-
Notifications
You must be signed in to change notification settings - Fork 158
docs(skills): add dpdata driver skill #953
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Merged
njzjz
merged 3 commits into
deepmodeling:master
from
njzjz-bot:skills/dpdata-driver-skill
Mar 23, 2026
+158
−0
Merged
Changes from all commits
Commits
File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -34,3 +34,7 @@ tests/data_*.h5 | |
| tests/data_*/ | ||
| tests/tmp.* | ||
| tests/.coverage | ||
|
|
||
| # local dev artifact | ||
| uv.lock | ||
| .venv/ | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| --- | ||
| name: dpdata-driver | ||
| description: 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. | ||
| license: LGPL-3.0-or-later | ||
| compatibility: Requires dpdata or uv for running dpdata | ||
| metadata: | ||
| author: njzjz-bot | ||
| version: '1.0' | ||
| --- | ||
|
|
||
| # 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 `System` into a `LabeledSystem` by 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: | ||
|
|
||
| ```python | ||
| 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: | ||
|
|
||
| - `ase` | ||
| - `dp` / `deepmd` / `deepmd-kit` | ||
| - `gaussian` | ||
| - `sqm` | ||
| - `hybrid` | ||
|
|
||
| (Exact set depends on dpdata version and installed extras.) | ||
|
|
||
| ## Minimal workflow | ||
|
|
||
| ```python | ||
| 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 | ||
|
|
||
| ```python | ||
| 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`. | ||
|
|
||
| ```python | ||
| # /// script | ||
| # requires-python = ">=3.8" | ||
| # dependencies = [ | ||
| # "dpdata", | ||
| # "numpy", | ||
| # "ase", | ||
njzjz-bot marked this conversation as resolved.
Show resolved
Hide resolved
|
||
| # ] | ||
| # /// | ||
| ``` | ||
|
|
||
| Script: | ||
|
|
||
| ```python | ||
| 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 | ||
|
|
||
| ```python | ||
| 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 `Driver` instance | ||
| - a dict like `{"type": "sqm", ...}` (type is the driver key) | ||
|
|
||
| Example (structure only; may require external executables): | ||
|
|
||
| ```python | ||
| 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: | ||
| - `dp` requires `deepmd-kit` + a model file | ||
| - `gaussian` requires Gaussian and a valid executable (default `g16`) | ||
| - `sqm` requires AmberTools `sqm` | ||
| - If you just need file format conversion, use the existing **dpdata CLI** skill instead. | ||
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.