pack-mm 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

pack_mm/cli/packmm.py

@@ -8,7 +8,9 @@ from __future__ import annotations
 
 from enum import Enum
 
-import typer
+from janus_core.cli.utils import yaml_converter_callback
+from typer import Exit, Option, Typer
+from typer_config import use_config
 
 from pack_mm.core.core import pack_molecules
 
@@ -41,98 +43,89 @@ class RelaxStrategy(str, Enum):
     MD = "md"
 
 
-app = typer.Typer(no_args_is_help=True)
+app = Typer(no_args_is_help=True)
 
 
 @app.command()
+@use_config(yaml_converter_callback)
 def packmm(
-    system: str | None = typer.Option(
+    system: str | None = Option(
         None,
         help="""The original box in which you want to add particles.
         If not provided, an empty box will be created.""",
     ),
-    molecule: str = typer.Option(
+    molecule: str = Option(
         "H2O",
         help="""Name of the molecule to be processed, ASE-recognizable or
         ASE-readable file.""",
     ),
-    nmols: int = typer.Option(-1, help="Target number of molecules to insert."),
-    ntries: int = typer.Option(
+    nmols: int = Option(-1, help="Target number of molecules to insert."),
+    ntries: int = Option(
         50, help="Maximum number of attempts to insert each molecule."
     ),
-    every: int = typer.Option(
+    every: int = Option(
         -1, help="Run MD-NVE or Geometry optimisation everyth insertion."
     ),
-    seed: int = typer.Option(2025, help="Random seed for reproducibility."),
-    md_steps: int = typer.Option(10, help="Number of steps to run MD."),
-    md_timestep: float = typer.Option(1.0, help="Timestep for MD integration, in fs."),
-    where: InsertionMethod = typer.Option(
+    seed: int = Option(2025, help="Random seed for reproducibility."),
+    md_steps: int = Option(10, help="Number of steps to run MD."),
+    md_timestep: float = Option(1.0, help="Timestep for MD integration, in fs."),
+    where: InsertionMethod = Option(
         InsertionMethod.ANYWHERE,
         help="""Where to insert the molecule. Choices: 'anywhere', 'sphere',
         'box', 'cylinderZ', 'cylinderY', 'cylinderX', 'ellipsoid'.""",
     ),
-    insert_strategy: InsertionStrategy = typer.Option(
+    insert_strategy: InsertionStrategy = Option(
         InsertionStrategy.MC,
         help="""How to insert a new molecule. Choices: 'mc', 'hmc',""",
     ),
-    relax_strategy: RelaxStrategy = typer.Option(
+    relax_strategy: RelaxStrategy = Option(
         RelaxStrategy.GEOMETRY_OPTIMISATION,
         help="""How to relax the system to get more favourable structures.
             Choices: 'geometry_optimisation', 'md',""",
     ),
-    centre: str | None = typer.Option(
+    centre: str | None = Option(
         None,
         help="""Centre of the insertion zone, coordinates in Å,
         e.g., '5.0, 5.0, 5.0'.""",
     ),
-    radius: float | None = typer.Option(
+    radius: float | None = Option(
         None,
         help="""Radius of the sphere or cylinder in Å,
         depending on the insertion volume.""",
     ),
-    height: float | None = typer.Option(None, help="Height of the cylinder in Å."),
-    a: float | None = typer.Option(
+    height: float | None = Option(None, help="Height of the cylinder in Å."),
+    a: float | None = Option(
         None,
         help="""Side of the box or semi-axis of the ellipsoid, in Å,
         depends on the insertion method.""",
     ),
-    b: float | None = typer.Option(
+    b: float | None = Option(
         None,
         help="""Side of the box or semi-axis of the ellipsoid, in Å,
         depends on the insertion method.""",
     ),
-    c: float | None = typer.Option(
+    c: float | None = Option(
         None,
         help="""Side of the box or semi-axis of the ellipsoid, in Å,
         depends on the insertion method.""",
     ),
-    device: str = typer.Option(
+    device: str = Option(
         "cpu", help="Device to run calculations on (e.g., 'cpu' or 'cuda')."
     ),
-    model: str = typer.Option("medium-omat-0", help="ML model to use."),
-    arch: str = typer.Option("mace_mp", help="MLIP architecture to use."),
-    temperature: float = typer.Option(
+    model: str = Option("medium-omat-0", help="ML model to use."),
+    arch: str = Option("mace_mp", help="MLIP architecture to use."),
+    temperature: float = Option(
         300.0, help="Temperature for the Monte Carlo acceptance rule."
     ),
-    md_temperature: float = typer.Option(
+    md_temperature: float = Option(
         100.0, help="Temperature for the Molecular dynamics relaxation."
     ),
-    cell_a: float = typer.Option(
-        20.0, help="Side of the empty box along the x-axis in Å."
-    ),
-    cell_b: float = typer.Option(
-        20.0, help="Side of the empty box along the y-axis in Å."
-    ),
-    cell_c: float = typer.Option(
-        20.0, help="Side of the empty box along the z-axis in Å."
-    ),
-    fmax: float = typer.Option(
-        0.1, help="force tollerance for optimisation if needed."
-    ),
-    geometry: bool = typer.Option(
-        True, help="Perform geometry optimization at the end."
-    ),
-    out_path: str = typer.Option(".", help="path to save various outputs."),
+    cell_a: float = Option(20.0, help="Side of the empty box along the x-axis in Å."),
+    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."),
+    geometry: bool = Option(True, help="Perform geometry optimization at the end."),
+    out_path: str = Option(".", help="path to save various outputs."),
 ):
     """Pack molecules into a system based on the specified parameters."""
     print("Script called with following input")
@@ -166,7 +159,7 @@ def packmm(
     print(f"{md_temperature=}")
     if nmols == -1:
         print("nothing to do, no molecule to insert")
-        raise typer.Exit(0)
+        raise Exit(0)
 
     center = centre
     if centre:

pack_mm/core/core.py

@@ -210,7 +210,7 @@ def pack_molecules(
     out_path: str = ".",
     every: int = -1,
     relax_strategy: str = "geometry_optimisation",
-    insert_strategy: str = "random",
+    insert_strategy: str = "mc",
     md_steps: int = 10,
     md_timestep: float = 1.0,
     md_temperature: float = 100.0,
@@ -277,7 +277,7 @@ def pack_molecules(
         sysname = ""
     elif isinstance(system, Atoms):
         sys = system.copy()
-        sysname = sys.get_chemical_formula()
+        sysname = sys.get_chemical_formula() + "+"
     else:
         sys = read(system)
         sysname = Path(system).stem + "+"

{pack_mm-0.1.1.dist-info → pack_mm-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pack-mm
-Version: 0.1.1
+Version: 0.1.3
 Summary: packing materials and molecules in boxes using for machine learnt interatomic potentials
 Author: Alin M. Elena
 Classifier: Programming Language :: Python
@@ -19,10 +19,13 @@ Requires-Dist: typer<1.0.0,>=0.12.5
 Requires-Dist: typer-config<2.0.0,>=1.4.2
 Description-Content-Type: text/markdown
 
+[![PyPI version][pypi-badge]][pypi-link]
 [![Python versions][python-badge]][python-link]
 [![Build Status][ci-badge]][ci-link]
 [![Coverage Status][cov-badge]][cov-link]
 [![License][license-badge]][license-link]
+[![DOI][doi-badge]][doi-link]
+[![Docs status][docs-badge]][docs-link]
 
 # what is packmm
 
@@ -33,12 +36,15 @@ It tries to generate realistic starting configuration by employing machine learn
 interatomic potential for describing interactions between atoms and Monte Carlo,
 Molecular Dynamics and hybrid Monte Carlo.
 
+It is using [janus-core](https://github.com/stfc/janus-core) for MLIPs ([mace mp](https://github.com/ACEsuit/mace-mp) is the default) and for MD and Geometry optimisation
+routines.
+
 It provides both a cli and a python api, with some examples below.
 
 ## Quick install
 
 ```bash
-
+   python3 -m pip install pack-mm   # or
    uv pip install pack-mm
 
 ```
@@ -46,14 +52,24 @@ or install the latest
 
 ```bash
 
+  python3 -m pip install git+https://github.com/ddmms/pack-mm.git # or
   uv pip install git+https://github.com/ddmms/pack-mm.git
 
 ```
 
+## Using gpu
+
+by default runs on cpu, if you want to use gpus (recommended for big systems) pass --device cuda to cli or device="cuda" to python
+API.
+
 ## 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)
+- [Surface](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/surface.ipynb)
+- [Water](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/water.ipynb)
+- [interstitials](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/interstitials.ipynb)
+- [Mof](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/mof.ipynb)
 
 ## CLI examples
 
@@ -248,6 +264,8 @@ after optimisation
 
 
 
+[doi-link]: https://zenodo.org/badge/latestdoi/937083576
+[doi-badge]: https://zenodo.org/badge/937083576.svg
 [python-badge]: https://img.shields.io/pypi/pyversions/pack-mm.svg
 [python-link]: https://pypi.org/project/pack-mm/
 [ci-badge]: https://github.com/ddmms/pack-mm/actions/workflows/build.yml/badge.svg?branch=main
@@ -256,3 +274,7 @@ after optimisation
 [cov-link]: https://coveralls.io/github/ddmms/pack-mm?branch=main
 [license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
 [license-link]: https://opensource.org/license/MIT
+[pypi-badge]: https://badge.fury.io/py/pack-mm.svg
+[pypi-link]: https://pypi.org/project/pack-mm/
+[docs-badge]: https://github.com/ddmms/pack-mm/actions/workflows/python-publish.yml/badge.svg
+[docs-link]: https://ddmms.github.io/pack-mm/

pack_mm-0.1.3.dist-info/RECORD

@@ -0,0 +1,8 @@
+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,,

pack_mm-0.1.1.dist-info/RECORD

@@ -1,8 +0,0 @@
-pack_mm-0.1.1.dist-info/METADATA,sha256=-Hv1zI5_LAmH0iJi37Z4d9xAgepWpXxrRM1DIVz3SmM,13804
-pack_mm-0.1.1.dist-info/WHEEL,sha256=thaaA2w1JzcGC48WYufAs8nrYZjJm8LqNfnXFOFyCC4,90
-pack_mm-0.1.1.dist-info/entry_points.txt,sha256=ajKA2oehIa_LCVCP2XTRxV0VNgjGl9c2wYkwk0BasrQ,66
-pack_mm-0.1.1.dist-info/licenses/LICENSE,sha256=ZOYkPdn_vQ8wYJqZnjesow79F_grMbVlHcJ9V91G1pE,1100
-pack_mm/__init__.py,sha256=ct7qfCmTDwhLYip6JKYWRLasmmaGYt0ColbK0CpvYZk,150
-pack_mm/cli/packmm.py,sha256=E63MmBrxvn9g5GQMK5vlyq6CmHL8hgQ8CICeX2N9z1E,6398
-pack_mm/core/core.py,sha256=vLTdnWaqnIOtkhtLBG9911RxhJMn-DWAWe5GzyFWSdc,15883
-pack_mm-0.1.1.dist-info/RECORD,,