jlmol

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Load Structure

Display

🔍

Edit

Orbital Controls

Orbital: 1

Use arrow keys ↑/↓ to navigate orbitals

XYZ Editor

Click atoms in the 3D structure or the rows below to select them.

ElemCo.jl Input

AO Basis Set:

JKfit Basis:

MPfit Basis:

Charge:

ms2 (2·S_z):

Calculation steps

Add step:

Generated input (editable):

Changing steps or options regenerates this script. You can also edit it directly (edits are overwritten on the next change).

xtb (g-xTB) Calculation

Options

Charge

Unpaired electrons

Extra xtb flags (optional)

Relax only selected atoms (freeze the rest)

During optimization, writes an xtb $fix block for every non-selected atom (--input). Select atoms by clicking them in the structure or XYZ viewer. Ignored if no atoms are selected.

Runs xtb <coord.xyz> --gxtb for the energy, or xtb <coord.xyz> --gxtb --opt to optimize and replace the current geometry. Requires the g-xTB distribution from grimme-lab/g-xtb on your PATH (see Settings → xtb).

⚙️ User Preferences

Application Behavior

Auto-load last molecule on startup

Automatically load the most recently opened molecule when the application starts

Remember window positions

Save and restore the positions of panels and windows

Show tooltips on hover

Display helpful tooltips when hovering over buttons and controls

Updates

Automatically check for updates on startup

Quietly check GitHub for a newer release when jlmol starts, and notify you if one is available

File Handling

Confirm before overwriting files

Ask for confirmation before overwriting existing files

Default export format:

Default file format for exports

Export PNG with transparent background

Export PNG images with transparent background (JPEG always uses white background)

Molecular Display

Default display mode:

Default molecular representation when loading structures

Auto-spin molecules when loaded

Automatically start rotation animation for new molecules

Show atom labels by default

Display element symbols on atoms

JSmol Configuration

Background color:

Background color for the molecular viewer

Enable antialiasing

Smooth edges for better visual quality (may affect performance)

Default zoom level:

Initial zoom level for loaded molecules

Performance

Enable hardware acceleration

Use GPU acceleration for better performance (restart required)

Render quality:

Rendering quality vs performance tradeoff

Memory limit (MB):

Maximum memory usage for molecular structures

Developer Options

Enable debug mode

Show additional debug information in console

Detailed error logging

Log detailed error information for troubleshooting

Julia Configuration

Julia command:

Command or path to Julia executable (supports WSL)

Calculation timeout (min):

Maximum time to wait for calculations to complete

Default Calculation Settings

Default basis set:

Default basis set for new calculations

Default method (molecule):

Default correlated method for molecular (geometry + basis) calculations. A DF-HF reference step is added automatically.

Default method (FCIDUMP):

Default correlated method for FCIDUMP calculations. No reference step is added.

Density fitting and the reference/correlation macros are now chosen per step in the ElemCo.jl panel (Reference and Method blocks).

Output Settings

Auto-clear output on new calculation

Automatically clear previous output when starting new calculations

Auto-save calculation output

Automatically save calculation results to file

xtb Configuration

xtb command:

Command or path to the xtb executable (supports WSL, e.g. wsl --shell-type login xtb). g-xTB calculations require the xtb binary from the g-xtb distribution, which bundles the parameters.

Download the g-xTB distribution from github.com/grimme-lab/g-xtb, extract it, and put its xtb binary on your PATH (or set the full path above). It includes the parameters — no separate download is needed.