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Plugin PySCF Calculator

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Hiromichi Yokoyama edited this page Aug 5, 2026 · 4 revisions

Plugin: PySCF Calculator

PySCF Calculator runs real quantum-chemistry calculations directly inside MoleditPy, using PySCF as the backend: single-point energies, geometry optimization, transition-state search, frequency analysis, TD-DFT, and rigid/relaxed potential-energy surface scans — plus an interactive 3D viewer for the resulting molecular orbitals, density, and electrostatic potential.
Repository moleditpy_pyscf-calculator
Version 3.3.2
Author HiroYokoyama
Supported OS macOS, Linux, WSL only (PySCF has no native Windows build)
Supported Python >=3.9, <3.15
Menu location Extensions ▸ PySCF Calculator...
Extra dependencies PySCF, GeomeTRIC, NumPy, Matplotlib, PyQt6

See Official Plugins for the full catalogue.

1. Overview

The dialog has two tabs — Calculation, where you configure and run a job on a background thread, and Visualization, where you load the job's output folder and inspect orbitals, density/ESP surfaces, an orbital-energy diagram, and (for frequency jobs) thermodynamic properties. Every run writes into its own output/job_N folder, so results and checkpoints from different jobs never collide.

2. Calculation tab

Calculation Settings:

Field Options
Job Type Energy, Geometry Optimization, Frequency, Optimization + Frequency, Transition State Optimization, TS Optimization + Frequency, TDDFT, Rigid Surface Scan, Relaxed Surface Scan
Configure Scan Button shown only for the two scan job types — opens the Scan Configuration dialog (§2.1)
N States Spinbox (1–100, default 10), shown only for TDDFT
Method RKS, RHF, UKS, UHF, ROKS, ROHF
Functional Enabled only for the K-methods. GGA (B3LYP, PBE, BP86, BLYP, PW91); Hybrid GGA (PBE0, B3PW91, HSE06); Meta-GGA (TPSS, SCAN, M06-L); Hybrid Meta-GGA (M06, M06-2X, TPSSh, M11); Range-Separated (ωB97X-D, CAM-B3LYP, LRC-ωPBE, LRC-ωPBEh); LDA (LDA, SVWN)
Basis Set Pople (STO-3G through 6-311++G(3df,3pd)), Dunning cc-pVDZ/TZ/QZ/5Z and aug- variants, Karlsruhe def2-SVP/TZVP/QZVP/TZVPP/QZVPP, minimally-augmented "ma-" def2 variants, LANL2DZ
Solvent None (Vacuum), Water, Ethanol, Methanol, Acetone, THF, Chloroform, Dichloromethane, Toluene, Benzene
Charge / Spin Multiplicity Charge -5..5, Multiplicity Singlet..Sextet; Auto Detect button fills both from the loaded molecule (and runs automatically ~100 ms after the dialog opens if a molecule is already loaded)
Max Threads / Max Memory 0 (auto) up to 64 threads; 500–256000 MB
Enable Symmetry / Break Initial Guess Symmetry Checkboxes — the latter helps converge spin-polarized UKS/UHF solutions
Max SCF Cycles 1–2000, default 100
Conv. Tolerance Text field, default 1e-9
DFT Grid Level 0–9, default 3
Output Dir Defaults to ~/PySCF_Results, with a Browse button

Save as Default persists the current Method/Basis/output path/etc. as the starting point for future sessions. Run Calculation / Stop control a background worker thread; an indeterminate progress bar and a log pane (showing the full PySCF stdout, including low-level warnings) update live.

2.1 Scan Configuration dialog

For the two scan job types, Configure Scan opens a dialog that asks you to click 2, 3, or 4 atoms in the 3D viewer — the count determines whether the scan coordinate is a bond, angle, or dihedral (detected automatically). It shows the current selection, coordinate type, and current value, plus Start/End/Steps fields (default 10 steps). It temporarily switches the main window into measurement-selection mode and polls the 3D selection every 200 ms so the preview stays live, restoring the previous mode when closed.

3. Visualization tab

  • Result Folder — read-only path plus Load Result Folder..., which auto-detects either a checkpoint-based result (pyscf.chk / checkpoint.chk) or a scan result folder (scan_results.csv + scan_trajectory.xyz).
  • Load Optimized Structure — pulls the optimized geometry back into the main 2D/3D editor.
  • Post-Calculation Analysis group: an auto-populated list of orbitals/properties (occupied/virtual MOs, HOMO/LUMO, density options), a manual MO-index entry for custom orbitals, Generate & Visualize Selected (builds cube files on demand), Show Orbital Energy Diagram, and Show Thermodynamic Properties (enabled only after a Frequency job).
  • Visualization Controls (for MO/density cubes): isovalue (0.0001–10.0, default 0.04), separate positive/negative color pickers, and an opacity slider (default 40%).
  • ESP Mapping Controls (shown only for mapped/ESP surfaces): surface isovalue (default 0.004), min/max color-range with a Fit button (auto-fits to the surface's value distribution), a colormap dropdown (jet, jet_r, bwr, bwr_r, seismic, seismic_r, coolwarm, coolwarm_r, viridis, viridis_r — default jet_r), and opacity.

3.1 Orbital Energy Diagram

An interactive HOMO/LUMO energy-level plot: click a level to generate (if needed) and visualize its cube in 3D, drag to zoom, scroll to pan, double-click to reset the view to the HOMO–LUMO gap, toggle eV/Hartree units, and Save to PNG (auto-hides the UI chrome for a clean figure).

3.2 Thermodynamic Properties dialog

A separate window (enabled after Frequency-type jobs) showing a table of thermochemical quantities, with Export CSV.

4. Typical workflow

  1. Build or load a molecule in MoleditPy, then Extensions ▸ PySCF Calculator....
  2. On the Calculation tab, pick Job Type, Method/Functional, Basis, Solvent, and charge/spin (or Auto Detect); set resource limits; for a scan job, click Configure Scan and pick atoms in the 3D viewer.
  3. Run Calculation — watch the log and progress bar, or Stop if needed.
  4. The dialog switches to the Visualization tab automatically on completion (or Load Result Folder to reopen a past job).
  5. Select orbitals/properties and Generate & Visualize; tune isovalue/colors/opacity or ESP colormap/range; open the Orbital Energy Diagram or Thermodynamic Properties as needed.

5. See also

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