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mcpy

Python package designed to run atomistic Monte Carlo simulations.

https://github.com/farrisric/mcpy

Science Score: 67.0%

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    CITATION.cff file
    Found CITATION.cff file
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    Found .zenodo.json file
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    Found 1 DOI reference(s) in README
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    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (10.4%) to scientific vocabulary

Keywords

monte-carlo monte-carlo-simulation
Last synced: 6 months ago · JSON representation ·

Repository

Python package designed to run atomistic Monte Carlo simulations.

Basic Info
  • Host: GitHub
  • Owner: farrisric
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 241 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
monte-carlo monte-carlo-simulation
Created about 1 year ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

DOI

mcpy

mcpy is a Python package designed to run atomistic Monte Carlo simulations. It provides tools for performing Grand Canonical Monte Carlo (GCMC) simulations using the Atomic Simulation Environment (ASE) and other dependencies.

Features

  • Grand Canonical Monte Carlo simulations
  • Integration with ASE for atomic simulations
  • Support for MACE calculator potential and other calculators
  • Configurable simulation parameters and logging

Installation

To install the mcpy package, ensure you have Python 3.11 or higher and run the following commands:

sh pip install .

Alternatively, you can install the package in editable mode:

sh pip install -e .

Please note that mpi4py should be installed using conda:

sh conda install mpi4py

Dependencies

The package requires the following dependencies:

  • ase>=3.23.0
  • mace-torch>=0.3.9
  • mpi4py>=4.0.1

Usage

Here is an example of how to use the mcpy package to run a GCMC simulation:

```python from mcpy.ensembles.grandcanonicalensemble import GrandCanonicalEnsemble from ase.calculators.lj import LennardJones from ase import Atoms from mcpy.moves import DeletionMove, InsertionMove, DisplacementMove from mcpy.moves.move_selector import MoveSelector

class Calculator(): def init(self) -> None: self.calculator = LennardJones(sigma=3.4, epsilon=0.010086, rc=10.2, smooth=True)

def get_potential_energy(self, atoms):
    atoms.calc = self.calculator
    return atoms.get_potential_energy()

lj = Calculator() atoms = Atoms('Ar', cell=[27.2, 27.2, 27.2], pbc=True) lj.getpotentialenergy(atoms)

box = atoms.get_cell() species = ['Ar']

movelist = [[25, 25, 50], [DeletionMove(species=species, seed=12, operatingbox=box), InsertionMove(species=species, seed=13, operatingbox=box), DisplacementMove(species=species, seed=14, maxdisplacement=1.7)]]

moveselector = MoveSelector(*movelist)

Temp = 87.79

gcmc = GrandCanonicalEnsemble( atoms=atoms, calculator=lj, mu={'Ar': -8.4*0.010086}, unitstype='metal', species=species, temperature=Temp, moveselector=moveselector, outfile=f'T{Temp}.out', trajectorywriteinterval=1, outfilewriteinterval=1, trajfile=f'T{Temp}.xyz')

gcmc.run(1000000) ```

Contributing

Contributions are welcome! Please fork the repository and submit a pull request with your changes.

License

This project is licensed under the MIT License. See the LICENSE file for details.

Owner

  • Name: Riccardo Farris
  • Login: farrisric
  • Kind: user
  • Company: @reac-nps

PhD Student in Theoretical and Computational Chemistry in the @reac-nps group at the Universidad de Barcelona,

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "mcpy: a python package designed to run atomistic Monte Carlo simulations"
authors:
  - family-names: "Farris"
    given-names: "Riccardo"
    affiliation: "Universitat de Barcelona"
  - family-names: "Telari"
    given-names: "Emanuele"
    affiliation: "Universitat de Barcelona"
date-released: "2025-05-01"
version: "1.0.0"
doi: "10.5072/zenodo.262131"
url: "https://github.com/farrisric/mcpy"
license: "MIT"

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Last synced: 6 months ago

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