Hosted GPU tier: endpoint, launcher, reaper, runner image, clients (GJOB-088) - #1

…ld Silicon branding

- Scrubber shows frame numbers under major ticks; major/minor grid spacing
  user-selectable (10/20/25/50% and 1/2/5/10%)
- Right-side inspector (View menu, ⌥⌘I, or sidebar button): timeline grid,
  atom size, background, orbit speed, camera reset, element legend — live via
  the same UserDefaults keys as Settings
- Brand: launching under ForceField Silicon (Gitinama Inc. trade name);
  bundle id com.forcefieldsilicon.mdengine; README/LICENSE/manual updated

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

…t agent-security note

- Bundle fe_oxidation.in/.xyz: bcc Fe slab + O2 gas via ffield.reax.Fe_O_C_H
  (ships with LAMMPS - nothing redistributed); 391 atoms, 13 frames, runs in
  ~17s on 6 omp threads. First step of the metal-oxidation focus; Al/O ReaxFF
  pending a force-field licensing check.
- CLI + MCP derive LAMMPS_POTENTIALS from the lmp install when unset, so decks
  can reference bare force-field names out of the box (verified end-to-end).
- README: decks-are-programs security note now states plainly that an agent on
  the MCP server can submit decks that execute with user privileges; sandboxing
  is scoped to the hosted tier.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- LammpsDumpParser: ITEM: TIMESTEP blocks from dump atom/custom; direct,
  unwrapped, and scaled (box-mapped) coordinates; element column when present,
  numeric type token otherwise; rows sorted by id. TrajectoryReader sniffs
  dump-vs-XYZ, and every reader (app Load File, CLI info/export/decimate, MCP
  trajectory tools) now goes through it. Verified: scaled and element dump
  variants parse bit-identical bboxes to the XYZ reference.
- Unknown element tokens (numeric types) get stable distinct hash colours.
- docker/runner: two-stage LAMMPS stable_29Aug2024 OpenMP build, non-root,
  potentials baked in; README documents the hardening flags that constitute
  the sandbox (no network, read-only, resource caps).

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

…robustness

From peer-session shakedown on real oxidation dumps (RUN-010, id type x y z q):
- Reported misparse (element=id, shifted coords, wrong counts) was a STALE
  RELEASE BINARY on PATH, not parser logic - release now rebuilt with every
  change; parser verified against 150-frame growing-count dump (8402->8421).
- Real fixes/features: -h/--help on subcommands (was 'cannot read --help');
  info prints the dump's per-atom field list and charge range; Arv carries q
  from native dumps; export/decimate --charges writes extended-XYZ
  (Properties=species:S:1:pos:R:3:charge:R:1); --elements O,Al maps numeric
  type tokens to symbols; rows with non-finite coords dropped (NaN-poisoned
  RUN-006 tail frames now parse with finite bbox). MCP: trajectory_info gains
  fields/charges, export_frame gains charges option.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

…dump)

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- Tests/AppTests: 11 XCTest cases over both parsers, reader sniffing, and the
  extended-XYZ writer (scaled coords, charges, id sort, growing counts,
  truncated in-flight tails, NaN drops); test target fixed to match its dir
  so 'swift test' actually runs it. All green.
- MCP: new job_files tool (locate a finished job's outputs); refuse >2GB
  trajectory loads with actionable guidance (CLI too); serverInfo 0.5.0.
- README: full MCP tool table, Claude Desktop registration, platform/limits.
- GitHub Actions CI (build + test + release build on macos-14), activates on
  first push.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

… scaffold

- Double-clicking .xyz/.extxyz/.lammpstrj/.traj/.dump now opens in MDEngine
  (CFBundleDocumentTypes + AppDelegate open-URL buffering for launch races)
- scripts/make_dmg.sh packages dist/MDEngine-<version>.dmg with /Applications
  symlink; make_app.sh signs with DEVELOPER_ID + notarizes/staples when
  NOTARY_PROFILE is set, ad-hoc otherwise - Apple-day is config-only
- Version 0.5.0 across app + MCP

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- Play/pause button beside the timeline with a Loop checkbox beneath it
  (checked = repeat from frame 1 when playback reaches the end; persisted)
- Live following: a loaded file is polled every 2s; frames appended by a
  running simulation extend the timeline automatically (green 'live' badge).
  Camera and scrub position are preserved; if the user was at the final frame
  the view follows the new final frame. Skipped above 512MB.
- Gesture terminology unified as Orbit / Pan / Zoom / Reset — window hint,
  manual, and code comments now all say 'Pan: double-click-drag'

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Root cause (hung on a 343MB growing oxidation dump): load() parsed on the
main thread, then live-follow re-parsed the WHOLE file every 2s, also on the
main thread. Fixes:
- All parsing moved to a background queue; UI shows 'Loading …' and stays
  responsive; results published on main
- Live-follow: in-flight guard (never overlapping parses), poll interval
  scales with file size (~45s at 350MB), 1GB follow cap, watch invalidated
  if a different file is loaded meanwhile
- App-side 2GB open guard with decimate guidance (CLI/MCP already had one)
- Arv drops its unused Identifiable UUID (millions of pointless allocations
  per parse); renderer builds GPU atom arrays per frame on demand instead of
  precomputing every frame (~350MB saved on 1276-frame trajectories)

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- Window scene replaces WindowGroup: macOS restoration was resurrecting blank
  duplicate windows; every window shared one trajectory anyway
- View menu + inspector View section: Perspective/Orthographic toggle (⌥⌘P).
  Ortho frames the height perspective would see at the current distance, so
  zoom works and switching holds framing; point size pre-divided by distance
  to match apparent atom size
- Window title shows the loaded file name

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Root cause (seen twice in screenshots: restored windows rendering window-bg
gray): AppKit recreates the MTKView while the representable's Coordinator -
and its uploaded-generation counter - survives. The fresh Renderer never
received the trajectory and every draw early-returned without painting.
makeNSView now resets the coordinator's generation so the next update
re-uploads, and draw() always encodes a clear pass so an atomless view shows
the intentional background instead of never painting.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

MTKView's internal display link silently never started for re-hosted windows
(process sample showed zero draw calls while UI stayed live). The view now
pauses the internal loop and owns a CADisplayLink created in
viewDidMoveToWindow — rendering runs exactly while the view is in a window.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Tracked on every successful load (deduped, most recent first, persisted).
Menu shows filenames with full-path tooltips; stale entries are pruned with
an explanatory alert; Clear Menu resets.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

- ZProfileAnalysis in LAMMPSCore: surface plane (top-5% substrate mean z),
  probe penetration depths, at-surface/in-flight counts, bound-probe mean
  charge, relative-z histogram; unit-tested; shared by app and MCP.
- Inspector: Z-profile section (substrate/probe pickers, live stats, mini
  histogram) + Scale bar toggle in the View section.
- Viewport scale bar: round 1/2/5x10^n A length, driven by camera distance
  and trajectory normalization via ViewportScale; exact at center depth.
- MCP: z_profile tool (frame/substrate/probe args, defaults to the two most
  abundant elements).
- Manual: Inspector analysis section.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Persisted as playbackFPS; retimes a running playback live.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… core

- New MDRender target: RenderCore (one shader/camera-math/palette shared by
  the interactive view and offscreen rendering), OffscreenRenderer, and
  VideoExporter (AVFoundation H.264 MP4 + ImageIO animated GIF).
- Annotations (scale bar + frame counter) baked by default, toggleable.
- Cinematic orbit option; sprite sizes scale with output resolution so 4K
  exports match the window (maxPointSize uniform added to the shader).
- App: File > Export Video... (shift-cmd-E) + Inspector Video-export section
  (resolution/fps/stride-with-auto/annotations/orbit, progress + cancel).
- Viewport View menu snaps to canonical Top/Bottom/Front/Rear (z-up rig);
  Inspector panes 2-4 add extra fixed-view viewports in a CAD-style grid.
- MCP: render_video tool (camera in degrees, stride, orbit, annotations,
  type->element mapping via 'elements'); element mapper moved to LAMMPSCore.
- Manual: Views + Video export sections.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…ed state)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… viewport View menu

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… view picker

Pane rows show a status summary (view name / Off) collapsed; pane 1 is the
main viewport (always on, Free + snap presets synced with the View menu).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…pans

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…deo export second-to-last

LazyVGrid collapsed rows after the first because Metal views have no
intrinsic size; the viewport grid now uses explicit HStack rows.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… in Restore Defaults

Home/reset camera = isometric (corner view, direction cosines 135/45/-45 to
the axes). Camera rig gains a roll axis so Left keeps z up. Restore Defaults
now resets pane 1-4 (Isometric main; 2/3/4 = Top/Left/Front, off).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

The bundled example now waits 0.4 s and yields to any real open event
(sourceName set = a load is underway, frames set = one landed).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…able)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…kbox overrides

Each extra pane now has its own camera publisher so its bar tracks its own
zoom; checkbox style distinguishes scale-bar controls from pane switches.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…/Left)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Restore Defaults / Reset Camera bumps one token for all panes; extra panes
now re-apply their assigned preset after the reset instead of inheriting
the main pane's isometric home.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

… renders

- VideoExporter.exportPNG: single frame -> PNG, same camera/style/annotation
  pipeline as video. contrastStyle(): minority species enlarged 1.8x and
  recolored to pop against the substrate.
- render_video and render_image accept colors ('O=red,Al=#3366ff' — named or
  hex), sizes ('O=1.8'), style: 'contrast'; shared arg parsing.
- README/manual updated with the new tools.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

…gle in the toolbar; signed DMG + tools tarball scripts

- Inspector ▸ Z-profile: numeric depth axis (Å rel. surface), labeled surface-plane
  marker, chart tooltip; Export CSV… / Export Excel… of the LAST frame
  (LAMMPSCore/ZProfileExport: sectioned CSV, dependency-free two-sheet .xlsx)
- Inspector toggle moved from the status bar to a full-size toolbar button
  (top-right, "Hide or show the Inspector"), matching Xcode
- make_dmg.sh signs + notarizes + staples the DMG when DEVELOPER_ID/NOTARY_PROFILE
  are set; new make_tools.sh packages signed CLI + MCP binaries
- version 0.6.1 (bundle + MCP serverInfo)

…host=, list_hosts, fetch_job

Same job contract, different machine: deck dir rsynced up (trajectories/
checkpoints/logs excluded), LAMMPS launched under nohup with the exit code
recorded remotely; job_status/job_log/job_files/cancel_job read state over ssh;
fetch_job pulls the run directory back for the analysis and render tools.
A GPU host is a launch template with the KOKKOS flags. Explicit 'cancelled'
state for local and remote jobs. Verified end to end against ssh localhost.

…I stage (GJOB-088 step 1)

…tates, billing

…en MDE_JOB_ID is set, sshd dev mode otherwise

…fline e2e verified (submit→pull→run→upload→done→results→debit)

…login/account/jobs/job; MCP host=cloud across all job tools; App Run Accelerated + Accelerated Runs window + Settings tab; results auto-open. Verified vs mock from all three surfaces; 20 tests

Co-Authored-By: Claude Code <noreply@anthropic.com>

…nt-key /welcome + Stripe webhook, admin CLI, Caddy/systemd/bootstrap/deploy, 19 tests; CONTRACT: purchase flow + pod lifecycle

…st real deploy

… GJOB-093)

… mkdir before potentials symlink

…llback, launch timeout, pod release on every terminal state; 33 tests; untrack pycache

…mport)

…s — Community cudaErrorUnknown was undiagnosable

…g; test covers live shape

…under timeout(wall+600) — CONTRACT pod-lifecycle enforcer 3; hourly sqlite backup timer

…tests)