JLmol offers deep integration with ElemCo.jl, a modern Julia-based quantum chemistry package. This enables users to go from structure visualization to high-level computation and back, all within a single interface. The integration is designed for both beginners and advanced users, with support for local, WSL, and remote execution.
Input Generation:
- Build a calculation from ordered “building blocks” — a reference, correlation methods, exports, custom Julia, or any ElemCo.jl macro — that you add, remove, reorder and collapse, with the generated Julia updating live.
- Select methods from grouped menus with a spin selector (closed-shell /
U / R): HF, MP2, the coupled-cluster and distinguishable-cluster families, ΛCCSD(T), quasi-variational (QV / OQV) methods, excited states (EOM), FCI and CIPHI — composed into the ElemCo.jl method string (e.g. UCCSD, EOM-UCCSD).
- Set any ElemCo.jl option through a searchable options browser: every option is pre-filled with its default and shows its description on hover, and only the values you change are written to the input.
- Choose correlation-consistent basis sets (cc-pVDZ/TZ, aug-cc-pVDZ/TZ) and auxiliary JK- and MP2-fitting sets, or switch to FCIDUMP mode to read integrals from a file instead of a geometry and basis.
- Set the charge and spin, add any macro exported by ElemCo.jl as a step (with its signature and docstring shown as help), then edit the generated input directly — with Julia syntax highlighting — or copy it to the clipboard.
- Molden orbital export: add an export step to dump the calculated orbitals in Molden format, ready to be reopened in JLmol or other tools for orbital visualization.
- Insert Selected Atoms: insert the atoms currently selected in the structure as a 1-based index list (e.g.
[1, 3, 5]) at the cursor of whichever field you're editing — useful for defining dummy atoms or active regions.
Calculation Runner:
- Run calculations locally, in WSL (Windows Subsystem for Linux), or remotely via SSH.
- Customizable Julia command and environment for advanced workflows. To run Julia under WSL, use a login shell so your environment and
PATH are picked up, e.g. wsl --shell-type login julia.
- Integrated log viewer for monitoring calculation progress and troubleshooting errors.
- For remote jobs, the bundled
runremote script uses ssh/scp to execute calculations on a more powerful Linux machine (works best with passwordless SSH).
- Supports batch jobs and large molecule calculations (subject to system resources).
User Preferences & Technical Details:
- Configure the Julia executable path, per-mode default methods (molecule and FCIDUMP), and the default basis set in the settings panel.
- Preferences are saved between sessions for a persistent workflow.
- Calculation output can be visualized directly (orbitals, energies, etc.).
- Handles errors gracefully and provides detailed feedback for failed jobs.
Best Practices & Troubleshooting:
- Set up your Julia environment and ElemCo.jl installation before running calculations.
- For remote jobs, ensure SSH keys and permissions are configured correctly.
- Check calculation logs for errors or warnings if results are unexpected.
- Use the integrated runner for rapid prototyping and the command line for large-scale jobs.
References: