Bulk Rnaseq
K-Dense-AI/scientific-agent-skills
Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression.
Calculate equation of state (bulk modulus, equilibrium volume) using MLIPs.
MITAuto-check passed
Install Mat Equation Of State
$ npx skills add learningmatter-mit/AtomisticSkills --skill mat-equation-of-state -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills mat-equation-of-state --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/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/mat-equation-of-state .claude/skills/mat-equation-of-state && 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 "mat-equation-of-state" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-equation-of-state into .claude/skills/mat-equation-of-state/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-equation-of-state", 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/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-equation-of-stateType 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 learningmatter-mit/AtomisticSkills --skill mat-equation-of-state -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills mat-equation-of-state --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/mat-equation-of-state .agents/skills/mat-equation-of-state && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "mat-equation-of-state" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-equation-of-state into .agents/skills/mat-equation-of-state/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-equation-of-state", 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 learningmatter-mit/AtomisticSkills --skill mat-equation-of-state -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills mat-equation-of-state --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/mat-equation-of-state .cursor/skills/mat-equation-of-state && 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 "mat-equation-of-state" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-equation-of-state into .cursor/skills/mat-equation-of-state/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-equation-of-state", 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/learningmatter-mit/AtomisticSkills.git --path skills/mat-equation-of-state--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 learningmatter-mit/AtomisticSkills --skill mat-equation-of-state -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills mat-equation-of-state --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/mat-equation-of-state .gemini/skills/mat-equation-of-state && 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 "mat-equation-of-state" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-equation-of-state into .gemini/skills/mat-equation-of-state/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-equation-of-state", 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 learningmatter-mit/AtomisticSkills mat-equation-of-stateInstalls 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 learningmatter-mit/AtomisticSkills --skill mat-equation-of-state -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/mat-equation-of-state .github/skills/mat-equation-of-state && 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 "mat-equation-of-state" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-equation-of-state into .github/skills/mat-equation-of-state/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-equation-of-state", 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 learningmatter-mit/AtomisticSkills --skill mat-equation-of-state -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills mat-equation-of-state --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/mat-equation-of-state .opencode/skills/mat-equation-of-state && 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 "mat-equation-of-state" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-equation-of-state into .opencode/skills/mat-equation-of-state/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-equation-of-state", 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
mat-equation-of-state- GitHub stars
- 176
- Token cost
- ~1.2k tokens
- SKILL.md length
- 549 words
- Files
- 6 (incl. scripts)
- Skills in repo
- 129
- Repo updated
- First seen
- Licence
- MIT
At a glance
Calculate equation of state (bulk modulus, equilibrium volume) using MLIPs.
- Works in 6 steps: Prerequisites → Choosing a Foundation Potential → Calculation Workflow → …
- SKILL.md covers Goal, 1. Prerequisites, 2. Choosing a Foundation… and 3. Calculation Workflow, plus 3 more sections
- Runs Python scripts from its folder
What it does
Mat Equation Of State is an agent skill from learningmatter-mit/AtomisticSkills. Calculate equation of state (bulk modulus, equilibrium volume) using MLIPs.
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 8 other files, including scripts (for example `examples/Si/README.md`, `examples/Si/eos_results.json` and `scripts/calculate_eos.py`).
The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.
Example prompts
- “/mat-equation-of-state”
Requirements
- Python 3
Workflow steps
6 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 6257444. 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
Ships 1 file in scripts/ (Python), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
github.com
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
Mat Equation Of State loads about 1.2k tokens when it runs. Until then it costs about 24 tokens; SKILL.md has 549 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); the scripts in this folder are not scanned.
SKILL.md
The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 549 words, ~1,184 tokens.
Download SKILL.mdSave it as
.claude/skills/mat-equation-of-state/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.- name
- mat-equation-of-state
- description
- Calculate equation of state (bulk modulus, equilibrium volume) using MLIPs.
- metadata.category
- materials
- metadata.venv
- mlip
Equation of State Skill
This skill provides tools for calculating the equation of state (EOS) of crystalline materials using Machine Learning Interatomic Potentials (MLIPs). The EOS describes the relationship between volume, energy, and pressure, allowing extraction of bulk modulus and equilibrium volume.
Goal
Calculate the equation of state for a material by applying volumetric strains, computing the energy-volume relationship, and fitting to the Birch-Murnaghan equation to determine the bulk modulus ($B_0$) and equilibrium volume ($V_0$).
1. Prerequisites
- The appropriate MLIP wrapper must be available (
MACEWrapper,MatGLWrapper, orFAIRCHEMWrapper). matcalcis included in themlipandfairchemenvironments.- A relaxed structure file (CIF, POSCAR, or other ASE-readable format).
2. Choosing a Foundation Potential
EOS calculations require accurate total energies across different volumes.
[!IMPORTANT]
- Use OMAT or MatPES trained models: These models (e.g.,
MACE-OMAT-0-small,CHGNet-MatPES-PBE,TensorNet-MatPES-r2SCAN) provide more reliable energy predictions.- MPtrj models can be used: Unlike phonon calculations, EOS is less sensitive to force accuracy, but OMAT/MatPES models are still recommended for best results.
Refer to the foundation-potentials skill for more details.
3. Calculation Workflow
To calculate the equation of state, use the calculate_eos.py script:
${CLAUDE_SKILL_DIR}/../../venv/run mlip python ${CLAUDE_SKILL_DIR}/scripts/calculate_eos.py \
--structure path/to/relaxed_structure.cif \
--model_type mace \
--model_name MACE-OMAT-0-small \
--n_points 11 \
--max_abs_strain 0.1 \
--relax_structure \
--output_dir research/my_folder/eosKey Parameters:
--n_points: Number of strain points (default: 11)--max_abs_strain: Maximum linear strain applied (default: 0.1 = ±10%, i.e. volumes spanning (1±0.1)^3)--relax_structure/--no-relax_structure(default on): fully relax the input cell (ions and cell vectors) before the strain scan, so the scan is centred on this model's own equilibrium volume rather than whatever volume the input file happens to have. It does not control the per-strain relaxation -- matcalc relaxes every strained point regardless.--allow_shape_change/--no-allow_shape_change(default on, matcalc >= 0.5): at each strain point relax the cell shape at constant volume as well as the ions. This is the E(V) a Birch-Murnaghan fit assumes -- the minimum energy at fixed volume. Symmetry forbids shape relaxation in cubic cells, so it changes nothing there; for anisotropic cells, freezing the shape overestimates B0.--fmax: Force convergence tolerance for relaxation (default: 0.1 eV/Å)
Show full SKILL.md (228 more words)Show less
4. Output Files
eos_results.json: Summary containing bulk modulus (GPa), equilibrium volume (ų), equilibrium energy (eV) and the R² of the fit. The equilibrium volume and energy are the Birch-Murnaghan minimum (v0, e0) -- not the volume or energy of any individual scan point.energies_volumes.dat: Energy-volume data points used for fitting. The same scan is repeated under theenergy_volume_curvekey ofeos_results.json, so the fit can always be reproduced from the summary alone.
5. Examples
See examples/ for detailed usage scenarios, including Silicon EOS calculation.
6. Constraints
- Environment: Scripts require an environment with MLIP packages installed (
venv/run <venv> ...):mlipfor MACE and MatGL/CHGNet modelsfairchemfor FairChem/UMA models
- Structure Relaxation: two distinct stages. The pre-relaxation (
--relax_structure) centres the scan on the model's equilibrium cell; the per-point relaxation always runs.--fmaxcurrently sets both -- the 0.1 eV/Å default is loose for a cell relaxation, and a pre-relaxation that stops early shifts the whole scan window and therefore B0. Tighten it (0.02-0.05) when B0 matters. V0 from the fit is far less sensitive than B0. - Strain Range: The default ±10% strain is suitable for most materials. For very soft or very hard materials, adjust
--max_abs_strainaccordingly. - Fitting Model: MatCalc fits the Birch-Murnaghan equation of state. Note that
--max_abs_strainis applied as a linear strain (target volume = (1+e)^3 x V0), despite matcalc's own docstring calling it volumetric.
Author: Bowen Deng Contact: GitHub @learningmatter-mit
© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 5 other files (scripts) in skills/mat-equation-of-state of learningmatter-mit/AtomisticSkills.
- SKILL.md
- examples/Si/README.md
- examples/Si/Si.cif
- examples/Si/energies_volumes.dat
- examples/Si/eos_results.json
- scripts/calculate_eos.py
Open the folder on GitHubat commit 6257444
Compare with similar skills
Mat Equation Of State 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 |
|---|---|---|---|---|---|---|
| Mat Equation Of State this skilllearningmatter-mit/AtomisticSkills | 176 | — | ~1.2k | Automated safety check: Pass | MIT | |
| Bulk RnaseqK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~4.2k | Automated safety check: Pass | MIT | |
| Eol Resistor Calculatorsickn33/agentic-awesome-skills | 47k | 1 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Geometric Volume CalculationInternScience/scp | 170 | 1 repos | ~527 | Automated safety check: Pass | MIT | |
| Material Density Volume CalculationInternScience/scp | 170 | 1 repos | ~497 | Automated safety check: Pass | MIT | |
| Bulk Ingestiongarrytan/gbrain | 31k | — | ~4.7k | Automated safety check: Pass | MIT |
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Questions about Mat Equation Of State
What does Mat Equation Of State do?
Calculate equation of state (bulk modulus, equilibrium volume) using MLIPs. Mat Equation Of State is an agent skill from learningmatter-mit/AtomisticSkills. Calculate equation of state (bulk modulus, equilibrium volume) using MLIPs.
How do I install Mat Equation Of State in Claude Code?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill mat-equation-of-state -a claude-code`. Or copy the skill folder (skills/mat-equation-of-state in learningmatter-mit/AtomisticSkills) into .claude/skills/mat-equation-of-state in your project. Claude Code loads it when a task matches its description.
How do I install Mat Equation Of State in Codex?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill mat-equation-of-state -a codex`. Or copy the skill folder (skills/mat-equation-of-state in learningmatter-mit/AtomisticSkills) into .agents/skills/mat-equation-of-state in your project. Codex loads it when a task matches its description.
Can I use Mat Equation Of State 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 learningmatter-mit/AtomisticSkills --skill mat-equation-of-state -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/mat-equation-of-state, .gemini/skills/mat-equation-of-state, .github/skills/mat-equation-of-state and .opencode/skills/mat-equation-of-state in your project.
What does Mat Equation Of State need to run?
Going by SKILL.md and its folder, Mat Equation Of State needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Mat Equation Of State access the network?
SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.
Is Mat Equation Of State 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Mat Equation Of State use?
Mat Equation Of State is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Mat Equation Of State 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.
What are the alternatives to Mat Equation Of State?
Skills that share tags, products or a category with Mat Equation Of State: Bulk Rnaseq (K-Dense-AI/scientific-agent-skills, 48k stars), Eol Resistor Calculator (sickn33/agentic-awesome-skills, 47k stars), Geometric Volume Calculation (InternScience/scp, 170 stars) and Material Density Volume Calculation (InternScience/scp, 170 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Mat Equation Of State?
learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.
Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.