ALCHEMI Toolkit is a Python framework that uses GPUs to run atomic simulations and train machine-learned models for chemistry and materials science. Researchers and developers use it for molecular dynamics, geometry relaxation, and model training across one or multiple GPUs. Its catalogue add-ons guide coding agents in using the toolkit’s APIs and repository conventions.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add NVIDIA/nvalchemi-toolkit --skill nvalchemi-dynamics-hooksgit clone --depth 1 https://github.com/NVIDIA/nvalchemi-toolkitWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/nvidia/nvalchemi-toolkit/nvalchemi-dynamics-hooks)<a href="https://agentmods.dev/skills/nvidia/nvalchemi-toolkit/nvalchemi-dynamics-hooks"><img src="https://agentmods.dev/badge/skills/nvidia/nvalchemi-toolkit/nvalchemi-dynamics-hooks/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/nvidia/nvalchemi-toolkit/nvalchemi-dynamics-hooks"><img src="https://agentmods.dev/badge/skills/nvidia/nvalchemi-toolkit/nvalchemi-dynamics-hooks.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00069 | $0.04091 |
| Opus 5.5 | $0.00028 | $0.01636 |
| Sonnet 5.5 | $0.00014 | $0.00818 |
| Haiku 4.5 | $0.00007 | $0.00409 |
Grade A, and why
nvalchemi-dynamics-hooks scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 495 lines — stays where its author put it; the contents beside it link to each section on GitHub.
nvalchemi Hooks
Overview
Hooks are callbacks that fire at specific points during each workflow step.
They observe or modify batch state without changing the engine itself.
The hook system is framework-wide: the same Hook protocol works for
dynamics and custom pipelines. Dynamics engines pass DynamicsContext;
custom engines can pass HookContext or their own context subclass.
from nvalchemi.hooks import (
BiasedPotentialHook,
DynamicsContext,
Hook,
HookContext,
HookRegistryMixin,
NeighborListHook,
WrapPeriodicHook,
)
from nvalchemi.dynamics.base import DynamicsStage
from nvalchemi.dynamics.hooks import (
EnergyDriftMonitorHook,
LoggingHook,
MaxForceClampHook,
NaNDetectorHook,
SnapshotHook,
StageTimingHook,
TorchProfilerHook,
)
Hook protocol
Any object with these attributes satisfies the Hook protocol (runtime-checkable):
class Hook(Protocol):
frequency: int # execute every N steps (1 = every step)
stage: Enum | None # stage enum value (None for stage-agnostic hooks)
def __call__(self, ctx: HookContext, stage: Enum) -> None:
"""Called with a context snapshot and the current stage."""
...
A hook fires when step_count % hook.frequency == 0 (so all hooks fire at
step 0), except ON_ADMISSION, which fires once per admission regardless of
frequency.
HookContext — base snapshot shared by hook-enabled workflows:
@dataclass(kw_only=True)
class HookContext:
batch: Batch # current batch (all engines)
model: BaseModelMixin | None = None
global_rank: int = 0 # distributed rank
workflow: Any = None # back-reference to the engine
DynamicsContext — context passed by dynamics engines:
@dataclass(kw_only=True)
class DynamicsContext(HookContext):
step_count: int = 0
converged_mask: torch.Tensor | None = None
active_graph_mask: torch.Tensor | None = None
graduated_mask: torch.Tensor | None = None # ON_GRADUATE only
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago Changed · +8 lines 2e9a40fdbb23
- 1mo ago Changed · +4 lines 75386676d366
- 1mo ago Changed · +20 lines 0d57c2d7e842
- 1mo ago Changed · +37 lines b7397e2ba0d8
- 2mo ago First seen · 426 lines · 69 tokens per session scan A 850829606aaf
nvalchemi-dynamics-hooks is a skill published in the GitHub repository NVIDIA/nvalchemi-toolkit (204 stars, last pushed yesterday), licensed Apache-2.0. It adds 69 tokens to every session and 4,091 once invoked, about $0.0003 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
nvalchemi-dynamics-hooks compared with skills from other repositories
| Mod | Type | Stars | Last push | Licence | Scan | Tokens | Works with |
|---|---|---|---|---|---|---|---|
| nvalchemi-dynamics-hooksNVIDIA/nvalchemi-toolkit | Skill | 204 | yesterday | Apache-2.0 | A | 69 | Claude Code |
| instrument-data-to-allotropeanthropics/knowledge-work-plugins | Skill | 35k | 2d ago | Apache-2.0 | A | 123 | Claude Code |
| exploratory-data-analysisK-Dense-AI/scientific-agent-skills | Skill | 56k | 4d ago | MIT | A | 83 | Claude Code |
| matlabK-Dense-AI/scientific-agent-skills | Skill | 56k | 4d ago | MIT | A | 44 | Claude Code |
| phylogeneticsK-Dense-AI/scientific-agent-skills | Skill | 56k | 4d ago | MIT | A | 71 | Claude Code, Codex |
| research-engineerdavila7/claude-code-templates | Skill | 33k | yesterday | MIT | A | 43 | Claude Code, Codex |
| mapping-to-snomedmaziyarpanahi/openmed | Skill | 5.8k | yesterday | Apache-2.0 | A | 205 | Claude Code |