Save input configuration

janus_core/cli/descriptors.py

@@ -79,8 +79,7 @@ def descriptors(
     calc_per_atom
         Whether to calculate descriptors for each atom. Default is False.
     arch
-        MLIP architecture to use for single point calculations.
-        Default is "mace_mp".
+        MLIP architecture to use for calculations. Default is "mace_mp".
     device
         Device to run model on. Default is "cpu".
     model_path
@@ -111,8 +110,9 @@ def descriptors(
         carbon_summary,
         check_config,
         end_summary,
+        get_config,
+        get_struct_info,
         parse_typer_dicts,
-        save_struct_calc,
         start_summary,
     )
 
@@ -127,6 +127,14 @@ def descriptors(
     if "filename" in write_kwargs:
         raise ValueError("'filename' must be passed through the --out option")
 
+    # Set initial config
+    all_kwargs = {
+        "read_kwargs": read_kwargs.copy(),
+        "calc_kwargs": calc_kwargs.copy(),
+        "write_kwargs": write_kwargs.copy(),
+    }
+    config = get_config(params=ctx.params, all_kwargs=all_kwargs)
+
     # Set default filname for writing structure with descriptors if not specified
     if out:
         write_kwargs["filename"] = out
@@ -162,24 +170,14 @@ def descriptors(
     ).absolute()
     log = descript.log_kwargs["filename"]
 
-    # Store inputs for yaml summary
-    inputs = descriptors_kwargs.copy()
-
     # Add structure, MLIP information, and log to inputs
-    save_struct_calc(
-        inputs=inputs,
+    info = get_struct_info(
         struct=descript.struct,
         struct_path=struct,
-        arch=arch,
-        device=device,
-        model_path=model_path,
-        read_kwargs=read_kwargs,
-        calc_kwargs=calc_kwargs,
-        log=log,
     )
 
     # Save summary information before calculation begins
-    start_summary(command="descriptors", summary=summary, inputs=inputs)
+    start_summary(command="descriptors", summary=summary, config=config, info=info)
 
     # Calculate descriptors
     descript.run()

janus_core/cli/eos.py

@@ -143,8 +143,9 @@ def eos(
         carbon_summary,
         check_config,
         end_summary,
+        get_config,
+        get_struct_info,
         parse_typer_dicts,
-        save_struct_calc,
         set_read_kwargs_index,
         start_summary,
     )
@@ -160,6 +161,15 @@ def eos(
     if eos_type not in get_args(EoSNames):
         raise ValueError(f"Fit type must be one of: {get_args(EoSNames)}")
 
+    # Set initial config
+    all_kwargs = {
+        "read_kwargs": read_kwargs.copy(),
+        "calc_kwargs": calc_kwargs.copy(),
+        "minimize_kwargs": minimize_kwargs.copy(),
+        "write_kwargs": write_kwargs.copy(),
+    }
+    config = get_config(params=ctx.params, all_kwargs=all_kwargs)
+
     # Read only first structure by default and ensure only one image is read
     set_read_kwargs_index(read_kwargs)
 
@@ -205,24 +215,14 @@ def eos(
     ).absolute()
     log = equation_of_state.log_kwargs["filename"]
 
-    # Store inputs for yaml summary
-    inputs = eos_kwargs.copy()
-
     # Add structure, MLIP information, and log to inputs
-    save_struct_calc(
-        inputs=inputs,
+    info = get_struct_info(
         struct=equation_of_state.struct,
         struct_path=struct,
-        arch=arch,
-        device=device,
-        model_path=model_path,
-        read_kwargs=read_kwargs,
-        calc_kwargs=calc_kwargs,
-        log=log,
     )
 
-    # Save summary information before calculations begin
-    start_summary(command="eos", summary=summary, inputs=inputs)
+    # Save summary information before calculation begins
+    start_summary(command="eos", summary=summary, config=config, info=info)
 
     # Run equation of state calculations
     equation_of_state.run()

janus_core/cli/geomopt.py

@@ -223,8 +223,9 @@ def geomopt(
         carbon_summary,
         check_config,
         end_summary,
+        get_config,
+        get_struct_info,
         parse_typer_dicts,
-        save_struct_calc,
         set_read_kwargs_index,
         start_summary,
     )
@@ -236,6 +237,15 @@ def geomopt(
         [read_kwargs, calc_kwargs, minimize_kwargs, write_kwargs]
     )
 
+    # Set initial config
+    all_kwargs = {
+        "read_kwargs": read_kwargs.copy(),
+        "calc_kwargs": calc_kwargs.copy(),
+        "minimize_kwargs": minimize_kwargs.copy(),
+        "write_kwargs": write_kwargs.copy(),
+    }
+    config = get_config(params=ctx.params, all_kwargs=all_kwargs)
+
     # Read only first structure by default and ensure only one image is read
     set_read_kwargs_index(read_kwargs)
 
@@ -296,24 +306,14 @@ def geomopt(
     ).absolute()
     log = optimizer.log_kwargs["filename"]
 
-    # Store inputs for yaml summary
-    inputs = optimize_kwargs.copy()
-
     # Add structure, MLIP information, and log to inputs
-    save_struct_calc(
-        inputs=inputs,
+    info = get_struct_info(
         struct=optimizer.struct,
         struct_path=struct,
-        arch=arch,
-        device=device,
-        model_path=model_path,
-        read_kwargs=read_kwargs,
-        calc_kwargs=calc_kwargs,
-        log=log,
     )
 
-    # Save summary information before optimization begins
-    start_summary(command="geomopt", summary=summary, inputs=inputs)
+    # Save summary information before calculation begins
+    start_summary(command="geomopt", summary=summary, config=config, info=info)
 
     # Run geometry optimization and save output structure
     optimizer.run()

janus_core/cli/md.py

@@ -354,8 +354,9 @@ def md(
         carbon_summary,
         check_config,
         end_summary,
+        get_config,
+        get_struct_info,
         parse_typer_dicts,
-        save_struct_calc,
         set_read_kwargs_index,
         start_summary,
     )
@@ -385,6 +386,17 @@ def md(
     if ensemble not in get_args(Ensembles):
         raise ValueError(f"ensemble must be in {get_args(Ensembles)}")
 
+    # Set initial config
+    all_kwargs = {
+        "read_kwargs": read_kwargs.copy(),
+        "calc_kwargs": calc_kwargs.copy(),
+        "minimize_kwargs": minimize_kwargs.copy(),
+        "ensemble_kwargs": ensemble_kwargs.copy(),
+        "write_kwargs": write_kwargs.copy(),
+        "post_process_kwargs": post_process_kwargs.copy(),
+    }
+    config = get_config(params=ctx.params, all_kwargs=all_kwargs)
+
     # Read only first structure by default and ensure only one image is read
     set_read_kwargs_index(read_kwargs)
 
@@ -553,23 +565,14 @@ def md(
     log = dyn.log_kwargs["filename"]
 
     # Store inputs for yaml summary
-    inputs = dyn_kwargs | {"ensemble": ensemble}
-
     # Add structure, MLIP information, and log to inputs
-    save_struct_calc(
-        inputs=inputs,
+    info = get_struct_info(
         struct=dyn.struct,
         struct_path=struct,
-        arch=arch,
-        device=device,
-        model_path=model_path,
-        read_kwargs=read_kwargs,
-        calc_kwargs=calc_kwargs,
-        log=log,
     )
 
-    # Save summary information before simulation begins
-    start_summary(command="md", summary=summary, inputs=inputs)
+    # Save summary information before calculation begins
+    start_summary(command="md", summary=summary, config=config, info=info)
 
     # Run molecular dynamics
     dyn.run()

janus_core/cli/neb.py

@@ -24,7 +24,7 @@
     Summary,
     WriteKwargs,
 )
-from janus_core.cli.utils import dict_paths_to_strs, yaml_converter_callback
+from janus_core.cli.utils import yaml_converter_callback
 
 app = Typer()
 
@@ -175,8 +175,9 @@ def neb(
         carbon_summary,
         check_config,
         end_summary,
+        get_config,
+        get_struct_info,
         parse_typer_dicts,
-        save_struct_calc,
         start_summary,
     )
     from janus_core.helpers.janus_types import Interpolators
@@ -204,6 +205,18 @@ def neb(
         ]
     )
 
+    # Set initial config
+    all_kwargs = {
+        "write_kwargs": write_kwargs.copy(),
+        "neb_kwargs": neb_kwargs.copy(),
+        "interpolator_kwargs": interpolator_kwargs.copy(),
+        "optimizer_kwargs": optimizer_kwargs.copy(),
+        "minimize_kwargs": minimize_kwargs.copy(),
+        "read_kwargs": read_kwargs.copy(),
+        "calc_kwargs": calc_kwargs.copy(),
+    }
+    config = get_config(params=ctx.params, all_kwargs=all_kwargs)
+
     if band_structs:
         if init_struct or final_struct:
             raise ValueError(
@@ -256,40 +269,24 @@ def neb(
     summary = neb._build_filename("neb-summary.yml", filename=summary).absolute()
     log = neb.log_kwargs["filename"]
 
-    # Store inputs for yaml summary
-    inputs = neb_inputs.copy()
-
-    del inputs["init_struct"]
-    del inputs["final_struct"]
-    del inputs["band_structs"]
-
     # Add structure, MLIP information, and log to inputs
-    save_struct_calc(
-        inputs=inputs,
+    info = get_struct_info(
         struct=neb.struct,
         struct_path=init_struct,
-        arch=arch,
-        device=device,
-        model_path=model_path,
-        read_kwargs=read_kwargs,
-        calc_kwargs=calc_kwargs,
-        log=log,
     )
+
     if band_structs:
-        inputs["band_structs"] = inputs.pop("traj")
+        info["band_structs"] = info.pop("traj")
     else:
-        inputs["init_struct"] = inputs.pop("struct")
-        inputs["final_struct"] = {
+        info["init_struct"] = info.pop("struct")
+        info["final_struct"] = {
             "n_atoms": len(neb.final_struct),
             "struct_path": final_struct,
             "formula": neb.final_struct.get_chemical_formula(),
         }
 
-    # Convert all paths to strings in inputs nested dictionary
-    dict_paths_to_strs(inputs)
-
     # Save summary information before calculations begin
-    start_summary(command="neb", summary=summary, inputs=inputs)
+    start_summary(command="neb", summary=summary, config=config, info=info)
 
     # Run equation of state calculations
     neb.run()

janus_core/cli/phonons.py

@@ -232,10 +232,10 @@ def phonons(
     from janus_core.cli.utils import (
         carbon_summary,
         check_config,
-        dict_tuples_to_lists,
         end_summary,
+        get_config,
+        get_struct_info,
         parse_typer_dicts,
-        save_struct_calc,
         set_read_kwargs_index,
         start_summary,
     )
@@ -261,6 +261,17 @@ def phonons(
         ]
     )
 
+    # Set initial config
+    all_kwargs = {
+        "displacement_kwargs": displacement_kwargs.copy(),
+        "read_kwargs": read_kwargs.copy(),
+        "calc_kwargs": calc_kwargs.copy(),
+        "minimize_kwargs": minimize_kwargs.copy(),
+        "dos_kwargs": dos_kwargs.copy(),
+        "pdos_kwargs": pdos_kwargs.copy(),
+    }
+    config = get_config(params=ctx.params, all_kwargs=all_kwargs)
+
     # Read only first structure by default and ensure only one image is read
     set_read_kwargs_index(read_kwargs)
 
@@ -340,27 +351,14 @@ def phonons(
     summary = phonon._build_filename("phonons-summary.yml", filename=summary).absolute()
     log = phonon.log_kwargs["filename"]
 
-    # Store inputs for yaml summary
-    inputs = phonons_kwargs.copy()
-
     # Add structure, MLIP information, and log to inputs
-    save_struct_calc(
-        inputs=inputs,
+    info = get_struct_info(
         struct=phonon.struct,
         struct_path=struct,
-        arch=arch,
-        device=device,
-        model_path=model_path,
-        read_kwargs=read_kwargs,
-        calc_kwargs=calc_kwargs,
-        log=log,
     )
 
-    # Convert all tuples to list in inputs nested dictionary
-    dict_tuples_to_lists(inputs)
-
-    # Save summary information before calculations begin
-    start_summary(command="phonons", summary=summary, inputs=inputs)
+    # Save summary information before calculation begins
+    start_summary(command="phonons", summary=summary, config=config, info=info)
 
     # Run phonon calculations
     phonon.run()

janus_core/cli/preprocess.py

@@ -49,10 +49,15 @@ def preprocess(
     from janus_core.cli.utils import carbon_summary, end_summary, start_summary
     from janus_core.training.preprocess import preprocess as run_preprocess
 
-    inputs = {"mlip_config": str(mlip_config)}
+    config = {
+        "mlip_config": mlip_config,
+        "log": log,
+        "tracker": tracker,
+        "summary": summary,
+    }
 
     # Save summary information before preprocessing begins
-    start_summary(command="preprocess", summary=summary, inputs=inputs)
+    start_summary(command="preprocess", summary=summary, config=config, info={})
 
     log_kwargs = {"filemode": "w"}
     if log: