpr file for running simulations in Gromacs.

diff --git a/openfe_gromacs/protocols/gromacs_utils/write_mdp.py b/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
@@ -56,6 +56,7 @@ def dict2mdp(settings_dict: dict, shared_basepath):
     non_mdps = [
         "forcefield_cache",
         "mdp_file",
+        "grompp_mdp_file",
         "tpr_file",
         "trr_file",
         "xtc_file",

diff --git a/openfe_gromacs/tests/data/MDProtocol_json_results.gz b/openfe_gromacs/tests/data/MDProtocol_json_results.gz
diff --git a/openfe_gromacs/tests/data/MDProtocol_json_results_no_EM.gz b/openfe_gromacs/tests/data/MDProtocol_json_results_no_EM.gz
diff --git a/openfe_gromacs/tests/protocols/test_gromacs_md.py b/openfe_gromacs/tests/protocols/test_gromacs_md.py
@@ -243,7 +243,7 @@ def test_get_mdp_filenames(self, protocolresult):
     def test_get_filenames_em(self, protocolresult):
         dict_file_path = protocolresult.get_filenames_em()
         assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
+        assert len(dict_file_path) == 8
         for name, file_path in dict_file_path.items():
             assert isinstance(file_path, list)
             assert len(file_path) == 1
@@ -264,7 +264,7 @@ def test_get_xtc_em_filename(self, protocolresult):
     def test_get_filenames_nvt(self, protocolresult):
         dict_file_path = protocolresult.get_filenames_nvt()
         assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
+        assert len(dict_file_path) == 8
         for name, file_path in dict_file_path.items():
             assert isinstance(file_path, list)
             assert len(file_path) == 1
@@ -285,7 +285,7 @@ def test_get_xtc_nvt_filenames(self, protocolresult):
     def test_get_filenames_npt(self, protocolresult):
         dict_file_path = protocolresult.get_filenames_npt()
         assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
+        assert len(dict_file_path) == 8
         for name, file_path in dict_file_path.items():
             assert isinstance(file_path, list)
             assert len(file_path) == 1
@@ -323,7 +323,7 @@ def test_reload_protocol_result(self, md_json_no_em):
     def test_get_filenames_em(self, protocolresult):
         dict_file_path = protocolresult.get_filenames_em()
         assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
+        assert len(dict_file_path) == 8
         for name, file_path in dict_file_path.items():
             assert isinstance(file_path, type(None))