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-reportinggit 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-reporting)<a href="https://agentmods.dev/skills/nvidia/nvalchemi-toolkit/nvalchemi-reporting"><img src="https://agentmods.dev/badge/skills/nvidia/nvalchemi-toolkit/nvalchemi-reporting/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-reporting"><img src="https://agentmods.dev/badge/skills/nvidia/nvalchemi-toolkit/nvalchemi-reporting.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Excessive Agency · line 280 Skill enables autonomous high-impact decisions without human-in-the-loop verification. Critical operations (destructive commands, financial transactions, data deletion) should require explicit user confirmation.Fix: Add human-in-the-loop confirmation for destructive, irreversible, or high-impact operations. Never auto-execute commands that modify files, send data, or alter system state.
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 | $0.00086 | $0.02200 |
| Opus 5.5 | $0.00034 | $0.00880 |
| Sonnet 5.5 | $0.00017 | $0.00440 |
| Haiku 4.5 | $0.00009 | $0.00220 |
Grade A, and why
nvalchemi-reporting 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 17d 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 — 290 lines — stays where its author put it; the contents beside it link to each section on GitHub.
nvalchemi Reporting
Overview
Use reporting for curated workflow summaries and dashboards. Use logging for
direct event records such as per-system dynamics rows. See
docs/userguide/reporting.md, docs/userguide/training.md,
docs/userguide/dynamics.md, and docs/userguide/hooks.md for full details.
from nvalchemi.hooks import (
ReportingOrchestrator,
RichReporter,
TensorBoardReporter,
)
from nvalchemi.dynamics.hooks import LoggingHook
Choose The Layer
Use ReportingOrchestrator when the user wants progress summaries, live Rich
dashboards, TensorBoard scalar snapshots, rank reductions, or one observability
hook that works across training, dynamics, and custom hook-enabled workflows.
ReportingOrchestrator is the hook to register with hooks=[...] or
register_hook(...); RichReporter, TensorBoardReporter, and custom
Reporter objects are sinks owned by that hook and are not registered directly.
Workflow engines enter and close hook context managers automatically during
run(), so user code should not wrap reporting hooks manually in normal cases.
Use nvalchemi.dynamics.hooks.LoggingHook when the user wants a
durable dynamics event stream with one row per graph or group. By default, it
computes dynamics observables such as energy, fmax, temperature, status, and
graph index, then writes one row per system to CSV, TensorBoard, or a custom writer.
With by_group=True, it writes one row per batch group with step, group_idx,
and status, even without custom scalars. Optional custom scalars add or override
columns with one value per group or a broadcast scalar.
Do not reuse the dynamics LoggingHook as a training logger. For training,
prefer reporters unless the task explicitly requires a raw training-event log;
then implement a training-specific hook with the same hook protocol.
Training Pattern
Attach the ReportingOrchestrator as a normal training hook. Pick stages by
enum name when the code already serializes hook specs or when avoiding imports
in config files. Use AFTER_OPTIMIZER_STEP for high-frequency loss and
learning-rate progress, and validation stages when summaries should align with
validation output.
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.
- 17d ago Changed · +4 lines 6c7849522266
- 1mo ago First seen · 286 lines · 86 tokens per session scan A 0e47cedbb114
nvalchemi-reporting is a skill published in the GitHub repository NVIDIA/nvalchemi-toolkit (192 stars, last pushed yesterday), licensed Apache-2.0. It adds 86 tokens to every session and 2,200 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.
Other skills, from other repositories
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…
exploratory-data-analysis
Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…
matlab
Builds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows. Use for arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.
phylogenetics
Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein…
research-engineer
An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.
presenting-conference-talks
Generates conference presentation slides (Beamer LaTeX PDF and editable PPTX) from a compiled paper with speaker notes and talk script. Use when preparing oral talks, spotlight presentations, or invited talks for ML and systems conferences.