doc: update README with architecture diagram

[skip-ci]

Author: plexoos

docs/architecture.md

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+## Architecture overview
+
+Simphony is a Geant4 plus OptiX optical photon transport stack. Geant4 owns the
+detector construction, material definitions, event loop, and optional reference
+tracking. `G4CXOpticks` is the bridge into the GPU stack: `SetGeometry(world)`
+translates a Geant4 world into Opticks/CSG data once, and `simulate(eventID,
+reset)` launches GPU photon generation and propagation for each event.
+
+Application-facing code lives mainly in `src/`, `config/`, `tests/`, and
+`optiphy/`. The lower-level packages are Opticks-derived framework libraries:
+`sysrap`, `CSG`, `qudarap`, `CSGOptiX`, `u4`, and `g4cx`. Optional DD4hep
+integration plugins live in `dd4hepplugins/` and are built only when DD4hep is
+available.
+
+### Layered view
+
+```mermaid
+
+flowchart TB
+  subgraph Inputs["Inputs"]
+    direction TB
+    userinputs["GDML<br/>Geant4 macro<br/>config/*.json"]
+  end
+
+  subgraph Apps["Application layer"]
+    direction TB
+    appcode["installed targets<br/>simg4ox<br/>GPUCerenkov<br/>GPURaytrace"]
+  end
+
+  subgraph Bridge["Geant4 bridge"]
+    direction TB
+    u4["u4<br/>Geant4 translation<br/>materials<br/>surfaces<br/>recorder utilities"]
+    g4cx["g4cx<br/>G4CXOpticks"]
+  end
+
+  subgraph Runtime["GPU runtime"]
+    direction TB
+    sysrap["sysrap<br/>NP arrays<br/>SEvt/SSim<br/>config<br/>photon types"]
+    csg["CSG<br/>CSGFoundry<br/>primitives<br/>geometry model"]
+    qudarap["qudarap<br/>QSim/QEvt<br/>RNG<br/>optical physics"]
+    csgoptix["CSGOptiX<br/>OptiX module<br/>GAS/IAS/SBT<br/>launch control"]
+  end
+
+  subgraph Outputs["Outputs"]
+    direction TB
+    persisted["NumPy arrays<br/>hit.npy<br/>photon.npy<br/>record.npy<br/>seq.npy"]
+    analysis["analysis with optiphy tools"]
+  end
+
+  userinputs --> appcode
+  appcode --> u4
+  u4 --> g4cx
+  u4 --> sysrap
+  u4 --> csg
+  sysrap --> csg
+  sysrap --> qudarap
+  csg --> csgoptix
+  qudarap --> csgoptix
+  g4cx --> csgoptix
+
+  csgoptix --> persisted
+  persisted --> analysis
+```
+
+### Build targets and packages
+
+The top-level CMake project is `simphony` and builds these core libraries in
+dependency order:
+
+| Layer | CMake target | Directory | Main role |
+|---|---|---|---|
+| System utilities | `SysRap` | `sysrap/` | `NP`/`NPFold`, `SEvt`, `SSim`, logging, config, photon and genstep types |
+| CSG geometry | `CSG` | `CSG/` | `CSGFoundry` and CSG primitive/intersection data |
+| CUDA simulation support | `QUDARap` | `qudarap/` | `QSim`, `QEvt`, RNG, and optical physics tables |
+| OptiX runtime | `CSGOptiX` | `CSGOptiX/` | OptiX PTX/module setup, acceleration structures, SBT, and launches |
+| Geant4 utilities | `U4` | `u4/` | Geant4 material/surface/geometry translation and recorder support |
+| G4-to-GPU bridge | `G4CX` | `g4cx/` | `G4CXOpticks` geometry setup, GPU simulation, and reset/finalization |
+
+The installed application targets from `src/` are:
+
+| Target | Purpose |
+|---|---|
+| `simg4ox` | General Geant4 application that loads GDML, reads a torch JSON config, runs Geant4, and launches GPU simulation at event end |
+| `GPUCerenkov` | Cerenkov-focused example using charged-particle genstep collection |
+| `GPURaytrace` | Cerenkov plus scintillation example with GPU ray tracing |
+| `GPUPhotonSource` | Torch-generated optical photons, with Geant4 and GPU tracking side by side |
+| `GPUPhotonSourceMinimal` | Torch-generated optical photons with GPU-only photon transport |
+| `GPUPhotonFileSource` | User-provided photon text file with GPU-only photon transport |
+| `consgeo` | GDML-to-CSG conversion helper |
+| `simtox` | Torch photon generator that writes `out/photons.npy` |
+
+`simphony_argparse` and `simphony_g4_deps` are interface targets used to share
+third-party argparse headers and common Geant4/G4CX link dependencies. The
+standalone `examples/` tree contains small consumer examples that use an
+installed `simphony` package; it is not added by the top-level `CMakeLists.txt`.
+
+### Runtime data flow
+
+There are two main runtime input modes:
+
+- **Charged-particle driven:** Geant4 tracks charged particles, Cerenkov and/or
+  scintillation gensteps are collected into `SEvt`, and the GPU generates and
+  propagates optical photons from those gensteps.
+- **Direct photon input:** the application injects an `NP` array of photons into
+  `SEvt` with `SetInputPhoton`, using photons generated from a torch JSON config
+  or parsed from a user-provided photon file.
+
+```mermaid
+%%{init: {
+  "flowchart": {
+    "nodeSpacing": 12,
+    "rankSpacing": 34,
+    "htmlLabels": true
+  }
+}}%%
+
+flowchart TB
+  subgraph Geometry["Geometry setup, once"]
+    direction TB
+    gdml2["GDML file"]
+    det["DetectorConstruction<br/>G4GDMLParser"]
+    sens["ConstructSDandField<br/>attach SensDet<br/>logical volumes"]
+    setgeo["G4CXOpticks::SetGeometry(world)"]
+    u4tree["U4Tree<br/>builds stree in SSim"]
+    foundry["CSGFoundry<br/>CreateFromSim"]
+    create["CSGOptiX::Create<br/>upload geometry<br/>build GAS/IAS/SBT<br/>load PTX"]
+  end
+
+  subgraph Event["Per-event work"]
+    direction TB
+    begin["SEvt::beginOfEvent"]
+    eventinput["event input mode<br/>Geant4 tracking to gensteps<br/>or direct photons to SetInputPhoton"]
+    evtend["SEvt gather<br/>endOfEvent"]
+    simulate["G4CXOpticks::simulate(eventID, false)"]
+    qsim["QSim<br/>generate and propagate"]
+    launch["OptiX launch<br/>CSG intersections"]
+    hits["GPU hits<br/>and event arrays"]
+    reset["G4CXOpticks::reset(eventID)"]
+  end
+
+  subgraph Persist["Persist and inspect"]
+    direction TB
+    eventout["opticks_hits_output.txt<br/>g4_hits_output.txt<br/>or o_hits.npy/g_hits.npy<br/><br/>/tmp/$USER/opticks/GEOM/...<br/>hit.npy<br/>photon.npy<br/>record.npy<br/>seq.npy"]
+    py["optiphy/ana<br/>optiphy/tools<br/>tests"]
+  end
+
+  gdml2 --> det --> sens --> setgeo --> u4tree --> foundry --> create
+  create --> simulate
+
+  begin --> eventinput
+  eventinput --> evtend
+  evtend --> simulate
+  simulate --> qsim --> launch --> hits --> reset
+
+  hits --> eventout
+  eventout --> py
+```
+
+### OptiX pipeline and extension points
+
+The fixed OptiX programs are built from `CSGOptiX/CSGOptiX7.cu` into a PTX
+object during the CMake build and installed with the libraries. User code
+usually changes scene content, photon/genstep inputs, or Geant4 actions rather
+than editing the OptiX programs directly.
+
+```mermaid
+%%{init: {
+  "flowchart": {
+    "nodeSpacing": 12,
+    "rankSpacing": 34,
+    "htmlLabels": true
+  }
+}}%%
+
+flowchart TB
+  subgraph User["User-controlled inputs"]
+    direction TB
+    usercontrolled["GDML scene<br/>optical properties<br/>sensor tags<br/><br/>gensteps<br/>or input photons<br/><br/>Geant4 app logic<br/>primary generator<br/>event/stepping/tracking actions"]
+  end
+
+  subgraph Launch["Launch preparation"]
+    direction TB
+    launchdata["SEvt/QEvt<br/>event buffers<br/><br/>CSGFoundry<br/>geometry buffers"]
+    sbt["CSGOptiX<br/>module<br/>pipeline<br/>SBT"]
+  end
+
+  subgraph Programs["CSGOptiX7.cu programs"]
+    direction TB
+    rg["__raygen__rg<br/>render<br/>simtrace<br/>simulate"]
+    simrg["simulate path<br/>qsim generate_photon<br/>qsim propagate"]
+    trace["optixTrace"]
+    shaderprograms["__intersection__is<br/>CSG primitive tests<br/><br/>__closesthit__ch<br/>boundary payload<br/><br/>__miss__ms<br/>miss payload"]
+  end
+
+  subgraph Extend["Lower-level extension points"]
+    direction TB
+    csgext["CSG/<br/>new primitives<br/>import rules"]
+    physext["qudarap/<br/>transport physics<br/>optical models"]
+    u4ext["u4/<br/>Geant4 mapping<br/>materials<br/>surfaces<br/>sensors"]
+  end
+
+  usercontrolled --> launchdata
+  launchdata --> sbt
+  sbt --> rg --> simrg --> trace
+  trace --> shaderprograms
+  csgext -.-> shaderprograms
+  physext -.-> simrg
+  u4ext -.-> launchdata
+```
+
+### What users typically provide
+
+| You provide | Where it enters | Purpose |
+|---|---|---|
+| GDML geometry with material and surface properties, plus `SensDet` aux tags when needed | `DetectorConstruction` -> `G4CXOpticks::SetGeometry` | Defines the world, optical media, and sensitive surfaces |
+| Geant4 macro | Geant4 run manager | Controls threads, `/run/beamOn`, visualization, and G4 optical-photon tracking settings |
+| Geant4 user actions in `src/` | Executable-specific app headers | Defines primary generation, event flow, optional G4 reference tracking, and output writing |
+| Torch JSON config in `config/` | `generate_photons` -> `SEvt::SetInputPhoton` | Direct optical photon injection without charged primaries |
+| Photon text file | `GPUPhotonFileSource` -> `SEvt::SetInputPhoton` | Replay or externally generated photon distributions |
+| DD4hep detector/application configuration, when enabled | `dd4hepplugins/` actions | Integrates Simphony GPU optical transport into DD4hep/DDG4 workflows |
+
+### Where to start in the tree
+
+- Start in `src/` if you are adding or changing an installed executable, input
+  mode, Geant4 primary generator, or Geant4 action.
+- Use `config/` for torch-source JSON presets and `tests/geom/` for GDML test
+  geometries.
+- Move to `g4cx/` and `u4/` when changing Geant4 integration, geometry
+  translation, materials, surfaces, sensitive-detector mapping, or event
+  recording.
+- Move to `CSG/` when adding a CSG primitive, changing CSG import, or debugging
+  geometry intersections.
+- Move to `qudarap/` and `CSGOptiX/` only when extending GPU transport physics,
+  event buffers, OptiX launches, or OptiX device programs.
+- Use `dd4hepplugins/` for DD4hep/DDG4 action plugin work.
+- Use `optiphy/ana/`, `optiphy/tools/`, and `tests/` to inspect outputs and
+  validate behavior.