jinzhezenggroup/computational-chemistry-agent-skills/dpdata-minimizer

dpdata-minimizer

Use dpdata “minimizer plugins” to optimize/minimize geometry and return a dpdata.LabeledSystem.

Key idea

• A Minimizer performs geometry optimization (updates coordinates) and returns labeled results.
• dpdata exposes this as:

System.minimize(*args, minimizer: str|Minimizer, **kwargs) -> LabeledSystem

List supported minimizer keys (runtime)

from dpdata.driver import Minimizer
print(sorted(Minimizer.get_minimizers().keys()))

In the current dpdata repo, minimizer keys include:

• ase
• sqm

Relationship to drivers (important)

Some minimizers require a dpdata Driver object.

Example: ASEMinimizer takes a dpdata Driver in its constructor:

• minimizer="ase" requires driver=<dpdata Driver> (e.g. the ASE driver wrapping an ASE calculator).

So you generally do:

1. Construct a driver
2. Construct a minimizer (or let dpdata do it by passing the right kwargs)
3. Call System.minimize(...)

Runnable example: ASE minimizer with an ASE calculator

Use uv inline script metadata so the example runs reproducibly with uv run.

# /// script
# requires-python = ">=3.12"
# dependencies = [
#   "dpdata",
#   "numpy",
#   "ase",
# ]
# ///
import numpy as np
from ase.calculators.emt import EMT
from dpdata.driver import Driver
from dpdata.system import System
open("tmp.xyz", "w").write("""2\n\nH 0 0 0\nH 0 0 0.74\n""")
sys = System("tmp.xyz", fmt="xyz")
# Build a dpdata driver that can provide energies/forces to ASE optimizers.
ase_driver = Driver.get_driver("ase")(calculator=EMT())
# Minimize using the ASE minimizer plugin.
# NOTE: ASEMinimizer expects `driver` (not `calculator`) as input.
ls = sys.minimize(minimizer="ase", driver=ase_driver, fmax=0.05, max_steps=5)
print("coords", np.array(ls.data["coords"]).shape)
print("energies", np.array(ls.data["energies"]))
print("forces", np.array(ls.data["forces"]).shape)

Notes / gotchas

• System.minimize(...) accepts either a minimizer key string or a Minimizer object.
• If you previously used System.predict(driver="ase", calculator=...), be aware that minimization is different: you need to pass a driver into the minimizer (ASEMinimizer does not accept calculator=).
• sqm minimizer requires AmberTools sqm executable and typically won’t be runnable in CI.