Changelog

Current version: v0.3.15

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—HTR complete cages now carry periodic-cell-aware centers produced by the shared Rust engine
—Canonical HTR cage signatures retain their machine labels through occupancy cutoff and theta calculations
—The supplied 4,500-water production structure now assigns all 161 highlighted guests inside their PBC-unwrapped cages

Changed

~Display labels are now applied only after scientific occupancy calculation

Fixed

•Boundary-crossing HTR cages no longer acquire false centers from averaging wrapped browser coordinates
•HTR small- and large-cage occupancy statistics no longer fall through the generic cage cutoff because of display typography

—Native GROMACS and mapped LAMMPS trajectories now run CHILL+ across the exact Start, End, and Step range selected in Analyze
—CHILL+ chart and CSV frame labels are one-based, matching the visible range controls and the other trajectory algorithms
—In-memory multi-frame GRO analysis keeps its bounded sampling path while native trajectory sources use the explicit range contract

Changed

~The shared trajectory range action now dispatches CHILL+ as well as TRACE, HTR, GRADE, F3, and F4
~Native GROMACS and mapped LAMMPS CHILL+ analysis validates the selected range against the source frame count before starting work

Fixed

•CHILL+ no longer replaces a requested native trajectory window with an evenly sampled 40-frame sweep
•CHILL+ completion and progress state now preserves the exact analyzed frame identities

—HTR, TRACE, and native GRADE now follow their own reference contracts instead of sharing one TRACE-shaped result
—Normal and large GRO, mapped LAMMPS, and native GROMACS trajectories now run selected TRACE, HTR, GRADE, and F3/F4 ranges with explicit frame provenance
—The Blender extension caches algorithm-owned analysis per frame and imports both schema v1 and provenance-rich schema v2 ClavisCage bundles
—F3/F4 aggregation and geometry now match independent and reference calculations on the supplied production fixture

Added

+A native three-family GRADE port for 5^12, 5^12 6^2, and 5^12 6^4 cages, including guest-filled counts
+Complete HTR and GRADE golden regressions plus algorithm-aware worker, bundle, and Blender round-trip coverage

Changed

~HTR uses its oxygen-only periodic topology, TRACE uses the reference ring and two-pass cup machinery, and GRADE no longer exposes arbitrary TRACE signatures
~Trajectory rows and Blender CSV exports retain the selected algorithm, source frame, display frame, parameters, and algorithm-specific payload

Fixed

•F3 now weights every neighbor triplet and F4 uses the maximum-distance minimum-image hydrogen pair
•Stale cross-algorithm trajectory, overlay, occupancy, and F3/F4 state is cleared when a new file or frame takes ownership
•The worker WASM import surface is synchronized with the committed browser artifact and protected by an instantiation contract

—PRO users can hand the current displayed scene to the Blender extension as an offline, editable ClavisCage bundle
—The worker-served WASM now stays synchronized with the package build and reproduces the exact sII 192 / sI 512 reference counts
—Path-traced output now carries active CHILL+ class colors, water-class filters, and the classified O–O network
—Large path-traced scenes use adaptive atom tessellation and batched bond geometry instead of millions of cloned meshes

Added

+A versioned .claviscage.zip action carrying the current frame, matching CHILL+/H-bond/HTR analyses, and supported editable styles into Blender

Fixed

•Stale current-frame analyses are omitted with a bundle warning instead of being attached to newer coordinates
•The July 13 release notes are correctly identified as v0.3.12
•CHILL+ no longer falls back to neutral path-traced atoms or drops its classified-water network
•Oversized path-tracer scenes now fail soft against GPU memory and CPU primitive ceilings before full geometry allocation or worker cloning

—The Render tab now provides one Export Center for standard and path-traced PNG images, frame ZIP archives, and WebGL or path-traced MP4 movies
—Export actions explain unavailable requirements and lock while another export is active
—Frame-sequence and movie exports now stop on an incomplete frame and restore the original frame and overlay visibility afterward
—CHILL+ now remains composable with hydrogen bonds and non-water residue rendering

Added

+A capability-aware Export Center that reuses the existing WebGL, path-tracing, ZIP, and browser-video pipelines

Fixed

•Batch and video capture no longer silently produce incomplete output when a frame cannot be captured
•Export sessions restore the exact cage, ring, hydrogen-bond, and guest overlay state that was active before rendering
•CHILL+ analysis and frame refresh retain a current hydrogen-bond network with controls in the CHILL+ results panel
•CHILL+ class isolation keeps non-water residues such as SDS and NA visible and preserves their atom and bond sizing
•Hiding SDS, NA, or other non-water residue channels no longer invalidates the active CHILL+ coloring and network
•Single-frame scenes omit frame-sequence and movie actions instead of showing an inapplicable multiple-frame requirement
•Rapid native GROMACS frame swaps keep the newest request without surfacing expected request supersession as a runtime error
•Unreleased changelog labels no longer render as vUnreleased

—CHILL+ visualization state now clears before TRACE, HTR, or GRADE takes over the scene, preventing stale CHILL network overlays from mixing with cage and H-bond overlays
—CHILL+ coloring and network overlays are tied to the analyzed frame identity, so same-size frame changes no longer reuse stale classification just because the water count matches
—Native GROMACS render-position frames now feed water extraction from the displayed coordinate buffer when it aligns with the rendered atoms

Fixed

•Cleared CHILL-only color/network state on non-CHILL analysis and broad analysis resets
•Added frame-key validation for CHILL+ color and network overlays
•Updated browser QA coverage for CHILL+ followed by TRACE, HTR, and GRADE in one session

—CHILL+ now draws the classified-water network — the O-O neighbor lattice — as a connected overlay colored by structure class, so ice and hydrate cages appear as connected polyhedra like the cage and H-bond overlays, not just colored dots
—The network respects the per-class filter: isolate "hydrate only" to see just the hydrate cage framework, and liquid waters are omitted so the ordered structures stand out
—A NETWORK STYLE panel controls the overlay bond width, opacity, and color (a single-color override or per-class colors)

Added

+ChillNetworkVisualization overlay driven by the O-O neighbor edges the cell-list CHILL+ search already computes (no extra cost), rendered per class in the CHILL+ palette and PBC-wrapped like the H-bond overlay
+Width / opacity / color controls for the CHILL+ network overlay in the results panel

—The CHILL+ time-series now runs on LAMMPS trajectories, in addition to native GROMACS and in-memory multi-frame .gro files — so you can track ice/hydrate/liquid fractions over a LAMMPS run too

Added

+LAMMPS trajectory support in the CHILL+ time-series sampler; the RUN CHILL+ TIME SERIES button now appears for a loaded multi-frame LAMMPS dump

—A new CHILL+ time-series samples up to 40 frames across a trajectory, classifies each, and plots the six structure-class fractions over time — so you can watch ice, gas-hydrate, and liquid populations evolve during a dissociation or growth run
—Runs on the fast v0.3.6 cell-list classifier, so a sampled multi-frame sweep completes without freezing the view
—Works on native GROMACS trajectories and in-memory multi-frame .gro files; the series exports to CSV

Added

+RUN CHILL+ TIME SERIES button in the CHILL+ analysis panel (shown when a multi-frame trajectory is loaded) and a ChillTimeSeries line chart with one line per class plus CSV download

—CHILL+ now recolors the 3D view by structure class the moment analysis finishes, so ice, gas-hydrate, and interfacial regions are visible at a glance instead of only as counts
—A new per-class show/hide filter in the results panel isolates specific structure types in 3D — for example show only gas hydrate and interfacial hydrate — mirroring the OVITO select-type, hide-the-rest workflow
—CHILL+ neighbor search switched from an all-pairs O(n^2) scan to an O(n) cell list, roughly 48x faster on a ~16k-water frame, so analysis no longer freezes the view
—Large native GROMACS trajectories now render full atoms and bonds once a frame is settled, instead of a bare point cloud, while playback keeps the fast capped preview

Added

+CHILL+ 3D color mode auto-applies on analysis, with HYDRATE ONLY / ICE ONLY / SHOW ALL quick actions and a per-class show/hide filter to isolate structure types

Changed

~CHILL+ neighbor search uses an orthorhombic cell list (with an O(n^2) fallback for triclinic boxes) that produces byte-identical classification to the previous brute-force search

Fixed

•Bonds are no longer permanently suppressed for large native trajectories; they render once a frame is settled and only collapse to the fast preview during loading or playback
•CHILL+ coloring now surfaces a visible notice when the displayed frame differs from the analyzed frame, instead of silently showing no colors

—A companion Model Context Protocol (MCP) server, clavis-mcp, lets an MCP client such as Claude Desktop run ClavisCage analyses by natural language
—Exposes CHILL+, cage detection (TRACE), HTR rings, and F3/F4 order parameters over the same native engine that powers the web app, so results match exactly
—Analyzes single .gro structures and extracts individual frames from .xtc/.trr trajectories for per-frame analysis
—File access is fail-closed to an operator-configured allowlist, with no network egress and size guards

Added

+clavis-cli native runner over the Rust engine (feature-gated so it stays out of the WebAssembly build) that prints analysis JSON for a .gro file
+clavis-mcp Python package (FastMCP) with tools chill_plus, detect_cages, detect_htr_rings, f3_f4_order, and analyze_trajectory_frame; 14 pytest tests plus a Claude Desktop configuration guide

—Native trajectory playback no longer flashes a blocking progress overlay on every frame, so scrubbing and playback stay smooth
—Capped previews of large systems now sample atoms evenly across the whole simulation box instead of taking the first ~20,000 atoms by file order, so molecules past the cut-off no longer vanish

Changed

~Capped large-scene previews use an evenly-spread stride sample (always keeping selected atoms), with selection-highlight and click-to-select remapped to stay aligned with the sampled atoms

Fixed

•The blocking work overlay is suppressed during active playback while genuine (non-playback) frame loads still show it

—CHILL+ (Nguyen & Molinero, 2015) classifies each water into six structure classes — other/liquid, hexagonal ice, cubic ice, interfacial ice, gas hydrate, and interfacial hydrate
—A 3D CHILL+ color mode paints each classified water oxygen by its class, so dissociation is visible spatially in the viewer
—Cross-validated against OVITO’s ChillPlusModifier: identical on ideal sI/sII lattices and 97–99.8% agreement on disordered systems

Added

+CHILL+ analysis algorithm alongside TRACE, HTR, and GRADE, with a per-class count and fraction breakdown
+CHILL+ color mode in the viewer’s COLOR BY controls (appears once a CHILL+ result exists)

—Guest detection now recognizes cyclopentane, propane, and other clathrate guests consistently across the engine and browser, while excluding counter-ions
—Water and guest extraction group atoms by contiguous residue blocks so distinct molecules are no longer merged when GROMACS residue numbers wrap past 99,999
—HTR results now show a structure-state verdict (hydrate / partial / amorphous) so a low cage count reads as dissociation rather than under-detection
—Documented that GRADE cage counts come from TRACE, and that HTR is a more conservative large-cage estimator than TRACE by design

Changed

~HTR results panel surfaces a crystallinity/structure-state verdict alongside SEC and nSEC/IC cage counts and ring statistics
~Documented the intentional HTR primitive-ring vs TRACE all-topological-rings divergence in cage detection

Fixed

•Engine and browser guest identification unified on a shared denylist (guest = non-water, non-ion/metal); keeps cyclopentane (CPN) and propane (PRO) and guests with metal-symbol atom names, excludes counter-ions (NA, CL)
•Engine guest positions use a minimum-image-aware centroid so a guest split across the periodic boundary is located correctly instead of at the box center
•Contiguous residue-block grouping in water and guest extraction fixes 5-digit residue-number wraparound merging distinct molecules on very large systems

—GROMACS .gro/.tpr + .xtc/.trr sessions now index trajectory frame byte ranges and use selected-frame decode instead of materializing every binary frame at open time
—LAMMPS .data + dump and dump-only workflows now use Blob/File-backed frame indexing and frame-slice reads so mapped playback no longer needs the full dump text in browser memory
—Large and long trajectory workflows stay browser-local while reusing worker progress, stale-frame guards, cancellation, and current-frame analysis surfaces
—Sampled TRACE/F3F4 ranges remain available where mapping yields valid waters; HTR/GRADE trajectory-wide analysis remains out of scope

Added

+Blob/File-backed LAMMPS dump scanner and per-frame reader for .lammpstrj, .dump, and .lammpsdump inputs
+Focused regression coverage proving LAMMPS trajectory files are posted to the worker as File objects rather than read with full file.text()

Changed

~Native GROMACS selected-frame playback now indexes XTC/TRR frame slices and decodes only the requested frame in the worker
~Mapped LAMMPS playback and sampled TRACE/F3F4 ranges now await async frame-slice loads with existing progress, done/error, cancellation, and stale request handling
~Large native GROMACS viewport playback stays on a capped preview path after each frame commit so PREV/NEXT/JUMP remain responsive while current-frame analysis can still request full frame data
~Upload and feature copy now describe large/long trajectory behavior across supported GROMACS native pairs, large GRO files, and mapped LAMMPS dumps without claiming GPU compute or full trajectory-wide HTR/GRADE

—LAMMPS .data, .lammpstrj, .dump, and .lammpsdump files are now recognized by upload contracts and trajectory-session planning
—A TypeScript LAMMPS parser core handles supported dump/data text, nm-unit cell conversion, atom-id-stable frames, and hydrate water/guest mapping validation
—A conservative mapping wizard lets users confirm unit style and atom-type roles, then worker-loads LAMMPS dump frames into the normal scene for playback, current-frame TRACE/HTR/GRADE and F3/F4 analysis, and trajectory-wide TRACE/F3F4 ranges
—Standalone LAMMPS dump files can now infer atom types from ITEM: ATOMS rows and use the same mapped playback/analysis path when mol-based water grouping is valid

Added

+Self-contained TypeScript LAMMPS text parsing groundwork for supported dump/data workflows
+Browser-worker LAMMPS frame loading path with cancellation and disposal hooks
+LAMMPS mapping wizard for unit-style selection and atom-type role confirmation before mapped frame loading
+Current-frame LAMMPS TRACE/HTR/GRADE and F3/F4 analysis wiring using mapped water extraction and triclinic cell-aware WASM wrappers where metadata is available
+Mapped LAMMPS TRACE cage trajectory ranges and F3/F4 trajectory ranges with progress, done/error messages, and cancellation
+Dump-only LAMMPS mapping fallback with fail-closed water validation for missing molecule ids or invalid 1 O + 2 H groupings
+LAMMPS dump frame-range scanning so playback and trajectory analysis keep raw dump text plus offsets and parse only requested frames

Changed

~Upload copy now describes paired .data + dump inputs as mapped playback with current-frame analysis plus TRACE/F3F4 trajectory ranges; HTR/GRADE trajectory-wide analysis remains out of scope
~Generated WASM package metadata now matches the app release version (0.3.0)
~Release audit notes now document the remaining moderate Next/PostCSS advisory waiver while high-severity npm audit checks pass and force-downgrade fixes remain intentionally unused

—Native .gro/.tpr + .xtc/.trr PAUSE stays clickable by mouse while dense frame commits are in flight
—Native multi-frame sessions now show movie export controls in RENDER using the decoded native frame count
—H-bond visualization refreshes to the selected native frame instead of showing previous-frame geometry

Fixed

•Native PLAY/PAUSE no longer disables the PAUSE button during frame loading, matching Space-key behavior
•Standard and path-traced movie export controls are visible for native trajectory sessions with more than one decoded frame
•Video export loads each native frame before preparing TRACE cages or H-bonds, so exports do not reuse frame-zero overlays
•Native frame navigation clears stale H-bond and cage geometry while preserving overlay intent for the current-frame TRACE refresh

—Native .gro/.tpr + .xtc/.trr uploads now offer continuous PLAY/PAUSE playback from the browser worker cache
—H-bond and hydrate-cage visualization context stays mounted while native frames advance
—Native frame controls block overlapping requests during dense commits while keeping PREV/NEXT/JUMP available

Added

+Browser-local native playback controls with loop and speed settings for decoded GROMACS trajectories

Fixed

•Native playback no longer clears analysis surfaces on ordinary view or playback frame changes
•Scene performance policy keeps active native TRACE/H-bond/cage overlays mounted during selected-frame loads
•Native playback clamps or wraps at trajectory boundaries instead of overflowing past the decoded frame count

—Native trajectories rendered bonds at rest for the then-current native scene policy; v0.3.1 supersedes this for large native capped previews
—Cage / H-bond overlays no longer vanish after advancing one native frame — they appear immediately for the current frame
—Fixed a crash when auto-analysis ran on a native frame advance

Changed

~Bonds were suppressed only during an in-flight native frame fetch for this release; v0.3.1 keeps large native previews capped at rest
~The analysis overlay gate reopens on the next paint after results commit instead of after a fixed delay

Fixed

•Native trajectory rendering matched static .gro at rest for this release; large native preview policy changed again in v0.3.1
•Per-frame auto-analysis no longer crashes on native trajectories and reads the correct current-frame coordinates
•Cage and H-bond overlays surface immediately after each native frame advance instead of requiring a second advance

—Large native GROMACS trajectories (.gro/.tpr + .xtc/.trr) moved from a flat point cloud to instanced-sphere rendering; v0.3.1 keeps dense native previews capped at rest
—Frame scrubbing stays responsive — coordinates stream into instance matrices without rebuilding topology or colors
—Unsupported TPR files (e.g. TPX 122) now guide you to load the matching .gro topology, which works and renders identically

Changed

~Scene performance policy capped preview atoms only during an in-flight native frame load in this release; v0.3.1 keeps large native previews capped at rest
~AtomCloud separates topology/appearance grouping from per-frame coordinate buffers so only instance matrices update per frame

Fixed

•Large native GROMACS trajectories render with the normal sphere-and-bond molecular style instead of tiny dots
•Unsupported-TPR errors point users to the .gro topology path instead of suggesting another TPR binary

—Large static systems (50k+ atoms) now render as full instanced spheres instead of a flat point cloud, matching the look of small systems
—Dense emulsion and solvated `.gro`/`.pdb` inputs no longer appear as tiny dots
—The point-cloud path is now reserved for large native GROMACS trajectory streaming where frame-scrub responsiveness needs it

Changed

~Scene performance policy now drives the point renderer only for large native trajectory scenes, not for large static structures
~The viewport render branch is now governed solely by the performance policy instead of a redundant raw atom-count threshold

Fixed

•Large static structures (50k+ atoms) render with the normal sphere-and-bond molecular style, restoring the expected appearance for big emulsion systems

—Large native GROMACS frame jumps now stay responsive by keeping dense viewport navigation on a capped point-preview path
—Native selected-frame updates stream worker coordinate buffers directly into render positions instead of rebuilding full atom objects
—Molecular point geometry and typed attributes are reused across same-count frame updates
—Position buffers are separated from residue style buffers so coordinate-only frame changes avoid color and opacity rebuilds
—Browser and Chrome QA now verify dense local TPR/XTC frame jumps with performance evidence

Added

+Native frame decode, post-decode, and commit timing measures for dense trajectory QA
+Large native trajectory Browser/Chromium and Chrome-channel evidence for frame 12/24/12 navigation

Changed

~Dense native GROMACS viewport rendering now keeps the capped point preview active after frame loading so the next frame command remains interactive
~Native view frame commits now use renderPositions while analysis requests can still materialize a full scientific Frame
~Point rendering now reuses geometry and style buffers when topology and visual settings are unchanged

Fixed

•Large native trajectory frame jumps no longer freeze the viewport for tens of seconds after the visible frame changes
•Dense native scenes no longer expand immediately back to full-detail atom rendering after every selected-frame update
•TRACE/HTR/GRADE overlay commit feedback stays bounded by the dense-scene performance policy while preserving current-frame analysis state

—.gro + .xtc and .gro + .trr uploads now preserve GRO residue and atom metadata during native binary playback
—Mixed TPR layouts now fail safely instead of being silently relabeled as all-SOL water when topology metadata is unsupported
—Dense residue/layer visual edits show busy feedback and coalesce rapid slider changes so large scenes feel active instead of frozen
—TRACE/H-bond overlays refresh by trajectory frame and share one preparation path for WebGL and path-traced video export
—Standard Export now follows Preview Mode render-frame crop and output dimensions while excluding preview-only guide artifacts
—Background-only path-traced renders now include recovery actions such as Center Frame and Reset 16:9

Added

+GRO topology metadata pairing for native XTC/TRR playback with atom-index validation and count-specific mismatch errors
+Frame-aware TRACE/H-bond cache keys across algorithm, layer, frame, cutoff, and active trajectory state
+Busy-work feedback for dense visual setting commits such as high-count residue opacity and size changes
+Background-only render recovery controls that update camera/crop state without requiring a page reload

Changed

~Exact-residue binary trajectory guidance now recommends .gro + .xtc/.trr when TPR metadata cannot be decoded faithfully
~WebGL and path-traced video exports now prepare active overlays through the same frame preparation helper
~Standard WebGL PNG export now uses the configured render frame when Preview Mode is active instead of raw viewport capture

Fixed

•GRO-paired binary trajectories no longer collapse HSL, SOL, SLAB, CH4, or other residue channels into a generic trajectory scene
•Unsupported mixed TPR topologies no longer fall through to the simple water recipe
•Trajectory frame changes no longer automatically discard active TRACE/H-bond overlay intent
•Native frame loading and analysis-commit overlays now show visibly animated indeterminate progress instead of a static-looking bar
•HTR/GRADE trajectory frame changes no longer start stale analysis-commit overlays when only TRACE has a frame-aware auto-refresh path
•Preview-only render-frame guides, focus markers, and light indicators are hidden during Standard Export capture
•HTR analysis visualization no longer triggers a Maximum update depth error while committing overlays

—Paired .tpr + .xtc and .tpr + .trr uploads now open as native browser-local trajectory sessions
—Binary GROMACS frames decode in a worker and use selected-frame PREV/NEXT/JUMP controls for dense native sessions
—Mixed-residue layers now expose residue channels for independent visibility and styling
—GROMACS upload copy now points users to paired native playback instead of conversion-first guidance

Added

+Stable TPR topology metadata decoding with real atom names, residue names, residue numbers, and molecule-block summaries
+GROMACS 2026.2 fixture-backed decoder proof for .tpr + .xtc and .tpr + .trr sessions
+Worker-backed native GROMACS trajectory loading with staged busy overlay progress
+Decoded-frame GRO adapter so trajectory analysis can run on native binary sessions
+Residue-aware layer channels for per-residue visibility, atom scale, stick width, opacity, color mode, and render style

Changed

~Dashboard file picker accepts paired topology/trajectory selections in one upload action
~Native binary GROMACS sessions now disable continuous scrubber playback and guide users toward selected-frame streaming
~Binary GROMACS capability copy now distinguishes paired playback from unsupported standalone .tpr files
~Path-traced render dimensions now start at a lighter 1280 x 720 default while keeping 1080p as an explicit preset

Fixed

•Corrupt binary trajectories now fail with typed decoder errors instead of stale scene mutation
•Native TRR playback uses a CLAVISCAGE padding-aware parser fallback for GROMACS 2026 TRR files

—Hydrate-water aliases such as HSL now participate in cage-water analysis instead of being treated as guest residues
—PDB and CIF/mmCIF text structures now load into the same browser-local frame model as GRO structures
—GROMACS XTC, TRR, and TPR uploads are recognized with topology/trajectory guidance instead of failing as unknown file types
—Large path-traced exports keep far molecular scenes inside the export camera clipping range

Added

+Shared residue taxonomy for water, hydrate-water, guest, metal/slab, geologic/mineral, biomolecule, and unknown categories
+PDB CRYST1 plus ATOM/HETATM coordinate parsing and CIF/mmCIF atom_site Cartesian coordinate parsing
+Metal and geologic residue coloring for structures such as SLAB/Fe and montmorillonite-like residues
+X/Y/Z viewport orientation controls that initialize and reset the camera from the selected positive axis toward the scene
+CPU Path Tracer availability now follows browser Worker/ImageData support by default, with explicit deployment opt-out support
+Mouse-pointer Drag Frame affordance for crop adjustment discovery
+Live scene busy overlay for file processing, frame streaming, and analysis work
+HTR complete-cage guest occupancy assignment when guest residues are present
+Richer staged loading and long-running-work overlays for startup, parsing, frame streaming, and analysis

Changed

~Dashboard upload controls now accept .gro, .pdb, .cif, .mmcif, .xtc, .trr, and .tpr inputs
~Water extraction, guest extraction, live preview colors, and path-traced colors now share residue classification logic
~H-bond visualization defaults now start at line width 2.0 and opacity 50% in preview and path-traced fallback surfaces

Fixed

•Orthographic close-zoom inspection no longer drops molecular batches when the camera frustum becomes tight
•CPU path-traced renders now use the live camera target and the same render-frame crop selection as GPU path tracing
•Path-traced render completion now rejects empty scenes and all-background outputs instead of presenting a blank preview/download as complete
•Algorithm-specific analysis snapshots prevent TRACE, HTR, and GRADE cage/occupancy overlays from mixing after algorithm switches
•New primary structure uploads clear stale analysis-complete popups before scene rebuild
•Recognized .xtc/.trr/.tpr inputs show topology/trajectory guidance instead of a red parser error

—Dashboard render IA now exposes clearer VIEW, ANALYZE, RESULTS, LAYERS, and RENDER states with semantic chips
—RAY-TRACED EXPORT now shows a Render Resource selector for GPU WebGL and the gated CPU still-image fallback
—Drag Frame crops now update output WIDTH/HEIGHT to match the drawn crop aspect while preserving pixel area

Added

+Desktop sidebar resizing with drag clamps while preserving the mobile layout
+CPU still-image fallback behind NEXT_PUBLIC_ENABLE_CPU_RENDERER=true with deterministic Worker rendering, progress, cancel, and typed render limits
+Render Resource controls that identify GPU WebGL as the default browser path-tracer backend and CPU as a feature-flagged still PNG path
+ARIA tab, tabpanel, aria-controls, aria-labelledby, roving focus, Home/End, and arrow-key support for dashboard sidebar tabs

Changed

~Dashboard navigation uses orientation-aware sidebar tabs on desktop plus semantic chips such as Render ready, Layers N, and Analysis pending
~Browser GPU Status and Render Resource cards prioritize concise summaries and hide dense GPU details behind disclosure
~Output Frame presents DRAG FRAME as the primary crop-adjustment action with a short scene hint
~Sidebar tab switching is controlled by React state instead of DOM query clicks

Fixed

•Drag Frame crops preserve pixel area while changing output dimensions, preventing stretched path-traced exports without runaway growth
•Render Resource backend cards stay contained at the minimum desktop sidebar width
•Local development without DATABASE_URL now returns JSON for AuthJS session and FREE usage checks instead of an HTML ClientFetchError
•Mobile sidebar tab labels stay readable by hiding compact icons/badges before the sm breakpoint
•Changelog accent buttons use black-on-yellow contrast for better readability
•The post-analysis VIEW RESULTS action now switches to RESULTS through React state instead of clicking a CSS selector

—RAY-TRACED EXPORT now shows a Render Resource selector so users can see the active GPU WebGL backend
—CPU path tracing is listed as unavailable instead of silently implying that WebGL rendering can be forced onto CPU
—The render button is guarded when an unavailable backend is selected, preventing misleading CPU render attempts

Added

+Render Resource controls for GPU WebGL versus CPU Path Tracer backend preference in the RENDER tab
+Truthful CPU path-tracing availability copy explaining that a separate JavaScript/WASM backend is required

Changed

~Path-traced render controls now report the selected compute resource before render starts

—The RENDER tab now reports browser GPU status so users can see when the WebGL path tracer is active
—Path-traced renders now request the browser high-performance GPU path and show render throughput metrics
—Atom geometry is grouped into baked merged BufferGeometry so the path tracer preserves atom positions while reducing scene object count

Added

+GPU capability probing for WebGL, WebGPU availability, exposed renderer details, and browser backend limitations
+Render metrics for scene build time, samples per second, mesh/object counts, triangle estimates, and path-tracer tile layout

Changed

~Path-traced renderer creation now consistently uses a high-performance WebGL context hint for both interactive renders and frame captures
~Atom path-tracing geometry now uses material/radius grouped baked BufferGeometry instead of cloning one sphere mesh per atom

—Path-traced output now matches the yellow Preview Mode render frame instead of stretching or zooming the scene into the wrong aspect
—Centered render frames and user-drawn crops now share the same viewport-normalized camera crop logic
—Orthographic and perspective path-traced cameras now start from the live preview viewport before applying the export crop

Added

+Shared render-frame helpers that resolve centered Preview Mode frames into explicit camera crop selections

Fixed

•Centered Preview Mode exports no longer ignore the yellow frame and render from a mismatched output aspect camera
•Orthographic path-traced exports now preserve the live viewport aspect before cropping to the requested output frame

—The public Features section now leads with the complete Clavis algorithm suite instead of implying cage detection is TRACE-only
—Landing feature cards now explicitly name TRACE, HTR, GRADE, F3/F4, guest occupancy, trajectory/layer workflows, and preview-matched exports
—The Features heading now frames the section as the Current Clavis Algorithm Suite for clearer scientific positioning

Changed

~Renamed the first landing feature card to Hydrate Algorithm Suite
~Rewrote visible feature-card copy to avoid deprecated TRACE-only or generic path-tracing language
~Updated structured-data and social metadata so SEO no longer frames Clavis as TRACE-only cage detection
~Bumped app metadata to v0.2.10 for the landing-copy clarification

—The public Features section now describes the current WASM-local Clavis workflow instead of older one-line capability blurbs
—Landing copy now names TRACE, HTR, GRADE, F3/F4, guest occupancy, trajectories, layers, and path-traced figure parity together
—Hero and SEO descriptions now emphasize browser-local analysis and no-backend upload expectations

Changed

~Renamed the landing feature heading to Current Clavis Workflow
~Refreshed feature cards for cage/ring detection, structure metrics, path-traced figures, trajectory/layer workflows, and guest occupancy filters
~Updated marketing metadata to match the current WASM-first product surface

—Path-traced renders now honor occupied guest highlights, guest size, guest bonds, cage occupancy emphasis, and hydrogen-bond width/opacity settings
—Drag Frame now uses the exact user-drawn crop instead of only deriving a centered aspect frame
—Dashboard theme changes carry into Changelog so dark/neon app sessions no longer open a light release page

Added

+Normalized render-frame crop selection shared by the scene overlay and path-traced camera view offsets
+Path-tracer guest highlight geometry with cyan neon halos and bonds for occupied guest molecules

Changed

~The former HD RESET control is now RESET 16:9 and resets both output dimensions and the crop frame
~Cage and H-bond path-traced geometry now follows the same visual controls used in the live preview more closely

Fixed

•Path-traced export no longer drops occupied guest emphasis or line-width settings compared with Preview Mode
•Small Drag Frame selections now define the exported crop instead of expanding back to a large centered frame
•Changelog theme state stays synchronized with the selected dashboard theme

—Marketing and dashboard layouts are easier to use on narrow mobile screens
—The #features landing-page anchor now resolves correctly from claviscage.app/#features
—Documentation and Terms now match the current WASM-first Clavis workflow

Added

+Responsive mobile menu behavior with an opaque foreground panel and body scroll lock
+Production-style Terms of Service copy covering scientific use, browser-local session state, and Lemon Squeezy billing

Changed

~Dashboard controls and tab lists now compact for mobile viewports instead of squeezing the scene
~Docs now describe Overall occupancy, occupied guest filters, render-frame export controls, browser-local recovery, and WASM/local processing more accurately

Fixed

•The landing-page Features navigation target is restored with an explicit features section anchor

—Camera position and OrbitControls target now restore with the recovered scene session
—Refresh/navigation recovery preserves the exact molecular viewing angle instead of only restoring settings

Fixed

•Recovered sessions no longer initialize the 3D scene back to the default camera view after settings restore

—Normal-size .gro scenes restore after accidental refresh or a quick Changelog visit
—Changelog entries now load as a folded timeline with the newest release expanded
—Release history remains scannable as more versions accumulate

Added

+Session-local scene recovery for recoverable .gro layers, view toggles, filters, and analysis overlays
+Accessible changelog accordion with latest-version default expansion

Changed

~The NEW badge can be used without discarding the current app scene session
~Large trajectory sessions intentionally skip Web Storage recovery to avoid quota failures

—Occupied guest SIZE now scales guest bonds together with atom cores
—Occupied guest highlight controls are accessible independently from cage wireframe visibility
—Guest visuals use a cleaner neon halo palette instead of warm/brown emphasis colors

Changed

~Guest bond thickness now follows the HIGHLIGHT OCCUPIED GUESTS size slider
~Multi-atom occupied guests receive translucent additive halos and cyan emissive bonds
~Single-atom occupied guest markers use brighter cyan-family emissive halos
~The aggregate metric label is now OVERALL OCCUPANCY where shown in the app UI

—Cage overlays no longer force occupied guest emphasis by default
—Occupied guests can be filtered by enclosing cage type and current GRADE structure bucket
—Single-atom guests now render as focused halo markers while multi-atom guests remain ball-and-stick

Added

+Explicit HIGHLIGHT OCCUPIED GUESTS toggle with visible/total guest count
+Guest-specific cage-type and current/global structure filters independent from cage wireframe filters
+Pure guest filter helpers with stale-selection reconciliation tests

Changed

~Guest highlights reset to off on new files, resets, and new cage-analysis results
~Single-atom occupied guests use a subtle emissive halo instead of the multi-atom molecule path

—RENDER tab now supports custom path-traced output width and height
—Preview Mode displays a centered Blender-style render frame overlay before export
—Drag Frame mode lets users set render aspect visually without changing normal scene navigation

Added

+OUTPUT FRAME controls with px inputs, common aspect presets, and HD reset
+Scene overlay that previews the centered render frame used by path-traced export
+Shared render dimension normalization and aspect helper tests

Changed

~Path-traced export no longer hardcodes 1920 × 1080; it uses user-selected dimensions
~Frontend test harness now pins jsdom 26.1 to keep Vitest compatible with the current local Node 20.9 environment

—Enclathrated CP/ECP guests now render as full atom-level molecules instead of one enlarged marker
—Guest occupancy uses molecule centroids while preserving cage assignment results
—RESULTS tab contrast improved for dark and neon themes

Added

+PBC-aware guest molecule extraction with per-atom metadata for .gro residues
+Ball-and-stick guest overlay for multi-atom enclathrated guests

Changed

~Guest SIZE control now scales atom-level guest overlays and keeps single-point fallback for legacy data

Fixed

•Multi-atom guests such as CP and ECP no longer collapse to a single yellow sphere in the cage view
•Several RESULTS cards and empty states now inherit theme text and border colors

—Calculate cage occupancy ratios (θ_S, θ_L) for guest molecules
—Multi-layer analysis with cross-layer guest detection
—Enclathrated guests visualized as spheres inside cage wireframes
—ENCLATHRATED GUESTS overlay panel with size control

Added

+Guest occupancy calculation via WASM calculate_occupancy
+Cross-layer guest collection from separate .gro layers
+ENCLATHRATED GUESTS checkbox and SIZE slider in overlay controls
+Guest sphere visualization (only enclathrated guests shown as spheres)

Fixed

•Guest layer click in LAYERS tab no longer shows error (silent ignore)
•Cage wire thickness restored to default 0.30 (was incorrectly set to 0.10)
•Filter used != null instead of !== null to correctly handle Rust Option::None → JS undefined

—Large .gro trajectory file support with background frame counting
—OAuth account linking fixed

Added

+Streaming large trajectory worker with frame anchoring

Fixed

•OAuth provider account linking
•WASM import compatibility

—TRACE, HTR, GRADE cage detection algorithms
—F3/F4 order parameters
—GPU path-traced rendering (PRO)
—MD trajectory support
—Layer management system

Added

+Core WASM engine with Rust-based cage detection
+React Three Fiber 3D visualization
+Lemon Squeezy payment integration
+Mintlify documentation site

Initializing ClavisCage

Large trajectories can take a moment. Work continues in your browser.

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Parsing structure workspace

Preparing WebGL viewport

Streaming molecular assets

Syncing analysis modules

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Changelog

Current version: v0.3.15

Versions

Highlights

139

Default

Latest open

—HTR complete cages now carry periodic-cell-aware centers produced by the shared Rust engine
—Canonical HTR cage signatures retain their machine labels through occupancy cutoff and theta calculations
—The supplied 4,500-water production structure now assigns all 161 highlighted guests inside their PBC-unwrapped cages

Changed

~Display labels are now applied only after scientific occupancy calculation

Fixed

•Boundary-crossing HTR cages no longer acquire false centers from averaging wrapped browser coordinates
•HTR small- and large-cage occupancy statistics no longer fall through the generic cage cutoff because of display typography

—Native GROMACS and mapped LAMMPS trajectories now run CHILL+ across the exact Start, End, and Step range selected in Analyze
—CHILL+ chart and CSV frame labels are one-based, matching the visible range controls and the other trajectory algorithms
—In-memory multi-frame GRO analysis keeps its bounded sampling path while native trajectory sources use the explicit range contract

Changed

~The shared trajectory range action now dispatches CHILL+ as well as TRACE, HTR, GRADE, F3, and F4
~Native GROMACS and mapped LAMMPS CHILL+ analysis validates the selected range against the source frame count before starting work

Fixed

•CHILL+ no longer replaces a requested native trajectory window with an evenly sampled 40-frame sweep
•CHILL+ completion and progress state now preserves the exact analyzed frame identities

—HTR, TRACE, and native GRADE now follow their own reference contracts instead of sharing one TRACE-shaped result
—Normal and large GRO, mapped LAMMPS, and native GROMACS trajectories now run selected TRACE, HTR, GRADE, and F3/F4 ranges with explicit frame provenance
—The Blender extension caches algorithm-owned analysis per frame and imports both schema v1 and provenance-rich schema v2 ClavisCage bundles
—F3/F4 aggregation and geometry now match independent and reference calculations on the supplied production fixture

Added

+A native three-family GRADE port for 5^12, 5^12 6^2, and 5^12 6^4 cages, including guest-filled counts
+Complete HTR and GRADE golden regressions plus algorithm-aware worker, bundle, and Blender round-trip coverage

Changed

~HTR uses its oxygen-only periodic topology, TRACE uses the reference ring and two-pass cup machinery, and GRADE no longer exposes arbitrary TRACE signatures
~Trajectory rows and Blender CSV exports retain the selected algorithm, source frame, display frame, parameters, and algorithm-specific payload

Fixed

•F3 now weights every neighbor triplet and F4 uses the maximum-distance minimum-image hydrogen pair
•Stale cross-algorithm trajectory, overlay, occupancy, and F3/F4 state is cleared when a new file or frame takes ownership
•The worker WASM import surface is synchronized with the committed browser artifact and protected by an instantiation contract

—PRO users can hand the current displayed scene to the Blender extension as an offline, editable ClavisCage bundle
—The worker-served WASM now stays synchronized with the package build and reproduces the exact sII 192 / sI 512 reference counts
—Path-traced output now carries active CHILL+ class colors, water-class filters, and the classified O–O network
—Large path-traced scenes use adaptive atom tessellation and batched bond geometry instead of millions of cloned meshes

Added

+A versioned .claviscage.zip action carrying the current frame, matching CHILL+/H-bond/HTR analyses, and supported editable styles into Blender

Fixed

•Stale current-frame analyses are omitted with a bundle warning instead of being attached to newer coordinates
•The July 13 release notes are correctly identified as v0.3.12
•CHILL+ no longer falls back to neutral path-traced atoms or drops its classified-water network
•Oversized path-tracer scenes now fail soft against GPU memory and CPU primitive ceilings before full geometry allocation or worker cloning

—The Render tab now provides one Export Center for standard and path-traced PNG images, frame ZIP archives, and WebGL or path-traced MP4 movies
—Export actions explain unavailable requirements and lock while another export is active
—Frame-sequence and movie exports now stop on an incomplete frame and restore the original frame and overlay visibility afterward
—CHILL+ now remains composable with hydrogen bonds and non-water residue rendering

Added

+A capability-aware Export Center that reuses the existing WebGL, path-tracing, ZIP, and browser-video pipelines

Fixed

•Batch and video capture no longer silently produce incomplete output when a frame cannot be captured
•Export sessions restore the exact cage, ring, hydrogen-bond, and guest overlay state that was active before rendering
•CHILL+ analysis and frame refresh retain a current hydrogen-bond network with controls in the CHILL+ results panel
•CHILL+ class isolation keeps non-water residues such as SDS and NA visible and preserves their atom and bond sizing
•Hiding SDS, NA, or other non-water residue channels no longer invalidates the active CHILL+ coloring and network
•Single-frame scenes omit frame-sequence and movie actions instead of showing an inapplicable multiple-frame requirement
•Rapid native GROMACS frame swaps keep the newest request without surfacing expected request supersession as a runtime error
•Unreleased changelog labels no longer render as vUnreleased

—CHILL+ visualization state now clears before TRACE, HTR, or GRADE takes over the scene, preventing stale CHILL network overlays from mixing with cage and H-bond overlays
—CHILL+ coloring and network overlays are tied to the analyzed frame identity, so same-size frame changes no longer reuse stale classification just because the water count matches
—Native GROMACS render-position frames now feed water extraction from the displayed coordinate buffer when it aligns with the rendered atoms

Fixed

•Cleared CHILL-only color/network state on non-CHILL analysis and broad analysis resets
•Added frame-key validation for CHILL+ color and network overlays
•Updated browser QA coverage for CHILL+ followed by TRACE, HTR, and GRADE in one session

—CHILL+ now draws the classified-water network — the O-O neighbor lattice — as a connected overlay colored by structure class, so ice and hydrate cages appear as connected polyhedra like the cage and H-bond overlays, not just colored dots
—The network respects the per-class filter: isolate "hydrate only" to see just the hydrate cage framework, and liquid waters are omitted so the ordered structures stand out
—A NETWORK STYLE panel controls the overlay bond width, opacity, and color (a single-color override or per-class colors)

Added

+ChillNetworkVisualization overlay driven by the O-O neighbor edges the cell-list CHILL+ search already computes (no extra cost), rendered per class in the CHILL+ palette and PBC-wrapped like the H-bond overlay
+Width / opacity / color controls for the CHILL+ network overlay in the results panel

—The CHILL+ time-series now runs on LAMMPS trajectories, in addition to native GROMACS and in-memory multi-frame .gro files — so you can track ice/hydrate/liquid fractions over a LAMMPS run too

Added

+LAMMPS trajectory support in the CHILL+ time-series sampler; the RUN CHILL+ TIME SERIES button now appears for a loaded multi-frame LAMMPS dump

—A new CHILL+ time-series samples up to 40 frames across a trajectory, classifies each, and plots the six structure-class fractions over time — so you can watch ice, gas-hydrate, and liquid populations evolve during a dissociation or growth run
—Runs on the fast v0.3.6 cell-list classifier, so a sampled multi-frame sweep completes without freezing the view
—Works on native GROMACS trajectories and in-memory multi-frame .gro files; the series exports to CSV

Added

+RUN CHILL+ TIME SERIES button in the CHILL+ analysis panel (shown when a multi-frame trajectory is loaded) and a ChillTimeSeries line chart with one line per class plus CSV download

—CHILL+ now recolors the 3D view by structure class the moment analysis finishes, so ice, gas-hydrate, and interfacial regions are visible at a glance instead of only as counts
—A new per-class show/hide filter in the results panel isolates specific structure types in 3D — for example show only gas hydrate and interfacial hydrate — mirroring the OVITO select-type, hide-the-rest workflow
—CHILL+ neighbor search switched from an all-pairs O(n^2) scan to an O(n) cell list, roughly 48x faster on a ~16k-water frame, so analysis no longer freezes the view
—Large native GROMACS trajectories now render full atoms and bonds once a frame is settled, instead of a bare point cloud, while playback keeps the fast capped preview

Added

+CHILL+ 3D color mode auto-applies on analysis, with HYDRATE ONLY / ICE ONLY / SHOW ALL quick actions and a per-class show/hide filter to isolate structure types

Changed

~CHILL+ neighbor search uses an orthorhombic cell list (with an O(n^2) fallback for triclinic boxes) that produces byte-identical classification to the previous brute-force search

Fixed

•Bonds are no longer permanently suppressed for large native trajectories; they render once a frame is settled and only collapse to the fast preview during loading or playback
•CHILL+ coloring now surfaces a visible notice when the displayed frame differs from the analyzed frame, instead of silently showing no colors

—A companion Model Context Protocol (MCP) server, clavis-mcp, lets an MCP client such as Claude Desktop run ClavisCage analyses by natural language
—Exposes CHILL+, cage detection (TRACE), HTR rings, and F3/F4 order parameters over the same native engine that powers the web app, so results match exactly
—Analyzes single .gro structures and extracts individual frames from .xtc/.trr trajectories for per-frame analysis
—File access is fail-closed to an operator-configured allowlist, with no network egress and size guards

Added

+clavis-cli native runner over the Rust engine (feature-gated so it stays out of the WebAssembly build) that prints analysis JSON for a .gro file
+clavis-mcp Python package (FastMCP) with tools chill_plus, detect_cages, detect_htr_rings, f3_f4_order, and analyze_trajectory_frame; 14 pytest tests plus a Claude Desktop configuration guide

—Native trajectory playback no longer flashes a blocking progress overlay on every frame, so scrubbing and playback stay smooth
—Capped previews of large systems now sample atoms evenly across the whole simulation box instead of taking the first ~20,000 atoms by file order, so molecules past the cut-off no longer vanish

Changed

~Capped large-scene previews use an evenly-spread stride sample (always keeping selected atoms), with selection-highlight and click-to-select remapped to stay aligned with the sampled atoms

Fixed

•The blocking work overlay is suppressed during active playback while genuine (non-playback) frame loads still show it

—CHILL+ (Nguyen & Molinero, 2015) classifies each water into six structure classes — other/liquid, hexagonal ice, cubic ice, interfacial ice, gas hydrate, and interfacial hydrate
—A 3D CHILL+ color mode paints each classified water oxygen by its class, so dissociation is visible spatially in the viewer
—Cross-validated against OVITO’s ChillPlusModifier: identical on ideal sI/sII lattices and 97–99.8% agreement on disordered systems

Added

+CHILL+ analysis algorithm alongside TRACE, HTR, and GRADE, with a per-class count and fraction breakdown
+CHILL+ color mode in the viewer’s COLOR BY controls (appears once a CHILL+ result exists)

—Guest detection now recognizes cyclopentane, propane, and other clathrate guests consistently across the engine and browser, while excluding counter-ions
—Water and guest extraction group atoms by contiguous residue blocks so distinct molecules are no longer merged when GROMACS residue numbers wrap past 99,999
—HTR results now show a structure-state verdict (hydrate / partial / amorphous) so a low cage count reads as dissociation rather than under-detection
—Documented that GRADE cage counts come from TRACE, and that HTR is a more conservative large-cage estimator than TRACE by design

Changed

~HTR results panel surfaces a crystallinity/structure-state verdict alongside SEC and nSEC/IC cage counts and ring statistics
~Documented the intentional HTR primitive-ring vs TRACE all-topological-rings divergence in cage detection

Fixed

•Engine and browser guest identification unified on a shared denylist (guest = non-water, non-ion/metal); keeps cyclopentane (CPN) and propane (PRO) and guests with metal-symbol atom names, excludes counter-ions (NA, CL)
•Engine guest positions use a minimum-image-aware centroid so a guest split across the periodic boundary is located correctly instead of at the box center
•Contiguous residue-block grouping in water and guest extraction fixes 5-digit residue-number wraparound merging distinct molecules on very large systems

—GROMACS .gro/.tpr + .xtc/.trr sessions now index trajectory frame byte ranges and use selected-frame decode instead of materializing every binary frame at open time
—LAMMPS .data + dump and dump-only workflows now use Blob/File-backed frame indexing and frame-slice reads so mapped playback no longer needs the full dump text in browser memory
—Large and long trajectory workflows stay browser-local while reusing worker progress, stale-frame guards, cancellation, and current-frame analysis surfaces
—Sampled TRACE/F3F4 ranges remain available where mapping yields valid waters; HTR/GRADE trajectory-wide analysis remains out of scope

Added

+Blob/File-backed LAMMPS dump scanner and per-frame reader for .lammpstrj, .dump, and .lammpsdump inputs
+Focused regression coverage proving LAMMPS trajectory files are posted to the worker as File objects rather than read with full file.text()

Changed

~Native GROMACS selected-frame playback now indexes XTC/TRR frame slices and decodes only the requested frame in the worker
~Mapped LAMMPS playback and sampled TRACE/F3F4 ranges now await async frame-slice loads with existing progress, done/error, cancellation, and stale request handling
~Large native GROMACS viewport playback stays on a capped preview path after each frame commit so PREV/NEXT/JUMP remain responsive while current-frame analysis can still request full frame data
~Upload and feature copy now describe large/long trajectory behavior across supported GROMACS native pairs, large GRO files, and mapped LAMMPS dumps without claiming GPU compute or full trajectory-wide HTR/GRADE

—LAMMPS .data, .lammpstrj, .dump, and .lammpsdump files are now recognized by upload contracts and trajectory-session planning
—A TypeScript LAMMPS parser core handles supported dump/data text, nm-unit cell conversion, atom-id-stable frames, and hydrate water/guest mapping validation
—A conservative mapping wizard lets users confirm unit style and atom-type roles, then worker-loads LAMMPS dump frames into the normal scene for playback, current-frame TRACE/HTR/GRADE and F3/F4 analysis, and trajectory-wide TRACE/F3F4 ranges
—Standalone LAMMPS dump files can now infer atom types from ITEM: ATOMS rows and use the same mapped playback/analysis path when mol-based water grouping is valid

Added

+Self-contained TypeScript LAMMPS text parsing groundwork for supported dump/data workflows
+Browser-worker LAMMPS frame loading path with cancellation and disposal hooks
+LAMMPS mapping wizard for unit-style selection and atom-type role confirmation before mapped frame loading
+Current-frame LAMMPS TRACE/HTR/GRADE and F3/F4 analysis wiring using mapped water extraction and triclinic cell-aware WASM wrappers where metadata is available
+Mapped LAMMPS TRACE cage trajectory ranges and F3/F4 trajectory ranges with progress, done/error messages, and cancellation
+Dump-only LAMMPS mapping fallback with fail-closed water validation for missing molecule ids or invalid 1 O + 2 H groupings
+LAMMPS dump frame-range scanning so playback and trajectory analysis keep raw dump text plus offsets and parse only requested frames

Changed

~Upload copy now describes paired .data + dump inputs as mapped playback with current-frame analysis plus TRACE/F3F4 trajectory ranges; HTR/GRADE trajectory-wide analysis remains out of scope
~Generated WASM package metadata now matches the app release version (0.3.0)
~Release audit notes now document the remaining moderate Next/PostCSS advisory waiver while high-severity npm audit checks pass and force-downgrade fixes remain intentionally unused

—Native .gro/.tpr + .xtc/.trr PAUSE stays clickable by mouse while dense frame commits are in flight
—Native multi-frame sessions now show movie export controls in RENDER using the decoded native frame count
—H-bond visualization refreshes to the selected native frame instead of showing previous-frame geometry

Fixed

•Native PLAY/PAUSE no longer disables the PAUSE button during frame loading, matching Space-key behavior
•Standard and path-traced movie export controls are visible for native trajectory sessions with more than one decoded frame
•Video export loads each native frame before preparing TRACE cages or H-bonds, so exports do not reuse frame-zero overlays
•Native frame navigation clears stale H-bond and cage geometry while preserving overlay intent for the current-frame TRACE refresh

—Native .gro/.tpr + .xtc/.trr uploads now offer continuous PLAY/PAUSE playback from the browser worker cache
—H-bond and hydrate-cage visualization context stays mounted while native frames advance
—Native frame controls block overlapping requests during dense commits while keeping PREV/NEXT/JUMP available

Added

+Browser-local native playback controls with loop and speed settings for decoded GROMACS trajectories

Fixed

•Native playback no longer clears analysis surfaces on ordinary view or playback frame changes
•Scene performance policy keeps active native TRACE/H-bond/cage overlays mounted during selected-frame loads
•Native playback clamps or wraps at trajectory boundaries instead of overflowing past the decoded frame count

—Native trajectories rendered bonds at rest for the then-current native scene policy; v0.3.1 supersedes this for large native capped previews
—Cage / H-bond overlays no longer vanish after advancing one native frame — they appear immediately for the current frame
—Fixed a crash when auto-analysis ran on a native frame advance

Changed

~Bonds were suppressed only during an in-flight native frame fetch for this release; v0.3.1 keeps large native previews capped at rest
~The analysis overlay gate reopens on the next paint after results commit instead of after a fixed delay

Fixed

•Native trajectory rendering matched static .gro at rest for this release; large native preview policy changed again in v0.3.1
•Per-frame auto-analysis no longer crashes on native trajectories and reads the correct current-frame coordinates
•Cage and H-bond overlays surface immediately after each native frame advance instead of requiring a second advance

—Large native GROMACS trajectories (.gro/.tpr + .xtc/.trr) moved from a flat point cloud to instanced-sphere rendering; v0.3.1 keeps dense native previews capped at rest
—Frame scrubbing stays responsive — coordinates stream into instance matrices without rebuilding topology or colors
—Unsupported TPR files (e.g. TPX 122) now guide you to load the matching .gro topology, which works and renders identically

Changed

~Scene performance policy capped preview atoms only during an in-flight native frame load in this release; v0.3.1 keeps large native previews capped at rest
~AtomCloud separates topology/appearance grouping from per-frame coordinate buffers so only instance matrices update per frame

Fixed

•Large native GROMACS trajectories render with the normal sphere-and-bond molecular style instead of tiny dots
•Unsupported-TPR errors point users to the .gro topology path instead of suggesting another TPR binary

—Large static systems (50k+ atoms) now render as full instanced spheres instead of a flat point cloud, matching the look of small systems
—Dense emulsion and solvated `.gro`/`.pdb` inputs no longer appear as tiny dots
—The point-cloud path is now reserved for large native GROMACS trajectory streaming where frame-scrub responsiveness needs it

Changed

~Scene performance policy now drives the point renderer only for large native trajectory scenes, not for large static structures
~The viewport render branch is now governed solely by the performance policy instead of a redundant raw atom-count threshold

Fixed

•Large static structures (50k+ atoms) render with the normal sphere-and-bond molecular style, restoring the expected appearance for big emulsion systems

—Large native GROMACS frame jumps now stay responsive by keeping dense viewport navigation on a capped point-preview path
—Native selected-frame updates stream worker coordinate buffers directly into render positions instead of rebuilding full atom objects
—Molecular point geometry and typed attributes are reused across same-count frame updates
—Position buffers are separated from residue style buffers so coordinate-only frame changes avoid color and opacity rebuilds
—Browser and Chrome QA now verify dense local TPR/XTC frame jumps with performance evidence

Added

+Native frame decode, post-decode, and commit timing measures for dense trajectory QA
+Large native trajectory Browser/Chromium and Chrome-channel evidence for frame 12/24/12 navigation

Changed

~Dense native GROMACS viewport rendering now keeps the capped point preview active after frame loading so the next frame command remains interactive
~Native view frame commits now use renderPositions while analysis requests can still materialize a full scientific Frame
~Point rendering now reuses geometry and style buffers when topology and visual settings are unchanged

Fixed

•Large native trajectory frame jumps no longer freeze the viewport for tens of seconds after the visible frame changes
•Dense native scenes no longer expand immediately back to full-detail atom rendering after every selected-frame update
•TRACE/HTR/GRADE overlay commit feedback stays bounded by the dense-scene performance policy while preserving current-frame analysis state

—.gro + .xtc and .gro + .trr uploads now preserve GRO residue and atom metadata during native binary playback
—Mixed TPR layouts now fail safely instead of being silently relabeled as all-SOL water when topology metadata is unsupported
—Dense residue/layer visual edits show busy feedback and coalesce rapid slider changes so large scenes feel active instead of frozen
—TRACE/H-bond overlays refresh by trajectory frame and share one preparation path for WebGL and path-traced video export
—Standard Export now follows Preview Mode render-frame crop and output dimensions while excluding preview-only guide artifacts
—Background-only path-traced renders now include recovery actions such as Center Frame and Reset 16:9

Added

+GRO topology metadata pairing for native XTC/TRR playback with atom-index validation and count-specific mismatch errors
+Frame-aware TRACE/H-bond cache keys across algorithm, layer, frame, cutoff, and active trajectory state
+Busy-work feedback for dense visual setting commits such as high-count residue opacity and size changes
+Background-only render recovery controls that update camera/crop state without requiring a page reload

Changed

~Exact-residue binary trajectory guidance now recommends .gro + .xtc/.trr when TPR metadata cannot be decoded faithfully
~WebGL and path-traced video exports now prepare active overlays through the same frame preparation helper
~Standard WebGL PNG export now uses the configured render frame when Preview Mode is active instead of raw viewport capture

Fixed

•GRO-paired binary trajectories no longer collapse HSL, SOL, SLAB, CH4, or other residue channels into a generic trajectory scene
•Unsupported mixed TPR topologies no longer fall through to the simple water recipe
•Trajectory frame changes no longer automatically discard active TRACE/H-bond overlay intent
•Native frame loading and analysis-commit overlays now show visibly animated indeterminate progress instead of a static-looking bar
•HTR/GRADE trajectory frame changes no longer start stale analysis-commit overlays when only TRACE has a frame-aware auto-refresh path
•Preview-only render-frame guides, focus markers, and light indicators are hidden during Standard Export capture
•HTR analysis visualization no longer triggers a Maximum update depth error while committing overlays

—Paired .tpr + .xtc and .tpr + .trr uploads now open as native browser-local trajectory sessions
—Binary GROMACS frames decode in a worker and use selected-frame PREV/NEXT/JUMP controls for dense native sessions
—Mixed-residue layers now expose residue channels for independent visibility and styling
—GROMACS upload copy now points users to paired native playback instead of conversion-first guidance

Added

+Stable TPR topology metadata decoding with real atom names, residue names, residue numbers, and molecule-block summaries
+GROMACS 2026.2 fixture-backed decoder proof for .tpr + .xtc and .tpr + .trr sessions
+Worker-backed native GROMACS trajectory loading with staged busy overlay progress
+Decoded-frame GRO adapter so trajectory analysis can run on native binary sessions
+Residue-aware layer channels for per-residue visibility, atom scale, stick width, opacity, color mode, and render style

Changed

~Dashboard file picker accepts paired topology/trajectory selections in one upload action
~Native binary GROMACS sessions now disable continuous scrubber playback and guide users toward selected-frame streaming
~Binary GROMACS capability copy now distinguishes paired playback from unsupported standalone .tpr files
~Path-traced render dimensions now start at a lighter 1280 x 720 default while keeping 1080p as an explicit preset

Fixed

•Corrupt binary trajectories now fail with typed decoder errors instead of stale scene mutation
•Native TRR playback uses a CLAVISCAGE padding-aware parser fallback for GROMACS 2026 TRR files

—Hydrate-water aliases such as HSL now participate in cage-water analysis instead of being treated as guest residues
—PDB and CIF/mmCIF text structures now load into the same browser-local frame model as GRO structures
—GROMACS XTC, TRR, and TPR uploads are recognized with topology/trajectory guidance instead of failing as unknown file types
—Large path-traced exports keep far molecular scenes inside the export camera clipping range

Added

+Shared residue taxonomy for water, hydrate-water, guest, metal/slab, geologic/mineral, biomolecule, and unknown categories
+PDB CRYST1 plus ATOM/HETATM coordinate parsing and CIF/mmCIF atom_site Cartesian coordinate parsing
+Metal and geologic residue coloring for structures such as SLAB/Fe and montmorillonite-like residues
+X/Y/Z viewport orientation controls that initialize and reset the camera from the selected positive axis toward the scene
+CPU Path Tracer availability now follows browser Worker/ImageData support by default, with explicit deployment opt-out support
+Mouse-pointer Drag Frame affordance for crop adjustment discovery
+Live scene busy overlay for file processing, frame streaming, and analysis work
+HTR complete-cage guest occupancy assignment when guest residues are present
+Richer staged loading and long-running-work overlays for startup, parsing, frame streaming, and analysis

Changed

~Dashboard upload controls now accept .gro, .pdb, .cif, .mmcif, .xtc, .trr, and .tpr inputs
~Water extraction, guest extraction, live preview colors, and path-traced colors now share residue classification logic
~H-bond visualization defaults now start at line width 2.0 and opacity 50% in preview and path-traced fallback surfaces

Fixed

•Orthographic close-zoom inspection no longer drops molecular batches when the camera frustum becomes tight
•CPU path-traced renders now use the live camera target and the same render-frame crop selection as GPU path tracing
•Path-traced render completion now rejects empty scenes and all-background outputs instead of presenting a blank preview/download as complete
•Algorithm-specific analysis snapshots prevent TRACE, HTR, and GRADE cage/occupancy overlays from mixing after algorithm switches
•New primary structure uploads clear stale analysis-complete popups before scene rebuild
•Recognized .xtc/.trr/.tpr inputs show topology/trajectory guidance instead of a red parser error

—Dashboard render IA now exposes clearer VIEW, ANALYZE, RESULTS, LAYERS, and RENDER states with semantic chips
—RAY-TRACED EXPORT now shows a Render Resource selector for GPU WebGL and the gated CPU still-image fallback
—Drag Frame crops now update output WIDTH/HEIGHT to match the drawn crop aspect while preserving pixel area

Added

+Desktop sidebar resizing with drag clamps while preserving the mobile layout
+CPU still-image fallback behind NEXT_PUBLIC_ENABLE_CPU_RENDERER=true with deterministic Worker rendering, progress, cancel, and typed render limits
+Render Resource controls that identify GPU WebGL as the default browser path-tracer backend and CPU as a feature-flagged still PNG path
+ARIA tab, tabpanel, aria-controls, aria-labelledby, roving focus, Home/End, and arrow-key support for dashboard sidebar tabs

Changed

~Dashboard navigation uses orientation-aware sidebar tabs on desktop plus semantic chips such as Render ready, Layers N, and Analysis pending
~Browser GPU Status and Render Resource cards prioritize concise summaries and hide dense GPU details behind disclosure
~Output Frame presents DRAG FRAME as the primary crop-adjustment action with a short scene hint
~Sidebar tab switching is controlled by React state instead of DOM query clicks

Fixed

•Drag Frame crops preserve pixel area while changing output dimensions, preventing stretched path-traced exports without runaway growth
•Render Resource backend cards stay contained at the minimum desktop sidebar width
•Local development without DATABASE_URL now returns JSON for AuthJS session and FREE usage checks instead of an HTML ClientFetchError
•Mobile sidebar tab labels stay readable by hiding compact icons/badges before the sm breakpoint
•Changelog accent buttons use black-on-yellow contrast for better readability
•The post-analysis VIEW RESULTS action now switches to RESULTS through React state instead of clicking a CSS selector

—RAY-TRACED EXPORT now shows a Render Resource selector so users can see the active GPU WebGL backend
—CPU path tracing is listed as unavailable instead of silently implying that WebGL rendering can be forced onto CPU
—The render button is guarded when an unavailable backend is selected, preventing misleading CPU render attempts

Added

+Render Resource controls for GPU WebGL versus CPU Path Tracer backend preference in the RENDER tab
+Truthful CPU path-tracing availability copy explaining that a separate JavaScript/WASM backend is required

Changed

~Path-traced render controls now report the selected compute resource before render starts

—The RENDER tab now reports browser GPU status so users can see when the WebGL path tracer is active
—Path-traced renders now request the browser high-performance GPU path and show render throughput metrics
—Atom geometry is grouped into baked merged BufferGeometry so the path tracer preserves atom positions while reducing scene object count

Added

+GPU capability probing for WebGL, WebGPU availability, exposed renderer details, and browser backend limitations
+Render metrics for scene build time, samples per second, mesh/object counts, triangle estimates, and path-tracer tile layout

Changed

~Path-traced renderer creation now consistently uses a high-performance WebGL context hint for both interactive renders and frame captures
~Atom path-tracing geometry now uses material/radius grouped baked BufferGeometry instead of cloning one sphere mesh per atom

—Path-traced output now matches the yellow Preview Mode render frame instead of stretching or zooming the scene into the wrong aspect
—Centered render frames and user-drawn crops now share the same viewport-normalized camera crop logic
—Orthographic and perspective path-traced cameras now start from the live preview viewport before applying the export crop

Added

+Shared render-frame helpers that resolve centered Preview Mode frames into explicit camera crop selections

Fixed

•Centered Preview Mode exports no longer ignore the yellow frame and render from a mismatched output aspect camera
•Orthographic path-traced exports now preserve the live viewport aspect before cropping to the requested output frame

—The public Features section now leads with the complete Clavis algorithm suite instead of implying cage detection is TRACE-only
—Landing feature cards now explicitly name TRACE, HTR, GRADE, F3/F4, guest occupancy, trajectory/layer workflows, and preview-matched exports
—The Features heading now frames the section as the Current Clavis Algorithm Suite for clearer scientific positioning

Changed

~Renamed the first landing feature card to Hydrate Algorithm Suite
~Rewrote visible feature-card copy to avoid deprecated TRACE-only or generic path-tracing language
~Updated structured-data and social metadata so SEO no longer frames Clavis as TRACE-only cage detection
~Bumped app metadata to v0.2.10 for the landing-copy clarification

—The public Features section now describes the current WASM-local Clavis workflow instead of older one-line capability blurbs
—Landing copy now names TRACE, HTR, GRADE, F3/F4, guest occupancy, trajectories, layers, and path-traced figure parity together
—Hero and SEO descriptions now emphasize browser-local analysis and no-backend upload expectations

Changed

~Renamed the landing feature heading to Current Clavis Workflow
~Refreshed feature cards for cage/ring detection, structure metrics, path-traced figures, trajectory/layer workflows, and guest occupancy filters
~Updated marketing metadata to match the current WASM-first product surface

—Path-traced renders now honor occupied guest highlights, guest size, guest bonds, cage occupancy emphasis, and hydrogen-bond width/opacity settings
—Drag Frame now uses the exact user-drawn crop instead of only deriving a centered aspect frame
—Dashboard theme changes carry into Changelog so dark/neon app sessions no longer open a light release page

Added

+Normalized render-frame crop selection shared by the scene overlay and path-traced camera view offsets
+Path-tracer guest highlight geometry with cyan neon halos and bonds for occupied guest molecules

Changed

~The former HD RESET control is now RESET 16:9 and resets both output dimensions and the crop frame
~Cage and H-bond path-traced geometry now follows the same visual controls used in the live preview more closely

Fixed

•Path-traced export no longer drops occupied guest emphasis or line-width settings compared with Preview Mode
•Small Drag Frame selections now define the exported crop instead of expanding back to a large centered frame
•Changelog theme state stays synchronized with the selected dashboard theme

—Marketing and dashboard layouts are easier to use on narrow mobile screens
—The #features landing-page anchor now resolves correctly from claviscage.app/#features
—Documentation and Terms now match the current WASM-first Clavis workflow

Added

+Responsive mobile menu behavior with an opaque foreground panel and body scroll lock
+Production-style Terms of Service copy covering scientific use, browser-local session state, and Lemon Squeezy billing

Changed

~Dashboard controls and tab lists now compact for mobile viewports instead of squeezing the scene
~Docs now describe Overall occupancy, occupied guest filters, render-frame export controls, browser-local recovery, and WASM/local processing more accurately

Fixed

•The landing-page Features navigation target is restored with an explicit features section anchor

—Camera position and OrbitControls target now restore with the recovered scene session
—Refresh/navigation recovery preserves the exact molecular viewing angle instead of only restoring settings

Fixed

•Recovered sessions no longer initialize the 3D scene back to the default camera view after settings restore

—Normal-size .gro scenes restore after accidental refresh or a quick Changelog visit
—Changelog entries now load as a folded timeline with the newest release expanded
—Release history remains scannable as more versions accumulate

Added

+Session-local scene recovery for recoverable .gro layers, view toggles, filters, and analysis overlays
+Accessible changelog accordion with latest-version default expansion

Changed

~The NEW badge can be used without discarding the current app scene session
~Large trajectory sessions intentionally skip Web Storage recovery to avoid quota failures

—Occupied guest SIZE now scales guest bonds together with atom cores
—Occupied guest highlight controls are accessible independently from cage wireframe visibility
—Guest visuals use a cleaner neon halo palette instead of warm/brown emphasis colors

Changed

~Guest bond thickness now follows the HIGHLIGHT OCCUPIED GUESTS size slider
~Multi-atom occupied guests receive translucent additive halos and cyan emissive bonds
~Single-atom occupied guest markers use brighter cyan-family emissive halos
~The aggregate metric label is now OVERALL OCCUPANCY where shown in the app UI

—Cage overlays no longer force occupied guest emphasis by default
—Occupied guests can be filtered by enclosing cage type and current GRADE structure bucket
—Single-atom guests now render as focused halo markers while multi-atom guests remain ball-and-stick

Added

+Explicit HIGHLIGHT OCCUPIED GUESTS toggle with visible/total guest count
+Guest-specific cage-type and current/global structure filters independent from cage wireframe filters
+Pure guest filter helpers with stale-selection reconciliation tests

Changed

~Guest highlights reset to off on new files, resets, and new cage-analysis results
~Single-atom occupied guests use a subtle emissive halo instead of the multi-atom molecule path

—RENDER tab now supports custom path-traced output width and height
—Preview Mode displays a centered Blender-style render frame overlay before export
—Drag Frame mode lets users set render aspect visually without changing normal scene navigation

Added

+OUTPUT FRAME controls with px inputs, common aspect presets, and HD reset
+Scene overlay that previews the centered render frame used by path-traced export
+Shared render dimension normalization and aspect helper tests

Changed

~Path-traced export no longer hardcodes 1920 × 1080; it uses user-selected dimensions
~Frontend test harness now pins jsdom 26.1 to keep Vitest compatible with the current local Node 20.9 environment

—Enclathrated CP/ECP guests now render as full atom-level molecules instead of one enlarged marker
—Guest occupancy uses molecule centroids while preserving cage assignment results
—RESULTS tab contrast improved for dark and neon themes

Added

+PBC-aware guest molecule extraction with per-atom metadata for .gro residues
+Ball-and-stick guest overlay for multi-atom enclathrated guests

Changed

~Guest SIZE control now scales atom-level guest overlays and keeps single-point fallback for legacy data

Fixed

•Multi-atom guests such as CP and ECP no longer collapse to a single yellow sphere in the cage view
•Several RESULTS cards and empty states now inherit theme text and border colors

—Calculate cage occupancy ratios (θ_S, θ_L) for guest molecules
—Multi-layer analysis with cross-layer guest detection
—Enclathrated guests visualized as spheres inside cage wireframes
—ENCLATHRATED GUESTS overlay panel with size control

Added

+Guest occupancy calculation via WASM calculate_occupancy
+Cross-layer guest collection from separate .gro layers
+ENCLATHRATED GUESTS checkbox and SIZE slider in overlay controls
+Guest sphere visualization (only enclathrated guests shown as spheres)

Fixed

•Guest layer click in LAYERS tab no longer shows error (silent ignore)
•Cage wire thickness restored to default 0.30 (was incorrectly set to 0.10)
•Filter used != null instead of !== null to correctly handle Rust Option::None → JS undefined

—Large .gro trajectory file support with background frame counting
—OAuth account linking fixed

Added

+Streaming large trajectory worker with frame anchoring

Fixed

•OAuth provider account linking
•WASM import compatibility

—TRACE, HTR, GRADE cage detection algorithms
—F3/F4 order parameters
—GPU path-traced rendering (PRO)
—MD trajectory support
—Layer management system

Added

+Core WASM engine with Rust-based cage detection
+React Three Fiber 3D visualization
+Lemon Squeezy payment integration
+Mintlify documentation site