Tako DocsProduct guide
Tako Docs
Tako is an atomistic simulation package that runs entirely in your browser. It combines structure building and visualization, quantum-chemical and machine-learned calculations, and a built-in research agent in one workspace.
Learn how to start using Tako for structures, calculations, analysis artifacts, workflows, and sharing. Pick a quick start if you are new, or jump to a reference chapter when you know the task.
Getting Started
- Tako DocsStart using Tako for browser-local atomistic structures, calculations, analysis, automation, and reproducible scientific examples.
- Before You StartBrowser requirements, model downloads, local storage, privacy, and backup expectations before running Tako calculations.
- Five-Minute Ethanol CalculationLoad ethanol, run a GFN2 single-point calculation, and verify its energy and Mulliken partial charges in under ten minutes.
- Workspace TourLearn where structures, tools, calculations, files, artifacts, and floating windows live in Tako.
- Molecule Tutorial: Optimize Water and Run VibrationsOptimize water with GFN2+D4, verify the relaxed minimum, calculate molecular vibrations, and interpret the IR spectrum.
- Crystal Tutorial: Check Silicon with Phonons and DOSRelax diamond silicon with a force-focused MLIP, check its phonon bands, then use GFN2 for a qualitative electronic DOS/PDOS view.
- Write Your First Tako ScriptWrite and execute a small reproducible JavaScript workflow using the same public calculation API as Tako's visible controls.
Build & Edit Structures
- Import a StructureOpen a structure as a new tab or import it into the active structure as a layer, then verify cell, periodicity, and atom data.
- Build a StructureStart from the Library, SMILES, individual atoms, or Tako Script while keeping the scientific origin and intended periodicity explicit.
- Edit Atoms and GeometrySelect, move, rotate, duplicate, replace, delete, measure, and annotate atoms while preserving an auditable structure state.
- Work with LayersSeparate host, guest, surface, adsorbate, annotations, and artifacts using visibility, locks, groups, and merge operations.
- Apply Atomic ConstraintsFix complete atoms or selected Cartesian coordinates and verify how constraints affect optimization and downstream calculations.
Run Calculations
- Calculation OverviewSelect the Tako operation that answers a scientific question and continue to its interface procedure or authoritative method chapter.
- Choose a CalculatorSelect a model in a calculation setup dialog, interpret asset and capability states, and configure the charge, spin, and SCF fields exposed for GFN2.
- Run a Single-Point CalculationOpen Single Point Setup, select a calculator and supported outputs, start the fixed-geometry evaluation, and open its artifacts.
- Optimize a StructureConfigure fixed-cell or variable-cell geometry optimization, follow its trajectory, and accept or reject the resulting structure.
- Run Molecular DynamicsConfigure and inspect a finite-temperature trajectory with the MD Setup dialog, including the effective ensemble selected by each thermostat and barostat combination.
- Calculate Molecular VibrationsConfigure a finite-difference molecular vibration calculation, request supported IR/Raman response, and inspect the resulting modes and spectra.
- Calculate Crystal PhononsConfigure a periodic finite-displacement phonon calculation, generate or edit a SeekPath band path, and inspect Gamma modes, a Gamma histogram, and the optional band result.
- Simulate a UV–Visible SpectrumOperate Tako's sTDA setup, distinguish response roots from Gaussian folding controls, and inspect raw artifacts without overstating viewer-derived assignments.
- Simulate a Powder Diffraction PatternOperate periodic Bragg diffraction or finite-cluster Debye scattering and interpret the controls, artifacts, and branch-specific limitations exactly.
- Calculate a Reaction Path with NEBConfigure and inspect an NEB or climbing-image NEB calculation in the Tako interface.
- Refine and Verify a Transition StateOperate the combined CI-NEB, dimer, and vibration-check workflow while distinguishing controls that affect the current transition-state runtime from controls used only by standalone reaction paths or dimers.
Results & Troubleshooting
- Monitor a CalculationFollow status, progress, logs, partial artifacts, cancellation, and completion without mistaking activity for scientific success.
- Read and Compare EnergiesLocate authoritative energy fields, reject failed or unconverged states, normalize reference conventions, and build comparison tables without calling model energies free energies.
- Inspect TrajectoriesOpen optimization, molecular-dynamics, reaction-path, and dimer frames; check geometry evolution; and extract an accepted structure.
- Inspect Spectra and PlotsOpen vibration, phonon, DOS, XRD, UV-Vis, SVG, and Plotly artifacts and verify axes, units, provenance, and plot semantics.
- Inspect Cube and Grid DataOpen, identify, render, slice, color-map, import, and export Gaussian cube fields while preserving grid geometry, units, and field identity.
- Diagnose Failed CalculationsClassify setup, download, SCF, optimization, model-domain, memory, and worker failures before changing settings or trusting partial output.
Agent & Automation
- Automation OverviewChoose between writing a Tako Script yourself and asking the Agent to create and run one under your review.
- Use the AgentConnect Codex, submit a scoped scientific task, read the plan, steer execution, and verify generated files before accepting the answer.
- Connect Tako in ChatGPTConnect the public Tako MCP endpoint in ChatGPT developer mode.
Share & Reproduce
- Share and Export WorkChoose a live read-only share, durable workspace archive, or individual structure/artifact export.
- Share a Live Read-Only WorkspaceCreate an owner-online link for selected non-ignored Explorer files and complete the peer connection safely.
- Export a Workspace ArchiveCreate a durable ZIP containing structures, Explorer files, calculations, manifests, and workspace metadata, then verify the archive.
- Export Structures and ArtifactsExport one structure, table, plot, report, or cube in an appropriate format and include enough context for reuse.
- Organize a Reproducible WorkspaceSeparate source, inputs, outputs, diagnostics, cache, and human interpretation so another reader can audit and rerun the work.
How Tako Works
- How Tako Runs CalculationsThe execution model shared by every Tako calculation — calculation state, normalization, browser workers, model assets, workspaces, completion states, and provenance.
- Choosing a MethodGFN2-xTB versus machine-learned potentials — what each theory captures, where each one fails, and how to pick a method for your system.
- Potential Energy SurfacesEnergies, gradients, Hessians, constraints, stationary points, trajectories, and model dependence as the scientific foundation of atomistic calculations.
- Single-Point Energies and PropertiesFixed-geometry energy, force, stress, charge, density, and electronic-property evaluation, including comparability, interpretation, and failure modes.
- Comparable Energies and Thermodynamic CyclesDefine model energies, relative and reaction energies, ZPE and thermal corrections, standard states, adsorption and voltage cycles, and the exact boundary of Tako's current outputs.
- Geometry OptimizationPotential energy surfaces, the BFGS/FIRE/MDMin optimizers, convergence control, cell relaxation, and constraints in Tako.
- Molecular Vibrations and IR/Raman SpectroscopyHarmonic normal-mode theory, finite-difference Hessians, infrared and Raman response, zero-point energy, numerical convergence, and Tako implementation boundaries.
- Crystal Phonons and Lattice DynamicsHarmonic lattice dynamics, finite-displacement force constants, dynamical matrices, acoustic sum rules, supercell convergence, reciprocal-space paths, DOS limits, and Tako implementation.
- Electronic Excitations and UV–Visible SpectraFrom vertical electronic excitation theory through Tako's sTDA-xTB response model, oscillator strengths, Gaussian folding, assignments, and defensible interpretation.
- Density Fields, NCI Analysis, and Volumetric DataElectron-density grids, reduced density gradient and sign(lambda2)rho theory, Tako's fixed-grid implementation, Gaussian cube semantics, isosurfaces, sections, and defensible interpretation.
- Powder X-ray DiffractionScattering geometry, reciprocal-lattice powder diffraction, finite-system Debye scattering, exact Tako behavior, and scientifically defensible comparison with experiment.
- Molecular DynamicsMolecular-dynamics theory and exact Tako runtime behavior: ensembles, integrators, thermostats, barostats, initialization, routing, constraints, trajectories, and restart limits.
- Molecular Dynamics: Statistics and ValidationEquilibration, convergence, autocorrelation, observables, ensemble-specific diagnostics, uncertainty, and reporting standards for Tako molecular-dynamics trajectories.
- Nudged Elastic Band MethodTheory, numerical implementation, convergence, and interpretation of NEB and climbing-image NEB in Tako.
- Transition States and the Dimer MethodFirst-order saddle points, min-mode following, NEB-to-dimer refinement, vibrational verification, and how to validate Tako's combined transition-state calculation.
- Reproducibility and ReportingThe shared record-keeping and reporting standard behind every Tako method chapter — what to preserve, how to phrase claims proportional to evidence, and how to report sensitivity, failures, and limitations.
Examples
- ExamplesFour complete Tako studies you can open, run, and read end to end — each starting from a real chemical question.
- Thiolate–CO₂ Adduct FormationDoes a benzyl thiolate anion chemically bite CO₂? A three-term GFN2-D4 energy cycle, run locally, reads the binding energy, a surviving ~1.8 Å S–C bond, and charge flowing onto CO₂ as converging signs of real chemisorption — the molecular move behind CO₂-philic capture liquids.
- Thymol and Carvacrol in Beta-CyclodextrinA host-guest inclusion study asking which of two near-identical flavour isomers, thymol or carvacrol, a beta-cyclodextrin cavity holds more tightly, using fixed-host GFN2-D4 inclusion energies and multiple docking poses to test whether the winner is real.
- CO₂ Binding in a CC3 Porous Organic CageDoes a fast laptop-scale method reproduce the CC3 cage's experimental CO₂ > CH₄ > N₂ preference, and how does its CO₂ binding line up against coupled cluster? A fixed-host site-energy study of gas capture in a porous organic cage, worked step by step in Tako's interface.
- Agent Demo: Water Stretch–Bend SurfaceYou ask Tako's agent how water's energy changes as its two O–H bonds stretch and its H–O–H angle opens and closes; it plans a 9×9 GFN2 scan, writes and runs the script, and hands back a single potential well you can rotate and read.
Tako Script
- Calculator Construction and ValidationConstruct GFN2 and machine-learned calculators in Tako Script, validate their capabilities, inspect required assets, and preserve calculator provenance.
- Single-Point Calculations with Tako ScriptValidate and run tako.singlePoint, interpret its promise and result channels, write authoritative artifacts, and construct comparable fixed-geometry series.
- Geometry Optimization with Tako ScriptValidate and run tako.optimize, control atomic and cell degrees of freedom, enforce convergence gates, continue staged relaxations, and write auditable outputs.
- Molecular Vibrations with Tako ScriptValidate and run tako.vibration, control finite differences and spectroscopy channels, inspect the exact result contract, and write auditable mode and spectrum data.
- Crystal Phonons with Tako ScriptValidate and run tako.phonon, control primitive-cell supercells and reciprocal paths, distinguish partial result branches, and write auditable stability evidence.
- Molecular Dynamics with Tako ScriptCall tako.molecularDynamics with an explicit effective integrator, validate the returned trajectory and trace, and keep independent replicas scientifically reproducible.
- NEB with Tako ScriptBuild, run, validate, and save a reaction-path calculation with the Tako Script API.
- Transition-State Search with Tako ScriptCall the combined NEB, dimer, and vibration workflow while validating its stage-specific convergence and current result-coherence boundary.
- Powder Diffraction with Tako ScriptRun periodic Bragg diffraction or finite Debye scattering, branch on the actual returned mode, and preserve branch-specific assumptions and result fields.
- UV–Visible Spectra with Tako ScriptRun sTDA with GFN2-xTB or g-xTB, converge roots and folding independently, read signed transition coefficients, and preserve the exact result boundary.
- NCI and Volumetric Data with Tako ScriptRequest native NCI cubes, parse and validate Gaussian cube geometry, use grid derivatives with explicit units, and write derived fields without confusing Script and native stencils.
- Energy Analysis with Tako ScriptExtract energies with exact helper precedence, guard convergence and provenance, build balanced reaction/binding/voltage cycles, combine matching ZPE, and avoid nonexistent helper APIs.
Technical Reference
- Terminology and GlossaryDistinguish operation, calculator, model, method, runtime, structure tab, layer, artifact, Tako Script, and Agent.
- UI Command ReferenceFind Tako menus, sidebars, panels, and the result surfaces they open.
- Structure Format ReferenceChoose an import or export format and understand which structure data it preserves.
- Calculation Artifact ReferenceIdentify Tako calculation files, their authority, and the viewer used to inspect them.
- Calculator ReferenceExact calculator identifiers, runtime and weight mappings, capability boundaries, state inputs, asset requirements, and provenance fields.
- Tako Script API ReferenceChoose a focused namespace reference for the supported Tako Script API.
- Known LimitationsCurrent implementation defects and hard limitations that affect Tako results, each with its scope, workaround, and the reference page that owns the exact contract.
Operation Reference
- Tako Script Operation SettingsChoose the calculation operation whose generated settings you need.
- tako.singlePoint SettingsGenerated signature, settings, result contract, and example for tako.singlePoint.
- tako.optimize SettingsGenerated signature, settings, result contract, and example for tako.optimize.
- tako.molecularDynamics SettingsGenerated signature, settings, result contract, and example for tako.molecularDynamics.
- tako.phonon SettingsGenerated signature, settings, result contract, and example for tako.phonon.
- tako.xrd SettingsGenerated signature, settings, result contract, and example for tako.xrd.
- tako.vibration SettingsGenerated signature, settings, result contract, and example for tako.vibration.
- tako.stda SettingsGenerated signature, settings, result contract, and example for tako.stda.
- tako.reactionPath SettingsGenerated signature, settings, result contract, and example for tako.reactionPath.
- tako.transitionState SettingsGenerated signature, settings, result contract, and example for tako.transitionState.