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Documentation

Documentation for using MATONE and for how its calculations are set up — from your first calculation and the web app's features to the defaults behind each calculation and a reference for every tool and output file.

  • Get started →What MATONE does, your first calculation, a workspace tour, accounts and limits, and Claude Code.
  • Guides →How to use the web app: chat, material search, structures, calculation settings, jobs, results, files, sharing and settings.
  • Tutorials →Step-by-step walkthroughs of research scenarios and recorded demo runs.
  • Calculation methods →Defaults and why — pseudopotentials, functionals, DFT+U, magnetism, 2D, workflows, error recovery, phonons, NEB, MD and molecular calculations.
  • Reference →Every MCP tool's arguments and result keys, analysis modules, output files, data sources and the support matrix.
  • Concepts →A glossary of the physics and numerical terms used across MATONE.

What is MATONE?

MATONE (Materials + ONE) turns research requests written in natural language into materials simulations. The AI reads the request, designs the calculation and hands it to a tool; the numbers are computed by Quantum ESPRESSO (periodic DFT), Psi4 (molecular quantum chemistry) and LAMMPS (classical molecular dynamics). It wraps 41 analysis modules and 101 deterministic MCP tools in a web interface; VASP is supported for input generation and output analysis only. It is a horizontal platform serving many research areas rather than one specialty.

From request to result

UserAIToolsEnginesAnalysisVisualizationChat / MCPdeterministic codeQE / Psi4 / LAMMPS

In web chat the AI is one of MATONE's Korean language models; in Claude Code (MCP) it is your own Claude. The AI only picks tools and arguments — deterministic code and the engines write the input files, run the calculations and analyse the results.

Key Principles

Conversational

Describe the calculation in natural language and the AI picks the right tool and arguments (material, calculation type, the theory settings you named). DFT parameters and input files are produced by deterministic code (presets + auto-detection), not by the AI; a theory setting the AI adds that you did not name is marked "assistant's choice" on the calculation plan.

Automated

A confirmed calculation plan runs end to end as a multi-step workflow: relaxation → SCF → bands → NSCF → DOS → automatic post-processing. An interrupted workflow can be resumed from its checkpoint.

Reproducible

Every calculation folder keeps the record needed to reproduce it. A workflow (run_workflow) writes per-step pw.in/pw.out, results_summary.json with the detection log behind each automatic choice, workflow_state.json for resuming, and file_manifest.json; input generation (generate_dft_input) writes README.md and run_info.json.

Extensible

(For source contributors) New analysis modules, engines and MCP tools are added following the repository's developer recipes; tools self-register through the @mcp.tool() decorator without touching the core. The web service has no way for users to add modules.

More:MATONE overview — what it does and does not do

Concept Glossary

Quick reference for the physics + numerical-method terms used across the platform.

Quick Start

Web Interface

✓ No installation needed — just a browser. All computation runs on our servers.

1

Sign up and verify your email

Sign up with email and password or with Google. With an email sign-up you must click the link in the verification email before you can submit calculations (Google accounts start verified). New accounts start on the trial plan; the free plan that follows the trial cannot run calculations. The operator opens and closes sign-up — if it is closed, contact support@matone.one.
2

Find a material

Type something like "Search Si" in the chat, or browse the materials database and pick a material. A bare formula opens material search results — it does not start a calculation.
3

Request and review the calculation

Ask for the calculation explicitly, e.g. "Calculate the band structure of Si", and a calculation plan card (relaxation → SCF → bands → NSCF → DOS) opens with its settings. Press "Run now" to submit it, or "Open in Workspace" to change detailed settings before submitting. On the cloud, getting a node ready can add up to about 10 minutes.
4

Check the results

When the job finishes, the band-structure and DOS plots and the analysis results open. You can ask about them in the chat (e.g. "What is the band gap?").

More:First calculation — Si band structure (step by step) · Accounts and limits

Claude Code (MCP)

Installing requires the source code. MATONE is not a PyPI package (`pip install matone` does not work) and the source repository is currently private — if you do not have access to it, use the web interface.

1

Install from source

git clone https://github.com/hipo-son/SHALOM.git
cd SHALOM
pip install -e ".[mcp,analysis,phonon,symmetry,plotting,reporting]"
2

Register MCP server

claude mcp add matone -- python -m matone.mcp_server

Or open Claude Code at the repository root and .mcp.json registers the server automatically. If the Python of the environment where MATONE is installed is not on PATH, set MATONE_PYTHON to its path.

3

Start using

Check the connection with /mcp in Claude Code, then ask in natural language. Start by checking the QE installation:
"Check whether the QE environment is set up"

Prerequisites — only for Claude Code (MCP) or a self-hosted install (not needed for the web interface)

  • •Python 3.11+ — conda (the repository's environment.yml, recommended) or venv
  • •Calculation engines — Quantum ESPRESSO (recommended; conda-forge `qe` or apt, Windows needs WSL2), Psi4 (molecules, conda only), LAMMPS (molecular dynamics). Not needed if you only build structures, generate input files or analyse existing outputs.
  • •Pseudopotentials — QE defaults to SSSP 1.3.0 PBE Efficiency (UPF). Missing files are downloaded by run_workflow into `$MATONE_PSEUDO_DIR` (default `~/pseudopotentials`); to fetch them ahead of time run `python -m matone.setup_pseudo`. Psi4 uses Gaussian basis sets instead of pseudopotentials.

More:Using MATONE from Claude Code — install, register, check QE

Example Prompts

> Calculate the band structure of Silicon
> Run a phonon calculation for MgO with thermal properties
> Search for Fe2O3
> Build a 2x2 Pt(111) slab
> Run a Li-migration NEB between the two uploaded structures

Calculations that need several structures are requested step by step. A surface energy comes from the energies of two SCF runs (bulk and slab), and an NEB needs a start and an end structure that you prepare.

Feature Details

A conversational AI interface for the main steps of a materials simulation.

💬

Natural Language Interface

Describe the simulation in everyday language. The AI reads the request and picks the right tool and arguments; deterministic code builds the input files from presets and auto-detection. On the web you review the settings on a plan card before anything runs.

🔄

Multi-Step Automated Workflows

The 5-step core pipeline runs vc-relax, SCF, bands, NSCF and DOS in order, and optional steps such as phonon, MD, elastic and EOS can be added per run. Each step uses the previous step's results. If the vc-relax or SCF step fails, it is retried automatically with progressive corrections chosen by error type; an interrupted workflow continues with resume_workflow.

🔍

Smart Material Detection

Spin polarisation is switched on when magnetic elements are present (ferromagnetic high-spin start; antiferromagnetic orderings are computed only when requested). DFT+U (Dudarev, PBE-fitted U values) is applied automatically to oxides and fluorides of magnetic transition metals; sulfides, selenides and tellurides need it switched on explicitly, and it is never applied automatically under HSE06 or SCAN. Vacuum layers identify 2D sheets, slabs and molecules, and the composition decides metal or insulator smearing.

📊

41 Analysis Modules

Post-processing covers elastic tensors, phonons, electronic structure, XRD, symmetry, magnetism, MD trajectories, EOS fitting, surface energies, Raman/IR, dielectric functions, Bader charges, defects and more. Each module has its own inputs and limits — see the analysis module catalog and reference.

📈

Interactive Visualization

Plotly-based interactive HTML plots for band structures, DOS, and phonon dispersions. Three.js crystal structure viewer with rotation, zoom, atom selection, and high-performance instancing.

📄

PDF Report Generation

Builds a PDF report from the results (structure, calculation parameters, detection log, workflow steps, analysis results, plots). The report written automatically after a workflow is in English; the PDF button in the workspace regenerates it in the interface language (Korean, English, Japanese or Spanish).

🤖

Autonomous Loop

Give a research goal and the AI drafts a multi-step calculation plan, which you review and edit in a workflow diagram before it runs. Results are validated after each calculation step; with an acceptance criterion, plan → run → evaluate repeats up to 5 times by default.

⚡

NEB Transition States

Climbing-image NEB with Quantum ESPRESSO neb.x (7 images by default). You supply the start and end structures (e.g. before and after a Li vacancy hop); if the endpoints are not relaxed, switch on endpoint relaxation (relax_endpoints) to get a physically meaningful barrier.

Standard Workflow: 5-Step Core Pipeline + Optional Steps

1.vc-relax→
2.SCF→
3.Bands→
4.NSCF→
5.DOS
+ OptionalPhononMDElasticEOS

Optional steps (phonon, MD, elastic, EOS, DFPT, PDOS, dielectric function, charge density, Bader and more) are enabled per run. DFPT is Γ-point and insulator-only and gives IR (dielectric tensor, Born effective charges); the Raman tensor is computed only with LDA, norm-conserving pseudopotentials, no spin polarisation and no +U or SOC. Automatic retry on failure exists only for the vc-relax and SCF steps — bands, NSCF, DOS and optional steps are not retried. A failed optional step is recorded and the rest of the results are kept.

More:Standard workflow · Automatic error recovery · DFT+U rules · Magnetic initialisation and ordering · Plan cards and autonomous mode · NEB reaction paths

Recipes

Recipes by calculation type. Clicking a card opens the workspace with that type selected in the calculation settings panel (sign-in required).

Basis Convergence

📊

Convergence Test

run_convergencebeginner

Convergence test (cutoff/k-points)

  • Interpret ecutwfc / k-point convergence sweep results
  • Prerequisite before production calculations
quantum espresso

Electronic Structure

⚡

DFT Workflow

run_workflowbeginner

Relaxation → SCF → Bands → DOS

  • Full pipeline: vc-relax → SCF → bands → DOS
  • Auto-extract band gap and Fermi energy
  • Auto-trigger post_process → PDF report
quantum espresso
🎯

HSE06 Hybrid Bands

run_workflowadvanced

Hybrid-functional band structure via Wannier90

  • HSE06 hybrid band gap (corrects PBE underestimate)
  • Wannier90 interpolation off the EXX SCF
  • Literature-grade gaps for semiconductors

"Skip relaxation" is ticked by default, so it computes the structure as given — open a PBE-relaxed one. With the default SSSP files (mostly ultrasoft/PAW) an HSE06 relaxation is refused; to relax, pick a norm-conserving library.

quantum espresso

Material Properties

🔊

Phonon Calculation

run_workflowintermediate

Phonon bands/DOS + thermal properties

  • Phonon band / DOS / thermal properties (C_v, S, F)
  • Detect dynamic stability via imaginary modes
  • Choose supercell size (typically 2×2×2)
quantum espresso
🌊

DFPT (IR; Raman when allowed)

run_workflowadvanced

Γ-point IR spectrum via ph.x (insulators only; Raman conditional)

  • Γ-point dynamical matrix via DFPT
  • Optical phonon mode classification

Γ point and insulators only. The default settings (PBE + SSSP) give IR only; Raman needs LDA, norm-conserving pseudopotentials and no spin polarisation.

quantum espresso
💎

Elastic Constants

run_workflowintermediate

Finite-strain Cij tensor calculation

  • 6×6 elastic tensor → bulk / shear / Young's modulus
  • Verify Born stability
  • Choose appropriate stress-strain pair magnitudes
quantum espresso
📐

Equation of State

run_workflowintermediate

Volume sweep + Birch-Murnaghan fit

  • 3rd-order Birch-Murnaghan EOS fit
  • Extract V₀, K₀, K₀′
  • Compressibility / pressure response
quantum espresso

Molecular Dynamics

🔬

Molecular Dynamics

run_mdadvanced

LAMMPS molecular dynamics simulation

  • Run LAMMPS NVT/NPT MD
  • Extract RDF / MSD / diffusion
  • Auto-detect thermalization and equilibration

Automatic force fields cover only element sets with a built-in potential (EAM metals, Tersoff/SW semiconductors, LJ noble gases). Other materials (e.g. Li compounds, oxides) need pair_style set explicitly.

lammps

Molecular QM

⚛️

Molecular Single-Point Energy

run_molecular_scfbeginner

Psi4 SCF/DFT single-point (total energy, HOMO-LUMO gap)

  • Psi4 single-point energy
  • Default B3LYP / def2-SVP workflow

Results: total energy and HOMO-LUMO gap (the dipole moment is not extracted). A molecular structure file must be open to submit.

psi4
⚛️

Molecular Geometry Optimization

run_molecular_optimizationbeginner

Psi4 geometry optimization (find equilibrium structure)

  • Molecular geometry optimization
  • Force convergence threshold
psi4
⚛️

Molecular Vibrational Analysis

run_molecular_frequenciesintermediate

Psi4 frequencies (imaginary-mode check; ZPE/thermochemistry only in the raw output)

Pick a finished "Molecular Geometry Optimization"; it computes from that run's folder. Results are the frequency list, the number of imaginary modes and the ideal-gas thermochemistry from them (ZPE, enthalpy, entropy and Gibbs energy corrections).

psi4

Structure-only

⚛️

Moiré angle scan

search_moire_anglesadvanced

Find commensurate supercells across a twist range

  • Search commensurate twist-angle supercells

With the defaults (at most 200 atoms) no commensurate cell is found at small twist angles. The 1.05° magic-angle cell is outside the search range and cannot be built.

⚛️

Subgroup analysis

analyze_subgroupsadvanced

Enumerate isotropy subgroups for a crystal structure

  • Distortion paths via group-subgroup relations
  • Starting point for phase-transition search

Lists only maximal subgroups (ITA), Glazer tilts (Pm-3m parents) and structural pseudo-symmetry candidates (irrep-driven isotropy subgroups are not supported). Needs a structure file.

Each recipe opens with that calculation type's default parameters — adjust the material, accuracy and advanced settings before submitting. To reuse a plan, save it with "Save template" in the workflow panel and bring it back with "Load template".

More:Calculation settings panel

Walkthroughs

End-to-end narratives for common research workflows.

Demos — example results

Examples of recorded calculation results. Each detail page shows the key numbers and their interpretation; entries marked "Planned" are plans with no computed results yet.

Demo detail pages need no sign-in. Viewing the 3D structure and plots with "Open in workspace" requires signing in.

Research Domains

The 7 research areas MATONE covers and the analyses for each. Calculations outside this scope and known limits are listed in the support matrix.

More:Support matrix and limits

Battery Research

Electronic structure and stability of cathode and anode materials, average insertion voltage (vs Li/Li⁺ — from a low-Li host, a high-Li host and Li metal; no intermediate-phase search), Li/Na/K migration barriers (NEB), and Psi4 calculations on electrolyte molecules (EC, DMC, …). Dedicated SEI-reaction or electrode–electrolyte-interface modelling is not supported.

✓Band structure & DOS of electrode materials (metallic or gapped)
✓NEB ion-migration barriers (you prepare the start and end structures)
✓Dynamical stability from phonons
✓Dopant site preference — compute each substituted structure and compare total energies
> Calculate the average voltage of LiCoO2

Heterogeneous Catalysis

Surface slab building, adsorption energies (a three-calculation plan: slab, adsorbed structure, gas molecule), NEB reaction barriers, CHE free-energy diagrams and overpotentials. Wulff equilibrium shapes are built from per-facet surface energies you have computed.

✓Surface energy (from slab and bulk total energies) & Wulff shape (from per-facet surface energies)
✓Adsorbate relaxation and adsorption energy (electronic energy; no ZPE or entropy correction)
✓NEB reaction barriers on surfaces
✓Bonding analysis: Bader charges (QE) — charge-density differences only from uploaded VASP CHGCAR files
> Create a Pt(111) slab and calculate CO adsorption energy

2D Materials

Graphene, TMDs, layered heterostructures with automatic 2D detection. Applies vacuum isolation, DFT-D3(BJ) van der Waals correction, and 2Dxy cell relaxation constraints.

✓Band structure with 2D-appropriate k-path
✓Phonon dispersion for dynamical stability
✓Elastic constants (in-plane stiffness)
✓Interface epitaxial matching for heterostructures
> Calculate band structure of monolayer MoS2

Defect Engineering

Build substitutional and vacancy point defects and compute defect supercells. Formation energies, charge-transition levels and binding energies are evaluated from the total energies of finished calculations plus the chemical potentials, the VBM and a finite-size correction that you enter. Charged cells (system.tot_charge) have no field in the web calculation settings and can only be set through user_overrides in an MCP call, and finite-size corrections are not computed automatically.

✓Defect formation energy (at one chosen Fermi level — from total energies, chemical potentials and the VBM)
✓Charge-transition levels ε(q/q′) (from per-charge formation energies)
✓Defect-complex binding energy (from complex and isolated-defect energies)
✓Supercell-size convergence — no automatic tool; build each size and compare
> Build a 2x2x2 supercell of TiO2

Electronic & optical

Band structure, density of states (including PDOS), direct/indirect band gaps, electron and hole effective masses. Spin–orbit coupling (fully relativistic pseudopotentials selected automatically) covers heavy elements and topological materials. Transport properties such as the Seebeck coefficient or electrical conductivity are not computed.

✓Band gap (direct/indirect), VBM/CBM positions
✓Electron and hole effective masses (parabolic fit at the band edges; scalars, not a tensor)
✓PDOS orbital decomposition
✓Dielectric function ε(ω) — epsilon.x, runs only with norm-conserving pseudopotentials (known issue: optical properties are not extracted yet)
> Calculate effective mass and band gap of GaAs

Phonon & Thermal

Phonon dispersion and DOS (phonopy finite displacements), thermal properties (Cv, entropy, free energy), Γ-point DFPT IR spectra of insulators (Raman only with LDA, norm-conserving pseudopotentials and no spin polarisation), and a quasi-harmonic Debye model on an E(V) curve (thermal expansion, Grüneisen parameter, Debye temperature).

✓Phonon band structure & DOS
✓Thermodynamic properties vs. temperature
✓IR-active modes and spectra (Raman is conditional — default PBE settings give IR only; metals are not supported)
✓Quasi-harmonic thermal expansion (Debye model from an E(V) curve, not phonon-based QHA)
> Compute the phonon dispersion and DFPT IR spectrum of MgO

Structural & Mechanical

Elastic tensor (finite-strain SCF stresses, clamped-ion) and derived moduli (bulk, shear, Young's), Poisson ratio, Born mechanical stability, equation-of-state fitting and XRD patterns. Phase diagrams are built from Materials Project data.

✓Elastic tensor (clamped-ion — no internal relaxation, so diamond-type C44 comes out too high) & Born stability
✓Birch-Murnaghan EOS (V0, K0, K0')
✓Phase diagram & convex hull (Materials Project entries — needs MP_API_KEY on the server; your own energies are not included)
✓XRD pattern for experimental comparison
> Calculate elastic constants and check mechanical stability of Diamond

Backend Reference

What the engines MATONE actually runs (Quantum ESPRESSO, Psi4, LAMMPS) support. VASP is input generation and output analysis only — it is never executed — and machine-learning potentials (MACE, CHGNet, UMA) are disabled.

Quantum ESPRESSO

QEFree / Open Source

The main DFT engine for periodic systems (plane waves + pseudopotentials). The pseudopotential family follows the functional — PBE and HSE06: SSSP 1.3.0 Efficiency; PBEsol: SSSP 1.3.0 PBEsol; LDA and SCAN: PseudoDojo norm-conserving; spin–orbit coupling: PseudoDojo fully relativistic. Other families (SSSP Precision, GBRV, SG15, …) can be chosen.

Supported Calculations

  • •vc-relax (variable-cell relaxation, ISIF=3 equivalent)
  • •SCF (self-consistent field)
  • •Bands (band structure along high-symmetry k-path)
  • •NSCF (non-self-consistent for DOS)
  • •DOS / PDOS (total and projected density of states)
  • •Phonons (phonopy finite displacements — dispersion, DOS, thermal properties)
  • •Γ-point DFPT (ph.x + dynmat.x, insulators only): IR always; the Raman tensor only with LDA, norm-conserving pseudopotentials, no spin polarisation, no +U or SOC

Key Features

  • ✓GGA+U with Dudarev scheme (HUBBARD card, QE 7.1+ syntax)
  • ✓Per-element recommended cutoffs (ecutwfc/ecutrho) from the chosen pseudopotential family, with per-preset minimums
  • ✓Automatic 2D detection: assume_isolated, DFT-D3(BJ), 2Dxy
  • ✓Progressive error recovery for the vc-relax and SCF steps (a correction strategy per error type; fatal errors are reported at once)
  • ✓3 k-path conventions (Setyawan-Curtarolo, HPKOT, Latimer-Munro)

More:QE calculation defaults and accuracy presets · Pseudopotentials and cutoffs · Functionals, dispersion and spin–orbit coupling · Phonons, DFPT and Raman/IR · Automatic error recovery

Psi4

PSI4Free / Open Source

Molecular quantum-chemistry engine for isolated molecules: SCF/DFT single points, geometry optimisation and frequencies. Psi4 requests from the web chat only write the input file and do not run it; runs happen from the calculation settings panel (molecular single point, geometry optimisation) or the autonomous loop.

Supported Calculations

  • •SCF / DFT single-point energy
  • •Geometry optimization
  • •Frequency analysis
  • •Thermochemistry (ZPE, enthalpy, Gibbs energy) — only in Psi4's raw output (output.dat), not extracted into the results
  • •HOMO-LUMO gap and orbital energies (the dipole moment is not extracted)

Key Features

  • ✓Psi4 input generation from molecule records or uploaded XYZ
  • ✓Method/basis presets for common molecular workflows
  • ✓Results are saved to result_summary.json in the calculation folder (not added to the molecule database)
  • ✓PCM implicit solvent (EC, PC, DMC, …) — via the calculation settings panel or the MCP solvent argument
  • ✓No proprietary license registration step

More:Molecular quantum chemistry (Psi4)

LAMMPS

LAMMPSFree / Open Source

Advanced option: classical molecular dynamics for large or long MD runs and classical-potential comparisons (use QE when accuracy matters). Automatic force fields cover only element sets with a built-in potential (EAM metals, Tersoff/SW semiconductors, LJ noble gases); if no single potential covers every element of the structure, the run is refused. For other materials, set pair_style yourself in the MD calculation settings.

Supported Calculations

  • •NVT (canonical ensemble, Nose-Hoover thermostat)
  • •NPT (isothermal-isobaric ensemble)
  • •NVE (microcanonical ensemble)
  • •Energy minimization

Key Features

  • ✓Automatic force-field detection: among force fields covering every element, priority EAM (eam/alloy) > Tersoff > EAM (funcfl) > Stillinger-Weber > LJ
  • ✓Per-element potential parameters from lammps_potentials.yaml
  • ✓Shorter per-force-field timestep chosen automatically when light elements (H, He, Li) are present
  • ✓Trajectory analysis: RDF, MSD, VACF, diffusion coefficient (MSD and diffusion are currently unreliable because of a periodic-boundary issue)
  • ✓2D detection: automatic p p f boundary conditions
  • ✓Lorentz-Berthelot mixing for LJ cross-pair interactions

More:Molecular dynamics (LAMMPS)

Analysis Module Catalog

173 analysis API entries that extract physical properties from DFT/MD results.

More:Analysis module reference — inputs, output units, limits · Automatic post-processing

🔧

Elastic

Bulk/shear/Young's modulus, Poisson ratio, mechanical stability

🔊

Phonon

Band structure, DOS, thermal properties, dynamical stability

⚡

Electronic

Band gap, VBM/CBM, effective mass, DOS at Fermi level

📡

XRD

Powder X-ray diffraction pattern from crystal structure

🔷

Symmetry

Space group, point group, crystal system, Wyckoff positions

🧲

Magnetic

Per-atom magnetic moments and total/absolute magnetisation from QE pw.out (Löwdin charges only when PDOS-step output exists)

🏃

MD

RDF, MSD, VACF, diffusion coefficient, equilibration detection (known issue in MSD and diffusion)

📉

EOS

Birch-Murnaghan 3rd-order equation of state fitting

🧱

Surface

Surface energy from slab/bulk energies (J/m²)

🚪

Work Function

Slab Φ = V_vacuum − E_F from VASP LOCPOT results (QE path not implemented — not usable yet on calculations MATONE runs)

🌈

Dielectric

Dielectric function, refractive index, optical absorption (known issue reading QE epsilon.x output)

🎵

Raman/IR

Vibrational mode frequencies, Raman/IR activity, broadened spectra (Lorentzian, 5 cm⁻¹ by default)

🔋

Charge

VASP CHGCAR only: density statistics, charge difference (ρ_AB − ρ_A − ρ_B), sphere integration

⚛️

Bader

Per-atom charge partition (Henkelman algorithm), oxidation states, basin volumes (needs the bader executable)

💎

Defect

Formation energy, charge-transition levels, binding energy (from the energies, chemical potentials, VBM and corrections you enter)

🤝

Adsorption

Adsorption, cohesive and interface binding energies (electronic energies — no ZPE or entropy correction in the tools or workflows)

🛤️

NEB

Climbing-image NEB + harmonic-TST ΔG‡(T) + Eyring rate k(T) + half-life (treat ΔG‡ and k(T) as indicative)

🧪

Pourbaix

Pourbaix diagram (pH vs potential) built from Materials Project entries (needs MP_API_KEY on the server)

📐

Phase Diagram

Formation-energy convex hull from Materials Project entries (1–4 elements, needs MP_API_KEY; your own energies are not included)

🔗

Interface

Film/substrate epitaxial matching (Zur-McGill ZSL)

🔥

Reaction Thermo

Reaction enthalpy, entropy, Gibbs energy, equilibrium constant

📈

Quasiharmonic

Thermal expansion, Grüneisen parameter and Debye temperature from a quasi-harmonic Debye model (pymatgen) on an E(V) curve (not a phonon calculation)

💠

Wulff Shape

Equilibrium crystal shape from per-facet surface energies

🌀

Moiré Potential

Real-space moiré potential maps (built-in MoSe₂/WSe₂ parameters only)

🔮

Exciton

Moiré exciton bands (continuum 225-band Hamiltonian for twisted TMD bilayers; built-in MoSe₂/WSe₂ parameters only)

🛡️

Exciton Keldysh

Keldysh interaction screening for 2D excitons (fixed hBN/WSe₂/MoSe₂ stack only)

🍃

Catalysis

CHE free-energy diagram, OER/ORR/HER/CO2RR overpotential, scaling relations

🧬

Molecular Symmetry

Point group of a molecule (non-periodic) — Schoenflies symbol, number of operations, equivalent atoms (Mulliken labels come with the character tables)

💨

Molecular Thermo

Molecular thermochemistry (ZPE, H, S, G) from frequencies — library function only, not connected to Psi4 calculations yet

🌳

Subgroup

Maximal subgroups (ITA), Glazer tilts (Pm-3m parents) and structural pseudo-symmetry candidates (irrep-driven isotropy subgroups not supported)

📋

Character Tables

Point-group character tables for Mulliken irrep assignment

🔬

STEM Imaging

Multi-sublattice atomic-column detection (Gatan .dm3/.dm4 + .png/.tif) — needs the optional [stem] dependencies, not in the hosted service yet

📚

Reference

Compare DFT results with experimental literature values for the built-in reference materials and with OPTIMADE structural data

✅

Validator

Cross-result physical-plausibility checks (band gap, elastic, phonon, lattice drift)

📊

PDOS

Projected density of states (orbital and site decomposition)

📁

File Manifest

Classify calc directory files by role (input/output/analysis/meta)

🔄

Post-Process

Auto-detect and run all applicable analyses on a calc directory

🧭

Band Topology

Euler class of an isolated two-band real subspace (Wilson loop — built-in models or a wannier90 _hr.dat)

⚖️

Comparison

Side-by-side table of scalar properties (band gap, energies, bulk modulus, …) across several finished calculations

🔀

Moiré Search

Commensurate moiré supercell search by twist angle and bilayer/multilayer assembly (search range limited at small angles)

🧾

Synthesis

Packs a calculation folder's results into a bundle for AI summaries and checks that numbers in a summary are backed by the results

Dependencies

The install commands below apply only to a self-install from a source checkout. The web service has the libraries it needs on its servers, except STEM analysis ([stem]), which is not included yet.

numpy + ASE — Electronic, Magnetic, MD, Surface, Raman/IR, Dielectric, Defect, Adsorption, Catalysis, NEB, Reaction Thermo
pip install -e ".[eos]" — EOS (scipy)
pip install -e ".[analysis]" — Elastic, XRD, Charge, Bader (+ bader binary), Interface, Wulff, Quasiharmonic, Work Function, Molecular Symmetry (pymatgen)
pip install -e ".[phonon]" — Phonon (phonopy)
pip install -e ".[symmetry]" — Symmetry, Subgroup (spglib)
pip install -e ".[mp]" + MP_API_KEY — Pourbaix, Phase Diagram (Materials Project)
pip install -e ".[stem]" — STEM Imaging (atomap, HyperSpy)

MCP Tool Reference

MATONE's 101 deterministic tools. Claude Code calls them directly over MCP, and the web chat uses the same tool functions.

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Quick Setup

Requires the source code: MATONE is not a PyPI package and the source repository is currently private.

git clone https://github.com/hipo-son/SHALOM.git && cd SHALOM
pip install -e ".[mcp,analysis,phonon,symmetry,plotting,reporting]"
claude mcp add matone -- python -m matone.mcp_server

More:Using MATONE from Claude Code — install, register, check QE

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