pack-mm 0.1.3__py3-none-any.whl → 0.1.11__py3-none-any.whl

pack_mm/cli/packmm.py

@@ -124,6 +124,12 @@ def packmm(
     cell_b: float = Option(20.0, help="Side of the empty box along the y-axis in Å."),
     cell_c: float = Option(20.0, help="Side of the empty box along the z-axis in Å."),
     fmax: float = Option(0.1, help="force tollerance for optimisation if needed."),
+    threshold: float = Option(
+        0.92,
+        help="""percentage of the single molecule energy above which
+                the acceptance energy difference must
+                be considered for acceptance.""",
+    ),
     geometry: bool = Option(True, help="Perform geometry optimization at the end."),
     out_path: str = Option(".", help="path to save various outputs."),
 ):
@@ -149,6 +155,7 @@ def packmm(
     print(f"{device=}")
     print(f"{temperature=}")
     print(f"{fmax=}")
+    print(f"{threshold=}")
     print(f"{geometry=}")
     print(f"{out_path=}")
     print(f"{every=}")
@@ -188,6 +195,7 @@ def packmm(
         temperature=temperature,
         ntries=ntries,
         fmax=fmax,
+        threshold=threshold,
         geometry=geometry,
         cell_a=cell_a,
         cell_b=cell_b,

pack_mm/core/core.py

@@ -189,9 +189,9 @@ def pack_molecules(
     system: str | Atoms = None,
     molecule: str = "H2O",
     nmols: int = -1,
-    arch: str = "cpu",
-    model: str = "mace_mp",
-    device: str = "medium-omat-0",
+    arch: str = "mace_mp",
+    model: str = "medium-omat-0",
+    device: str = "cpu",
     where: str = "anywhere",
     center: tuple[float, float, float] = None,
     radius: float = None,
@@ -204,6 +204,7 @@ def pack_molecules(
     ntries: int = 50,
     geometry: bool = False,
     fmax: float = 0.1,
+    threshold: float = 0.92,
     cell_a: float = None,
     cell_b: float = None,
     cell_c: float = None,
@@ -243,6 +244,9 @@ def pack_molecules(
         md_temperature (float): Temperature in Kelvin for MD.
         md_steps (int): Number of steps for MD.
         md_timestep (float): Timestep in fs for MD.
+        fmax (float): Max force for geometry optimisation.
+        threshold (float): Percentage of the single molecule energy above which
+                           the move is to be considered for acceptance.
         insert_strategy (str): Insert strategy, "random" or "md"
         relax_strategy (str): Relax strategy, "geometry_optimisation" or "md"
 
@@ -298,6 +302,10 @@ def pack_molecules(
 
     e = sys.get_potential_energy() if len(sys) > 0 else 0.0
 
+    mol = load_molecule(molecule)
+    mol.calc = calc
+    emol = mol.get_potential_energy()
+
     csys = sys.copy()
     i = 0
     while i < nmols:
@@ -316,7 +324,7 @@ def pack_molecules(
 
             if every > 0 and _itry / every == 0:
                 tsys = save_the_day(
-                    struct_path=tsys,
+                    struct=tsys,
                     device=device,
                     arch=arch,
                     model=model,
@@ -336,7 +344,7 @@ def pack_molecules(
             u = random.random()
             print(f"Old energy={e}, new energy={en}, {de=}, {acc=}, random={u}")
 
-            if u <= acc:
+            if abs(de / emol) > threshold and u <= acc:
                 accept = True
                 break
         if accept:
@@ -367,13 +375,13 @@ def pack_molecules(
     # Perform final geometry optimization if requested
     if geometry:
         energy_final, csys = optimize_geometry(
-            Path(out_path) / f"{sysname}{nmols}{Path(molecule).stem}.cif",
-            device,
-            arch,
-            model,
-            fmax,
-            out_path,
-            True,
+            struct=Path(out_path) / f"{sysname}{nmols}{Path(molecule).stem}.cif",
+            device=device,
+            arch=arch,
+            model=model,
+            fmax=fmax,
+            out_path=out_path,
+            opt_cell=True,
         )
     return (energy_final, csys)
 
@@ -418,7 +426,7 @@ def rotate_molecule(mol):
 
 
 def save_the_day(
-    struct_path: str | Atoms,
+    struct: str | Atoms,
     device: str = "",
     arch: str = "",
     model: str = "",
@@ -432,7 +440,7 @@ def save_the_day(
     """Geometry optimisation or MD to get a better structure."""
     if relax_strategy == "geometry_optimisation":
         _, a = optimize_geometry(
-            struct_path,
+            struct,
             device,
             arch,
             model,
@@ -442,13 +450,13 @@ def save_the_day(
         return a
     if relax_strategy == "md":
         return run_md_nve(
-            struct_path, md_temperature, md_steps, md_timestep, arch, model, device
+            struct, md_temperature, md_steps, md_timestep, arch, model, device
         )
     return None
 
 
 def run_md_nve(
-    struct_path: str | Atoms,
+    struct: str | Atoms,
     temp: float = 100.0,
     steps: int = 10,
     timestep: float = 1.0,
@@ -457,34 +465,22 @@ def run_md_nve(
     device: str = "",
 ) -> Atoms:
     """Run nve simulation."""
-    if isinstance(struct_path, Atoms):
-        md = NVE(
-            struct=struct_path,
-            temp=temp,
-            device=device,
-            arch=arch,
-            calc_kwargs={"model_paths": model},
-            stats_every=1,
-            steps=steps,
-            timestep=timestep,
-        )
-    else:
-        md = NVE(
-            struct_path=struct_path,
-            temp=temp,
-            device=device,
-            arch=arch,
-            calc_kwargs={"model_paths": model},
-            stats_every=1,
-            steps=steps,
-            timestep=timestep,
-        )
+    md = NVE(
+        struct=struct,
+        temp=temp,
+        device=device,
+        arch=arch,
+        calc_kwargs={"model_paths": model},
+        stats_every=1,
+        steps=steps,
+        timestep=timestep,
+    )
     md.run()
     return md.struct
 
 
 def optimize_geometry(
-    struct_path: str | Atoms,
+    struct: str | Atoms,
     device: str,
     arch: str,
     model: str,
@@ -493,25 +489,15 @@ def optimize_geometry(
     opt_cell: bool = False,
 ) -> tuple(float, Atoms):
     """Optimize the geometry of a structure."""
-    if isinstance(struct_path, Atoms):
-        geo = GeomOpt(
-            struct=struct_path,
-            device=device,
-            arch=arch,
-            fmax=fmax,
-            calc_kwargs={"model_paths": model},
-            filter_kwargs={"hydrostatic_strain": opt_cell},
-        )
-        geo.run()
-    else:
-        geo = GeomOpt(
-            struct_path=struct_path,
-            device=device,
-            arch=arch,
-            fmax=fmax,
-            calc_kwargs={"model_paths": model},
-            filter_kwargs={"hydrostatic_strain": opt_cell},
-        )
-        geo.run()
-        write(Path(out_path) / f"{Path(struct_path).stem}-opt.cif", geo.struct)
+    geo = GeomOpt(
+        struct=struct,
+        device=device,
+        arch=arch,
+        fmax=fmax,
+        calc_kwargs={"model_paths": model},
+        filter_kwargs={"hydrostatic_strain": opt_cell},
+    )
+    geo.run()
+    if isinstance(struct, Path):
+        write(Path(out_path) / f"{struct.stem}-opt.cif", geo.struct)
     return (geo.struct.get_potential_energy(), geo.struct)

{pack_mm-0.1.3.dist-info → pack_mm-0.1.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pack-mm
-Version: 0.1.3
+Version: 0.1.11
 Summary: packing materials and molecules in boxes using for machine learnt interatomic potentials
 Author: Alin M. Elena
 Classifier: Programming Language :: Python
@@ -14,7 +14,7 @@ Classifier: Development Status :: 4 - Beta
 Project-URL: Repository, https://github.com/ddmms/pack-mm/
 Project-URL: Documentation, https://ddmms.github.io/pack-mm/
 Requires-Python: >=3.10
-Requires-Dist: janus-core>=0.7.2
+Requires-Dist: janus-core[mace]>=0.7.2
 Requires-Dist: typer<1.0.0,>=0.12.5
 Requires-Dist: typer-config<2.0.0,>=1.4.2
 Description-Content-Type: text/markdown

pack_mm-0.1.11.dist-info/RECORD

@@ -0,0 +1,8 @@
+pack_mm-0.1.11.dist-info/METADATA,sha256=o4IdCZX_1an8XCAIN4a2qD2oI9QCp2loR9oNRkZM5lg,15589
+pack_mm-0.1.11.dist-info/WHEEL,sha256=thaaA2w1JzcGC48WYufAs8nrYZjJm8LqNfnXFOFyCC4,90
+pack_mm-0.1.11.dist-info/entry_points.txt,sha256=ajKA2oehIa_LCVCP2XTRxV0VNgjGl9c2wYkwk0BasrQ,66
+pack_mm-0.1.11.dist-info/licenses/LICENSE,sha256=ZOYkPdn_vQ8wYJqZnjesow79F_grMbVlHcJ9V91G1pE,1100
+pack_mm/__init__.py,sha256=ct7qfCmTDwhLYip6JKYWRLasmmaGYt0ColbK0CpvYZk,150
+pack_mm/cli/packmm.py,sha256=B_GtIfSMxxCuo7077hSnGFY4Jql0EliFCAewmBhyvoU,6584
+pack_mm/core/core.py,sha256=Zn3kFof9Gkz0C70iOC4WLZkckyC92NWuXQUhieN02vU,15567
+pack_mm-0.1.11.dist-info/RECORD,,

pack_mm-0.1.3.dist-info/RECORD

@@ -1,8 +0,0 @@
-pack_mm-0.1.3.dist-info/METADATA,sha256=O1R3mqp12KVeizVU372ZInNl8ljidaVsKCPmv64QQR4,15582
-pack_mm-0.1.3.dist-info/WHEEL,sha256=thaaA2w1JzcGC48WYufAs8nrYZjJm8LqNfnXFOFyCC4,90
-pack_mm-0.1.3.dist-info/entry_points.txt,sha256=ajKA2oehIa_LCVCP2XTRxV0VNgjGl9c2wYkwk0BasrQ,66
-pack_mm-0.1.3.dist-info/licenses/LICENSE,sha256=ZOYkPdn_vQ8wYJqZnjesow79F_grMbVlHcJ9V91G1pE,1100
-pack_mm/__init__.py,sha256=ct7qfCmTDwhLYip6JKYWRLasmmaGYt0ColbK0CpvYZk,150
-pack_mm/cli/packmm.py,sha256=2WJRReS9BSmLadWPU6_m-0MPl1AHnKHZmDruD8aXBDQ,6303
-pack_mm/core/core.py,sha256=lFDFIVrt_WAb45c0da_8Sey7Ku21oJqXCUIEtK6j-po,15885
-pack_mm-0.1.3.dist-info/RECORD,,