Dpdata driver
Skill jinzhezenggroup/computational-chemistry-agent-skills/tools/dpdata-driver
Use dpdata Python Driver plugins to label systems (energies/forces/virials) via System.predict(), list available drivers, and build Driver objects (ase/deepmd/gaussian/sqm/hybrid). Use when working with dpdata Python API (not CLI) and you need driver-based energy/force prediction, plugin registration keys, or examples of using dpdata with ASE calculators or DeePMD models.From its SKILL.md
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SKILL.md
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dpdata-driver
Use dpdata “driver plugins” to label a dpdata.System (predict energies/forces/virials) and obtain a dpdata.LabeledSystem.
Key idea
- A Driver converts an unlabeled
Systeminto aLabeledSystemby computing:energies(required)forces(optional but common)virials(optional)
In dpdata, this is exposed as:
System.predict(*args, driver="dp", **kwargs) -> LabeledSystem
driver can be:
- a string key (plugin name), e.g.
"ase","dp","gaussian" - a Driver object, e.g.
Driver.get_driver("ase")(...)
List supported driver keys (runtime)
When unsure what drivers exist in this dpdata version/env, query them at runtime:
import dpdata
from dpdata.driver import Driver
print(sorted(Driver.get_drivers().keys()))
import dpdata ensures built-in plugins are loaded before listing registered drivers.
In the current repo state, keys include:
asedp/deepmd/deepmd-kitgaussiansqmhybrid
(Exact set depends on dpdata version and installed extras.)
Minimal workflow
import dpdata
from dpdata.system import System
sys = System("input.xyz", fmt="xyz")
ls = sys.predict(driver="ase", calculator=...) # returns dpdata.LabeledSystem
Verify you got a labeled system
assert "energies" in ls.data
# optional:
# assert "forces" in ls.data
# assert "virials" in ls.data
Example: use the ASE driver with an ASE calculator (runnable)
This is the easiest fully runnable example because it doesn’t require external QM software.
Dependencies (recommended): declare script dependencies with uv inline metadata, then run with uv run.
# /// script
# requires-python = ">=3.8"
# dependencies = [
# "dpdata",
# "numpy",
# "ase",
# ]
# ///
Script:
from pathlib import Path
import numpy as np
from ase.calculators.lj import LennardJones
from dpdata.system import System
# write a tiny molecule
Path("tmp.xyz").write_text("""2\n\nH 0 0 0\nH 0 0 0.74\n""")
sys = System("tmp.xyz", fmt="xyz")
ls = sys.predict(driver="ase", calculator=LennardJones())
print("energies", np.array(ls.data["energies"]))
print("forces shape", np.array(ls.data["forces"]).shape)
if "virials" in ls.data:
print("virials shape", np.array(ls.data["virials"]).shape)
else:
print("virials: <not provided by this driver/calculator>")
Example: pass a Driver object instead of a string
from ase.calculators.lj import LennardJones
from dpdata.driver import Driver
from dpdata.system import System
sys = System("tmp.xyz", fmt="xyz")
ase_driver = Driver.get_driver("ase")(calculator=LennardJones())
ls = sys.predict(driver=ase_driver)
Hybrid driver
Use driver="hybrid" to sum energies/forces/virials from multiple drivers.
The HybridDriver accepts drivers=[ ... ] where each item is either:
- a
Driverinstance - a dict like
{"type": "sqm", ...}(type is the driver key)
Example (structure only; may require external executables):
from dpdata.driver import Driver
hyb = Driver.get_driver("hybrid")(
drivers=[
{"type": "sqm", "qm_theory": "DFTB3"},
{"type": "dp", "dp": "frozen_model.pb"},
]
)
# ls = sys.predict(driver=hyb)
Notes / gotchas
- Many drivers require extra dependencies or external programs:
dprequiresdeepmd-kit+ a model filegaussianrequires Gaussian and a valid executable (defaultg16)sqmrequires AmberToolssqm
- If you just need file format conversion, use the existing dpdata CLI skill instead.
What ships with it
Read from the repository
Just SKILL.md. No reference files, no scripts.