Add rare events simulations (PLUMED)

[ElliottKasoar]

https://wiki.fysik.dtu.dk/ase//ase/calculators/plumed.html

[alinelena]

a simple poc is something like this

# -*- coding: utf-8 -*-
# Author; alin m elena, [email protected]
# Contribs;
# Date: 25-02-2025
# ©alin m elena, GPL v3 https://www.gnu.org/licenses/gpl-3.0.en.html
from ase import units
from ase.io import read

from janus_core.helpers.mlip_calculators import choose_calculator
from janus_core.calculations.md import NVT

from ase.calculators.plumed import Plumed


timestep = 0.001
steps = 1000
T = 300.0

arch = "mace_mp"
model = "small-0b2"
device = "cpu"

calc = choose_calculator(arch=arch,device=device,model_path=model)
with open("umbrella.dat") as f:
    plumed_config = [ x.strip("\n") for x in f.readlines() ]

butane = read('butane.extxyz')
plumed_config = [f"UNITS LENGTH=A TIME={1/(1000 * units.fs)} ENERGY={units.mol/units.kJ}"]  + plumed_config
plumed_calc = Plumed(calc=calc,
                    input=plumed_config,
                    timestep=timestep,
                    atoms=butane,
                    kT=units.kB*T)
md = NVT(struct=butane,
         temp=T,
         device=device,
         arch=arch,
         calc_kwargs={"model_paths": model},
         stats_every=1,
         steps=steps,
         timestep=1.0,
         friction=0.005,
         minimize=False)

md.struct.calc = plumed_calc

md.run()

units may need checked and seems to expose also a bug...