hillclimber
hillclimber is a Python framework for enhanced sampling with PLUMED. It provides high-level, Pythonic interfaces for configuring metadynamics simulations, making it easy to explore rare events and climb energy barriers in molecular dynamics simulations.
Installation
uv add hillclimber
Or with pip:
pip install hillclimber
Units
hillclimber uses ASE units throughout the package:
- Distances: Ångström / Å
- Energies: electronvolt / eV
- Time: femtoseconds / fs
- Temperature: Kelvin / K
Python Collective Variables (PyCV)
hillclimber supports custom Python-based collective variables through PLUMED's PYCVINTERFACE. This allows you to define arbitrary CVs in Python with full access to atomic coordinates and gradients.
Defining a PyCV
Create a subclass of PyCV with a compute method:
# cv.py
import numpy as np
from ase import Atoms
from hillclimber.pycv import PyCV
class DistanceCV(PyCV):
"""Custom distance CV between first two selected atoms."""
def compute(self, atoms: Atoms) -> tuple[float, np.ndarray]:
"""Compute CV value and gradients.
Parameters
----------
atoms : Atoms
ASE Atoms object containing ONLY the selected atoms.
Indices start at 0 and go up to len(atoms) - 1.
Returns
-------
tuple[float, np.ndarray]
CV value and gradients array of shape (n_atoms, 3).
"""
positions = atoms.get_positions()
diff = positions[1] - positions[0]
distance = float(np.linalg.norm(diff))
# Compute gradients for the selected atoms
grad = np.zeros((len(atoms), 3))
grad[0] = -diff / distance
grad[1] = diff / distance
return distance, grad
Atom Selection Options
The atoms parameter in PyCV accepts three types of input:
# Option 1: Direct indices (0-based)
cv = DistanceCV(atoms=[0, 1], prefix="dist")
# Option 2: None to select all atoms
cv = DistanceCV(atoms=None, prefix="dist_all")
# Option 3: AtomSelector for dynamic selection
import hillclimber as hc
cv = DistanceCV(atoms=hc.HeavyAtomSelector(), prefix="heavy")
cv = DistanceCV(atoms=hc.ElementSelector(symbols=["C", "O"]), prefix="co")
cv = DistanceCV(atoms=hc.SMARTSSelector(pattern="[OH]"), prefix="oh")
Important: In your compute() method:
- The
atomsparameter is an ASE Atoms object containing only the selected atoms (not the full system). Indices in this object start at 0. self.atomsis still your original selector/list/None if you need to access it for any reason.
Using PyCV with ZnTrack
PyCV integrates seamlessly with ZnTrack workflows:
# main.py
import zntrack
import ipsuite as ips
import hillclimber as hc
from cv import DistanceCV # Import from standalone module
# Define your model (e.g., MACE, LJ, etc.)
class MyModel(zntrack.Node):
def get_calculator(self, **kwargs):
# Return your ASE calculator
...
project = zntrack.Project()
with project:
data = ... # Your data node providing atoms
# Create the PyCV
cv = DistanceCV(atoms=[0, 1], prefix="dist")
# Configure the bias
bias = hc.MetadBias(
cv=cv,
sigma=0.1,
grid_min=2.0,
grid_max=6.0,
grid_bin=100,
)
# Configure metadynamics
config = hc.MetaDynamicsConfig(
height=0.01,
pace=10,
temp=300.0,
)
# Create the biased model
metad = hc.MetaDynamicsModel(
config=config,
data=data.frames,
bias_cvs=[bias],
model=MyModel(),
)
# Run MD with ipsuite
md = ips.ASEMD(
data=data.frames,
data_ids=-1,
model=metad,
thermostat=ips.LangevinThermostat(
temperature=300.0,
friction=0.01,
time_step=1.0,
),
steps=1000,
sampling_rate=10,
)
project.repro()
Important: The PyCV class should be defined in a standalone module (not __main__) that can be imported by PLUMED's Python interface. The module should only import what's necessary for the CV computation to avoid import issues in the PLUMED subprocess.
Documentation
Currently, there is no documentation available. Please refer to /examples for usage examples.
Metadata
Release files for hillclimber 0.1.8
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| hillclimber-0.1.8.tar.gz | 4.4 MB | With provenance | Details |
Built distributions (wheels)
Total release size: 623.2 MB
Release files / hillclimber-0.1.8.tar.gz
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