Academic Paper Writing Pipeline
Imbad0202/academic-research-skills
Runs a 12-agent pipeline that plans, drafts, cites, reviews and formats academic papers, with modes for revision, rebuttals, abstracts and citation checks.
Extract concrete computational tasks from papers, supplementary information, peer-review files, reviewer comments, reports, or manuscript PDFs, and seed .research evidence artifacts such as…
Install Literature To Calculation
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill literature-to-calculation -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist literature-to-calculation --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .claude/skills && cp -r skills-src/procedures/literature-to-calculation .claude/skills/literature-to-calculation && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "literature-to-calculation" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/procedures/literature-to-calculation into .claude/skills/literature-to-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-to-calculation", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/procedures/literature-to-calculationType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill literature-to-calculation -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist literature-to-calculation --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .agents/skills && cp -r skills-src/procedures/literature-to-calculation .agents/skills/literature-to-calculation && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "literature-to-calculation" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/procedures/literature-to-calculation into .agents/skills/literature-to-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-to-calculation", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill literature-to-calculation -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist literature-to-calculation --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/procedures/literature-to-calculation .cursor/skills/literature-to-calculation && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "literature-to-calculation" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/procedures/literature-to-calculation into .cursor/skills/literature-to-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-to-calculation", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/JCLiuGroup/AI-Computational-Chemist.git --path procedures/literature-to-calculation--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill literature-to-calculation -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist literature-to-calculation --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/procedures/literature-to-calculation .gemini/skills/literature-to-calculation && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "literature-to-calculation" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/procedures/literature-to-calculation into .gemini/skills/literature-to-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-to-calculation", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install JCLiuGroup/AI-Computational-Chemist literature-to-calculationInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill literature-to-calculation -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .github/skills && cp -r skills-src/procedures/literature-to-calculation .github/skills/literature-to-calculation && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "literature-to-calculation" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/procedures/literature-to-calculation into .github/skills/literature-to-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-to-calculation", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill literature-to-calculation -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist literature-to-calculation --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/procedures/literature-to-calculation .opencode/skills/literature-to-calculation && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "literature-to-calculation" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/procedures/literature-to-calculation into .opencode/skills/literature-to-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-to-calculation", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
literature-to-calculation- GitHub stars
- 148
- Used in
- 1 other repo
- Token cost
- ~1.2k tokens
- SKILL.md length
- 482 words
- Files
- 2 (incl. references)
- Skills in repo
- 21
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Extract concrete computational tasks from papers, supplementary information, peer-review files, reviewer comments, reports, or manuscript PDFs, and seed .research evidence artifacts such as…
- Works in 8 steps: Source: title, document type,… → Claim or concern requiring computation,… → System: composition, structure/phase,… → …
- Codex must turn document evidence into DFT
- SKILL.md covers Extract, Reproduction vs. Exploration, Seed .research Evidence and Route, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Literature To Calculation is an agent skill from JCLiuGroup/AI-Computational-Chemist. Extract concrete computational tasks from papers, supplementary information, peer-review files, reviewer comments, reports, or manuscript PDFs, and seed .research evidence artifacts such as method-fingerprint, model-observable-decision, and triage-plan before routing to computational chemistry workflow or tool skills. Use when Codex must turn document evidence into DFT, quantum chemistry, MD, MLP, structure-preparation, or analysis work.
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/research-artifacts.md`).
It sits in Research & Science.
When your agent uses it
- Codex must turn document evidence into DFT
- Quantum chemistry
- Structure-preparation
Example prompts
- “/literature-to-calculation”
Workflow steps
8 steps, taken from the first numbered list in SKILL.md.
- Source: title, document type, DOI/arXiv/report ID if available, and exact page, section, table, or figure.
- Claim or concern requiring computation, quoted only briefly when needed and otherwise tightly paraphrased.
- System: composition, structure/phase, surface and termination, defects, adsorbates, charge, spin, temperature, pressure, solvent…
- Method: code/version, functional, basis or pseudopotentials, U values, dispersion, force field, k-mesh/cutoff, convergence criteria…
- Required inputs: structures, coordinates, tables, trajectories, prior outputs, model parameters, and whether each is actually provided.
- Expected outputs: energies, barriers, structures, charges, DOS/bands, phonons, spectra, trajectories, free energies, step diagrams, plots…
- Comparison target: the paper's value, a trend, a reviewer threshold, or an experimental observable, with units and sign convention.
- Missing items that block a true reproduction.
What it can do on your machine
Read from SKILL.md and the folder at commit e27b555. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Literature To Calculation loads about 1.2k tokens when it runs, and up to ~2.9k if it reads all its reference files. Until then it costs about 117 tokens; SKILL.md has 482 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 482 words (~1,186 tokens).
“Use this before any calculation when the task originates from a document. The goal is a concrete, checkable calculation target and durable evidence, not a paper summary.”
- name
- literature-to-calculation
Files
SKILL.md and 1 other file (references) in procedures/literature-to-calculation of JCLiuGroup/AI-Computational-Chemist.
- SKILL.md
- references/research-artifacts.md
Open the folder on GitHubat commit e27b555
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in JCLiuGroup/AI-Computational-Chemist, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Literature To Calculation next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Literature To Calculation this skillJCLiuGroup/AI-Computational-Chemist | 148 | 1 repos | ~1.2k | Automated safety check: Pass | Custom licence | |
| Academic Paper Writing PipelineImbad0202/academic-research-skills | 51k | — | ~16k | Automated safety check: Pass | Custom licence | |
| Scientific Venue Templatesdavila7/claude-code-templates | 33k | 9 repos | ~5.1k | Automated safety check: Notes | MIT | |
| Horizontal-Vertical Deep ResearchKKKKhazix/khazix-skills | 21k | — | ~2.1k | Automated safety check: Pass | MIT | |
| Econ Writehanlulong/econ-writing-skill | 651 | 2 repos | ~14k | Automated safety check: Pass | MIT | |
| Math Modeling Competition WorkflowXiaoMaColtAI/math-modeling-skill | 1.9k | — | ~1.2k | Automated safety check: Pass | None |
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Related
Categories
Questions about Literature To Calculation
What does Literature To Calculation do?
Extract concrete computational tasks from papers, supplementary information, peer-review files, reviewer comments, reports, or manuscript PDFs, and seed .research evidence artifacts such as…. Literature To Calculation is an agent skill from JCLiuGroup/AI-Computational-Chemist.research evidence artifacts such as method-fingerprint, model-observable-decision, and triage-plan before routing to computational chemistry workflow or tool skills.
When should I use Literature To Calculation?
Literature To Calculation fits situations like: Codex must turn document evidence into DFT; quantum chemistry; structure-preparation.
How do I install Literature To Calculation in Claude Code?
Run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill literature-to-calculation -a claude-code`. Or copy the skill folder (procedures/literature-to-calculation in JCLiuGroup/AI-Computational-Chemist) into .claude/skills/literature-to-calculation in your project. Claude Code loads it when a task matches its description.
How do I install Literature To Calculation in Codex?
Run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill literature-to-calculation -a codex`. Or copy the skill folder (procedures/literature-to-calculation in JCLiuGroup/AI-Computational-Chemist) into .agents/skills/literature-to-calculation in your project. Codex loads it when a task matches its description.
Can I use Literature To Calculation in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill literature-to-calculation -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/literature-to-calculation, .gemini/skills/literature-to-calculation, .github/skills/literature-to-calculation and .opencode/skills/literature-to-calculation in your project.
What does Literature To Calculation need to run?
SKILL.md names no scripts, command-line tools or credentials: Literature To Calculation is instructions for the agent only.
Does Literature To Calculation access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Literature To Calculation safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Literature To Calculation use?
Literature To Calculation has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Literature To Calculation use?
About 1.2k tokens (SKILL.md is roughly 4.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.7k tokens, read only when the agent opens those files.
What are the alternatives to Literature To Calculation?
Skills that share tags, products or a category with Literature To Calculation: Academic Paper Writing Pipeline (Imbad0202/academic-research-skills, 51k stars), Scientific Venue Templates (davila7/claude-code-templates, 33k stars), Horizontal-Vertical Deep Research (KKKKhazix/khazix-skills, 21k stars) and Econ Write (hanlulong/econ-writing-skill, 651 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Literature To Calculation?
JCLiuGroup (a GitHub organization) maintains it in JCLiuGroup/AI-Computational-Chemist, which has 148 GitHub stars. The repository holds 21 skills in this directory. The repository was last updated on September 27, 2026.
Source: JCLiuGroup/AI-Computational-Chemist on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.