pack-mm 0.0.22__tar.gz → 0.0.24__tar.gz

{pack_mm-0.0.22 → pack_mm-0.0.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pack-mm
-Version: 0.0.22
+Version: 0.0.24
 Summary: packing materials and molecules in boxes using for machine learnt interatomic potentials
 Author: Alin M. Elena
 Classifier: Programming Language :: Python
@@ -50,6 +50,11 @@ or install the latest
 
 ```
 
+## Jupyter notebook examples
+
+
+- [Basics](docs/source/tutorials/basics.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ddmms/pack-mm/blob/main/docs/source/tutorials/basic.ipynb)
+
 ## CLI examples
 
 

{pack_mm-0.0.22 → pack_mm-0.0.24}/README.md

@@ -29,6 +29,11 @@ or install the latest
 
 ```
 
+## Jupyter notebook examples
+
+
+- [Basics](docs/source/tutorials/basics.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ddmms/pack-mm/blob/main/docs/source/tutorials/basic.ipynb)
+
 ## CLI examples
 
 

{pack_mm-0.0.22 → pack_mm-0.0.24}/pack_mm/core/core.py

@@ -186,7 +186,7 @@ def set_defaults(
 
 
 def pack_molecules(
-    system: str = None,
+    system: str | Atoms = None,
     molecule: str = "H2O",
     nmols: int = -1,
     arch: str = "cpu",
@@ -214,13 +214,13 @@ def pack_molecules(
     md_steps: int = 10,
     md_timestep: float = 1.0,
     md_temperature: float = 100.0,
-) -> float:
+) -> tuple(float, Atoms):
     """
     Pack molecules into a system based on the specified parameters.
 
     Parameters
     ----------
-        system (str): Path to the system file or name of the system.
+        system (str|Atoms): Path to the system file or name of the system.
         molecule (str): Path to the molecule file or name of the molecule.
         nmols (int): Number of molecules to insert.
         arch (str): Architecture for the calculator.
@@ -246,6 +246,11 @@ def pack_molecules(
         insert_strategy (str): Insert strategy, "random" or "md"
         relax_strategy (str): Relax strategy, "geometry_optimisation" or "md"
 
+    Returns
+    -------
+        tuple: A tuple energy and Atoms object containing
+               original system and added molecules..
+
     """
     kbt = temperature * kB
     validate_value("temperature", temperature)
@@ -270,6 +275,9 @@ def pack_molecules(
     if system is None:
         sys = Atoms(cell=[cell_a, cell_b, cell_c], pbc=[True, True, True])
         sysname = ""
+    elif isinstance(system, Atoms):
+        sys = system.copy()
+        sysname = sys.get_chemical_formula()
     else:
         sys = read(system)
         sysname = Path(system).stem + "+"
@@ -306,6 +314,20 @@ def pack_molecules(
                     tsys, md_temperature, md_steps, md_timestep, arch, model, device
                 )
 
+            if every > 0 and _itry / every == 0:
+                tsys = save_the_day(
+                    struct_path=tsys,
+                    device=device,
+                    arch=arch,
+                    model=model,
+                    fmax=fmax,
+                    out_path=out_path,
+                    md_temperature=md_temperature,
+                    md_steps=md_steps,
+                    md_timestep=md_timestep,
+                    relax_strategy=relax_strategy,
+                )
+
             tsys.calc = calc
             en = tsys.get_potential_energy()
             de = en - e
@@ -317,20 +339,6 @@ def pack_molecules(
             if u <= acc:
                 accept = True
                 break
-            if every > 0 and _itry / every == 0:
-                csys = save_the_day(
-                    Path(out_path) / f"{sysname}{i}{Path(molecule).stem}.cif",
-                    device,
-                    arch,
-                    model,
-                    fmax,
-                    out_path,
-                    md_temperature,
-                    md_steps,
-                    md_timestep,
-                    relax_strategy,
-                )
-
         if accept:
             csys = tsys.copy()
             e = en
@@ -342,7 +350,7 @@ def pack_molecules(
             # once you hit here is bad, this can keep looping
             print(f"Failed to insert particle {i + 1} after {ntries} tries")
             csys = save_the_day(
-                Path(out_path) / f"{sysname}{i}{Path(molecule).stem}.cif",
+                csys,
                 device,
                 arch,
                 model,
@@ -358,7 +366,7 @@ def pack_molecules(
 
     # Perform final geometry optimization if requested
     if geometry:
-        energy_final = optimize_geometry(
+        energy_final, csys = optimize_geometry(
             Path(out_path) / f"{sysname}{nmols}{Path(molecule).stem}.cif",
             device,
             arch,
@@ -367,7 +375,7 @@ def pack_molecules(
             out_path,
             True,
         )
-    return energy_final
+    return (energy_final, csys)
 
 
 def load_molecule(molecule: str):
@@ -410,7 +418,7 @@ def rotate_molecule(mol):
 
 
 def save_the_day(
-    struct_path: str = "",
+    struct_path: str | Atoms,
     device: str = "",
     arch: str = "",
     model: str = "",
@@ -423,7 +431,7 @@ def save_the_day(
 ) -> Atoms:
     """Geometry optimisation or MD to get a better structure."""
     if relax_strategy == "geometry_optimisation":
-        _ = optimize_geometry(
+        _, a = optimize_geometry(
             struct_path,
             device,
             arch,
@@ -431,7 +439,7 @@ def save_the_day(
             fmax,
             out_path,
         )
-        return read(Path(out_path) / f"{Path(struct_path).stem}-opt.cif")
+        return a
     if relax_strategy == "md":
         return run_md_nve(
             struct_path, md_temperature, md_steps, md_timestep, arch, model, device
@@ -476,23 +484,34 @@ def run_md_nve(
 
 
 def optimize_geometry(
-    struct_path: str,
+    struct_path: str | Atoms,
     device: str,
     arch: str,
     model: str,
     fmax: float,
     out_path: str = ".",
     opt_cell: bool = False,
-) -> float:
+) -> tuple(float, Atoms):
     """Optimize the geometry of a structure."""
-    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)
-    return geo.struct.get_potential_energy()
+    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)
+    return (geo.struct.get_potential_energy(), geo.struct)

{pack_mm-0.0.22 → pack_mm-0.0.24}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pack-mm"
-version = "0.0.22"
+version = "0.0.24"
 description = "packing materials and molecules in boxes using for machine learnt interatomic potentials"
 authors = [
     { name = "Alin M. Elena" },
@@ -53,6 +53,8 @@ docs = [
     "sphinx-autodoc-typehints<3.0.0,>=2.5.0",
     "sphinx-collapse>=0.1.3",
     "sphinx-copybutton<1.0.0,>=0.5.2",
+    "data-tutorials",
+    "weas-widget",
 ]
 pre-commit = [
     "pre-commit<4.0.0,>=3.6.0",

pack_mm-0.0.24/tests/test_advanced.py

@@ -0,0 +1,85 @@
+"""Advanced tests for packmm."""
+
+# Author; alin m elena, alin@elena.re
+# Contribs;
+# Date: 23-02-2025
+# ©alin m elena,
+from __future__ import annotations
+
+from ase.build import bulk
+from ase.io import read, write
+import pytest
+from typer.testing import CliRunner
+
+from pack_mm.cli.packmm import app
+
+runner = CliRunner()
+
+err = 1.0e-8
+
+
+def test_packmm_hmc(tmp_path):
+    """Check values."""
+    result = runner.invoke(
+        app,
+        [
+            "--nmols",
+            "2",
+            "--model",
+            "small-0b2",
+            "--insert-strategy",
+            "hmc",
+            "--seed",
+            "2042",
+            "--cell-a",
+            "10",
+            "--cell-b",
+            "10",
+            "--cell-c",
+            "10",
+            "--out-path",
+            tmp_path,
+        ],
+    )
+    assert result.exit_code == 0
+    assert (tmp_path / "1H2O.cif").exists()
+    assert (tmp_path / "2H2O.cif").exists()
+    f = read(tmp_path / "2H2O.cif")
+    assert f[0].position == pytest.approx([7.83420049, 6.21661184, 5.21814887], abs=err)
+    assert (tmp_path / "2H2O-opt.cif").exists()
+    f = read(tmp_path / "2H2O-opt.cif")
+    assert f[0].position == pytest.approx([7.83120709, 6.21742874, 5.22597213], abs=err)
+
+
+def test_packmm_every(tmp_path):
+    """Check values."""
+    na = bulk("NaCl", "rocksalt", a=5.61, cubic=True)
+    write(tmp_path / "system.cif", na)
+    write("system.cif", na)
+
+    result = runner.invoke(
+        app,
+        [
+            "--system",
+            tmp_path / "system.cif",
+            "--molecule",
+            "H2",
+            "--every",
+            "1",
+            "--nmols",
+            "2",
+            "--model",
+            "small-0b2",
+            "--seed",
+            "2042",
+            "--out-path",
+            tmp_path,
+            "--no-geometry",
+        ],
+    )
+    assert result.exit_code == 0
+    assert (tmp_path / "system.cif").exists()
+    assert (tmp_path / "system+1H2.cif").exists()
+    assert (tmp_path / "system+2H2.cif").exists()
+    f = read(tmp_path / "system+2H2.cif")
+    assert f[0].position == pytest.approx([1.24701529, 0.024216, 0.11632905], abs=err)

{pack_mm-0.0.22 → pack_mm-0.0.24}/tests/test_core.py

@@ -236,7 +236,7 @@ def test_optimize_geometry(tmp_path):
     molecule.set_pbc([True, True, True])
     structure_file = tmp_path / "water.cif"
     write(structure_file, molecule)
-    optimized_energy = optimize_geometry(
+    optimized_energy, _ = optimize_geometry(
         str(structure_file),
         device="cpu",
         arch="mace_mp",
@@ -256,7 +256,7 @@ def test_pack_molecules(tmp_path):
     system_file = tmp_path / "system.cif"
     write(system_file, system)
 
-    e = pack_molecules(
+    e, _ = pack_molecules(
         system=str(system_file),
         molecule="H2O",
         nmols=2,
@@ -279,6 +279,33 @@ def test_pack_molecules(tmp_path):
     assert e == pytest.approx(-29.21589570470306, abs=err)
 
 
+def test_pack_molecules_atoms(tmp_path):
+    """Test pack molecule."""
+    system = Atoms(
+        "Ca", positions=[(5.0, 5.0, 5.0)], cell=[10, 10, 10], pbc=[True, True, True]
+    )
+
+    e, _ = pack_molecules(
+        system=system,
+        molecule="H2O",
+        nmols=2,
+        arch="mace_mp",
+        model="small-0b2",
+        device="cpu",
+        where="sphere",
+        center=(5.0, 5.0, 5.0),
+        radius=5.0,
+        seed=2042,
+        temperature=300,
+        ntries=10,
+        geometry=False,
+        fmax=0.1,
+        out_path=tmp_path,
+    )
+
+    assert e == pytest.approx(-29.21589570470306, abs=err)
+
+
 def test_pack_molecules_2(tmp_path, capsys):
     """Test pack molecule."""
     system = Atoms(
@@ -287,7 +314,7 @@ def test_pack_molecules_2(tmp_path, capsys):
     system_file = tmp_path / "system.cif"
     write(system_file, system)
 
-    e = pack_molecules(
+    e, _ = pack_molecules(
         system=str(system_file),
         molecule="H2O",
         nmols=3,
@@ -307,7 +334,7 @@ def test_pack_molecules_2(tmp_path, capsys):
     captured = capsys.readouterr()
 
     assert "Failed to insert particle 3 after 2 tries" in captured.out
-    assert e == pytest.approx(-47.19506254437384, abs=err)
+    assert e == pytest.approx(-47.194755808249454, abs=err)
 
 
 def test_save_the_day(tmp_path):
@@ -318,7 +345,6 @@ def test_save_the_day(tmp_path):
     molecule.center()
     structure_file = tmp_path / "water.cif"
     write(structure_file, molecule)
-    print(molecule.positions)
     s = save_the_day(
         str(structure_file),
         device="cpu",
@@ -327,7 +353,6 @@ def test_save_the_day(tmp_path):
         fmax=0.01,
         out_path=tmp_path,
     )
-    print(s.positions)
     assert s[0].position == pytest.approx([5.0, 4.99619815, 5.30704738], abs=err)
 
 
@@ -339,7 +364,6 @@ def test_save_the_day_md(tmp_path):
     molecule.center()
     structure_file = tmp_path / "water.cif"
     write(structure_file, molecule)
-    print(molecule.positions)
     s = save_the_day(
         str(structure_file),
         device="cpu",
@@ -350,10 +374,30 @@ def test_save_the_day_md(tmp_path):
         md_steps=10.0,
         md_temperature=100.0,
     )
-    print(s.positions)
     assert s[0].position == pytest.approx([4.99684244, 5.00440785, 5.2987255], abs=err)
 
 
+def test_save_the_day_invalid(tmp_path):
+    """Test save the day."""
+    molecule = build_molecule("H2O")
+    molecule.set_cell([10, 10, 10])
+    molecule.set_pbc([True, True, True])
+    molecule.center()
+    structure_file = tmp_path / "water.cif"
+    write(structure_file, molecule)
+    s = save_the_day(
+        str(structure_file),
+        device="cpu",
+        arch="mace_mp",
+        model="small-0b2",
+        relax_strategy="invalid_stratregy",
+        md_timestep=1.0,
+        md_steps=10.0,
+        md_temperature=100.0,
+    )
+    assert s is None
+
+
 def test_run_md(tmp_path):
     """Test md."""
     molecule = build_molecule("H2O")