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 agentmods add skills/internscience/chemclaw/pdf-dft-extractornpx skills add InternScience/ChemClaw --skill pdf-dft-extractorgit clone --depth 1 https://github.com/InternScience/ChemClawWrote 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/internscience/chemclaw/pdf-dft-extractor)<a href="https://agentmods.dev/skills/internscience/chemclaw/pdf-dft-extractor"><img src="https://agentmods.dev/badge/skills/internscience/chemclaw/pdf-dft-extractor.svg" alt="Measured on agentmods" height="20"></a>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 | $0.00066 | $0.02596 |
| Opus 5 | $0.00033 | $0.01298 |
| Sonnet 5 | $0.00013 | $0.00519 |
| Haiku 4.5 | $0.00007 | $0.00260 |
Grade A, and why
pdf-dft-extractor 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 5d 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 — 294 lines — stays where its author put it; the contents beside it link to each section on GitHub.
PDF DFT Extractor | DFT坐标提取器
Extract DFT calculation coordinates from PDF files (especially supplementary materials) and generate Gaussian input files (.gjf). Supports batch processing with separate output folders for each PDF. 从PDF文件（特别是论文支撑材料）中提取DFT计算坐标，生成Gaussian输入文件(gjf)。支持批量处理，每个PDF文件单独生成一个输出文件夹。
功能特性
- 📄 PDF转Markdown: 使用MinerU API将PDF转换为结构化Markdown
- 🧮 自动提取DFT坐标: 从计算化学部分自动识别和提取分子坐标
- 📁 批量处理: 支持同时处理多个PDF文件
- 📂 独立输出: 每个PDF文件生成单独的输出文件夹
- ⚙️ 可配置参数: 支持自定义CPU核数、内存、计算方法等
快速开始
命令行使用
# 单个PDF文件
python extract_dft.py paper.pdf
# 批量处理整个目录
python extract_dft.py ./pdfs/
# 指定输出目录和计算参数
python extract_dft.py ./pdfs/ -o ./output/ --cpu 64 --mem 128GB
Python API使用
from extract_dft import process_pdf, batch_process
# 处理单个PDF
result = process_pdf(
pdf_path="paper.pdf",
output_dir="./output/paper1",
cpu=64,
mem="128GB",
method="B3PW91/def2TZVP em=d3bj"
)
# 批量处理
results = batch_process(
pdf_dir="./pdfs/",
output_base_dir="./output",
cpu=64,
mem="128GB"
)
参数说明
| 参数 | 默认值 | 说明 |
|---|---|---|
-o, --output |
./dft_output |
输出目录 |
--cpu |
64 | CPU核数 |
--mem |
128GB | 内存 |
--method |
B3PW91/def2TZVP em=d3bj | 计算方法和色散校正 |
--solvent |
SMD(toluene) | 溶剂模型 |
--charge |
0 | 电荷 |
--multiplicity |
1 | 自旋多重度 |
--keywords |
opt freq | 计算关键词 |
--keep-temp |
False | 保留临时文件 |
关于Gaussian计算方法的写法
在Gaussian中，色散校正需要单独使用em=关键词指定，不要写成B3PW91-D3(BJ)的形式。
✅ 正确写法：
# B3PW91/def2TZVP em=d3bj opt freq
❌ 错误写法：
# B3PW91-D3(BJ)/def2TZVP opt freq ← 这种写法Gaussian不识别
常用色散校正关键词：
| 色散校正 | 关键词 |
|---|---|
| D3 with Becke-Johnson damping | em=d3bj |
| D3 with zero damping | em=d3 or em=gd3 |
| D3(BJ) for DFT-D3 | em=d3bj |
| Grimme's GD3 | em=gd3 |
| GD3BJ | em=gd3bj |
示例对比：
# B3PW91 with D3BJ
--method "B3PW91/def2TZVP em=d3bj"
# B3LYP with GD3
--method "B3LYP/6-31G(d) em=gd3"
# PBE0 with D3BJ
--method "PBE1PBE/def2TZVP em=d3bj"
# ωB97X-D (已内置色散，无需额外添加)
--method "wB97XD/def2TZVP"
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
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.
- 5d ago First seen · 294 lines · 66 tokens per session scan A 699c5dc8dc23
pdf-dft-extractor is a skill published in the GitHub repository InternScience/ChemClaw (52 stars, last pushed 5mo ago), licensed MIT. It adds 66 tokens to every session and 2,596 once invoked, about $0.0003 per session on Opus 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.
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