feat: add MSD and self-diffusion coefficient workflow

amorphouspy/src/amorphouspy/__init__.py

@@ -27,6 +27,14 @@
     cte_from_npt_fluctuations,
     cte_from_volume_temperature_data,
 )
+from amorphouspy.properties.diffusion import (
+    compute_msd,
+    diffusion_simulation,
+    fit_arrhenius,
+    get_diffusion,
+    log_linear_dump_steps,
+    save_frames,
+)
 from amorphouspy.properties.elastic import elastic_simulation
 from amorphouspy.properties.structural.all import (
     analyze_structure,
@@ -63,6 +71,7 @@
     "compute_cavities",
     "compute_coordination",
     "compute_guttmann_rings",
+    "compute_msd",
     "compute_network_connectivity",
     "compute_projected_rdf",
     "compute_qn",
@@ -74,10 +83,12 @@
     "cte_from_fluctuations_simulation",
     "cte_from_npt_fluctuations",
     "cte_from_volume_temperature_data",
+    "diffusion_simulation",
     "elastic_simulation",
     "extract_composition",
     "extract_equilibration_frames",
     "find_rdf_minimum",
+    "fit_arrhenius",
     "fit_vft",
     "formula_mass_g_per_mol",
     "frames_from_melt_quench_result",
@@ -87,11 +98,13 @@
     "get_ase_structure",
     "get_atomic_mass",
     "get_composition",
+    "get_diffusion",
     "get_glass_density_from_model",
     "get_neighbors",
     "get_structure_dict",
     "get_viscosity",
     "load_lammps_dump",
+    "log_linear_dump_steps",
     "md_simulation",
     "melt_quench_simulation",
     "parse_formula",
@@ -100,6 +113,7 @@
     "run_melt_quench",
     "run_structural_analysis",
     "running_mean",
+    "save_frames",
     "structure_from_parsed_output",
     "temperature_scan_simulation",
     "type_to_dict",

amorphouspy/src/amorphouspy/lammps/io.py

@@ -150,13 +150,18 @@ def frames_from_melt_quench_result(
             atoms.set_velocities(stage_data["velocities"][i])
         if "indices" in stage_data:
             atoms.set_array("indices", stage_data["indices"][i])
-        atoms.info["temperature"] = stage_data["temperature"][i]
-        atoms.info["energy_pot"] = stage_data["energy_pot"][i]
-        atoms.info["energy_tot"] = stage_data["energy_tot"][i]
-        atoms.info["volume"] = stage_data["volume"][i]
-        atoms.info["pressure"] = stage_data["pressures"][i]
-        if "steps" in stage_data and i < len(stage_data["steps"]):
-            atoms.info["step"] = stage_data["steps"][i]
+        # Thermo-derived scalars are logged on a separate (thermo) cadence, so they can be shorter than
+        # the per-frame dump arrays (e.g. with a log-spaced dump schedule); guard each access.
+        for info_key, data_key in (
+            ("temperature", "temperature"),
+            ("energy_pot", "energy_pot"),
+            ("energy_tot", "energy_tot"),
+            ("volume", "volume"),
+            ("pressure", "pressures"),
+            ("step", "steps"),
+        ):
+            if data_key in stage_data and i < len(stage_data[data_key]):
+                atoms.info[info_key] = stage_data[data_key][i]
         if "forces" in stage_data:
             atoms.arrays["forces"] = stage_data["forces"][i]
         if "unwrapped_positions" in stage_data:

amorphouspy/src/amorphouspy/lammps/md.py

@@ -27,6 +27,7 @@ def md_simulation(
     langevin: bool = False,
     seed: int = 12345,
     tmp_working_directory: str | Path | None = None,
+    input_control_file: dict | None = None,
 ) -> dict:  # pylint: disable=too-many-positional-arguments
     """Perform a molecular dynamics simulation using LAMMPS.
 
@@ -56,6 +57,8 @@ def md_simulation(
             With the specification of tmp_working_directory, the temporary directory is created in the specified
             location. Therefore, tmp_working_directory needs to exist beforehand. Data will be cleaned after the
             simulation is finished.
+        input_control_file: Optional LAMMPS input overrides merged on top of the
+            default generated controls.
 
     Returns:
         A dictionary containing the simulation steps and temperature data.
@@ -80,6 +83,7 @@ def md_simulation(
         langevin=langevin,
         seed=seed,
         server_kwargs=server_kwargs,
+        input_control_file=input_control_file,
     )
 
     result = parsed_output.get("generic", None)