quantui 0.9.0__tar.gz → 0.11.1__tar.gz

{quantui-0.9.0 → quantui-0.11.1}/CHANGELOG.md

@@ -7,6 +7,462 @@ and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.ht
 
 ## [Unreleased]
 
+## [0.11.1] - 2026-11-02
+
+### Changed
+
+- Documentation site: an "Open the Viewer" link in the Home sidebar and on
+  the home page, a two-column Features page, and shorter text throughout.
+
+### Fixed
+
+- **IRC no longer ends both directions in the same minimum.** Sella's
+  iterative estimate of the starting Hessian could carry a spurious mode,
+  so from a transition state converged only to the force threshold the
+  first step went sideways and both directions fell into one valley. The
+  IRC now starts from PySCF's analytic Hessian, as the transition-state
+  search already does. If Sella's inner loop fails, the direction is
+  finished by mass-weighted steepest descent before a short-step BFGS;
+  if both ends still match, the verdict says so rather than reporting a
+  connection.
+- Viewer installer builds use the `macos-15` runner (`macos-14` is retired).
+
+## [0.11.0] - 2026-11-01
+
+### Added
+
+- **IRC calc type** (M-TS TS.3, engine Sella): follows the reaction path
+  downhill from a transition state in both directions, in mass-weighted
+  coordinates, to the two minima it connects. Pick the Transition State
+  result under *Start from*. The card gives the barrier from each side and
+  a verdict; the PES Scan panel plots energy against the reaction coordinate
+  (click a point to jump the Trajectory panel there); Trajectory plays
+  reactant → TS → product; History replays both. Steps of 0.2 Å·amu½ with
+  Sella's gamma at 0.4 (measured: 35–71 SCFs per direction where the
+  defaults stalled); if Sella's inner loop gives out near a minimum, that
+  direction is finished by minimizing and the card says so. PCM supported.
+  Also a batch job (`--calc irc`, usually `--from` a Transition State job;
+  no mid-path resume) in `quantui submit`, `quantui-batch` and the app's
+  SLURM path; `results` prints the barriers and verdict.
+- **Full symmetry labels for D4h, D4, C4v and D2d** vibrational modes
+  (square-planar, square-pyramidal and allene-type molecules) instead of
+  their D2h/C2v/D2 subgroup labels. B1 and B2 follow the usual convention
+  (C2′ axes, or σv planes, through the ligands), so a square-planar AB4's
+  B1g is the in-plane stretch. Point-group detection for mode labels no
+  longer drops to a lower group at the loose tolerance (an exact square
+  pyramid was labelled C2v).
+- **The Viewer draws the HOMO and LUMO** (M-VIEWER VW.7): when orbitals are
+  saved (app or batch job), the HOMO and LUMO, each spin for unrestricted
+  results, are also saved as gzipped cubes at the Isosurface panel's
+  default grid (about 0.4 MB each; `frontier_cubes/`). The desktop and
+  browser Viewer, which have no PySCF, draw those; for any other orbital,
+  density or ESP they say to open the result in the full QuantUI. Set
+  `QUANTUI_FRONTIER_CUBES=0` to skip them.
+- **`quantui view` opens the last folder it showed** when started without
+  one (desktop shortcuts), instead of the home directory.
+- **`quantui jobs`** (M-BATCH2 B2.9): your batch jobs, newest first, with
+  where each one is: waiting, running (with the worker's progress),
+  done or failed. With `squeue` on PATH it refreshes the job records from
+  the queue first; without it (an OnDemand session) it reads each job
+  folder. `--running` lists unfinished jobs, `--all` every job.
+- **History lists batch jobs not finished yet** (B2.10): on app start and
+  on Refresh, jobs submitted from a terminal show their state and progress
+  from their job folders, since OnDemand has no `squeue`. A
+  terminal-submitted job's record is marked succeeded when its result is
+  saved to History.
+- **Transition State as a batch job** (M-TS TS.5): `quantui submit`,
+  `quantui-batch submit --calc transition_state` and the app's SLURM path
+  run the same Sella search and frequency check as the window, PCM included.
+  A killed job resumes the search from its last step, never redoes a
+  finished search, and keeps the frequency check's finished displacements.
+  History shows the stationary point found with its search path;
+  `results` prints the verdict; `--from` a TS job starts from its saddle
+  point. A post-HF method is refused before the job queues. Both Apptainer
+  images now install the `[ts]` extra (Sella), which Transition State needs
+  on the cluster in the window as well.
+- **Clarity and layout pass** (M-UIPOLISH, from a rendered-UI walk-through):
+  - Molecules open facing the camera in every viewer (principal axes), so
+    water no longer looks linear and the dipole arrow is visible.
+  - The library finds common names ("water", "ammonia", "benzene"); QM9
+    entries come after the curated ones and duplicates are listed once.
+  - Two-column layouts on wide screens: Calculate (molecule | setup + run),
+    Results (card | structure), and the Analysis viewer, Mulliken,
+    Vibrational and Orbital panels; they stack on narrow windows.
+  - One-line header with the toolbar, a one-line step indicator, the
+    "Calculation complete" links right under Run, and a shorter, resizable
+    log that hides internal bookkeeping lines.
+  - Analysis lists the panels that have data first; plots opened from a
+    collapsed panel fill their width; Raman follows the IR axis direction.
+  - UV-Vis shows vacuum-UV bands (the window started at 100 nm) and lists
+    the excited states; NMR groups equivalent nuclei and uses one
+    Atom | σ | δ table.
+  - Live and History result cards show the same rows; frequencies are
+    listed with their symmetry labels; formulas read NH3, not H3N.
+  - Compare uses checkboxes and renders its chart; History offers recent
+    results as links with the other filters folded away; Help and Report
+    Issue open as side drawers (Esc closes both).
+  - Shorter copy throughout, a 12 px minimum text size, clearer section
+    headings, neutral Report Issue / Exit / idle Cancel buttons.
+  - Fixed: the System Settings GPU row could stay at "checking…" forever.
+- **Vibrational-mode symmetry labels** (M-SPECTRA2 SPC2.4) — after a Frequency
+  calculation each normal mode gets its irreducible representation: a *Sym.*
+  column and a Γvib caption in the Vibrational mode table (NH₃: 2A₁ + 2E), the
+  label in the mode dropdown, and a *Symmetry* line in the IR and Raman stick
+  hovers. Works for live results and History reloads (computed from the saved
+  displacements). Full-group labels for abelian groups, C3v, D3h, D3, D3d, D6h,
+  Td, Oh and linear molecules (σ/π); other groups (e.g. D4h) show labels in
+  PySCF's computational subgroup, said so in the caption.
+  `quantui.symmetry.label_mode_irreps()`.
+- **Diffuse basis sets** — `6-31+G*`, `6-31++G**`, `aug-cc-pVDZ` and
+  `def2-SVPD` join the basis menu (each next to the set it extends), for
+  anions, radical anions and weakly bound species. Available with PySCF in the
+  app, `quantui submit` and `quantui-batch`; PyFock's menu is unchanged.
+  `6-31+G(d)` / `6-31++G(d,p)` are accepted as the same sets. The basis card
+  marks them *Diffuse*, the educational notes explain them and nudge an anion
+  on a non-diffuse basis toward one, and the basis-set help topic has a new
+  *Anions need diffuse functions* paragraph. SLURM memory factors and the time
+  estimator's basis-function table cover the new sets.
+  `config.DIFFUSE_BASIS_SETS` / `config.is_diffuse_basis()` list them.
+- **`quantui results JOB_DIR`** — the `quantui-batch results` summary
+  (convergence, energy, imaginary modes, strongest IR bands, excited states,
+  NMR shifts) from inside the image. Both now also note a saddle-point
+  retry.
+- **Site limits for batch jobs** — `QUANTUI_SLURM_MAX_MEMORY_GB`,
+  `QUANTUI_SLURM_ESTIMATE_MAX_MEMORY_GB` and `QUANTUI_SLURM_MAX_CORES` set the
+  hard limits and the automatic estimate's own memory ceiling (defaults
+  unchanged: 128 GB, 32 cores). Set them in the image environment before
+  `quantui install-launcher` so `quantui-batch` uses the same values.
+- **Viewer mode (`quantui view [FOLDER]`)** — a lightweight QuantUI with only
+  the History and Analysis tabs, pointed at a results folder, needing no quantum
+  engine. `QuantUIApp(viewer=True, results_dir=...)` adds a results-folder bar
+  above the tabs; `quantui view` starts Voilà on a free `127.0.0.1` port and
+  opens the browser. Packaging for two delivery routes lives in
+  `packaging/viewer/` (unsigned conda-constructor desktop installers and a
+  Voici/Pyodide browser build), built by the new `viewer-builds` workflow.
+- **QuantUI Viewer in the docs** — new *QuantUI Viewer* page
+  (`/viewer/`) with a link to the browser Viewer, which the Pages workflow now
+  builds and publishes at `/viewer/app/` on each release and docs change.
+  Publishing a release also attaches the three Viewer installers to it.
+- **SLURM GPU and account settings** — `QUANTUI_SLURM_GRES`,
+  `QUANTUI_SLURM_QOS` and `QUANTUI_SLURM_ACCOUNT` add `#SBATCH --gres`,
+  `--qos` and `--account` lines to generated batch scripts (app, `quantui
+  submit` and `quantui-batch`). A GRES that asks for a GPU also turns on
+  `apptainer exec --nv`; `QUANTUI_SLURM_NV=1`/`0` overrides that.
+- **Batch Geometry Opt results are complete** — a SLURM `geometry_opt`
+  result now records the optimized geometry (`final_molecule`), the final
+  SCF's dipole moment and Mulliken charges, so History and
+  `quantui-batch results` show them without a follow-up single point.
+  `--from` chaining reads the recorded geometry.
+
+### Changed
+
+- **`quantui view` needs a per-run token.** It listened on 127.0.0.1 with
+  no authentication, so any local process or web page could start kernels
+  on its port; it now starts Voila with a random token and opens the URL
+  that carries it. A request without it gets a login page. (Standalone
+  Voila has no XSRF setting, so the `disable_check_xsrf` flag was never in
+  effect for the viewer; DEC-001's container setting is unchanged.)
+- **Frequency results check the geometry** — every Frequency run now
+  computes the forces at the input geometry. When the largest force is above
+  the Geometry Opt threshold (0.05 eV/Å) the result card (live and History)
+  and the Analysis thermochemistry box warn that the geometry is not a
+  stationary point, so its frequencies and thermochemistry are not
+  meaningful, and say how to fix it. `FreqResult.max_force_ev_per_ang`;
+  saved as `spectra.ir.max_force_ev_per_ang`.
+- **IR spectra run 4000 → 400 cm⁻¹ by default** (FTIR convention). An
+  **Axis** dropdown on the IR panel switches back to 400 → 4000; the choice
+  is remembered (`viz.ir_axis` in user settings). `plot_ir_spectrum()` gains
+  `descending=`.
+- **Energy-level diagram hides core orbitals by default** — occupied
+  orbitals more than 50 eV below the HOMO (e.g. water's O 1s) no longer set
+  the Y range and squeeze the valence levels into a sliver; the subtitle says
+  how many are hidden and a **Show core orbitals** checkbox restores them.
+  The HOMO–LUMO gap label no longer overlaps the axis labels.
+- **Dipole arrow convention** — the Mulliken panel says which end the arrow
+  head marks and offers both conventions (− → +, IUPAC/physics, default; or
+  + → −, the chemistry crossed arrow), remembered as `viz.dipole_arrow`.
+- **Frequency card** — title reads "H2O · B3LYP/6-31G* (RKS)"; H and G are
+  shown with their thermal correction vs E in kJ/mol instead of an absolute
+  kJ/mol value.
+- **Less duplication, tidier layout** — viewers no longer repeat the molecule
+  facts in a "Molecule Information" box; the launcher notebook drops its
+  duplicate "QuantUI" heading; result tables are compact and left-aligned;
+  the empty Calculate tab no longer reserves a blank viewer block.
+- **Esc closes the Help panel** (as does its Close button).
+- **Clearer controls** — no more truncated labels or "?.." buttons; PES atom
+  chips read "O1"; XYZ table headers line up; a **Done** button closes the
+  molecule editor; the Help panel has a **Close** button; System Settings
+  groups all settings in one card and says PlotlyMol; the activity indicator
+  is a neutral status chip; History, Compare and the Analysis heading show
+  readable times ("2026-10-25 04:31").
+- **Context-aware extras** — the spin-state helper appears only for molecules
+  with a transition metal; "Use mode → new Frequency calc" only when there
+  are imaginary modes; Analysis panels that don't apply say what they need in
+  their title; dark themes give 3D viewers the panel colour (also in PNG
+  exports) instead of black.
+- `import quantui` no longer loads numpy, RDKit, ASE, Plotly, IPython or
+  requests; every public name is resolved when first used. `quantui`
+  command-line tools and the batch worker start in a fraction of the time,
+  which matters on cluster login nodes (slow shared filesystems, per-user
+  thread limits).
+
+### Fixed
+
+- **"Copy path" in the browser viewer** no longer raises: Pyodide cannot
+  start the thread that resets the label, so the label just stays.
+- **`quantui-batch check` prints a fix hint only under a failed or warning
+  line.** Passing lines showed their hint too (`[ok  ] image …` followed by
+  "ask your instructor: the course image is missing or unreadable"), which
+  read as an error to students.
+- **Generate Isosurface works again for molecular orbitals** — it failed for
+  every MO with `unexpected keyword argument 'esp_range'` since the ESP-map
+  release. The orbital gallery was not affected.
+- **Edit Structure stays available after a molecule loads** — loading or
+  changing a molecule rebuilt the Calculate panel without it.
+- **Mulliken viewer** opens charge-coloured with the dipole arrow when those
+  boxes are ticked, instead of only after a box was toggled.
+- **Sliders are visible on every theme** (ipywidgets 8 sliders were unstyled:
+  no visible track, and a white handle on the Light theme), and the selected
+  option of toggle-button groups and History filter chips is now highlighted.
+- The QM pre-optimization checkbox no longer keeps the PES Scan wording
+  ("…before scan") after switching to another calculation type.
+- The Files tab re-lists its folder when opened, so newly saved results show
+  without clicking Refresh.
+- PES Scan: suggested Start/Stop values are rounded (0.001 Å / 0.1°) and the
+  unit label sits after Stop rather than after Points.
+- **Time-estimate basis-function counts** — the per-element table behind
+  `calc_log.count_basis_functions` had drifted from PySCF for 75 entries
+  (every element in def2-TZVP, e.g. H 14 instead of 6; Li/Be and Na–Ar in
+  the 6-31G*, cc-pV*Z and def2-SVP rows; Al–Ar in 3-21G/6-31G). It is now
+  generated from PySCF's AO counts and a test checks every entry. History
+  records logged before this keep their old `n_basis`, so estimates for
+  def2-TZVP and second-row/heavier molecules settle as new runs are logged.
+- **CPU image no longer overrides a caller's `QUANTUI_RESULTS_DIR` /
+  `QUANTUI_FREQ_PARALLEL`** (M-BATCH2 B2.12). `apptainer/quantui.def`
+  hard-exported both, so a site module or job script setting either was
+  silently clobbered inside the container. Both are now defaults
+  (`${VAR:-default}`), matching `quantui-gpu.def`.
+
+- History's **Refresh** button also saves batch jobs that finished since
+  the app started; before, they appeared only after a restart or a Cluster
+  Jobs refresh.
+- The batch resource estimate knows def2-SVP, def2-TZVP and LANL2DZ (they
+  used a generic factor), treats `6-31G(d)` / `6-31G(d,p)` like `6-31G*` /
+  `6-31G**`, and adds walltime for TD-DFT runs with more than 10 states and
+  PES scans with more than 10 points.
+- Batch `live.log` files no longer contain a copy of QuantUI's worker
+  source. PySCF writes the running script into its output at the log level
+  QuantUI uses; in a batch job that script is the worker (~900 lines per
+  calculation). PySCF's version and input summary are still logged.
+- Batch job and folder names write Pople bases the usual way: `6-31G*` →
+  `6-31Gd`, `6-31G(d,p)` → `6-31Gdp`, `6-31+G*` → `6-31pGd` (was
+  `6-31Gx`, `6-31Gxdxpx`, …).
+- `quantui submit` and `quantui-batch` refuse an XYZ file whose first line
+  gives a different atom count from the atoms listed (a cut-off or padded
+  file). The app still only warns, where you see the structure.
+- `quantui submit` (and Resubmit) syncs job states with the SLURM queue before
+  checking the concurrent-job limit. With no app open, finished jobs stayed
+  "submitted" in the registry and kept counting, so after two submissions
+  every further one was refused.
+- Generated SLURM scripts ask for one task with N CPUs
+  (`--ntasks=1 --cpus-per-task=N`) instead of N tasks, which is what the
+  single multi-threaded worker uses; a `SLURM_CPUS_PER_TASK` inherited from
+  the submitting allocation no longer sets the thread count.
+- `apptainer exec --nv` is no longer used for CPU jobs, and the worker runs
+  the batch image's own `python` instead of the submitting process's
+  interpreter path, which need not exist in that image.
+- SLURM jobs resume again after a resubmission. Since job folders got one
+  attempt folder per run, the checkpoint and the cached pre-opt geometry
+  were kept inside the attempt folder, which the next attempt never sees,
+  so killed geometry optimizations, PES scans and frequency runs restarted
+  from scratch. Both now live in the job folder.
+- The geometry optimization before a Frequency calculation (app and batch)
+  now converges to 0.01 eV/Å instead of 0.05. Residual forces at 0.05 left
+  soft modes such as methyl rotors wrong, or imaginary (CHEM-3200 Lab 4).
+  Plain Geometry Opt and the pre-opt for other calc types are unchanged.
+- When that pre-optimized Frequency run still finds an imaginary mode below
+  20i cm⁻¹ (usually a methyl or other rotor stuck at its eclipsed saddle
+  point), QuantUI displaces along the mode, re-optimizes and repeats the
+  frequencies once (app and batch). The result card and `result.json`
+  (`spectra.ir.imaginary_mode_retry`) say what was done; a mode still
+  imaginary after the retry is reported, not retried again.
+- **Viewer installers: the shortcut opened and closed a console without
+  starting anything.** `quantui view` looked for the `voila` command on
+  `PATH`, which a shortcut launch of an unactivated install does not set; it
+  printed "Voilà is not installed or not on PATH" and exited. It now runs
+  Voilà as `python -m voila` from its own interpreter and puts the install's
+  folders on `PATH` for the server. The Windows shortcut runs through
+  `cmd /c ... || pause`, so any future failure stays on screen. Stopping
+  `quantui view` now stops Voilà too, instead of leaving it serving. The
+  installer CI smoke test starts the viewer the way a shortcut does and
+  fetches a page (it previously only ran `quantui view --help`).
+
+- History → "View Results" / "View Analysis" navigated by fixed tab index, so
+  with the Cluster Jobs tab visible they landed one tab early. They now look
+  the tab up by name.
+- Background renders (vibrational animation, isosurface, export) and the
+  activity-light timer fall back to running inline when threads are
+  unavailable instead of leaving the panel stuck.
+
+## [0.10.0] - 2026-10-03
+
+### Added
+
+- **Upload structure files** — new **Upload File** tab (Calculate → Molecule
+  Input) and **Load as molecule** on the Files tab: XYZ (last frame), MOL,
+  SDF, MOL2, PDB, CIF, Gaussian `.gjf`/`.com` and `.log`/`.out`. Charge and
+  multiplicity are read from the file when it records them; 2-D MOL/SDF
+  drawings are embedded in 3-D.
+- **Download to your computer** — every export (structure files, script,
+  bundle, cubes, PNGs, plots, CSV, animations) now offers a browser download
+  link, and the Files tab has a **Download** button. Works on remote
+  Voilà/OnDemand sessions; files over 25 MB get a notice instead.
+- **Implicit solvent for optimizations, frequencies and TD-DFT** — Geometry
+  Opt is solvated at every step; Frequency uses PySCF's PCM Hessian and
+  solvated IR displacements (Raman is skipped in solvent); TD-DFT uses an
+  equilibrium ground state and non-equilibrium excitations with each
+  solvent's own optical dielectric. Also in SLURM batch jobs.
+- **Point groups and orbital symmetry labels** — the molecule summary and
+  result cards show the point group (0.01 Å tolerance, with a "nearly X"
+  hint); the orbital energy diagram labels orbitals textbook-style
+  (1a₁, 2a₁, 1b₂, 3a₁, 1b₁ for water; σ/π for linear molecules; C₃ᵥ labels
+  for NH₃).
+- **Density, spin-density and ESP surfaces** — the Isosurface panel draws the
+  electron density, the spin density (α − β) and the electrostatic potential
+  mapped on the density surface (red = negative, blue = positive, with a
+  colour bar), and α/β orbitals for unrestricted results.
+- **Vibration viewer** — displacement arrows, an amplitude slider and a table
+  of every mode with IR intensity and Raman activity.
+- **Thermochemistry at any temperature and pressure** — recomputed from the
+  stored frequencies (no new calculation), with U, H, S, G, Cv, Cp and the
+  rotational symmetry number.
+- **Edit Structure** — set a bond length, angle or dihedral to a value,
+  delete atoms, add a hydrogen, change an element, undo; pick atoms by
+  clicking the viewer. **Freeze atoms** for a constrained Geometry Opt.
+- **Orbital gallery** — the Isosurface panel's **Orbital gallery** button
+  shows the orbitals around the HOMO–LUMO gap (2, 3 or 4 on each side) as
+  small viewers that rotate together, each labelled with its symmetry and
+  energy; follows the α/β choice for unrestricted results.
+- **Transition State calc type** — searches for the saddle point near the
+  input geometry with Sella (starting from the analytic Hessian, with the
+  same PySCF settings as an optimization: PCM, density fitting, D3, GPU, SCF
+  rescue), then runs a frequency calculation and says plainly whether it
+  found a transition state (exactly one imaginary frequency), a minimum, or
+  a higher-order saddle point. Results open on the Vibrational panel to
+  animate the imaginary mode, plus IR, search trajectory, orbitals and
+  populations. Needs the optional extra: `pip install "quantui[ts]"`.
+  Local runs only for now (not SLURM batch).
+- **Populations and Isosurface for Frequency and TD-DFT results** — both
+  record the reference SCF's Mulliken charges, dipole and orbitals (both spin
+  channels for UHF/UKS), so the Populations, Isosurface and (TD-DFT) Energies
+  panels fill for them too, locally and from SLURM. Frequency Molden files
+  now include the orbitals.
+- **⟨S²⟩ for open-shell results** — single points record and show ⟨S²⟩
+  next to the ideal S(S+1), flagged when off by more than 10 % (spin
+  contamination). Reorganization-energy results record it at all four
+  points of each channel (`s2_*` fields in `result.json`), so a
+  spin-contaminated ion SCF can be filtered out of a λ dataset.
+- **Submit from a login node with `quantui-batch`** — a standard-library
+  Python 3.6+ launcher for SSH users. It never starts the image or imports
+  QuantUI on the login node: it writes the same job folder as
+  `SlurmBackend.prepare()` (constants copied from QuantUI at install time,
+  logic held equal by tests) and calls `sbatch`; the calculation runs in the
+  image on a compute node. Install once per image, e.g.
+  `apptainer exec IMAGE quantui install-launcher /shared/bin`.
+  `quantui-batch submit mol.xyz --calc frequency --method B3LYP --basis def2-SVP`;
+  `status`, `log`, `rerun` (e.g. `--mem=64G` after running out of memory),
+  `cancel`, `estimate` and `path` follow it. At most
+  `QUANTUI_MAX_CONCURRENT_JOBS` (default 2) QuantUI jobs may be queued or
+  running per user, counted from the real queue.
+- **`quantui-batch` workflow commands** — `--preset NAME` (shared
+  `presets.json` beside the launcher, plus per-user presets); `--from JOB`
+  starts from another job's optimized geometry, waiting on it with an
+  `afterok` dependency if it is still running (the worker loads the geometry
+  at run time, `quantui/backends/batch_chain.py`); `--queue-rest` lines jobs
+  up behind the user's running ones instead of refusing them; a duplicate
+  guard (`--again` to override); `rerun --more-memory` / `--more-time`;
+  `results JOB` (energy, convergence, imaginary modes, strongest IR bands,
+  excited states, shifts); `presets`; and `check` (python, image, Slurm
+  commands, job folders and free space, presets).
+- **Every QuantUI batch job is tagged `#SBATCH --comment=quantui`**, so an
+  operator can list all of them with `squeue -o "%k"`.
+- **`quantui submit` accepts `.xyz` files** with `--calc`, `--method`,
+  `--basis`, `--charge`, `--mult`, `--solvent`, `--preopt` and repeatable
+  `--option KEY=VALUE`; an impossible charge/multiplicity is refused before
+  anything is queued. The same flags override a request JSON's values.
+- **`quantui submit --prepare-only`** writes the job folder (`request.json` +
+  `submit.slurm`) without calling `sbatch` and prints the script path. Its
+  registry record has the new non-active status `prepared`.
+
+### Changed
+
+- **The GPU image builds from the working tree, like the CPU image** —
+  `quantui-gpu.def` copies the same `%files` allowlist as `quantui.def` and
+  installs it editable, instead of a pinned PyPI release, so a GPU node runs
+  the code that was just tested. `build-gpu.sh` records the commit
+  (`git describe`) in the image's `QuantUICommit` label and
+  `/opt/build-info/quantui-commit.txt`; its `--version` flag is gone — check
+  out a release tag to build that release.
+- **Finished batch attempts reach History when the app starts**, even where
+  SLURM is unavailable (e.g. an OnDemand session), so jobs submitted from a
+  terminal show up without opening the Cluster Jobs tab.
+
+### Fixed
+
+- **PBE-D3 now includes D3** — it needed `pyscf.dftd3`, which no QuantUI
+  environment installed, so PBE-D3 ran as plain PBE (with a warning). D3
+  (zero damping) is now applied through PySCF's built-in dispersion
+  (`pyscf-dispersion`, added to the `[pyscf]` extra, the conda environment
+  and the CPU image), including in gradients and Hessians.
+- **Rotational symmetry number** — thermochemistry detected symmetry at
+  PySCF's strict tolerance, so slightly unsymmetric geometries (any
+  optimized water or ammonia) used σ = 1, overstating the entropy by R ln σ.
+  Symmetric molecules' S and G change.
+- **`quantui submit --depends-on`** accepts a request id or a SLURM job id
+  and resolves it; it used to write the request id into
+  `--dependency=afterok:` and validate nothing.
+- **"Geometry optimization before the calculation" on SLURM** — Single
+  Point and NMR batch jobs ignored the checkbox (the local run honoured it).
+- **Mode-displaced Frequency seeds are re-optimized** — picking "displace
+  along mode" as the Frequency seed disabled the pre-optimization, so the
+  frequencies were computed at a geometry that is not a stationary point.
+  The checkbox is now ticked for that seed (left on, user can untick).
+- **Reorganization Energy shows its optimizer settings** — the run used the
+  max-force and max-steps fields while they were hidden, so values left over
+  from Geometry Opt or PES Scan applied unseen.
+- **No placeholder Raman spectrum** — when Raman activities were not
+  computed (PCM run, or `pyscf-properties` missing), the Raman panel drew
+  every mode at the same height. It now says why there is no spectrum.
+- **Disconnected structures are flagged for every source** — the molecule
+  summary notes separate fragments for pasted, library, uploaded, edited and
+  History structures, not only Online Search results.
+- **Pasting a multi-frame XYZ** says what it is and how to load it, instead
+  of "Line N: not enough values".
+- **Export Script follows the calculation** — it used to write a gas-phase
+  single point whatever was set up. It now applies the selected PCM solvent
+  and density fitting, adds the Hessian + thermochemistry for Frequency and
+  the excited states (with the solvent's optical dielectric) for TD-DFT, and
+  says plainly when it covers only the SCF (Geometry Opt, NMR, PES Scan,
+  Reorganization Energy).
+- **CPU image: NMR and analytical Raman** — the image installed QuantUI
+  without the `[pyscf]` extra, so `pyscf-properties` was missing. It now
+  installs the extra, and the build fails if `pyscf.prop.nmr` or
+  `pyscf.dispersion` cannot be imported.
+- **Solvent names are case-insensitive**; an unknown solvent is an error.
+  A request with `"water"` used to run in the gas phase.
+- **Export Script** writes into the result folder instead of the server's
+  working directory.
+
+- **Solvated batch requests the worker cannot run are refused up front** —
+  `quantui submit` and `quantui-batch` reject an unknown solvent, and a
+  solvent on a calc type the batch worker runs gas-phase only (e.g. `nmr`),
+  instead of letting the job queue and then fail. The supported set now
+  lives in one place (`batch_input.SOLVENT_CALC_TYPES`).
+- **SLURM memory estimate for transition-metal complexes** —
+  `estimate_slurm_resources()` used a short element table without Mn, Co,
+  Ni, Mo and most other metals, so a metal counted as 0 electrons and the
+  memory estimate came out low. It now uses the full table.
+
 ## [0.9.0] - 2026-09-26
 
 ### Added
@@ -934,7 +1390,10 @@ 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/v0.9.0...HEAD
+[Unreleased]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.11.1...HEAD
+[0.11.1]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.11.0...v0.11.1
+[0.11.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.10.0...v0.11.0
+[0.10.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.9.0...v0.10.0
 [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