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The offline molecular workbench

Save a molecule and selected results in one HTML file, then open it in a browser. You can inspect the structure, available fields and spectra offline; no hosted service is needed.

Stable interface support covers the tested desktop Chromium scope. Keep JSON or CSV results alongside it. The workbench is a visual aid, not a numerical reference. Displaying an analysis does not change its validation status.

openwfn ./openwfn-examples/water.fchk workbench water-workbench.html --open

For a Gaussian frequency output containing typed vibrational records:

openwfn water_freq.log workbench water-vibrations.html --open

For a supported Gaussian, ORCA, or Q-Chem excited-state output:

openwfn tddft.log workbench tddft-workbench.html --open

Without --open, open the resulting file in a modern browser. It works through file://; no localhost server or openWFN process must remain running.

What the file contains

The export can include molecular coordinates, bonds, calculation provenance, analysis properties, volumetric fields, vibrational mode records, excited-state records, UV–Vis arrays, CSS, JavaScript, and the molecular renderer. This portability has a privacy consequence: anyone who receives the file can inspect its embedded molecular data. Do not publish a workbench generated from a confidential calculation.

Molecular rendering is provided by 3Dmol.js under the BSD-3-Clause license. The renderer and its attribution are embedded in the output, so opening a workbench does not fetch the library from a CDN.

Workspace tour

Switching workspaces clears the previous field surfaces and measurement selections. Changing a field or its isovalue replaces the displayed surface rather than stacking another copy. The molecule and ghost-center labels remain visible.

Structure

Rotate, zoom, and recenter the molecule and inspect atom identity. Bond display follows openWFN's geometry-based connectivity model and should not be interpreted as a calculated bond order.

Orbitals

Inspect available frontier information and, when the calculation contains compatible coefficients and basis data, orbital fields. Positive and negative phases are represented separately; color indicates phase, not charge.

Vibrations

When the file contains supported normal-mode data, a Vibrations workspace appears. It uses the same vibrations, ir-spectrum, raman-spectrum and normal-mode results as the Python API.

The workspace provides:

  • a mode selector showing one-based mode number and signed source frequency;
  • source mode metadata, including IR intensity and Raman activity when available;
  • embedded IR and Raman-activity curves from the same deterministic broadened arrays used elsewhere;
  • clickable source spectral sticks that select the corresponding mode;
  • displacement arrows when source Cartesian normal-mode vectors are present;
  • an amplitude control that changes only arrow length for display.

The amplitude control does not alter or renormalize source displacement vectors, frequencies, reduced masses, force constants, IR intensities, or Raman activities. If displacement vectors are absent, the workspace says so explicitly; it does not synthesize motion.

The spectroscopy calculations remain Experimental even though the Workbench interface itself is Stable. Gaussian Raman values are displayed as Raman activities, not converted experimental intensities. See Vibrational spectroscopy.

Excited States

When the file contains supported excited-state data, an Excited States workspace appears. It uses the same excited-states, transition-dipoles and uvvis-spectrum results as Python, CLI, reports and MCP.

The workspace provides:

  • job/state selection using one-based indices;
  • source excitation energy and derived wavelength;
  • source oscillator strength, multiplicity, symmetry, method family, and transition dipole when available;
  • an embedded UV–Vis oscillator-strength profile using the same broadened arrays as the registered analysis;
  • clickable source spectral sticks that select the corresponding state;
  • an explicit source-value note distinguishing parsed quantities from visualization-only broadening.

The Workbench does not invent missing oscillator strengths or dipoles, does not clamp negative source oscillator strengths, and does not reinterpret method-specific amplitudes. The UV–Vis curve remains Experimental and is a deterministic visualization profile, not absorbance/extinction or an instrument model. See Excited states and UV–Vis.

Density and ESP

Review available density/ESP fields together with isovalue and grid provenance. Embedded coarse grids are visualization data unless separately converged and validated. Grid-derived electronic/total ESP remain Experimental; do not remove that qualification in screenshots or reports.

Measurements

Select two atoms for a distance, three for an angle, or four for a signed dihedral. Selection order matters, especially for the torsion sign. CLI atom numbering is one-based.

A careful review workflow

  1. Run doctor and summary in the terminal.
  2. For spectroscopy, run the relevant source-table command and desired spectra command and preserve JSON/CSV output.
  3. Generate the Workbench under a new, descriptive filename.
  4. Confirm molecular charge, multiplicity, formula, atom ordering, and selected mode/state number.
  5. Compare at least one displayed value with machine-readable CLI/Python output.
  6. Check the capability and validation label for every displayed scientific result or field.
  7. Preserve the exact openWFN version and input checksum with the artifact.

Workbench versus report

Use a workbench for interactive spatial/source-data exploration. Use a report for a fixed research record with selected analyses and command provenance. Archive machine-readable tables as well; neither the workbench nor a screenshot should be the sole numerical record.

For vibrational work, the Workbench is particularly useful for connecting a selected source spectral line with a 3D normal-mode direction. For excited states, it connects source state metadata with the corresponding UV–Vis stick/profile. The report is better for fixed mode/state tables and plots.

Troubleshooting

  • If an older HTML file keeps previous surfaces visible, regenerate it with the updated openWFN installation. Exported HTML files contain their own viewer code and do not update when you upgrade the package.
  • If the browser does not open, omit --open and open the reported HTML path manually.
  • If a panel has no data, run doctor; the source file may lack required records.
  • If the Vibrations workspace is absent, the parsed input contains no typed vibrational record.
  • If spectra exist but arrows do not, source displacement vectors are missing; this is a supported unavailable state.
  • If the Excited States workspace is absent, the parsed input contains no typed excited-state collection.
  • If excited states are present but no UV–Vis curve appears, the selected job may have no eligible source oscillator strengths; source states remain inspectable.
  • If generation refuses to replace a file, choose a new filename or deliberately add the global --overwrite option before the input file.
  • If a volumetric surface is slow, use coarser exploratory data first, then converge settings separately.

See Formats and exports, Security, and Validation status.

Browser validation scope

The stable Workbench line validates the established everyday-QC workspaces in offline desktop Chromium with workspace/surface interaction and geometry readouts matching the Python API. The canvas is contained in the viewer so it cannot intercept sidebar clicks. Evidence with input/CI provenance is captured in validation/everyday-qc/browser-report.json; CI reruns the browser validator.

The vibrational and excited-state features additionally have payload/HTML contract tests that require the Workbench to reuse registered numerical data and represent unavailable source properties explicitly. Browser CI remains the gate for preserving existing workspaces as new workspaces are added. This scope does not certify every GPU, browser, or mobile device.

Each preview field retains its scientific validation and conservation status independently of the interface. Coarse density fields are partial when their integration diagnostic fails. Vibrational and excited-state workspaces likewise preserve Experimental scientific status; interface rendering is not independent scientific validation.