quantui 0.8.1__tar.gz → 0.9.0__tar.gz

{quantui-0.8.1 → quantui-0.9.0}/CHANGELOG.md

@@ -7,6 +7,139 @@ and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.ht
 
 ## [Unreleased]
 
+## [0.9.0] - 2026-09-26
+
+### Added
+
+- **SLURM job folders with per-attempt subfolders (M-JOBDIRS)** — each cluster
+  job gets a readable folder (`<formula>_<calc>_<method>_<basis>`, or the
+  optional **Job name** on the Calculate tab) that doubles as the SLURM job
+  name. Every run of its `submit.slurm` creates a new `attempt-NN_job<id>/`
+  subfolder, so **Resubmit** (new, Cluster Jobs tab) and a hand-run
+  `sbatch submit.slurm` never overwrite an earlier attempt. The job root is
+  configurable in **System Settings** (or `QUANTUI_STAGING_DIR`), for
+  clusters with small home quotas.
+- **SLURM results marked in History** — entries show
+  `🖥 SLURM <job id>·a<attempt>` and the result card has a "Ran on" row with
+  the job folder. Hand-run attempts are added to History on the next Cluster
+  Jobs refresh; failed attempts stay in the job folder only.
+- **GPU offload for geometry optimization** — gpu4pyscf offload now reaches
+  every SCF/gradient step of a geometry optimization, not just single points.
+  A separate, guarded CuPy GPU path for PyFock, GPU provenance
+  (`gpu_used` / `gpu_name`) on optimization results, and
+  `quantui gpu check --engine pyfock`.
+- **PyFock backend (M-PYFOCK)** — Phase 1: normalized engine dispatch,
+  native-Windows PBE/def2 single points for neutral closed-shell molecules,
+  capability-driven calculation menus, engine provenance in logs and saved
+  results, a pinned `pyfock` install extra, and a Windows water parity gate
+  against PySCF; unsupported hybrids, ions, open-shell systems, solvent,
+  checkpoints and orbital analysis are rejected before compute. Phase 2:
+  geometry optimization via PyFock's ASE calculator with analytical
+  density-fitted gradients; results keep orbital arrays, Mulliken charges,
+  dipoles, and engine-native cube generation.
+- **`quantui submit` CLI** — submit request JSON files to SLURM from a script
+  (with `--job-name`, `--dry-run`, resource and mail options); resource
+  estimates account for parallel IR/Raman workers.
+- **Checkpoint/resume for batch and Frequency runs** — the SLURM batch worker
+  resumes Geometry Optimization, PES Scan and Frequency runs from their
+  checkpoints; Frequency (interactive and batch) banks each finished
+  displacement so a restart skips completed ones.
+- **SCF rescue for hard open-shell cases (M-SCF-ROBUST)** — one shared
+  convergence-rescue helper at every SCF call site, with provenance lines in
+  the log.
+- **RKS/UKS/RHF/UHF label** on every result card, live and saved.
+
+### Changed
+
+- **SLURM output layout** — new submissions use the job-folder layout above
+  instead of `~/.quantui/staging/<request_id>/`. Jobs submitted earlier keep
+  their old folders and still list, reconnect and ingest.
+- **Unconverged results are no longer reported as converged** — CCSD/CCSD(T)
+  amplitudes, TD-DFT roots, frequency Hessians, and optimizer gradients from an
+  unconverged SCF are now flagged instead of shown as a clean result. Saved
+  cards name the step that failed rather than blaming the SCF.
+- **Parallel IR/Raman worker pools** are sized from the SLURM/cgroup
+  allocation, not the node's full CPU count.
+
+### Fixed
+
+- **Thermochemistry** — entropy units no longer corrupt the Gibbs free energy;
+  thermochemistry is saved and shown again when a frequency result is
+  reopened from History.
+- **Raman activities** — added the missing a₀³→ų polarizability conversion.
+- **Functionals** — ωB97X-D resolves to the real functional (not `wb97x`+D3),
+  and the D3 dispersion status is shown instead of silently dropped.
+- **ECP systems** — ECPs are passed to parallel IR/Raman workers and embedded
+  in exported scripts; charge/spin inference handles ROHF and ECP systems.
+- **Exported scripts** for MP2/CCSD/CCSD(T) now run the requested method
+  instead of a DFT branch.
+- **Solvation** — PCM requested for a calc type that cannot use it is
+  rejected instead of silently ignored; solvated Geometry Optimization works
+  in the SLURM batch worker.
+- **SLURM ingest** keeps computed properties and provenance (dipole, charges,
+  SCF variant, solvent, GPU); reconnecting to a finished SLURM job no longer
+  saves a second copy of its result to History.
+- **SLURM scripts** quote paths containing spaces, and no longer export an
+  unused `QUANTUI_RESULTS_DIR`.
+- **Checkpoints** — PES Scan checkpoint identity is coordinate-aware, and the
+  interactive Frequency run uses its own checkpoint.
+- **NMR** fallback-reference metadata is saved and shown.
+- **Parallel IR/Raman workers** honor density fitting and SCF rescue.
+- **Batch results** carry Mulliken charges and dipoles; UHF Molden export is
+  complete.
+- **Spectra** — the x-range covers every real mode; exported NPZ files carry
+  the fields the cube helper needs, and cube provenance can't be overwritten.
+- **Packaging** — the built wheel ships `quantui.engines`.
+- **Theme** — Plotly axis and zero lines follow the active palette instead of
+  staying pale blue-gray on dark themes.
+
+## [0.8.2] - 2026-08-30
+
+### Added
+
+- **SLURM batch execution (M-CLUSTER2)** — optional cluster backend when
+  `QUANTUI_ENABLE_SLURM=1` and `sbatch` is on PATH: submit from the same UI,
+  monitor on the **Cluster Jobs** tab, hybrid `squeue`/`sacct` polling, submit
+  cooldown, and stale-registry cleanup. All Calculate-tab calc types supported
+  on the batch worker path.
+- **`QUANTUI_ENABLE_SLURM` site gate** — SLURM batch stays hidden and
+  undispatchable until an operator sets this environment variable. Student CPU
+  images and JupyterHub profiles can omit it (default off); instructors enable
+  cluster testing with `QUANTUI_ENABLE_SLURM=1` without any extra student
+  command.
+- **`quantui setup` and `quantui run app`** — writes `~/QuantUI.ipynb` for
+  NCShare/JupyterLab (Render with Voilà). `run app` detects Apptainer +
+  Jupyter and exits with Voilà instructions instead of opening an unreachable
+  second port.
+- **Parallel IR intensity displacements (CPU)** — Settings checkbox
+  (`compute.freq_parallel`) plus `QUANTUI_FREQ_PARALLEL` env override fans out
+  the 6N finite-difference SCF loop on hosts with ≥4 cores and ≥2 atoms. The
+  **CPU teaching SIF** sets `QUANTUI_FREQ_PARALLEL=1` by default; the checkbox
+  reflects the deployment value and locks while the env var is set.
+- **Imaginary-mode perturbation** for Frequency reruns seeded from History.
+- **Stage-aware frequency cost estimate** and per-phase run status labels (NMR,
+  Hessian, post-HF).
+- **Preset theme palettes** replacing the invert filter (M-THEME THEME.6).
+- **Quantum engine registry** (`quantui/engines/`) and
+  `ComputeSettings.quantum_engine` field (M-PYFOCK PYF.1 groundwork).
+- **Static Raman spectrum** on the Analysis tab (M-SPECTRA2).
+
+### Fixed
+
+- **Mulliken 3D viewer** could render blank after geometry persistence and lazy
+  panel activation (#103).
+- **`apptainer/quantui-gpu.def` never installed the `xtb` extra**, so GFN-FF
+  metal-capable classical pre-optimization (DEC-018) was unavailable in every
+  GPU/HPC image — the app correctly reported the honest-failure message
+  ("RDKit could not perceive bonds ... and the GFN-FF (xtb) metal backend is
+  not installed"), but the underlying cause was a container gap, not a
+  missing local install. Fixed by pinning the image's Python to 3.11 via the
+  deadsnakes PPA (Ubuntu 24.04's own repos ship 3.12 only, and `xtb`'s PyPI
+  wheels stop at `cp311`) and adding `xtb` to the pip extras. `quantui.def`
+  (the CPU teaching image) gained the equivalent `xtb-python` conda-forge
+  package, which it had also been missing despite `local-setup/environment.yml`
+  already carrying it for local conda installs.
+
 ## [0.8.1] - 2026-08-26
 
 ### Added
@@ -801,7 +934,12 @@ Initial public scaffolding of the QuantUI package: `quantui` package with
 `calculator.py`, basic notebook launcher, Apptainer container definition,
 MIT license, and project metadata.
 
-[Unreleased]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.6.1...HEAD
+[Unreleased]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.9.0...HEAD
+[0.9.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.8.2...v0.9.0
+[0.8.2]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.8.1...v0.8.2
+[0.8.1]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.8.0...v0.8.1
+[0.8.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.7.0...v0.8.0
+[0.7.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.6.1...v0.7.0
 [0.6.1]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.6.0...v0.6.1
 [0.6.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.5.2...v0.6.0
 [0.5.2]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.5.1...v0.5.2

{quantui-0.8.1/quantui.egg-info → quantui-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: quantui
-Version: 0.8.1
+Version: 0.9.0
 Summary: An open-source frontend for DFT and post-HF quantum chemistry with PySCF
 Author-email: Jonathan Schultz <nccu-schultz-lab@users.noreply.github.com>
 License: MIT License
@@ -55,11 +55,17 @@ Requires-Dist: numpy<3,>=1.24.0
 Requires-Dist: requests<3,>=2.28.0
 Requires-Dist: py3Dmol<3,>=2.0.0
 Requires-Dist: matplotlib<4,>=3.7.0
-Requires-Dist: plotly<7,>=5.0.0
+Requires-Dist: plotly<8,>=5.0.0
 Requires-Dist: plotlymol<1,>=0.2.1
+Requires-Dist: kaleido<2,>=0.2.1
 Provides-Extra: pyscf
 Requires-Dist: pyscf<3,>=2.13.0; extra == "pyscf"
 Requires-Dist: pyscf-properties; extra == "pyscf"
+Provides-Extra: pyfock
+Requires-Dist: pyfock<0.3,>=0.1.7; extra == "pyfock"
+Requires-Dist: ase<4,>=3.22.0; extra == "pyfock"
+Requires-Dist: scipy<2,>=1.10; extra == "pyfock"
+Requires-Dist: numba<0.68,>=0.57; extra == "pyfock"
 Provides-Extra: ase
 Requires-Dist: ase<4,>=3.22.0; extra == "ase"
 Provides-Extra: xtb
@@ -76,6 +82,10 @@ Provides-Extra: gpu-cuda13x
 Requires-Dist: gpu4pyscf-cuda13x; extra == "gpu-cuda13x"
 Requires-Dist: cupy-cuda13x; extra == "gpu-cuda13x"
 Requires-Dist: cutensor-cu13; extra == "gpu-cuda13x"
+Provides-Extra: pyfock-gpu-cuda12x
+Requires-Dist: cupy-cuda12x; extra == "pyfock-gpu-cuda12x"
+Provides-Extra: pyfock-gpu-cuda13x
+Requires-Dist: cupy-cuda13x; extra == "pyfock-gpu-cuda13x"
 Provides-Extra: notebook
 Requires-Dist: nbmake>=1.4.0; extra == "notebook"
 Requires-Dist: ipykernel<8,>=6.0.0; extra == "notebook"
@@ -84,6 +94,7 @@ Requires-Dist: pytest>=7.0.0; extra == "dev"
 Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
 Requires-Dist: pytest-mock>=3.10.0; extra == "dev"
 Requires-Dist: pytest-xdist>=3.0.0; extra == "dev"
+Requires-Dist: build>=1.0.0; extra == "dev"
 Requires-Dist: mypy<2.4,>=1.10; extra == "dev"
 Requires-Dist: types-requests>=2.28.0; extra == "dev"
 Requires-Dist: black~=26.5.1; python_version >= "3.10" and extra == "dev"
@@ -101,7 +112,8 @@ Dynamic: license-file
 [![Python](https://img.shields.io/badge/python-3.9%20|%203.10%20|%203.11-blue)](https://www.python.org)
 
 A powerful open-source frontend for DFT and post-HF quantum chemistry.
-QuantUI puts [PySCF](https://pyscf.org) behind an interactive Jupyter/Voilà
+QuantUI puts [PySCF](https://pyscf.org) and a guarded
+[PyFock](https://github.com/manassharma07/PyFock) subset behind an interactive Jupyter/Voilà
 UI so you can build molecules, run calculations locally, and visualize the
 results — no cluster account, no SLURM, no queueing.
 
@@ -119,24 +131,24 @@ Real output from QuantUI, straight from the app:
 <table>
   <tr>
     <td width="50%" align="center" valign="top">
-      <img src="docs/images/cisplatin_lumo.png" alt="Cisplatin LUMO isosurface" width="400"><br>
+      <img src="https://raw.githubusercontent.com/The-Schultz-Lab/QuantUI/main/docs/images/cisplatin_lumo.png" alt="Cisplatin LUMO isosurface" width="400"><br>
       <b>Cisplatin LUMO</b><br>
       <sub>Molecular-orbital isosurface · B3LYP/LANL2DZ (ECP on Pt &amp; Cl)</sub>
     </td>
     <td width="50%" align="center" valign="top">
-      <img src="docs/images/aspartame_orbital_diagram.png" alt="Aspartame orbital energy-level diagram" width="300"><br>
+      <img src="https://raw.githubusercontent.com/The-Schultz-Lab/QuantUI/main/docs/images/aspartame_orbital_diagram.png" alt="Aspartame orbital energy-level diagram" width="300"><br>
       <b>Aspartame orbital energies</b><br>
       <sub>Occupied/virtual levels · HOMO–LUMO gap 6.09 eV · B3LYP/6-31G*</sub>
     </td>
   </tr>
   <tr>
     <td width="50%" align="center" valign="top">
-      <img src="docs/images/benzene_ir_spectrum.png" alt="Benzene IR spectrum" width="400"><br>
+      <img src="https://raw.githubusercontent.com/The-Schultz-Lab/QuantUI/main/docs/images/benzene_ir_spectrum.png" alt="Benzene IR spectrum" width="400"><br>
       <b>Benzene IR spectrum</b><br>
       <sub>Analytical Hessian · ωB97X-D/6-31G · the four IR-active bands</sub>
     </td>
     <td width="50%" align="center" valign="top">
-      <img src="docs/images/cisplatin_optimization.png" alt="Cisplatin geometry-optimization energy convergence" width="400"><br>
+      <img src="https://raw.githubusercontent.com/The-Schultz-Lab/QuantUI/main/docs/images/cisplatin_optimization.png" alt="Cisplatin geometry-optimization energy convergence" width="400"><br>
       <b>Geometry optimization</b><br>
       <sub>Cisplatin relaxing over 21 BFGS steps · B3LYP/LANL2DZ</sub>
     </td>
@@ -165,7 +177,10 @@ Real output from QuantUI, straight from the app:
   your default-backend preference between sessions
 - **In-session calculations** — RHF, UHF, 9 DFT functionals, MP2, CCSD,
   CCSD(T), NMR shielding, TD-DFT UV-Vis, and 1D PES scans via PySCF, running
-  in your Python kernel (no batch submission)
+  in your Python kernel. Optional PyFock 0.1.x adds native-Windows PBE
+  single points and geometry optimizations for neutral, closed-shell molecules
+  with def2-SVP/def2-TZVP, including orbital and population analysis;
+  engine capabilities automatically gate the setup menus
 - **Implicit solvent** — PCM solvation (Water, Ethanol, THF, DMSO,
   Acetonitrile) via a single checkbox
 - **Rich results** — total energy, HOMO-LUMO gap, Mulliken charges, dipole
@@ -198,10 +213,12 @@ Real output from QuantUI, straight from the app:
 - **Plot export** — save IR, UV-Vis, PES, and orbital diagrams as standalone
   HTML
 - **Optional GPU acceleration** — when [gpu4pyscf](https://github.com/pyscf/gpu4pyscf)
-  and a CUDA-capable NVIDIA GPU are present, SCF calculations auto-offload
+  and a CUDA-capable NVIDIA GPU are present, single-point SCF calculations auto-offload
   via `mf.to_gpu()` (RHF / UHF / RKS / UKS supported; CCSD(T) stays on CPU).
   The Status tab + every result card show which compute device was used.
   Set `QUANTUI_DISABLE_GPU=1` to force CPU even when the GPU is available.
+  Geometry-optimization SCF steps are currently CPU-only; that limitation was
+  reproduced on real GPU hardware and remains an open optimizer-path fix.
 - **Timing calibration** — one-click benchmark suite populates the time
   estimator with real machine data so predictions are accurate from the first run
 - **Voilà app mode** — serve the notebook as a polished widget-only UI (no
@@ -216,11 +233,29 @@ Real output from QuantUI, straight from the app:
 | --- | --- | --- |
 | Linux / macOS | Full | PySCF installs natively |
 | WSL (Windows) | Full | Use an Ubuntu WSL environment |
-| Windows (native) | Partial | All UI and visualization features work; PySCF calculations require the Apptainer container |
+| Windows (native) | Partial | PyFock runs guarded PBE single points and geometry optimizations; use WSL/Apptainer for the full PySCF feature set |
 
-### Windows users: Apptainer container
+### Windows users: native PyFock or the full container
 
-PySCF does not install on Windows natively. The
+For native Windows, install the PyFock subset:
+
+```powershell
+py -3.11 -m venv .venv
+.venv\Scripts\Activate.ps1
+python -m pip install "quantui[pyfock,ase,app]"
+```
+
+In **System Settings → Quantum engine**, select PyFock (or leave Automatic
+selected when PySCF is absent). The validated subset supports neutral,
+closed-shell PBE single points and geometry optimizations with def2-SVP or
+def2-TZVP. Density fitting is always enabled, analytical gradients drive
+optimization, and orbital, Mulliken, dipole, and cube analysis are retained.
+Hybrids, charged/open-shell systems, solvent, and checkpoint warm starts remain
+PySCF-only. Optional PyFock GPU acceleration is available separately through
+CuPy; geometry optimization uses numerical forces on GPU because PyFock 0.1.7
+does not yet provide analytical GPU gradients.
+
+PySCF does not install on Windows natively. For the complete feature set, the
 [`apptainer/quantui.def`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/apptainer/quantui.def) container bundles
 the complete environment and runs anywhere Apptainer/Singularity is available.
 See [`apptainer/README.md`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/apptainer/README.md) for build and run instructions.
@@ -246,6 +281,12 @@ pip install -e ".[pyscf,ase,app]"
 python -m pip install quantui[pyscf,ase,app]
 ```
 
+For the limited native-Windows engine instead:
+
+```bash
+python -m pip install quantui[pyfock,ase,app]
+```
+
 ### Option C — Apptainer container (Windows / reproducible deployment)
 
 See [apptainer/README.md](https://github.com/The-Schultz-Lab/QuantUI/blob/main/apptainer/README.md).
@@ -306,6 +347,27 @@ and result cards will display the compute device.
 Whenever gpu4pyscf can't offload a particular call, QuantUI falls back
 to CPU automatically and the result card reflects which device ran.
 
+### Optional: PyFock GPU acceleration
+
+PyFock uses its own CuPy/Numba CUDA implementation; it does not use
+`gpu4pyscf`. Install the PyFock engine and the CUDA-suffixed CuPy extra that
+matches the NVIDIA driver reported by `nvidia-smi`:
+
+```bash
+# CUDA 13.x driver
+pip install "quantui[pyfock,pyfock-gpu-cuda13x]"
+
+# CUDA 12.x driver
+pip install "quantui[pyfock,pyfock-gpu-cuda12x]"
+```
+
+PyFock GPU use is guarded independently: QuantUI requires CuPy to import and
+report a CUDA device, and still honors the Settings GPU toggle and
+`QUANTUI_DISABLE_GPU=1`. If the probe fails, PyFock falls back to CPU and
+reports the reason. GPU single points use PyFock's GPU SCF/integral/XC path;
+GPU geometry optimizations use numerical finite-difference forces because the
+installed PyFock release's analytical gradient implementation is CPU-only.
+
 ### Optional: GFN-FF metal pre-optimization (xtb)
 
 The classical (MMFF/UFF) pre-optimizer relies on RDKit's organic valence

{quantui-0.8.1 → quantui-0.9.0}/README.md

@@ -7,7 +7,8 @@
 [![Python](https://img.shields.io/badge/python-3.9%20|%203.10%20|%203.11-blue)](https://www.python.org)
 
 A powerful open-source frontend for DFT and post-HF quantum chemistry.
-QuantUI puts [PySCF](https://pyscf.org) behind an interactive Jupyter/Voilà
+QuantUI puts [PySCF](https://pyscf.org) and a guarded
+[PyFock](https://github.com/manassharma07/PyFock) subset behind an interactive Jupyter/Voilà
 UI so you can build molecules, run calculations locally, and visualize the
 results — no cluster account, no SLURM, no queueing.
 
@@ -25,24 +26,24 @@ Real output from QuantUI, straight from the app:
 <table>
   <tr>
     <td width="50%" align="center" valign="top">
-      <img src="docs/images/cisplatin_lumo.png" alt="Cisplatin LUMO isosurface" width="400"><br>
+      <img src="https://raw.githubusercontent.com/The-Schultz-Lab/QuantUI/main/docs/images/cisplatin_lumo.png" alt="Cisplatin LUMO isosurface" width="400"><br>
       <b>Cisplatin LUMO</b><br>
       <sub>Molecular-orbital isosurface · B3LYP/LANL2DZ (ECP on Pt &amp; Cl)</sub>
     </td>
     <td width="50%" align="center" valign="top">
-      <img src="docs/images/aspartame_orbital_diagram.png" alt="Aspartame orbital energy-level diagram" width="300"><br>
+      <img src="https://raw.githubusercontent.com/The-Schultz-Lab/QuantUI/main/docs/images/aspartame_orbital_diagram.png" alt="Aspartame orbital energy-level diagram" width="300"><br>
       <b>Aspartame orbital energies</b><br>
       <sub>Occupied/virtual levels · HOMO–LUMO gap 6.09 eV · B3LYP/6-31G*</sub>
     </td>
   </tr>
   <tr>
     <td width="50%" align="center" valign="top">
-      <img src="docs/images/benzene_ir_spectrum.png" alt="Benzene IR spectrum" width="400"><br>
+      <img src="https://raw.githubusercontent.com/The-Schultz-Lab/QuantUI/main/docs/images/benzene_ir_spectrum.png" alt="Benzene IR spectrum" width="400"><br>
       <b>Benzene IR spectrum</b><br>
       <sub>Analytical Hessian · ωB97X-D/6-31G · the four IR-active bands</sub>
     </td>
     <td width="50%" align="center" valign="top">
-      <img src="docs/images/cisplatin_optimization.png" alt="Cisplatin geometry-optimization energy convergence" width="400"><br>
+      <img src="https://raw.githubusercontent.com/The-Schultz-Lab/QuantUI/main/docs/images/cisplatin_optimization.png" alt="Cisplatin geometry-optimization energy convergence" width="400"><br>
       <b>Geometry optimization</b><br>
       <sub>Cisplatin relaxing over 21 BFGS steps · B3LYP/LANL2DZ</sub>
     </td>
@@ -71,7 +72,10 @@ Real output from QuantUI, straight from the app:
   your default-backend preference between sessions
 - **In-session calculations** — RHF, UHF, 9 DFT functionals, MP2, CCSD,
   CCSD(T), NMR shielding, TD-DFT UV-Vis, and 1D PES scans via PySCF, running
-  in your Python kernel (no batch submission)
+  in your Python kernel. Optional PyFock 0.1.x adds native-Windows PBE
+  single points and geometry optimizations for neutral, closed-shell molecules
+  with def2-SVP/def2-TZVP, including orbital and population analysis;
+  engine capabilities automatically gate the setup menus
 - **Implicit solvent** — PCM solvation (Water, Ethanol, THF, DMSO,
   Acetonitrile) via a single checkbox
 - **Rich results** — total energy, HOMO-LUMO gap, Mulliken charges, dipole
@@ -104,10 +108,12 @@ Real output from QuantUI, straight from the app:
 - **Plot export** — save IR, UV-Vis, PES, and orbital diagrams as standalone
   HTML
 - **Optional GPU acceleration** — when [gpu4pyscf](https://github.com/pyscf/gpu4pyscf)
-  and a CUDA-capable NVIDIA GPU are present, SCF calculations auto-offload
+  and a CUDA-capable NVIDIA GPU are present, single-point SCF calculations auto-offload
   via `mf.to_gpu()` (RHF / UHF / RKS / UKS supported; CCSD(T) stays on CPU).
   The Status tab + every result card show which compute device was used.
   Set `QUANTUI_DISABLE_GPU=1` to force CPU even when the GPU is available.
+  Geometry-optimization SCF steps are currently CPU-only; that limitation was
+  reproduced on real GPU hardware and remains an open optimizer-path fix.
 - **Timing calibration** — one-click benchmark suite populates the time
   estimator with real machine data so predictions are accurate from the first run
 - **Voilà app mode** — serve the notebook as a polished widget-only UI (no
@@ -122,11 +128,29 @@ Real output from QuantUI, straight from the app:
 | --- | --- | --- |
 | Linux / macOS | Full | PySCF installs natively |
 | WSL (Windows) | Full | Use an Ubuntu WSL environment |
-| Windows (native) | Partial | All UI and visualization features work; PySCF calculations require the Apptainer container |
+| Windows (native) | Partial | PyFock runs guarded PBE single points and geometry optimizations; use WSL/Apptainer for the full PySCF feature set |
 
-### Windows users: Apptainer container
+### Windows users: native PyFock or the full container
 
-PySCF does not install on Windows natively. The
+For native Windows, install the PyFock subset:
+
+```powershell
+py -3.11 -m venv .venv
+.venv\Scripts\Activate.ps1
+python -m pip install "quantui[pyfock,ase,app]"
+```
+
+In **System Settings → Quantum engine**, select PyFock (or leave Automatic
+selected when PySCF is absent). The validated subset supports neutral,
+closed-shell PBE single points and geometry optimizations with def2-SVP or
+def2-TZVP. Density fitting is always enabled, analytical gradients drive
+optimization, and orbital, Mulliken, dipole, and cube analysis are retained.
+Hybrids, charged/open-shell systems, solvent, and checkpoint warm starts remain
+PySCF-only. Optional PyFock GPU acceleration is available separately through
+CuPy; geometry optimization uses numerical forces on GPU because PyFock 0.1.7
+does not yet provide analytical GPU gradients.
+
+PySCF does not install on Windows natively. For the complete feature set, the
 [`apptainer/quantui.def`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/apptainer/quantui.def) container bundles
 the complete environment and runs anywhere Apptainer/Singularity is available.
 See [`apptainer/README.md`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/apptainer/README.md) for build and run instructions.
@@ -152,6 +176,12 @@ pip install -e ".[pyscf,ase,app]"
 python -m pip install quantui[pyscf,ase,app]
 ```
 
+For the limited native-Windows engine instead:
+
+```bash
+python -m pip install quantui[pyfock,ase,app]
+```
+
 ### Option C — Apptainer container (Windows / reproducible deployment)
 
 See [apptainer/README.md](https://github.com/The-Schultz-Lab/QuantUI/blob/main/apptainer/README.md).
@@ -212,6 +242,27 @@ and result cards will display the compute device.
 Whenever gpu4pyscf can't offload a particular call, QuantUI falls back
 to CPU automatically and the result card reflects which device ran.
 
+### Optional: PyFock GPU acceleration
+
+PyFock uses its own CuPy/Numba CUDA implementation; it does not use
+`gpu4pyscf`. Install the PyFock engine and the CUDA-suffixed CuPy extra that
+matches the NVIDIA driver reported by `nvidia-smi`:
+
+```bash
+# CUDA 13.x driver
+pip install "quantui[pyfock,pyfock-gpu-cuda13x]"
+
+# CUDA 12.x driver
+pip install "quantui[pyfock,pyfock-gpu-cuda12x]"
+```
+
+PyFock GPU use is guarded independently: QuantUI requires CuPy to import and
+report a CUDA device, and still honors the Settings GPU toggle and
+`QUANTUI_DISABLE_GPU=1`. If the probe fails, PyFock falls back to CPU and
+reports the reason. GPU single points use PyFock's GPU SCF/integral/XC path;
+GPU geometry optimizations use numerical finite-difference forces because the
+installed PyFock release's analytical gradient implementation is CPU-only.
+
 ### Optional: GFN-FF metal pre-optimization (xtb)
 
 The classical (MMFF/UFF) pre-optimizer relies on RDKit's organic valence

{quantui-0.8.1 → quantui-0.9.0}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "quantui"
-version = "0.8.1"
+version = "0.9.0"
 description = "An open-source frontend for DFT and post-HF quantum chemistry with PySCF"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -30,8 +30,9 @@ classifiers = [
     # PyPI shows the licence from this classifier in the sidebar; the
     # [project] license table alone is not enough for the old-style display.
     "License :: OSI Approved :: MIT License",
-    # PySCF is Linux/macOS only, so Windows users need the container. Saying so
-    # in metadata means `pip` users see it before they hit an install failure.
+    # The complete PySCF feature set is Linux/macOS only. Native Windows has a
+    # smaller optional PyFock backend, documented in README; add a Windows
+    # classifier after its dedicated real-calculation CI gate is green.
     "Operating System :: POSIX :: Linux",
     "Operating System :: MacOS",
     "Environment :: Web Environment",
@@ -62,8 +63,9 @@ dependencies = [
     "requests>=2.28.0,<3",
     "py3Dmol>=2.0.0,<3",
     "matplotlib>=3.7.0,<4",
-    "plotly>=5.0.0,<7",
+    "plotly>=5.0.0,<8",
     "plotlymol>=0.2.1,<1",
+    "kaleido>=0.2.1,<2",
 ]
 
 [project.urls]
@@ -81,8 +83,19 @@ Issues = "https://github.com/The-Schultz-Lab/QuantUI/issues"
 # the terminal (``quantui log tail -n 50``, etc.). See ``quantui/cli.py``.
 quantui = "quantui.cli:main"
 
-[tool.setuptools]
-packages = ["quantui"]
+[tool.setuptools.packages.find]
+# AUDIT F20 — this used to be an explicit `packages = ["quantui",
+# "quantui.backends"]` list under [tool.setuptools]. quantui.engines is a
+# real subpackage (quantui/engines/__init__.py + base.py/pyscf_engine.py/
+# pyfock_engine.py) that was never added to that list: the built wheel
+# silently omitted it entirely (ModuleNotFoundError importing
+# quantui.engines from an installed, non-editable wheel), while every CI
+# run stayed green because CI installs editable (`pip install -e`), which
+# doesn't go through this list at all. Automatic discovery means the next
+# new subpackage ships by construction instead of needing a second edit
+# here that's easy to forget.
+include = ["quantui", "quantui.*"]
+exclude = ["tests", "tests.*"]
 
 [tool.setuptools.package-data]
 # Bundled molecule library (M-STRUCT): the indexed SQLite store + the
@@ -113,6 +126,20 @@ pyscf = [
     "pyscf-properties",
 ]
 
+# Native-Windows-capable pure-Python DFT backend (M-PYFOCK). PyFock 0.1.7
+# imports SciPy but does not declare it in its own wheel metadata, so QuantUI's
+# extra supplies and caps that runtime dependency explicitly.
+pyfock = [
+    "pyfock>=0.1.7,<0.3",
+    # PyFock's ASE calculator is the geometry-optimization path used by
+    # QuantUI; include ASE here so the documented backend extra is complete.
+    "ase>=3.22.0,<4",
+    "scipy>=1.10,<2",
+    # 0.68.0rc1 can be selected by PyFock's permissive floor and brought a
+    # prerelease llvmlite that crashed at import on Linux/Python 3.12.
+    "numba>=0.57,<0.68",
+]
+
 # ASE: structure I/O, extended molecule library, geometry optimisation
 ase = [
     "ase>=3.22.0,<4",
@@ -163,6 +190,16 @@ gpu-cuda13x = [
     "cutensor-cu13",
 ]
 
+# PyFock GPU acceleration is a separate CuPy-only path.  Do not install or
+# probe gpu4pyscf for a PyFock calculation: the two engines have independent
+# CUDA implementations and capability gates.
+pyfock-gpu-cuda12x = [
+    "cupy-cuda12x",
+]
+pyfock-gpu-cuda13x = [
+    "cupy-cuda13x",
+]
+
 # Notebook smoke-test dependencies
 notebook = [
     "nbmake>=1.4.0",
@@ -175,6 +212,13 @@ dev = [
     "pytest-cov>=4.0.0",
     "pytest-mock>=3.10.0",
     "pytest-xdist>=3.0.0",  # parallel test execution (-n=auto in addopts)
+    # AUDIT F20 — the PEP 517 build frontend, used by
+    # tests/test_packaging.py to build a real wheel and inspect its
+    # contents (import/package-data smoke test against a *built* wheel,
+    # not the editable install every other test runs against — the gap
+    # that let quantui.engines silently vanish from the shipped package
+    # while CI, always editable, stayed green).
+    "build>=1.0.0",
     "mypy>=1.10,<2.4",  # pinned, not an open floor — same reasoning as
     # black/ruff below: it must agree with .pre-commit-config.yaml's rev,
     # which is what CI enforces (M-TYPECHECK TYPE.2). A newer mypy silently
@@ -255,6 +299,7 @@ strict_equality = true
 [[tool.mypy.overrides]]
 module = [
     "pyscf.*",
+    "pyfock.*",
     "py3Dmol.*",
     "IPython.*",
     "ipywidgets.*",
@@ -293,6 +338,9 @@ markers = [
     "unit: marks tests as unit tests",
     "network: marks tests that require network connectivity",
     "notebook: marks notebook smoke tests",
+    "pyfock: marks real PyFock integration/parity tests (opt in with QUANTUI_RUN_PYFOCK_INTEGRATION=1)",
+    "gpu_integration: marks real NVIDIA GPU integration tests (opt in with QUANTUI_RUN_GPU_INTEGRATION=1)",
+    "pyfock_gpu: marks real PyFock CuPy GPU tests (opt in with QUANTUI_RUN_PYFOCK_GPU_INTEGRATION=1)",
 ]
 
 [tool.coverage.run]

{quantui-0.8.1 → quantui-0.9.0}/quantui/__init__.py

@@ -7,7 +7,7 @@ Calculations run locally in the Jupyter session — no cluster or SLURM required
 PySCF requires Linux/macOS/WSL. Windows users should use the Apptainer container.
 """
 
-__version__ = "0.8.1"
+__version__ = "0.9.0"
 
 import logging
 from typing import Any