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Calculation Types

All Run Mode calculations use the method selected at the top of the panel.

Single Point Energy​

Run a single point calculation when you want the energy and forces at the current geometry — no atoms move. It is the fastest calculation and a good first step before any heavier workflow.

When to use it: Sanity-checking a geometry, comparing the energy of two structures, or generating reference data for a scan.

To run one: select Single Point Energy in the left panel and click Run. The energy and force data appear in the results panel when the calculation finishes, reported in Hartree and Hartree/Angstrom. Force arrows can be toggled on in the display options to visualize the forces on each atom.

Geometry Optimization​

Minimum​

Relaxes the structure toward the nearest local minimum. The geometry updates live in the viewport while the optimization runs, so you can watch it converge.

When to use it: Before vibrational analysis, before a scan, or any time you want a relaxed geometry rather than the raw input.

Parameters:

  • Max steps — upper limit on the number of optimization steps
  • Force threshold (fMax) — convergence criterion for the maximum force on any atom, shown in Hartree/Angstrom

Transition State​

Searches for a first-order saddle point rather than a minimum. Works best when you already have a good starting guess — for example, from a TS geodesic interpolation in the reaction tools.

Parameters:

  • Max steps — upper limit on the number of optimization steps
  • Force threshold (fMax) — convergence criterion, shown in Hartree/Angstrom
  • Hessian update interval — how often the Hessian is recomputed during the search

Vibrational Analysis​

Computes harmonic frequencies for a stationary geometry. When complete, you get:

  • Normal mode frequencies
  • Zero-point energy
  • Animated vibrational mode visualization — click any mode to see it

Before running this: Optimize the geometry first. Vibrational analysis on a non-minimum geometry gives modes that are physically meaningless.

Thermochemistry​

Computes thermochemical properties from vibrational data:

  • Enthalpy
  • Entropy
  • Gibbs free energy corrections

If vibrational data is not already available, the viewer automatically runs a vibrational analysis first.

1D Scan​

Tracks energy along a single internal coordinate — a bond length, angle, or dihedral — while all other degrees of freedom are held fixed.

How to set it up:

  1. Select 2, 3, or 4 atoms in the viewport (this determines whether you are scanning a distance, angle, or dihedral).
  2. Open the scan controls in the left panel.
  3. Set the start, end, and number of steps.
  4. Optionally enable geometry relaxation at each step.
  5. Click Run.

The resulting energy profile appears as a plot. Clicking a point on the plot jumps the viewer to that frame.

Generates and ranks candidate minimum-energy structures. Useful when you want to explore the conformational space of a flexible molecule rather than assuming a single geometry.

The search generates conformers, then ranks them by single-point energy. An energy cutoff filters out high-energy structures automatically.

A variant of the conformer search tailored for transition state structures. Generates and ranks TS-like conformations.

COSMO Surface​

Generates a COSMO solvation surface using the GFN2-xTB method. The calculation runs xtb with --tmcosmo infinity to produce a Turbomole-compatible COSMO file. The result is a 3D surface overlay on the molecule, colored by segment charge density.

When to use it: When you need a solvation surface for COSMO-RS analysis, visualizing charge distribution on the solvent-accessible surface, or preparing input for COSMO-based solvation models.

Availability: Only visible when GFN2-xTB is selected as the method. GFN-FF does not support COSMO surface generation. The Cosmo button appears automatically in the calculation grid.

Result panel shows:

  • Total energy (Hartree)
  • Dielectric energy (if available)
  • Number of surface segments
  • Total surface area (Ų)
  • Surface charge statistics

Visualization: The COSMO surface is rendered as a colored overlay on the molecule. Use the display options to toggle the surface on/off and enable smoothing. The colorbar shows the charge density scale.

Mulliken Charges​

Computes Mulliken population charges using GFN2-xTB. Each atom gets a partial charge that is directly visualised — atoms are colored on a blue (negative) → white (neutral) → red (positive) scale.

When to use it: Checking charge distribution, identifying electrophilic/nucleophilic sites, comparing polarity across a molecule, or preparing charge data for downstream workflows.

Availability: Only visible when GFN2-xTB is selected. GFN-FF does not support population analysis. The Mulliken button appears automatically in the calculation grid.

Result panel shows:

  • Total energy (Hartree)
  • Sum of charges (should be close to net charge)
  • Charge range (min – max)
  • Top 5 atoms by absolute charge

Visualization: Atoms are recolored based on charge. Use the Mulliken toggle in display options to switch between standard element colors and charge-based coloring. A colorbar shows the charge scale.

Molden Orbitals​

Generates a molden orbital file using GFN2-xTB and converts it to volumetric cube surfaces via Multiwfn. The result is a set of 3D isosurfaces that can be toggled individually in the viewer.

When to use it: Visualizing molecular orbitals (HOMO, LUMO, etc.), analyzing electron density, or inspecting frontier orbital shapes.

Availability: Only visible when GFN2-xTB is selected. GFN-FF does not support orbital generation. The Molden button appears automatically in the calculation grid.

Result panel shows:

  • Total energy (Hartree)
  • Number of orbital surfaces generated
  • Surface names

Visualization: Each orbital appears as a colored volumetric isosurface. Use the volumetric display options panel to toggle individual surfaces on/off, adjust isovalues, and change opacity.

tip

For scans and any coordinate-based workflow, select your atoms in the viewport before opening the calculation controls — the UI uses that selection to decide which parameters to show.