From 91020714e7bdb99be242298787f45aa7f7720225 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 11:20:31 +0200
Subject: [PATCH 01/33] add CLAUDE.md with build, test, and architecture
 documentation

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 CLAUDE.md | 78 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 CLAUDE.md

diff --git a/CLAUDE.md b/CLAUDE.md
new file mode 100644
index 0000000..e266a11
--- /dev/null
+++ b/CLAUDE.md
@@ -0,0 +1,78 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+miniCaloSim is a Geant4-based calorimeter simulator designed for teaching. It exposes a Python API via pybind11 so students can define calorimeter geometries, run batch simulations, and visualise results — all from a Jupyter notebook.
+
+## Build
+
+Requires Geant4 (v11.1.2), pybind11 (submodule at `lib/pybind11`), and Python 3 development headers.
+
+```bash
+mkdir build && cd build
+cmake ..
+make -j$(nproc)
+```
+
+This produces two artifacts:
+- `build/minicalo.so` — the pybind11 Python module
+- `build/exampleB4a` — a standalone Geant4 executable (for reference only)
+
+After building, copy the Python files to the Python path for use outside the `bind/` directory (the Dockerfile shows the canonical install paths):
+```bash
+cp build/minicalo*.so bind/G4Calo.py bind/minicalo_tools.py bind/minipandas.py /target/python/path/
+cp bind/G4Calo_exec.py /usr/local/bin/
+```
+
+## Testing
+
+Run the minipandas unit tests (no Geant4 required):
+```bash
+cd bind && python3 test_minipandas.py
+```
+
+Run the TempFileManager unit tests:
+```bash
+cd bind && python3 -m unittest minicalo_tools.TestTempFileManager
+```
+
+There are no automated tests for the full simulation — student usage is the primary validation path.
+
+## Architecture
+
+### C++ / Geant4 layer (`src/`, `include/`)
+
+The simulation is a standard Geant4 application derived from example B4a. The key extension is that geometry is driven externally via `GeometryDescriptor` rather than hardcoded:
+
+- **`GeometryDescriptor`** (`include/GeometryDescriptor.hh`) — the central geometry object. Holds a list of `Layer` objects, each of which contains `Sensor` objects after construction. Sensors accumulate deposited energy during a run. Fully pickle-able via `__getstate__`/`__setstate__`.
+- **`Layer`** — describes one slab: material (NIST name), thickness (cm), active/passive, and an `nx × ny` sensor grid.
+- **`Sensor`** — stores position, size, and `mutable energy` (reset between events via `GeometryDescriptor::resetSensorEnergies()`).
+- **`DetectorConstruction`** (`src/DetectorConstruction.cc`) — reads `GeometryDescriptor` and builds Geant4 volumes. Uses `G4PVParameterised` + `LayerParametrisation` for the sensor grid. Active sensors have their `G4VPhysicalVolume*` assigned back into the `Layer`, enabling lookup in `SteppingAction`.
+- **`SteppingAction`** — on each step, maps the physical volume back to a `Sensor` via `GeometryDescriptor::getSensorByVolume()` and accumulates energy.
+- **`RunAction`** — writes a ROOT ntuple named `"Hits"` with per-event scalars (`true_energy`, `total_dep_energy`, `N_layers`, ...) and per-sensor arrays (`sensor_energy`, `sensor_x/y/z`, `sensor_dx/dy/dz`, `sensor_layer`, `sensor_copy_number`).
+- **`G4System`** (`include/G4System.hh`) — owns the Geant4 run manager lifetime. `init(GeometryDescriptor&, seed)` sets everything up; `run_batch(...)` fires events to a ROOT file. One `G4System` per process — instantiated inside the subprocess (`G4Calo_exec.py`) to avoid Geant4 singleton issues.
+
+### pybind11 bindings (`bind/bindings.cpp`)
+
+Exposes `Sensor`, `Layer`, `GeometryDescriptor`, and `G4System` to Python as the `minicalo` module.
+
+### Python layer (`bind/`)
+
+- **`G4Calo.py`** — the public student API. `run_batch()` parallelises events across CPU cores using `ThreadPoolExecutor`; each worker subprocess calls `G4Calo_exec.py`, which instantiates a fresh `G4System` to avoid Geant4 singleton issues. Results are written as temporary ROOT files in `/dev/shm` (fallback: `/tmp`), read back with `uproot`/`awkward`, and merged into a `MiniFrame`. `display_event()` runs a single event and renders a 3D Plotly figure.
+- **`G4Calo_exec.py`** — the worker subprocess entry point. Reads a pickled `GeometryDescriptor` + parameters, runs the simulation, writes a ROOT file, and returns the path. Must be on `$PATH` as an executable.
+- **`minicalo_tools.py`** — `TempFileManager`: context manager for `/dev/shm`-backed pickle IPC files between the main process and worker subprocesses.
+- **`minipandas.py`** — `MiniFrame`: a minimal NumPy-backed dataframe. Supports scalar columns `(N,)` and fixed-size vector columns `(N, M)`. Converts to `pandas.DataFrame` via `to_pandas()` and serialises with `to_pickle()`/`read_pickle()`.
+
+### Subprocess isolation pattern
+
+Geant4 uses global singletons that cannot be re-initialised within a process. Therefore, each simulation batch (even in "single-core" mode) runs in a fresh subprocess spawned by `G4Calo_exec.py`. Communication uses pickle files via `TempFileManager`; ROOT output files are used for event data.
+
+### Coordinate conventions
+
+Geant4 internal units are mm; sensor positions stored in `Sensor` are in Geant4 internal units. The Plotly visualisation multiplies layer dimensions by 10 to convert from cm to mm and labels axes with `[mm]`.
+
+## Docker
+
+`docker/Dockerfile` builds a JupyterHub-based image with Geant4 v11.1.2 (multithreading disabled, `GEANT4_BUILD_MULTITHREADED=OFF`), the minicalo package, and ML dependencies (PyTorch, PyG). `docker/Dockerfile-cpu` is the CPU-only variant.

From 19b1ef125bbb0c97ea19f542cb45e3e95faa1335 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 11:37:39 +0200
Subject: [PATCH 02/33] add per-step kinematics ntuple ("Steps") to ROOT output

Adds a second ntuple alongside the existing "Hits" ntuple with one row
per Geant4 step. Records event_id, track_id, step_no, PDG code, and
pre/post position + kinetic energy for every step in the simulation.

Also extends run_batch() with return_steps=False; when True, returns
(hits_mf, steps_mf) instead of just hits_mf.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 bind/G4Calo.py        | 17 +++++++++++++----
 src/RunAction.cc      | 15 +++++++++++++++
 src/SteppingAction.cc | 32 +++++++++++++++++++++++++-------
 3 files changed, 53 insertions(+), 11 deletions(-)

diff --git a/bind/G4Calo.py b/bind/G4Calo.py
index 09a8951..eb93c4d 100644
--- a/bind/G4Calo.py
+++ b/bind/G4Calo.py
@@ -334,7 +334,8 @@ def run_batch(
         maxEnergy_GeV: float = -1.0,
         filename: str = "",
         no_mp: bool = False,
-        manual_seed : int = -1):
+        manual_seed : int = -1,
+        return_steps: bool = False):
     """
 Run a full Geant4 simulation batch with automatic parallelisation.
 
@@ -361,12 +362,17 @@ no_mp : bool, optional
     Disable multiprocessing (run single-threaded) for debugging.
 manual_seed : int, optional
     Optional random seed. If < 0, seeds are generated automatically.
+return_steps : bool, optional
+    If True, also return a MiniFrame of step-level data (one row per
+    Geant4 step across all events). Returns a tuple (hits, steps).
 
 Returns
 -------
-MiniFrame
-    Table-like structure with one row per event, containing both scalar
-    values and fixed-size sensor arrays.
+MiniFrame or tuple[MiniFrame, MiniFrame]
+    If return_steps is False (default): event-level MiniFrame with one
+    row per event. If return_steps is True: (hits, steps) where steps
+    has one row per Geant4 step with columns event_id, track_id,
+    step_no, pdg, pre_x/y/z, pre_E, post_x/y/z, post_E.
 
 Notes
 -----
@@ -463,6 +469,9 @@ Example
             if os.path.exists(f):
                 os.remove(f)
     print('G4Calo: concatenation finished after {:.2f} seconds'.format(sw.elapsed()))
+    if return_steps:
+        steps_df = _assemble_results_to_mini_df(rp, tree_name="Steps")
+        return df, steps_df
     return df
 
 def _fill_event(gd : GeometryDescriptor, 
diff --git a/src/RunAction.cc b/src/RunAction.cc
index 160f566..b19eed9 100644
--- a/src/RunAction.cc
+++ b/src/RunAction.cc
@@ -80,7 +80,22 @@ RunAction::RunAction()
   analysisManager->CreateNtupleIColumn("sensor_layer",hitLayer);
   analysisManager->CreateNtupleIColumn("sensor_copy_number",hitCopyNumber);
 
+  analysisManager->FinishNtuple();
 
+  // Steps ntuple (one row per step, ntuple id=1)
+  analysisManager->CreateNtuple("Steps", "Steps");
+  analysisManager->CreateNtupleIColumn("event_id");   // col 0
+  analysisManager->CreateNtupleIColumn("track_id");   // col 1
+  analysisManager->CreateNtupleIColumn("step_no");    // col 2
+  analysisManager->CreateNtupleIColumn("pdg");        // col 3
+  analysisManager->CreateNtupleDColumn("pre_x");      // col 4
+  analysisManager->CreateNtupleDColumn("pre_y");      // col 5
+  analysisManager->CreateNtupleDColumn("pre_z");      // col 6
+  analysisManager->CreateNtupleDColumn("pre_E");      // col 7
+  analysisManager->CreateNtupleDColumn("post_x");     // col 8
+  analysisManager->CreateNtupleDColumn("post_y");     // col 9
+  analysisManager->CreateNtupleDColumn("post_z");     // col 10
+  analysisManager->CreateNtupleDColumn("post_E");     // col 11
   analysisManager->FinishNtuple();
 }
 
diff --git a/src/SteppingAction.cc b/src/SteppingAction.cc
index ec80e5d..1f84d52 100644
--- a/src/SteppingAction.cc
+++ b/src/SteppingAction.cc
@@ -33,6 +33,9 @@
 
 #include "G4Step.hh"
 #include "G4RunManager.hh"
+#include "G4AnalysisManager.hh"
+#include "G4Track.hh"
+#include "G4ParticleDefinition.hh"
 
 using namespace B4;
 
@@ -68,16 +71,31 @@ void SteppingAction::UserSteppingAction(const G4Step* step)
 
   
   auto sensor = DetectorConstruction::getDetectorConstruction()->getGeometryDescriptor()->getSensorByVolume(volume);
-  if(sensor == nullptr){
-    //can simply be not an active volume, so no need to throw an error
-    //G4cout << "Sensor not found in" << volume->GetName() << G4endl; //DEBUG
-    return;
+  if(sensor != nullptr){
+    //G4cout << "Sensor found in " << volume->GetName() << " with copy number " << volume->GetCopyNo()<< G4endl; //DEBUG
+    sensor->energy += edep;
   }
-  //G4cout << "Sensor found in " << volume->GetName() << " with copy number " << volume->GetCopyNo()<< G4endl; //DEBUG
-  sensor->energy += edep;
-  //find sensor by volume copy number
 
+  // Record step kinematics for every step
+  auto analysisManager = G4AnalysisManager::Instance();
+  auto pre   = step->GetPreStepPoint();
+  auto post  = step->GetPostStepPoint();
+  auto track = step->GetTrack();
+  int evtId  = G4RunManager::GetRunManager()->GetCurrentEvent()->GetEventID();
 
+  analysisManager->FillNtupleIColumn(1, 0, evtId);
+  analysisManager->FillNtupleIColumn(1, 1, track->GetTrackID());
+  analysisManager->FillNtupleIColumn(1, 2, track->GetCurrentStepNumber());
+  analysisManager->FillNtupleIColumn(1, 3, track->GetDefinition()->GetPDGEncoding());
+  analysisManager->FillNtupleDColumn(1, 4, pre->GetPosition().x());
+  analysisManager->FillNtupleDColumn(1, 5, pre->GetPosition().y());
+  analysisManager->FillNtupleDColumn(1, 6, pre->GetPosition().z());
+  analysisManager->FillNtupleDColumn(1, 7, pre->GetKineticEnergy());
+  analysisManager->FillNtupleDColumn(1, 8, post->GetPosition().x());
+  analysisManager->FillNtupleDColumn(1, 9, post->GetPosition().y());
+  analysisManager->FillNtupleDColumn(1, 10, post->GetPosition().z());
+  analysisManager->FillNtupleDColumn(1, 11, post->GetKineticEnergy());
+  analysisManager->AddNtupleRow(1);
 }
 
 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

From 4bc94278d85fef259194104b3737a25c758c908a Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 11:47:51 +0200
Subject: [PATCH 03/33] fix Docker build: initialise pybind11 submodule before
 cmake

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 docker/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index aed03b6..8fe7345 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -94,6 +94,7 @@ ARG USER
 ADD minicalosim /root/minicalosim
 
 RUN cd  /root/minicalosim && git checkout $COMMIT && \
+    git submodule update --init && \
     mkdir -p build && cd build && rm -rf * && cmake ../ && make -j4
 
 

From 0c3f68d0cfb20b2e597e6f467868a58ae62ba68e Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 12:30:47 +0200
Subject: [PATCH 04/33] change container entrypoint from start-notebook.sh to
 bash

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 docker/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 8fe7345..06ff5bb 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -128,5 +128,5 @@ RUN rm -rf /root/minicalosim
 RUN pip3 install pyarrow fastparquet
 
 USER ${NB_UID}
-CMD ["start-notebook.sh"]
+CMD ["bash"]
 

From aaf0b33413f4d1b47f3192c93253f9265d68b2ed Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 12:38:52 +0200
Subject: [PATCH 05/33] add minimal Docker image (no CUDA, no Jupyter,
 batch-only Geant4)

Dockerfile-mini builds a lightweight image with only what's needed to
run the bind/ examples: Geant4 v11.1.2 (batch mode, no visualization),
Python 3.10, and numpy/pandas/uproot/awkward/plotly/ipython.
Examples are copied to /examples which is also the working directory.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 docker/Dockerfile-mini | 67 ++++++++++++++++++++++++++++++++++++++
 docker/build_mini.sh   | 74 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 141 insertions(+)
 create mode 100644 docker/Dockerfile-mini
 create mode 100755 docker/build_mini.sh

diff --git a/docker/Dockerfile-mini b/docker/Dockerfile-mini
new file mode 100644
index 0000000..756d509
--- /dev/null
+++ b/docker/Dockerfile-mini
@@ -0,0 +1,67 @@
+FROM ubuntu:22.04
+
+SHELL ["/bin/bash", "-c"]
+
+USER root
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Build tools + minimal Python
+RUN apt-get update -y && apt-get install -y \
+    python3 python3-dev python3-pip \
+    cmake g++ gcc binutils \
+    libssl-dev wget git \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN python3 -m pip install --upgrade pip && \
+    python3 -m pip install numpy pandas uproot awkward plotly ipython && \
+    ln -sf /usr/bin/python3 /usr/bin/python
+
+# Geant4 v11.1.2 — batch mode only (no visualization, no multithreading)
+RUN wget -q https://gitlab.cern.ch/geant4/geant4/-/archive/v11.1.2/geant4-v11.1.2.tar.gz && \
+    tar -xzf geant4-v11.1.2.tar.gz -C /tmp && \
+    rm geant4-v11.1.2.tar.gz && \
+    mkdir /tmp/geant4-v11.1.2-build && \
+    cmake \
+        -S /tmp/geant4-v11.1.2 \
+        -B /tmp/geant4-v11.1.2-build \
+        -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \
+        -DCMAKE_RULE_MESSAGES=OFF \
+        -DGEANT4_INSTALL_DATA=ON \
+        -DGEANT4_BUILD_MULTITHREADED=OFF \
+        -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
+        > /dev/null && \
+    cmake --build /tmp/geant4-v11.1.2-build --parallel $(nproc) > /dev/null && \
+    cmake --install /tmp/geant4-v11.1.2-build > /dev/null && \
+    rm -rf /tmp/geant4-v11.1.2 /tmp/geant4-v11.1.2-build
+
+ENV LD_LIBRARY_PATH="/opt/geant4-v11.1.2/lib:${LD_LIBRARY_PATH}"
+
+# Build minicalo
+ARG BUILD_DATE
+ARG COMMIT
+ARG USER
+LABEL org.label-schema.build-date=$BUILD_DATE
+
+ADD minicalosim /root/minicalosim
+
+RUN cd /root/minicalosim && git checkout $COMMIT && \
+    git submodule update --init && \
+    cmake \
+        -S . -B build \
+        -DWITH_GEANT4_UIVIS=OFF \
+        > /dev/null && \
+    cmake --build build --parallel $(nproc) && \
+    cp build/minicalo*.so /usr/local/lib/python3.10/dist-packages/
+
+RUN cp /root/minicalosim/bind/G4Calo.py \
+       /root/minicalosim/bind/minicalo_tools.py \
+       /root/minicalosim/bind/minipandas.py \
+       /usr/local/lib/python3.10/dist-packages/ && \
+    install -m 755 /root/minicalosim/bind/G4Calo_exec.py /usr/local/bin/G4Calo_exec.py
+
+# Copy examples
+RUN cp -r /root/minicalosim/bind /examples && \
+    rm -rf /root/minicalosim
+
+WORKDIR /examples
+CMD ["bash"]
diff --git a/docker/build_mini.sh b/docker/build_mini.sh
new file mode 100755
index 0000000..3cd5f08
--- /dev/null
+++ b/docker/build_mini.sh
@@ -0,0 +1,74 @@
+#!/usr/bin/bash
+
+if [ -n "$1" ]; then
+    if [ "$1" == "--no-cache" ]; then
+        FORCE_NO_CACHE="--no-cache"
+        COMMIT=$(git rev-parse --short HEAD)
+    else
+        COMMIT=$1
+        if ! git cat-file -e $COMMIT^{commit} 2>/dev/null; then
+            echo "ERROR: Commit $COMMIT not found in local repository."
+            exit 1
+        fi
+    fi
+else
+    COMMIT=$(git rev-parse --short HEAD)
+fi
+
+if [ "$COMMIT" == "$(git rev-parse --short HEAD)" ]; then
+    if [ -n "$(git status --porcelain)" ]; then
+        echo "WARNING: You are building the latest commit ${COMMIT}, but you have uncommitted changes."
+        echo "         This means that the image will not be reproducible."
+        echo "         If you want to build the latest commit, please commit your changes first."
+        read -p "Do you want to continue anyway? [y/N] " -n 1 -r
+        echo
+        if [[ ! $REPLY =~ ^[Yy]$ ]]; then
+            exit 1
+        fi
+    fi
+fi
+
+check_remote_commit_exists() {
+    local url="$1"
+    local commit="$2"
+    local tmpdir
+    tmpdir="$(mktemp -d)"
+    trap 'rm -rf "$tmpdir"' RETURN
+    git -C "$tmpdir" init -q
+    git -C "$tmpdir" remote add origin "$url"
+    if git -C "$tmpdir" fetch --quiet --depth=1 origin "$commit" 2>/dev/null; then
+        echo "✅ Commit $commit exists on remote."
+        return 0
+    else
+        echo "❌ ERROR: Commit $commit not found on remote."
+        echo "Refs currently visible on remote:"
+        git ls-remote --heads --tags "$url"
+        return 1
+    fi
+}
+
+if ! check_remote_commit_exists https://github.com/jkiesele/minicalosim $COMMIT; then
+    echo "WARNING: Commit $COMMIT not found in remote repository."
+fi
+
+if [ "$2" == "--no-cache" ]; then
+    FORCE_NO_CACHE="--no-cache"
+fi
+
+cd "$(dirname "$0")"
+cd ../../
+echo "Building minicalosim-mini:$COMMIT"
+echo "Current working directory: $(pwd)"
+
+docker build $FORCE_NO_CACHE \
+    -t jkiesele/minicalosim-mini:$COMMIT \
+    --build-arg USER=$USER \
+    --build-arg BUILD_DATE="$(date)" \
+    --build-arg COMMIT=$COMMIT \
+    -f minicalosim/docker/Dockerfile-mini .
+
+echo "successfully built container jkiesele/minicalosim-mini:${COMMIT}"
+
+docker tag jkiesele/minicalosim-mini:$COMMIT jkiesele/minicalosim-mini:latest
+
+echo "also tagged as jkiesele/minicalosim-mini:latest"

From 03b615cd3abdf71fe68831b943a439a2253f00a8 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 12:57:38 +0200
Subject: [PATCH 06/33] fix LD_LIBRARY_PATH warning in Dockerfile-mini

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 docker/Dockerfile-mini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/Dockerfile-mini b/docker/Dockerfile-mini
index 756d509..f795d3c 100644
--- a/docker/Dockerfile-mini
+++ b/docker/Dockerfile-mini
@@ -34,7 +34,7 @@ RUN wget -q https://gitlab.cern.ch/geant4/geant4/-/archive/v11.1.2/geant4-v11.1.
     cmake --install /tmp/geant4-v11.1.2-build > /dev/null && \
     rm -rf /tmp/geant4-v11.1.2 /tmp/geant4-v11.1.2-build
 
-ENV LD_LIBRARY_PATH="/opt/geant4-v11.1.2/lib:${LD_LIBRARY_PATH}"
+ENV LD_LIBRARY_PATH="/opt/geant4-v11.1.2/lib"
 
 # Build minicalo
 ARG BUILD_DATE

From 7a62a46fe6e92441165530f0b412e477f074a0c8 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 13:59:01 +0200
Subject: [PATCH 07/33] add run_pbwo4.py and include examples dir in both
 Docker images

run_pbwo4.py simulates 10 events in a single 20cm G4_PbWO4 layer
(10x10 sensor grid, 1 GeV e-) and saves results as a pickle next to
the script. Both images now expose /examples containing all bind/ files.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 bind/run_pbwo4.py | 14 ++++++++++++++
 docker/Dockerfile |  2 ++
 2 files changed, 16 insertions(+)
 create mode 100644 bind/run_pbwo4.py

diff --git a/bind/run_pbwo4.py b/bind/run_pbwo4.py
new file mode 100644
index 0000000..5eb80e4
--- /dev/null
+++ b/bind/run_pbwo4.py
@@ -0,0 +1,14 @@
+import os
+from G4Calo import run_batch
+from minicalo import GeometryDescriptor
+
+output_dir = os.path.dirname(os.path.abspath(__file__))
+
+gd = GeometryDescriptor()
+gd.addLayer(20.0, "G4_PbWO4", True, 10, 10)
+
+df = run_batch(gd, 10, "e-", 1.0)
+
+out = os.path.join(output_dir, "pbwo4_10events.pkl")
+df.to_pickle(out)
+print(f"Saved {len(df)} events to {out}")
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 06ff5bb..843f2fe 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -102,6 +102,8 @@ RUN cp /root/minicalosim/build/minicalo* /root/minicalosim/bind/G4Calo.py /root/
 
 RUN cp /root/minicalosim/bind/G4Calo_exec.py /usr/local/bin/
 
+RUN cp -r /root/minicalosim/bind /examples
+
 RUN cp /root/minicalosim/docker/start-notebook.py /usr/local/bin/
 RUN cp /root/minicalosim/docker/start-notebook.sh /usr/local/bin/
 RUN cp /root/minicalosim/docker/start-singleuser.py /usr/local/bin/

From 5f01ab6d35573286603f9015a753a84061c53f02 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 14:18:05 +0200
Subject: [PATCH 08/33] save hits and steps to separate pickles in run_pbwo4.py

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 bind/run_pbwo4.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/bind/run_pbwo4.py b/bind/run_pbwo4.py
index 5eb80e4..ce7218e 100644
--- a/bind/run_pbwo4.py
+++ b/bind/run_pbwo4.py
@@ -7,8 +7,11 @@ output_dir = os.path.dirname(os.path.abspath(__file__))
 gd = GeometryDescriptor()
 gd.addLayer(20.0, "G4_PbWO4", True, 10, 10)
 
-df = run_batch(gd, 10, "e-", 1.0)
+hits, steps = run_batch(gd, 10, "e-", 1.0, return_steps=True)
 
-out = os.path.join(output_dir, "pbwo4_10events.pkl")
-df.to_pickle(out)
-print(f"Saved {len(df)} events to {out}")
+hits_out  = os.path.join(output_dir, "pbwo4_10events_hits.pkl")
+steps_out = os.path.join(output_dir, "pbwo4_10events_steps.pkl")
+hits.to_pickle(hits_out)
+steps.to_pickle(steps_out)
+print(f"Saved {len(hits)} events to {hits_out}")
+print(f"Saved {len(steps)} steps  to {steps_out}")

From df3faa841ca819cd53117f9254204d99f647d270 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 14:18:40 +0200
Subject: [PATCH 09/33] assemble steps inside try block to ensure temp file
 cleanup

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 bind/G4Calo.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/bind/G4Calo.py b/bind/G4Calo.py
index eb93c4d..e59c21a 100644
--- a/bind/G4Calo.py
+++ b/bind/G4Calo.py
@@ -462,15 +462,17 @@ Example
     sw.reset()
     sw.start()
     df = None
+    steps_df = None
     try:
         df = _assemble_results_to_mini_df(rp)
-    finally: #make sure to delete temp files
+        if return_steps:
+            steps_df = _assemble_results_to_mini_df(rp, tree_name="Steps")
+    finally:
         for f in tmpfile:
             if os.path.exists(f):
                 os.remove(f)
     print('G4Calo: concatenation finished after {:.2f} seconds'.format(sw.elapsed()))
     if return_steps:
-        steps_df = _assemble_results_to_mini_df(rp, tree_name="Steps")
         return df, steps_df
     return df
 

From f9a7f2d1f14ffad1a289323e9fb386905bbc2c40 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 15:55:25 +0200
Subject: [PATCH 10/33] add Geant4 source as shallow submodule (lib/geant4)

Tracks HEAD of https://github.com/Geant4/geant4.git at depth 1 for
reference browsing. shallow=true ensures others also get a shallow clone.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .gitmodules | 4 ++++
 lib/geant4  | 1 +
 2 files changed, 5 insertions(+)
 create mode 160000 lib/geant4

diff --git a/.gitmodules b/.gitmodules
index f7047fb..50e41c1 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -2,3 +2,7 @@
 	path = lib/pybind11
 	url = https://github.com/pybind/pybind11
 	branch = stable
+[submodule "lib/geant4"]
+	path = lib/geant4
+	url = https://github.com/Geant4/geant4.git
+	shallow = true
diff --git a/lib/geant4 b/lib/geant4
new file mode 160000
index 0000000..41f2dd7
--- /dev/null
+++ b/lib/geant4
@@ -0,0 +1 @@
+Subproject commit 41f2dd79968018de4efb966f2546970b30c4af78

From 4ffb2f78b8f8ad1fb09778102a13372212932ce1 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 16:07:17 +0200
Subject: [PATCH 11/33] extend Steps ntuple and switch Docker to Geant4
 submodule source

Add 15 new columns to the Steps ntuple: edep, step_length, parent_id,
process name, layer_id, material, pre-step momentum direction, and
B/E field components (in T and V/m) at the pre-step point.

Replace wget Geant4 tarball download in all three Dockerfiles with
ADD of the lib/geant4 submodule source; narrow submodule init to
lib/pybind11 only so builds no longer require network access for Geant4.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 docker/Dockerfile      | 34 ++++++++++++-----------
 docker/Dockerfile-cpu  | 35 +++++++++++++-----------
 docker/Dockerfile-mini | 22 +++++++--------
 src/RunAction.cc       | 17 +++++++++++-
 src/SteppingAction.cc  | 61 ++++++++++++++++++++++++++++++++++++++++++
 5 files changed, 124 insertions(+), 45 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 843f2fe..d9eace4 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -50,22 +50,24 @@ RUN mkdir dawn-source \
     && make clean && make guiclean && make && make install \
     && cd - && rm -rf "dawn-source"
 
-## main package
+## main package — build Geant4 from submodule source
+ADD minicalosim/lib/geant4 /tmp/geant4-src
 
-RUN cd && wget -q https://gitlab.cern.ch/geant4/geant4/-/archive/v11.1.2/geant4-v11.1.2.tar.gz && \
-    tar -xzf geant4-v11.1.2.tar.gz -C /tmp && \    
-    mkdir /tmp/geant4-v11.1.2-build && \
-    cd /tmp/geant4-v11.1.2-build && \
-    cmake -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 -DCMAKE_RULE_MESSAGES=OFF -DGEANT4_INSTALL_DATA=ON \
-    -DGEANT4_USE_GDML=ON -DGEANT4_USE_OPENGL_X11=ON \
-             -DGEANT4_BUILD_MULTITHREADED=OFF \
-             -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
-    -DGEANT4_USE_RAYTRACER_X11=ON /tmp/geant4-v11.1.2 >/dev/null && \
-    make -j24 >/dev/null && \
-    make install >/dev/null
-
-RUN rm -rf /tmp/geant4-v11.1.2 && \
-    rm -rf /tmp/geant4-v11.1.2-build
+RUN cmake \
+        -S /tmp/geant4-src \
+        -B /tmp/geant4-build \
+        -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \
+        -DCMAKE_RULE_MESSAGES=OFF \
+        -DGEANT4_INSTALL_DATA=ON \
+        -DGEANT4_USE_GDML=ON \
+        -DGEANT4_USE_OPENGL_X11=ON \
+        -DGEANT4_BUILD_MULTITHREADED=OFF \
+        -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
+        -DGEANT4_USE_RAYTRACER_X11=ON \
+        >/dev/null && \
+    cmake --build /tmp/geant4-build --parallel $(nproc) >/dev/null && \
+    cmake --install /tmp/geant4-build >/dev/null && \
+    rm -rf /tmp/geant4-src /tmp/geant4-build
 
 
 RUN python3 -m pip install geant4-pybind
@@ -94,7 +96,7 @@ ARG USER
 ADD minicalosim /root/minicalosim
 
 RUN cd  /root/minicalosim && git checkout $COMMIT && \
-    git submodule update --init && \
+    git submodule update --init lib/pybind11 && \
     mkdir -p build && cd build && rm -rf * && cmake ../ && make -j4
 
 
diff --git a/docker/Dockerfile-cpu b/docker/Dockerfile-cpu
index 62c7f4b..b6d00ed 100644
--- a/docker/Dockerfile-cpu
+++ b/docker/Dockerfile-cpu
@@ -50,22 +50,24 @@ RUN mkdir dawn-source \
     && make clean && make guiclean && make && make install \
     && cd - && rm -rf "dawn-source"
 
-## main package
+## main package — build Geant4 from submodule source
+ADD minicalosim/lib/geant4 /tmp/geant4-src
 
-RUN cd && wget -q https://gitlab.cern.ch/geant4/geant4/-/archive/v11.1.2/geant4-v11.1.2.tar.gz && \
-    tar -xzf geant4-v11.1.2.tar.gz -C /tmp && \    
-    mkdir /tmp/geant4-v11.1.2-build && \
-    cd /tmp/geant4-v11.1.2-build && \
-    cmake -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 -DCMAKE_RULE_MESSAGES=OFF -DGEANT4_INSTALL_DATA=ON \
-    -DGEANT4_USE_GDML=ON -DGEANT4_USE_OPENGL_X11=ON \
-             -DGEANT4_BUILD_MULTITHREADED=ON \
-             -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
-    -DGEANT4_USE_RAYTRACER_X11=ON /tmp/geant4-v11.1.2 >/dev/null && \
-    make -j4 >/dev/null && \
-    make install >/dev/null
-
-RUN rm -rf /tmp/geant4-v11.1.2 && \
-    rm -rf /tmp/geant4-v11.1.2-build
+RUN cmake \
+        -S /tmp/geant4-src \
+        -B /tmp/geant4-build \
+        -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \
+        -DCMAKE_RULE_MESSAGES=OFF \
+        -DGEANT4_INSTALL_DATA=ON \
+        -DGEANT4_USE_GDML=ON \
+        -DGEANT4_USE_OPENGL_X11=ON \
+        -DGEANT4_BUILD_MULTITHREADED=ON \
+        -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
+        -DGEANT4_USE_RAYTRACER_X11=ON \
+        >/dev/null && \
+    cmake --build /tmp/geant4-build --parallel $(nproc) >/dev/null && \
+    cmake --install /tmp/geant4-build >/dev/null && \
+    rm -rf /tmp/geant4-src /tmp/geant4-build
 
 
 RUN python3 -m pip install geant4-pybind
@@ -94,7 +96,8 @@ ARG USER
 ADD minicalosim /root/minicalosim
 
 RUN cd  /root/minicalosim && git checkout $COMMIT && \
-    mkdir -p build && cd build && rm -rf * && cmake ../ && make -j4 &&\  
+    git submodule update --init lib/pybind11 && \
+    mkdir -p build && cd build && rm -rf * && cmake ../ && make -j$(nproc) &&\
     cp minicalo* ../bind/G4Calo.py /usr/local/lib/python3.8/dist-packages/
 
 
diff --git a/docker/Dockerfile-mini b/docker/Dockerfile-mini
index f795d3c..941e968 100644
--- a/docker/Dockerfile-mini
+++ b/docker/Dockerfile-mini
@@ -16,23 +16,21 @@ RUN python3 -m pip install --upgrade pip && \
     python3 -m pip install numpy pandas uproot awkward plotly ipython && \
     ln -sf /usr/bin/python3 /usr/bin/python
 
-# Geant4 v11.1.2 — batch mode only (no visualization, no multithreading)
-RUN wget -q https://gitlab.cern.ch/geant4/geant4/-/archive/v11.1.2/geant4-v11.1.2.tar.gz && \
-    tar -xzf geant4-v11.1.2.tar.gz -C /tmp && \
-    rm geant4-v11.1.2.tar.gz && \
-    mkdir /tmp/geant4-v11.1.2-build && \
-    cmake \
-        -S /tmp/geant4-v11.1.2 \
-        -B /tmp/geant4-v11.1.2-build \
+# Geant4 — build from submodule source (batch mode only, no visualization, no multithreading)
+ADD minicalosim/lib/geant4 /tmp/geant4-src
+
+RUN cmake \
+        -S /tmp/geant4-src \
+        -B /tmp/geant4-build \
         -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \
         -DCMAKE_RULE_MESSAGES=OFF \
         -DGEANT4_INSTALL_DATA=ON \
         -DGEANT4_BUILD_MULTITHREADED=OFF \
         -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
         > /dev/null && \
-    cmake --build /tmp/geant4-v11.1.2-build --parallel $(nproc) > /dev/null && \
-    cmake --install /tmp/geant4-v11.1.2-build > /dev/null && \
-    rm -rf /tmp/geant4-v11.1.2 /tmp/geant4-v11.1.2-build
+    cmake --build /tmp/geant4-build --parallel $(nproc) > /dev/null && \
+    cmake --install /tmp/geant4-build > /dev/null && \
+    rm -rf /tmp/geant4-src /tmp/geant4-build
 
 ENV LD_LIBRARY_PATH="/opt/geant4-v11.1.2/lib"
 
@@ -45,7 +43,7 @@ LABEL org.label-schema.build-date=$BUILD_DATE
 ADD minicalosim /root/minicalosim
 
 RUN cd /root/minicalosim && git checkout $COMMIT && \
-    git submodule update --init && \
+    git submodule update --init lib/pybind11 && \
     cmake \
         -S . -B build \
         -DWITH_GEANT4_UIVIS=OFF \
diff --git a/src/RunAction.cc b/src/RunAction.cc
index b19eed9..c14ef49 100644
--- a/src/RunAction.cc
+++ b/src/RunAction.cc
@@ -95,7 +95,22 @@ RunAction::RunAction()
   analysisManager->CreateNtupleDColumn("post_x");     // col 8
   analysisManager->CreateNtupleDColumn("post_y");     // col 9
   analysisManager->CreateNtupleDColumn("post_z");     // col 10
-  analysisManager->CreateNtupleDColumn("post_E");     // col 11
+  analysisManager->CreateNtupleDColumn("post_E");      // col 11
+  analysisManager->CreateNtupleDColumn("edep");        // col 12 [MeV]
+  analysisManager->CreateNtupleDColumn("step_length"); // col 13 [mm]
+  analysisManager->CreateNtupleIColumn("parent_id");   // col 14
+  analysisManager->CreateNtupleSColumn("process");     // col 15
+  analysisManager->CreateNtupleIColumn("layer_id");    // col 16  (-1 = outside all layers)
+  analysisManager->CreateNtupleSColumn("material");    // col 17
+  analysisManager->CreateNtupleDColumn("pre_dx");      // col 18
+  analysisManager->CreateNtupleDColumn("pre_dy");      // col 19
+  analysisManager->CreateNtupleDColumn("pre_dz");      // col 20
+  analysisManager->CreateNtupleDColumn("Bx");          // col 21 [T]
+  analysisManager->CreateNtupleDColumn("By");          // col 22 [T]
+  analysisManager->CreateNtupleDColumn("Bz");          // col 23 [T]
+  analysisManager->CreateNtupleDColumn("Ex");          // col 24 [V/m]
+  analysisManager->CreateNtupleDColumn("Ey");          // col 25 [V/m]
+  analysisManager->CreateNtupleDColumn("Ez");          // col 26 [V/m]
   analysisManager->FinishNtuple();
 }
 
diff --git a/src/SteppingAction.cc b/src/SteppingAction.cc
index 1f84d52..964c28c 100644
--- a/src/SteppingAction.cc
+++ b/src/SteppingAction.cc
@@ -36,6 +36,10 @@
 #include "G4AnalysisManager.hh"
 #include "G4Track.hh"
 #include "G4ParticleDefinition.hh"
+#include "G4TransportationManager.hh"
+#include "G4FieldManager.hh"
+#include "G4Field.hh"
+#include "G4SystemOfUnits.hh"
 
 using namespace B4;
 
@@ -95,6 +99,63 @@ void SteppingAction::UserSteppingAction(const G4Step* step)
   analysisManager->FillNtupleDColumn(1, 9, post->GetPosition().y());
   analysisManager->FillNtupleDColumn(1, 10, post->GetPosition().z());
   analysisManager->FillNtupleDColumn(1, 11, post->GetKineticEnergy());
+
+  // A: energy deposited in medium at this step (≠ pre_E - post_E when secondaries are created)
+  analysisManager->FillNtupleDColumn(1, 12, edep);
+
+  // B: geometric step length
+  analysisManager->FillNtupleDColumn(1, 13, step->GetStepLength());
+
+  // C: parent track ID (0 for primary)
+  analysisManager->FillNtupleIColumn(1, 14, track->GetParentID());
+
+  // D: process that ended this step
+  G4String processName = "";
+  const auto* postProc = post->GetProcessDefinedStep();
+  if (postProc) processName = postProc->GetProcessName();
+  analysisManager->FillNtupleSColumn(1, 15, processName);
+
+  // E: layer index (-1 if outside all layers) and material name at pre-step point
+  int layerId = -1;
+  const auto& layers = cw->getLayers();
+  for (int i = 0; i < (int)layers.size(); i++) {
+    if (layers[i].physicalVolume == volume) { layerId = i; break; }
+  }
+  G4String materialName = pre->GetMaterial() ? pre->GetMaterial()->GetName() : "";
+  analysisManager->FillNtupleIColumn(1, 16, layerId);
+  analysisManager->FillNtupleSColumn(1, 17, materialName);
+
+  // F: pre-step momentum direction (unit vector)
+  const auto dir = pre->GetMomentumDirection();
+  analysisManager->FillNtupleDColumn(1, 18, dir.x());
+  analysisManager->FillNtupleDColumn(1, 19, dir.y());
+  analysisManager->FillNtupleDColumn(1, 20, dir.z());
+
+  // Field: B [T] and E [V/m] at pre-step position; zero if no field is registered
+  G4double Bx=0, By=0, Bz=0, Ex=0, Ey=0, Ez=0;
+  const auto* fm = G4TransportationManager::GetTransportationManager()->GetFieldManager();
+  if (fm && fm->DoesFieldExist()) {
+    const G4Field* field = fm->GetDetectorField();
+    if (field) {
+      const G4double point[4] = {pre->GetPosition().x(), pre->GetPosition().y(),
+                                  pre->GetPosition().z(), pre->GetGlobalTime()};
+      G4double fieldVal[6] = {0,0,0,0,0,0};
+      field->GetFieldValue(point, fieldVal);
+      Bx = fieldVal[0] / tesla;
+      By = fieldVal[1] / tesla;
+      Bz = fieldVal[2] / tesla;
+      Ex = fieldVal[3] / (volt/m);
+      Ey = fieldVal[4] / (volt/m);
+      Ez = fieldVal[5] / (volt/m);
+    }
+  }
+  analysisManager->FillNtupleDColumn(1, 21, Bx);
+  analysisManager->FillNtupleDColumn(1, 22, By);
+  analysisManager->FillNtupleDColumn(1, 23, Bz);
+  analysisManager->FillNtupleDColumn(1, 24, Ex);
+  analysisManager->FillNtupleDColumn(1, 25, Ey);
+  analysisManager->FillNtupleDColumn(1, 26, Ez);
+
   analysisManager->AddNtupleRow(1);
 }
 

From f5c832fd44c9d5082c8e6904b8aaac2aa69676ba Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 16:09:55 +0200
Subject: [PATCH 12/33] fix Geant4 cmake git-dirty check when building from
 submodule ADD

The submodule leaves a .git *file* (not directory) pointing to
../../.git/modules/lib/geant4, which passes G4GitUtilities' guard
but causes a FATAL_ERROR when git status fails in the bare /tmp dir.
Remove .git before cmake so the guard fires and the check is skipped.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 docker/Dockerfile      | 3 ++-
 docker/Dockerfile-cpu  | 3 ++-
 docker/Dockerfile-mini | 3 ++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index d9eace4..3b91acf 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -53,7 +53,8 @@ RUN mkdir dawn-source \
 ## main package — build Geant4 from submodule source
 ADD minicalosim/lib/geant4 /tmp/geant4-src
 
-RUN cmake \
+RUN rm -f /tmp/geant4-src/.git && \
+    cmake \
         -S /tmp/geant4-src \
         -B /tmp/geant4-build \
         -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \
diff --git a/docker/Dockerfile-cpu b/docker/Dockerfile-cpu
index b6d00ed..2c60cf0 100644
--- a/docker/Dockerfile-cpu
+++ b/docker/Dockerfile-cpu
@@ -53,7 +53,8 @@ RUN mkdir dawn-source \
 ## main package — build Geant4 from submodule source
 ADD minicalosim/lib/geant4 /tmp/geant4-src
 
-RUN cmake \
+RUN rm -f /tmp/geant4-src/.git && \
+    cmake \
         -S /tmp/geant4-src \
         -B /tmp/geant4-build \
         -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \
diff --git a/docker/Dockerfile-mini b/docker/Dockerfile-mini
index 941e968..004314b 100644
--- a/docker/Dockerfile-mini
+++ b/docker/Dockerfile-mini
@@ -19,7 +19,8 @@ RUN python3 -m pip install --upgrade pip && \
 # Geant4 — build from submodule source (batch mode only, no visualization, no multithreading)
 ADD minicalosim/lib/geant4 /tmp/geant4-src
 
-RUN cmake \
+RUN rm -f /tmp/geant4-src/.git && \
+    cmake \
         -S /tmp/geant4-src \
         -B /tmp/geant4-build \
         -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \

From 5fc50bcefc012925ed1289a3d329b07a7001af38 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 8 Jun 2026 16:35:31 +0200
Subject: [PATCH 13/33] print commit hash on import; fix event_id offset in
 multi-core steps

G4Calo.py prints the commit at import time, resolved via a
minicalo_version.py file (baked in by Docker) or git rev-parse
from the file's directory as fallback.

event_id in the Steps ntuple restarts from 0 in each subprocess;
_assemble_results_to_mini_df now accepts per-file event_id_offsets
so IDs are globally unique after merging. run_batch passes cumulative
nevents as offsets when loading the Steps tree.

Dockerfiles write minicalo_version.py before copying Python files.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 bind/G4Calo.py         | 39 ++++++++++++++++++++++++++++++++++-----
 docker/Dockerfile      |  4 +++-
 docker/Dockerfile-cpu  |  3 ++-
 docker/Dockerfile-mini |  4 +++-
 4 files changed, 42 insertions(+), 8 deletions(-)

diff --git a/bind/G4Calo.py b/bind/G4Calo.py
index e59c21a..d3470d4 100644
--- a/bind/G4Calo.py
+++ b/bind/G4Calo.py
@@ -171,6 +171,27 @@ from IPython.display import Image, display
 from minipandas import MiniFrame
 
 
+def _get_commit():
+    try:
+        from minicalo_version import commit as _c
+        return _c
+    except ImportError:
+        pass
+    try:
+        r = subprocess.run(
+            ['git', 'rev-parse', '--short', 'HEAD'],
+            capture_output=True, text=True,
+            cwd=os.path.dirname(os.path.abspath(__file__))
+        )
+        if r.returncode == 0:
+            return r.stdout.strip()
+    except Exception:
+        pass
+    return 'unknown'
+
+print(f"miniCaloSim: commit {_get_commit()}")
+
+
 #### helpers #####
 
 class Stopwatch(object):
@@ -238,11 +259,14 @@ def _count_total_entries(root_paths, tree_name: str = "Hits") -> int:
             total += int(f[tree_name].num_entries)
     return total
 
-def _assemble_results_to_mini_df(root_paths, tree_name: str = "Hits"):
+def _assemble_results_to_mini_df(root_paths, tree_name: str = "Hits", event_id_offsets=None):
     """
     Returns:
       scalars: dict[col, np.ndarray]  # shape (N,)
       arrays:  dict[col, np.ndarray]  # shape (N, M[col])
+
+    event_id_offsets: optional list[int], one per file — added to the
+    'event_id' column so that IDs are globally unique across batches.
     """
     # 1) learn schema & sizes from first file
     scalar_cols, array_cols, array_sizes, dtypes_scalar, dtypes_array, _ = \
@@ -257,19 +281,22 @@ def _assemble_results_to_mini_df(root_paths, tree_name: str = "Hits"):
 
     # 4) fill by slices
     pos = 0
-    for p in root_paths:
+    for file_idx, p in enumerate(root_paths):
         with uproot.open(p) as f:
             arr = f[tree_name].arrays(library="ak")
         n = len(arr)
         sl = slice(pos, pos + n)
 
         for c in scalar_cols:
-            scalars[c][sl] = np.asarray(arr[c])
+            data = np.asarray(arr[c])
+            if c == 'event_id' and event_id_offsets is not None:
+                data = data + event_id_offsets[file_idx]
+            scalars[c][sl] = data
         for c in array_cols:
             arrays[c][sl, :] = ak.to_numpy(arr[c])  # (n, fixed_size)
 
         pos += n
-    
+
     #merge the dicts
     merged = {**scalars, **arrays}
     return MiniFrame(merged)
@@ -412,6 +439,7 @@ Example
     #print(f"Running {nEventsLastCore} events on last core")
     
     nevents = [nEventsPerCore if i < nCores - 1 else nEventsLastCore for i in range(nCores)]
+    event_id_offsets = [sum(nevents[:i]) for i in range(nCores)]
 
     if manual_seed >= 0:
         seed = manual_seed 
@@ -466,7 +494,8 @@ Example
     try:
         df = _assemble_results_to_mini_df(rp)
         if return_steps:
-            steps_df = _assemble_results_to_mini_df(rp, tree_name="Steps")
+            steps_df = _assemble_results_to_mini_df(rp, tree_name="Steps",
+                                                     event_id_offsets=event_id_offsets)
     finally:
         for f in tmpfile:
             if os.path.exists(f):
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 3b91acf..ef4a2a4 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -101,7 +101,9 @@ RUN cd  /root/minicalosim && git checkout $COMMIT && \
     mkdir -p build && cd build && rm -rf * && cmake ../ && make -j4
 
 
-RUN cp /root/minicalosim/build/minicalo* /root/minicalosim/bind/G4Calo.py /root/minicalosim/bind/minicalo_tools.py /root/minicalosim/bind/minipandas.py /usr/local/lib/python3.10/dist-packages/
+RUN echo "commit = '${COMMIT}'" > /root/minicalosim/bind/minicalo_version.py
+
+RUN cp /root/minicalosim/build/minicalo* /root/minicalosim/bind/G4Calo.py /root/minicalosim/bind/minicalo_tools.py /root/minicalosim/bind/minipandas.py /root/minicalosim/bind/minicalo_version.py /usr/local/lib/python3.10/dist-packages/
 
 RUN cp /root/minicalosim/bind/G4Calo_exec.py /usr/local/bin/
 
diff --git a/docker/Dockerfile-cpu b/docker/Dockerfile-cpu
index 2c60cf0..6ec54ca 100644
--- a/docker/Dockerfile-cpu
+++ b/docker/Dockerfile-cpu
@@ -99,7 +99,8 @@ ADD minicalosim /root/minicalosim
 RUN cd  /root/minicalosim && git checkout $COMMIT && \
     git submodule update --init lib/pybind11 && \
     mkdir -p build && cd build && rm -rf * && cmake ../ && make -j$(nproc) &&\
-    cp minicalo* ../bind/G4Calo.py /usr/local/lib/python3.8/dist-packages/
+    echo "commit = '${COMMIT}'" > ../bind/minicalo_version.py && \
+    cp minicalo* ../bind/G4Calo.py ../bind/minicalo_version.py /usr/local/lib/python3.8/dist-packages/
 
 
 
diff --git a/docker/Dockerfile-mini b/docker/Dockerfile-mini
index 004314b..7949860 100644
--- a/docker/Dockerfile-mini
+++ b/docker/Dockerfile-mini
@@ -52,9 +52,11 @@ RUN cd /root/minicalosim && git checkout $COMMIT && \
     cmake --build build --parallel $(nproc) && \
     cp build/minicalo*.so /usr/local/lib/python3.10/dist-packages/
 
-RUN cp /root/minicalosim/bind/G4Calo.py \
+RUN echo "commit = '${COMMIT}'" > /root/minicalosim/bind/minicalo_version.py && \
+    cp /root/minicalosim/bind/G4Calo.py \
        /root/minicalosim/bind/minicalo_tools.py \
        /root/minicalosim/bind/minipandas.py \
+       /root/minicalosim/bind/minicalo_version.py \
        /usr/local/lib/python3.10/dist-packages/ && \
     install -m 755 /root/minicalosim/bind/G4Calo_exec.py /usr/local/bin/G4Calo_exec.py
 

From 18de7dd3db6226c00497f1a42b7e44a354cde196 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Wed, 10 Jun 2026 08:20:27 +0200
Subject: [PATCH 14/33] limit Docker build parallelism to min(nproc, 16)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 docker/Dockerfile      | 4 ++--
 docker/Dockerfile-cpu  | 4 ++--
 docker/Dockerfile-mini | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index ef4a2a4..a59ee64 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -66,7 +66,7 @@ RUN rm -f /tmp/geant4-src/.git && \
         -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
         -DGEANT4_USE_RAYTRACER_X11=ON \
         >/dev/null && \
-    cmake --build /tmp/geant4-build --parallel $(nproc) >/dev/null && \
+    cmake --build /tmp/geant4-build --parallel $(( $(nproc) < 16 ? $(nproc) : 16 )) >/dev/null && \
     cmake --install /tmp/geant4-build >/dev/null && \
     rm -rf /tmp/geant4-src /tmp/geant4-build
 
@@ -98,7 +98,7 @@ ADD minicalosim /root/minicalosim
 
 RUN cd  /root/minicalosim && git checkout $COMMIT && \
     git submodule update --init lib/pybind11 && \
-    mkdir -p build && cd build && rm -rf * && cmake ../ && make -j4
+    mkdir -p build && cd build && rm -rf * && cmake ../ && make -j$(( $(nproc) < 16 ? $(nproc) : 16 ))
 
 
 RUN echo "commit = '${COMMIT}'" > /root/minicalosim/bind/minicalo_version.py
diff --git a/docker/Dockerfile-cpu b/docker/Dockerfile-cpu
index 6ec54ca..9f5d447 100644
--- a/docker/Dockerfile-cpu
+++ b/docker/Dockerfile-cpu
@@ -66,7 +66,7 @@ RUN rm -f /tmp/geant4-src/.git && \
         -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
         -DGEANT4_USE_RAYTRACER_X11=ON \
         >/dev/null && \
-    cmake --build /tmp/geant4-build --parallel $(nproc) >/dev/null && \
+    cmake --build /tmp/geant4-build --parallel $(( $(nproc) < 16 ? $(nproc) : 16 )) >/dev/null && \
     cmake --install /tmp/geant4-build >/dev/null && \
     rm -rf /tmp/geant4-src /tmp/geant4-build
 
@@ -98,7 +98,7 @@ ADD minicalosim /root/minicalosim
 
 RUN cd  /root/minicalosim && git checkout $COMMIT && \
     git submodule update --init lib/pybind11 && \
-    mkdir -p build && cd build && rm -rf * && cmake ../ && make -j$(nproc) &&\
+    mkdir -p build && cd build && rm -rf * && cmake ../ && make -j$(( $(nproc) < 16 ? $(nproc) : 16 )) &&\
     echo "commit = '${COMMIT}'" > ../bind/minicalo_version.py && \
     cp minicalo* ../bind/G4Calo.py ../bind/minicalo_version.py /usr/local/lib/python3.8/dist-packages/
 
diff --git a/docker/Dockerfile-mini b/docker/Dockerfile-mini
index 7949860..7a45b7c 100644
--- a/docker/Dockerfile-mini
+++ b/docker/Dockerfile-mini
@@ -29,7 +29,7 @@ RUN rm -f /tmp/geant4-src/.git && \
         -DGEANT4_BUILD_MULTITHREADED=OFF \
         -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
         > /dev/null && \
-    cmake --build /tmp/geant4-build --parallel $(nproc) > /dev/null && \
+    cmake --build /tmp/geant4-build --parallel $(( $(nproc) < 16 ? $(nproc) : 16 )) > /dev/null && \
     cmake --install /tmp/geant4-build > /dev/null && \
     rm -rf /tmp/geant4-src /tmp/geant4-build
 
@@ -49,7 +49,7 @@ RUN cd /root/minicalosim && git checkout $COMMIT && \
         -S . -B build \
         -DWITH_GEANT4_UIVIS=OFF \
         > /dev/null && \
-    cmake --build build --parallel $(nproc) && \
+    cmake --build build --parallel $(( $(nproc) < 16 ? $(nproc) : 16 )) && \
     cp build/minicalo*.so /usr/local/lib/python3.10/dist-packages/
 
 RUN echo "commit = '${COMMIT}'" > /root/minicalosim/bind/minicalo_version.py && \

From 01df646aa9ddc2877da07322ac9d8adb9bbb8291 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Wed, 10 Jun 2026 09:19:55 +0200
Subject: [PATCH 15/33] add run_pbwo4 C++ executable; fix missing std headers
 for Geant4 11.4

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 CMakeLists.txt                    |  3 +++
 include/PrimaryGeneratorAction.hh |  2 ++
 include/RunAction.hh              |  1 +
 run_pbwo4.cc                      | 36 +++++++++++++++++++++++++++++++
 4 files changed, 42 insertions(+)
 create mode 100644 run_pbwo4.cc

diff --git a/CMakeLists.txt b/CMakeLists.txt
index fb75b02..642a1a4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -58,6 +58,9 @@ target_link_libraries(minicalo PUBLIC ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
 add_executable(exampleB4a exampleB4a.cc ${sources} ${headers})
 target_link_libraries(exampleB4a ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
 
+add_executable(run_pbwo4 run_pbwo4.cc ${sources} ${headers})
+target_link_libraries(run_pbwo4 ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
+
 #----------------------------------------------------------------------------
 # Copy all scripts to the build directory, i.e. the directory in which we
 # build B4a. This is so that we can run the executable directly because it
diff --git a/include/PrimaryGeneratorAction.hh b/include/PrimaryGeneratorAction.hh
index 0366a7f..3cc9219 100644
--- a/include/PrimaryGeneratorAction.hh
+++ b/include/PrimaryGeneratorAction.hh
@@ -32,6 +32,8 @@
 
 #include "G4VUserPrimaryGeneratorAction.hh"
 #include "globals.hh"
+#include <vector>
+#include <string>
 
 class G4ParticleGun;
 class G4Event;
diff --git a/include/RunAction.hh b/include/RunAction.hh
index 6c89fc2..854bb55 100644
--- a/include/RunAction.hh
+++ b/include/RunAction.hh
@@ -32,6 +32,7 @@
 
 #include "G4UserRunAction.hh"
 #include "globals.hh"
+#include <vector>
 
 class G4Run;
 
diff --git a/run_pbwo4.cc b/run_pbwo4.cc
new file mode 100644
index 0000000..1754eb1
--- /dev/null
+++ b/run_pbwo4.cc
@@ -0,0 +1,36 @@
+#include "GeometryDescriptor.hh"
+#include "G4System.hh"
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+int main(int argc, char** argv) {
+    int nEvents = 10;
+
+    if (argc > 2) {
+        std::cerr << "Usage: run_pbwo4 [nEvents]" << std::endl;
+        return 1;
+    }
+    if (argc == 2) {
+        try {
+            nEvents = std::stoi(argv[1]);
+            if (nEvents <= 0) throw std::invalid_argument("must be positive");
+        } catch (const std::exception& e) {
+            std::cerr << "Invalid nEvents '" << argv[1] << "': " << e.what() << std::endl;
+            return 1;
+        }
+    }
+
+    std::string outfile = "pbwo4_" + std::to_string(nEvents) + "events_hits.root";
+
+    GeometryDescriptor gd;
+    gd.addLayer(20.0, "G4_PbWO4", true, 10, 10);
+
+    G4System g4;
+    g4.init(gd, -1);
+    g4.run_batch(nEvents, {"e-"}, 1.0, 1.0, outfile);
+
+    std::cout << "Saved " << nEvents << " events to " << outfile << std::endl;
+    return 0;
+}

From 718f9361f7af0d36035bcf7693076f9a5baf6820 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 11 Jun 2026 10:22:43 +0200
Subject: [PATCH 16/33] docs: archive parent_step_no design plan

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 docs/plan_parent_step_no.md | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 docs/plan_parent_step_no.md

diff --git a/docs/plan_parent_step_no.md b/docs/plan_parent_step_no.md
new file mode 100644
index 0000000..4198d59
--- /dev/null
+++ b/docs/plan_parent_step_no.md
@@ -0,0 +1,31 @@
+# Design: `parent_step_no` Column on Steps Ntuple
+
+## Problem
+
+The Steps ntuple records `parent_id` (which track created a secondary) but not *at which step* of the parent the secondary was born. Finding this after the fact requires a position join: match the secondary's first pre-step point against the parent's post-step points across ntuple rows.
+
+## Proposed solution
+
+Add a `parent_step_no` integer column to the Steps ntuple. Value is `-1` for the primary particle and the parent's step number for every step of any secondary.
+
+## Mechanism
+
+Use `G4VUserTrackInformation` to carry the parent step number forward from creation time to the secondary's tracking phase:
+
+1. **Tag at creation** — in `UserSteppingAction`, iterate `step->GetSecondaryInCurrentStep()` and attach a `TrackUserInfo(track->GetCurrentStepNumber())` object to each secondary via `const_cast<G4Track*>(sec)->SetUserInformation(...)`. Geant4 takes ownership and deletes it with the track.
+
+2. **Read at tracking** — when filling a Steps ntuple row, retrieve `dynamic_cast<TrackUserInfo*>(track->GetUserInformation())` and write `info->parentStepNo`, or `-1` if null (primary).
+
+## Files
+
+- `include/TrackUserInfo.hh` — new: minimal `G4VUserTrackInformation` subclass storing `int parentStepNo`
+- `src/RunAction.cc` — add column 27 `parent_step_no` (Integer) to ntuple 1 (`Steps`)
+- `src/SteppingAction.cc` — tag new secondaries; fill column 27
+
+## Note on `const_cast`
+
+`GetSecondaryInCurrentStep()` returns `const G4Track*`. The `const` is a conservative API choice, not a physics invariant. `G4VUserTrackInformation` is an explicit user-side side-channel; using `const_cast` here is standard Geant4 practice.
+
+## Superseded by
+
+This approach was superseded by the `Spawning` ntuple (branch `spawning-ntuple`), which avoids the per-row overhead and `const_cast` by pre-assigning track IDs in `G4SteppingManager` and writing a dedicated secondary-birth table.

From 9ea071813904e7629d33818469da70c93ce5daa4 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 11 Jun 2026 10:25:08 +0200
Subject: [PATCH 17/33] add Spawning ntuple recording secondary births per step

Each step that spawns secondaries now writes one row per secondary to a
new Spawning ntuple (event_id, parent_track_id, parent_step_no,
child_track_id). This enables direct shower-tree reconstruction without
position joins. Requires the companion Geant4 submodule change that
pre-assigns track IDs in ProcessSecondariesFromParticleChange.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 lib/geant4            |  2 +-
 src/RunAction.cc      |  8 ++++++++
 src/SteppingAction.cc | 12 ++++++++++++
 3 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/lib/geant4 b/lib/geant4
index 41f2dd7..e7827c9 160000
--- a/lib/geant4
+++ b/lib/geant4
@@ -1 +1 @@
-Subproject commit 41f2dd79968018de4efb966f2546970b30c4af78
+Subproject commit e7827c9b07aa6788f37e70658302945d6f129c70
diff --git a/src/RunAction.cc b/src/RunAction.cc
index c14ef49..d9d9afa 100644
--- a/src/RunAction.cc
+++ b/src/RunAction.cc
@@ -112,6 +112,14 @@ RunAction::RunAction()
   analysisManager->CreateNtupleDColumn("Ey");          // col 25 [V/m]
   analysisManager->CreateNtupleDColumn("Ez");          // col 26 [V/m]
   analysisManager->FinishNtuple();
+
+  // Spawning ntuple (one row per secondary born, ntuple id=2)
+  analysisManager->CreateNtuple("Spawning", "Spawning");
+  analysisManager->CreateNtupleIColumn("event_id");        // col 0
+  analysisManager->CreateNtupleIColumn("parent_track_id"); // col 1
+  analysisManager->CreateNtupleIColumn("parent_step_no");  // col 2
+  analysisManager->CreateNtupleIColumn("child_track_id");  // col 3
+  analysisManager->FinishNtuple();
 }
 
 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
diff --git a/src/SteppingAction.cc b/src/SteppingAction.cc
index 964c28c..4a6ac67 100644
--- a/src/SteppingAction.cc
+++ b/src/SteppingAction.cc
@@ -87,6 +87,18 @@ void SteppingAction::UserSteppingAction(const G4Step* step)
   auto track = step->GetTrack();
   int evtId  = G4RunManager::GetRunManager()->GetCurrentEvent()->GetEventID();
 
+  // Write one Spawning row per secondary born in this step (track IDs pre-assigned)
+  const auto* secondaries = step->GetSecondaryInCurrentStep();
+  if (secondaries) {
+    for (const G4Track* sec : *secondaries) {
+      analysisManager->FillNtupleIColumn(2, 0, evtId);
+      analysisManager->FillNtupleIColumn(2, 1, track->GetTrackID());
+      analysisManager->FillNtupleIColumn(2, 2, track->GetCurrentStepNumber());
+      analysisManager->FillNtupleIColumn(2, 3, sec->GetTrackID());
+      analysisManager->AddNtupleRow(2);
+    }
+  }
+
   analysisManager->FillNtupleIColumn(1, 0, evtId);
   analysisManager->FillNtupleIColumn(1, 1, track->GetTrackID());
   analysisManager->FillNtupleIColumn(1, 2, track->GetCurrentStepNumber());

From 517ba2ecb2a9b6da29d021c051bb1fd7fa461422 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 11 Jun 2026 10:30:36 +0200
Subject: [PATCH 18/33] add child_track_ids array column to Steps; remove
 parent_id
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Each Steps row now carries a variable-length child_track_ids int array
containing the track IDs of all secondaries spawned during that step.
The parent_id column is removed — parentage is now expressed
unidirectionally (parent→children) via child_track_ids and the Spawning
ntuple, rather than bidirectionally.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 include/RunAction.hh        |  2 ++
 include/SteppingAction.hh   |  4 ++++
 src/ActionInitialization.cc |  1 +
 src/RunAction.cc            | 26 +++++++++++++-------------
 src/SteppingAction.cc       | 33 +++++++++++++++++----------------
 5 files changed, 37 insertions(+), 29 deletions(-)

diff --git a/include/RunAction.hh b/include/RunAction.hh
index 854bb55..20a1e8d 100644
--- a/include/RunAction.hh
+++ b/include/RunAction.hh
@@ -83,6 +83,8 @@ class RunAction : public G4UserRunAction
   mutable std::vector<int> hitLayer;
   mutable std::vector<int> hitCopyNumber;
 
+  mutable std::vector<int> stepChildIds;
+
   mutable G4String filename;
 
 };
diff --git a/include/SteppingAction.hh b/include/SteppingAction.hh
index 85cdd0f..6cf86cb 100644
--- a/include/SteppingAction.hh
+++ b/include/SteppingAction.hh
@@ -33,6 +33,7 @@
 #include "G4UserSteppingAction.hh"
 #include "GeometryDescriptor.hh"
 #include "DetectorConstruction.hh"
+#include "RunAction.hh"
 
 
 namespace B4a
@@ -54,8 +55,11 @@ public:
 
   void UserSteppingAction(const G4Step* step) override;
 
+  void setRunAction(const B4::RunAction* runAction) { fRunAction = runAction; }
+
 private:
   EventAction* fEventAction = nullptr;
+  const B4::RunAction* fRunAction = nullptr;
 };
 
 }
diff --git a/src/ActionInitialization.cc b/src/ActionInitialization.cc
index d862832..5383cea 100644
--- a/src/ActionInitialization.cc
+++ b/src/ActionInitialization.cc
@@ -70,6 +70,7 @@ void ActionInitialization::Build() const
   eventAction->setPrimaryGeneratorAction(gen);
   SetUserAction(eventAction);
   auto steppingAction = new SteppingAction(eventAction);
+  steppingAction->setRunAction(runact);
   SetUserAction(steppingAction);
 }
 
diff --git a/src/RunAction.cc b/src/RunAction.cc
index d9d9afa..2d7507f 100644
--- a/src/RunAction.cc
+++ b/src/RunAction.cc
@@ -98,19 +98,19 @@ RunAction::RunAction()
   analysisManager->CreateNtupleDColumn("post_E");      // col 11
   analysisManager->CreateNtupleDColumn("edep");        // col 12 [MeV]
   analysisManager->CreateNtupleDColumn("step_length"); // col 13 [mm]
-  analysisManager->CreateNtupleIColumn("parent_id");   // col 14
-  analysisManager->CreateNtupleSColumn("process");     // col 15
-  analysisManager->CreateNtupleIColumn("layer_id");    // col 16  (-1 = outside all layers)
-  analysisManager->CreateNtupleSColumn("material");    // col 17
-  analysisManager->CreateNtupleDColumn("pre_dx");      // col 18
-  analysisManager->CreateNtupleDColumn("pre_dy");      // col 19
-  analysisManager->CreateNtupleDColumn("pre_dz");      // col 20
-  analysisManager->CreateNtupleDColumn("Bx");          // col 21 [T]
-  analysisManager->CreateNtupleDColumn("By");          // col 22 [T]
-  analysisManager->CreateNtupleDColumn("Bz");          // col 23 [T]
-  analysisManager->CreateNtupleDColumn("Ex");          // col 24 [V/m]
-  analysisManager->CreateNtupleDColumn("Ey");          // col 25 [V/m]
-  analysisManager->CreateNtupleDColumn("Ez");          // col 26 [V/m]
+  analysisManager->CreateNtupleSColumn("process");     // col 14
+  analysisManager->CreateNtupleIColumn("layer_id");    // col 15  (-1 = outside all layers)
+  analysisManager->CreateNtupleSColumn("material");    // col 16
+  analysisManager->CreateNtupleDColumn("pre_dx");      // col 17
+  analysisManager->CreateNtupleDColumn("pre_dy");      // col 18
+  analysisManager->CreateNtupleDColumn("pre_dz");      // col 19
+  analysisManager->CreateNtupleDColumn("Bx");          // col 20 [T]
+  analysisManager->CreateNtupleDColumn("By");          // col 21 [T]
+  analysisManager->CreateNtupleDColumn("Bz");          // col 22 [T]
+  analysisManager->CreateNtupleDColumn("Ex");          // col 23 [V/m]
+  analysisManager->CreateNtupleDColumn("Ey");          // col 24 [V/m]
+  analysisManager->CreateNtupleDColumn("Ez");          // col 25 [V/m]
+  analysisManager->CreateNtupleIColumn("child_track_ids", stepChildIds); // col 26 (variable-length array)
   analysisManager->FinishNtuple();
 
   // Spawning ntuple (one row per secondary born, ntuple id=2)
diff --git a/src/SteppingAction.cc b/src/SteppingAction.cc
index 4a6ac67..cb4146f 100644
--- a/src/SteppingAction.cc
+++ b/src/SteppingAction.cc
@@ -87,10 +87,13 @@ void SteppingAction::UserSteppingAction(const G4Step* step)
   auto track = step->GetTrack();
   int evtId  = G4RunManager::GetRunManager()->GetCurrentEvent()->GetEventID();
 
-  // Write one Spawning row per secondary born in this step (track IDs pre-assigned)
+  // Write one Spawning row per secondary born in this step (track IDs pre-assigned);
+  // also populate stepChildIds for the child_track_ids vector column in Steps.
+  fRunAction->stepChildIds.clear();
   const auto* secondaries = step->GetSecondaryInCurrentStep();
   if (secondaries) {
     for (const G4Track* sec : *secondaries) {
+      fRunAction->stepChildIds.push_back(sec->GetTrackID());
       analysisManager->FillNtupleIColumn(2, 0, evtId);
       analysisManager->FillNtupleIColumn(2, 1, track->GetTrackID());
       analysisManager->FillNtupleIColumn(2, 2, track->GetCurrentStepNumber());
@@ -118,14 +121,11 @@ void SteppingAction::UserSteppingAction(const G4Step* step)
   // B: geometric step length
   analysisManager->FillNtupleDColumn(1, 13, step->GetStepLength());
 
-  // C: parent track ID (0 for primary)
-  analysisManager->FillNtupleIColumn(1, 14, track->GetParentID());
-
   // D: process that ended this step
   G4String processName = "";
   const auto* postProc = post->GetProcessDefinedStep();
   if (postProc) processName = postProc->GetProcessName();
-  analysisManager->FillNtupleSColumn(1, 15, processName);
+  analysisManager->FillNtupleSColumn(1, 14, processName);
 
   // E: layer index (-1 if outside all layers) and material name at pre-step point
   int layerId = -1;
@@ -134,14 +134,14 @@ void SteppingAction::UserSteppingAction(const G4Step* step)
     if (layers[i].physicalVolume == volume) { layerId = i; break; }
   }
   G4String materialName = pre->GetMaterial() ? pre->GetMaterial()->GetName() : "";
-  analysisManager->FillNtupleIColumn(1, 16, layerId);
-  analysisManager->FillNtupleSColumn(1, 17, materialName);
+  analysisManager->FillNtupleIColumn(1, 15, layerId);
+  analysisManager->FillNtupleSColumn(1, 16, materialName);
 
   // F: pre-step momentum direction (unit vector)
   const auto dir = pre->GetMomentumDirection();
-  analysisManager->FillNtupleDColumn(1, 18, dir.x());
-  analysisManager->FillNtupleDColumn(1, 19, dir.y());
-  analysisManager->FillNtupleDColumn(1, 20, dir.z());
+  analysisManager->FillNtupleDColumn(1, 17, dir.x());
+  analysisManager->FillNtupleDColumn(1, 18, dir.y());
+  analysisManager->FillNtupleDColumn(1, 19, dir.z());
 
   // Field: B [T] and E [V/m] at pre-step position; zero if no field is registered
   G4double Bx=0, By=0, Bz=0, Ex=0, Ey=0, Ez=0;
@@ -161,12 +161,13 @@ void SteppingAction::UserSteppingAction(const G4Step* step)
       Ez = fieldVal[5] / (volt/m);
     }
   }
-  analysisManager->FillNtupleDColumn(1, 21, Bx);
-  analysisManager->FillNtupleDColumn(1, 22, By);
-  analysisManager->FillNtupleDColumn(1, 23, Bz);
-  analysisManager->FillNtupleDColumn(1, 24, Ex);
-  analysisManager->FillNtupleDColumn(1, 25, Ey);
-  analysisManager->FillNtupleDColumn(1, 26, Ez);
+  analysisManager->FillNtupleDColumn(1, 20, Bx);
+  analysisManager->FillNtupleDColumn(1, 21, By);
+  analysisManager->FillNtupleDColumn(1, 22, Bz);
+  analysisManager->FillNtupleDColumn(1, 23, Ex);
+  analysisManager->FillNtupleDColumn(1, 24, Ey);
+  analysisManager->FillNtupleDColumn(1, 25, Ez);
+  // col 26 child_track_ids: vector column, auto-read from fRunAction->stepChildIds at AddNtupleRow
 
   analysisManager->AddNtupleRow(1);
 }

From 121aab961f4b2f00455d2ed7b1e9c0913f0cb4ec Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 11 Jun 2026 10:36:05 +0200
Subject: [PATCH 19/33] point geant4 submodule at personal GitLab fork

Switch from upstream Geant4/geant4 on GitHub to lbogner/geant4 on
GitLab, which carries the minicalosim-spawning branch with the
pre-assigned track ID changes.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .gitmodules | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 50e41c1..ec6b94e 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -4,5 +4,4 @@
 	branch = stable
 [submodule "lib/geant4"]
 	path = lib/geant4
-	url = https://github.com/Geant4/geant4.git
-	shallow = true
+	url = git@gitlab.etp.kit.edu:lbogner/geant4.git

From e265a6aa6308d0a72057559e3eed3e193d8f9f6a Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 11 Jun 2026 10:41:47 +0200
Subject: [PATCH 20/33] add superbuild to compile Geant4 from submodule source
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

superbuild/CMakeLists.txt uses ExternalProject_Add to give three targets:

  cmake -B build -S superbuild/
  cmake --build build --target geant4      # build Geant4 → build/geant4-install
  cmake --build build --target run_pbwo4   # build minicalosim against it
  cmake --build build                      # both

The existing root CMakeLists.txt (find_package Geant4) is unchanged
for the system-Geant4 workflow.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 superbuild/CMakeLists.txt | 48 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 superbuild/CMakeLists.txt

diff --git a/superbuild/CMakeLists.txt b/superbuild/CMakeLists.txt
new file mode 100644
index 0000000..4a64abe
--- /dev/null
+++ b/superbuild/CMakeLists.txt
@@ -0,0 +1,48 @@
+cmake_minimum_required(VERSION 3.16)
+project(minicalosim-superbuild NONE)
+
+include(ExternalProject)
+include(ProcessorCount)
+
+ProcessorCount(NPROC)
+if(NOT NPROC OR NPROC EQUAL 0)
+  set(NPROC 4)
+endif()
+# Cap at 16 to avoid memory exhaustion on large machines (mirrors Dockerfile)
+if(NPROC GREATER 16)
+  set(NPROC 16)
+endif()
+
+set(G4_INSTALL ${CMAKE_BINARY_DIR}/geant4-install)
+set(G4_SRC     ${CMAKE_SOURCE_DIR}/../lib/geant4)
+set(MINI_SRC   ${CMAKE_SOURCE_DIR}/..)
+
+option(GEANT4_INSTALL_DATA "Download Geant4 physics data files (~2 GB)" ON)
+
+# ── Geant4 ────────────────────────────────────────────────────────────────────
+ExternalProject_Add(geant4
+  SOURCE_DIR  ${G4_SRC}
+  BINARY_DIR  ${CMAKE_BINARY_DIR}/geant4-build
+  INSTALL_DIR ${G4_INSTALL}
+  CMAKE_ARGS
+    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+    -DCMAKE_BUILD_TYPE=Release
+    -DGEANT4_INSTALL_DATA=${GEANT4_INSTALL_DATA}
+    -DGEANT4_USE_GDML=ON
+    -DGEANT4_BUILD_MULTITHREADED=OFF
+    -DGEANT4_BUILD_TLS_MODEL=global-dynamic
+  BUILD_COMMAND   cmake --build <BINARY_DIR> --parallel ${NPROC}
+  INSTALL_COMMAND cmake --install <BINARY_DIR>
+)
+
+# ── minicalosim (run_pbwo4) ───────────────────────────────────────────────────
+ExternalProject_Add(run_pbwo4
+  SOURCE_DIR  ${MINI_SRC}
+  BINARY_DIR  ${CMAKE_BINARY_DIR}/minicalosim-build
+  CMAKE_ARGS
+    -DCMAKE_PREFIX_PATH=${G4_INSTALL}
+    -DWITH_GEANT4_UIVIS=OFF
+  BUILD_COMMAND   cmake --build <BINARY_DIR> --target run_pbwo4 --parallel ${NPROC}
+  INSTALL_COMMAND ""
+  DEPENDS geant4
+)

From 2a0a23a45b4b98995ad299b84814a839880c2b08 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 11 Jun 2026 10:45:17 +0200
Subject: [PATCH 21/33] remove example files, mac files, and unused docker
 variants

Keep only the core C++ source and docker/Dockerfile-mini. Removes:
- exampleB4a (example executable and associated scripts)
- Geant4 macro (.mac) files
- ROOT plotting scripts
- GNUmakefile (old non-CMake build system)
- All Dockerfiles and scripts except Dockerfile-mini

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 CMakeLists.txt             |   30 +-
 GNUmakefile                |   21 -
 docker/Dockerfile          |  139 -----
 docker/Dockerfile-cpu      |  132 -----
 docker/build.sh            |   95 ---
 docker/build_cpu.sh        |   73 ---
 docker/build_mini.sh       |   74 ---
 docker/check_cuda_torch.py |   26 -
 docker/fix-permissions     |   33 --
 docker/start-notebook.py   |   44 --
 docker/start-notebook.sh   |   35 --
 docker/start-singleuser.py |   26 -
 docker/start-singleuser.sh |    5 -
 exampleB4.in               |   23 -
 exampleB4a.cc              |  285 ---------
 exampleB4a.out             | 1111 ------------------------------------
 gui.mac                    |   37 --
 init_vis.mac               |   17 -
 plotHisto.C                |   43 --
 plotNtuple.C               |   42 --
 run1.mac                   |   44 --
 run2.mac                   |   17 -
 vis.mac                    |   82 ---
 23 files changed, 1 insertion(+), 2433 deletions(-)
 delete mode 100644 GNUmakefile
 delete mode 100644 docker/Dockerfile
 delete mode 100644 docker/Dockerfile-cpu
 delete mode 100755 docker/build.sh
 delete mode 100755 docker/build_cpu.sh
 delete mode 100755 docker/build_mini.sh
 delete mode 100755 docker/check_cuda_torch.py
 delete mode 100755 docker/fix-permissions
 delete mode 100755 docker/start-notebook.py
 delete mode 100755 docker/start-notebook.sh
 delete mode 100755 docker/start-singleuser.py
 delete mode 100755 docker/start-singleuser.sh
 delete mode 100644 exampleB4.in
 delete mode 100644 exampleB4a.cc
 delete mode 100644 exampleB4a.out
 delete mode 100644 gui.mac
 delete mode 100644 init_vis.mac
 delete mode 100644 plotHisto.C
 delete mode 100644 plotNtuple.C
 delete mode 100644 run1.mac
 delete mode 100644 run2.mac
 delete mode 100644 vis.mac

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 642a1a4..b0133e5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -55,38 +55,10 @@ target_link_libraries(minicalo PUBLIC ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
 #----------------------------------------------------------------------------
 # Add the executable, and link it to the Geant4 and Python libraries
 #
-add_executable(exampleB4a exampleB4a.cc ${sources} ${headers})
-target_link_libraries(exampleB4a ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
-
 add_executable(run_pbwo4 run_pbwo4.cc ${sources} ${headers})
 target_link_libraries(run_pbwo4 ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
 
-#----------------------------------------------------------------------------
-# Copy all scripts to the build directory, i.e. the directory in which we
-# build B4a. This is so that we can run the executable directly because it
-# relies on these scripts being in the current working directory.
-#
-set(EXAMPLEB4A_SCRIPTS
-  exampleB4a.out
-  exampleB4.in
-  gui.mac
-  init_vis.mac
-  plotHisto.C
-  plotNtuple.C
-  run1.mac
-  run2.mac
-  vis.mac
-)
-
-foreach(_script ${EXAMPLEB4A_SCRIPTS})
-  configure_file(
-    ${PROJECT_SOURCE_DIR}/${_script}
-    ${PROJECT_BINARY_DIR}/${_script}
-    COPYONLY
-  )
-endforeach()
-
 #----------------------------------------------------------------------------
 # Install the executable to 'bin' directory under CMAKE_INSTALL_PREFIX
 #
-#install(TARGETS exampleB4a DESTINATION bin)
+#install(TARGETS run_pbwo4 DESTINATION bin)
diff --git a/GNUmakefile b/GNUmakefile
deleted file mode 100644
index c84b365..0000000
--- a/GNUmakefile
+++ /dev/null
@@ -1,21 +0,0 @@
-# --------------------------------------------------------------
-# GNUmakefile for examples module.  Gabriele Cosmo, 06/04/98.
-# --------------------------------------------------------------
-
-name := exampleB4a
-G4TARGET := $(name)
-G4EXLIB := true
-
-ifndef G4INSTALL
-  G4INSTALL = ../../..
-endif
-
-.PHONY: all
-all: lib bin
-
-include $(G4INSTALL)/config/binmake.gmk
-
-visclean:
-	rm -f g4*.prim g4*.eps g4*.wrl
-	rm -f .DAWN_*
-
diff --git a/docker/Dockerfile b/docker/Dockerfile
deleted file mode 100644
index a59ee64..0000000
--- a/docker/Dockerfile
+++ /dev/null
@@ -1,139 +0,0 @@
-FROM nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04
-
-SHELL ["/bin/sh", "-c"]
-
-USER root
-
-ENV DEBIAN_FRONTEND=noninteractive
-
-RUN /usr/bin/ls
-RUN sed -i "s,# deb http://archive.canonical.com/ubuntu,deb http://archive.canonical.com/ubuntu,g" /etc/apt/sources.list
-
-## Install some deps
-#RUN ls /etc/apt/
-RUN apt-get update -y 
-RUN apt-get install -y software-properties-common
-RUN add-apt-repository ppa:deadsnakes/ppa
-RUN apt-get update -y && apt-get upgrade -y
-RUN apt-get install -y python3 python3-dev python3-venv python3-pip
-#RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 100
-
-RUN apt-get install -y dpkg-dev cmake g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev 
-
-#RUN python3 --version && python3 -m ensurepip
-RUN python3 -m pip install --upgrade pip
-
-RUN python3 -m pip install pandas numpy matplotlib MarkupSafe wandb uproot setuptools awkward-pandas plotly
-RUN python3 -m pip install --no-cache-dir torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
-RUN python3 -m pip install torch_geometric
-RUN python3 -m pip install torch-cluster -f https://data.pyg.org/whl/torch-2.1.0+cu118.html
-
-# # # # GEANT
-RUN apt-get -y install libxmu-dev \
-        libgl1-mesa-dev \
-        libxerces-c-dev \
-        libexpat1 \
-        libx11-dev \
-        libglu1-mesa-dev \
-        freeglut3-dev \
-        mesa-common-dev \
-        imagemagick \
-        gv  wget autotools-dev libicu-dev libbz2-dev
-
-
-
-## DAWN FOR VIS
-
-RUN mkdir dawn-source \
-    && wget -q -O - http://geant4.kek.jp/~tanaka/src/dawn_3_91a.tgz | tar xzf - -C "dawn-source" \
-    && export DAWN_PS_PREVIEWER=NONE && cd dawn-source/dawn_3_91a \
-    && make clean && make guiclean && make && make install \
-    && cd - && rm -rf "dawn-source"
-
-## main package — build Geant4 from submodule source
-ADD minicalosim/lib/geant4 /tmp/geant4-src
-
-RUN rm -f /tmp/geant4-src/.git && \
-    cmake \
-        -S /tmp/geant4-src \
-        -B /tmp/geant4-build \
-        -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \
-        -DCMAKE_RULE_MESSAGES=OFF \
-        -DGEANT4_INSTALL_DATA=ON \
-        -DGEANT4_USE_GDML=ON \
-        -DGEANT4_USE_OPENGL_X11=ON \
-        -DGEANT4_BUILD_MULTITHREADED=OFF \
-        -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
-        -DGEANT4_USE_RAYTRACER_X11=ON \
-        >/dev/null && \
-    cmake --build /tmp/geant4-build --parallel $(( $(nproc) < 16 ? $(nproc) : 16 )) >/dev/null && \
-    cmake --install /tmp/geant4-build >/dev/null && \
-    rm -rf /tmp/geant4-src /tmp/geant4-build
-
-
-RUN python3 -m pip install geant4-pybind
-
-ENV LD_LIBRARY_PATH="/opt/geant4-v11.1.2/lib:${LD_LIBRARY_PATH}"
-
-RUN apt-get install -y git
-
-RUN python3 -m pip install ipython
-RUN apt-get install -y tk # for dawn
-
-# add jupyter packages for UC2 on top so they don't need to be installed every time
-RUN python3 -m pip install jupyterlab jupyterhub==4.1.5 batchspawner
-RUN ln -s /usr/bin/python3 /usr/bin/python
-
-
-RUN python3 -m pip install torch-scatter -f https://data.pyg.org/whl/torch-2.1.0+cu118.html
-
-#finally the package; use the commit hash to check out the correct version and only get them here, such that the rest can be cached
-ARG BUILD_DATE
-LABEL org.label-schema.build-date=$BUILD_DATE
-ARG COMMIT
-ARG USER
-
-# copy minicalosim and checkout the correct commit
-ADD minicalosim /root/minicalosim
-
-RUN cd  /root/minicalosim && git checkout $COMMIT && \
-    git submodule update --init lib/pybind11 && \
-    mkdir -p build && cd build && rm -rf * && cmake ../ && make -j$(( $(nproc) < 16 ? $(nproc) : 16 ))
-
-
-RUN echo "commit = '${COMMIT}'" > /root/minicalosim/bind/minicalo_version.py
-
-RUN cp /root/minicalosim/build/minicalo* /root/minicalosim/bind/G4Calo.py /root/minicalosim/bind/minicalo_tools.py /root/minicalosim/bind/minipandas.py /root/minicalosim/bind/minicalo_version.py /usr/local/lib/python3.10/dist-packages/
-
-RUN cp /root/minicalosim/bind/G4Calo_exec.py /usr/local/bin/
-
-RUN cp -r /root/minicalosim/bind /examples
-
-RUN cp /root/minicalosim/docker/start-notebook.py /usr/local/bin/
-RUN cp /root/minicalosim/docker/start-notebook.sh /usr/local/bin/
-RUN cp /root/minicalosim/docker/start-singleuser.py /usr/local/bin/
-RUN cp /root/minicalosim/docker/start-singleuser.sh /usr/local/bin/
-RUN cp /root/minicalosim/docker/fix-permissions /usr/local/bin/
-RUN cp /root/minicalosim/docker/check_cuda_torch.py /usr/local/bin/
-
-ARG NB_USER="jovyan"
-ARG NB_UID="1000"
-ARG NB_GID="100"
-
-USER root
-
-#RUN groupadd -g ${NB_GID} ${NB_USER} && \
-RUN    useradd -m -s /bin/bash -N -u ${NB_UID} -g ${NB_GID} ${NB_USER}
-
-RUN mkdir /etc/jupyter
-RUN fix-permissions /etc/jupyter/
-
-
-# clean up
-RUN rm -rf /root/minicalosim
-
-RUN pip3 install pyarrow fastparquet
-
-USER ${NB_UID}
-CMD ["bash"]
-
diff --git a/docker/Dockerfile-cpu b/docker/Dockerfile-cpu
deleted file mode 100644
index 9f5d447..0000000
--- a/docker/Dockerfile-cpu
+++ /dev/null
@@ -1,132 +0,0 @@
-FROM ubuntu:20.04
-
-SHELL ["/bin/sh", "-c"]
-
-USER root
-
-ENV DEBIAN_FRONTEND=noninteractive
-
-RUN /usr/bin/ls
-RUN sed -i "s,# deb http://archive.canonical.com/ubuntu,deb http://archive.canonical.com/ubuntu,g" /etc/apt/sources.list
-
-## Install some deps
-#RUN ls /etc/apt/
-RUN apt-get update -y 
-RUN apt-get install -y software-properties-common
-RUN add-apt-repository ppa:deadsnakes/ppa
-RUN apt-get update -y && apt-get upgrade -y
-RUN apt-get install -y python3 python3-dev python3-venv python3-pip
-#RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 100
-
-RUN apt-get install -y dpkg-dev cmake g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev 
-
-#RUN python3 --version && python3 -m ensurepip
-RUN python3 -m pip install --upgrade pip
-
-RUN python3 -m pip install pandas numpy matplotlib MarkupSafe wandb uproot setuptools awkward-pandas plotly
-RUN python3 -m pip install --no-cache-dir torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
-RUN python3 -m pip install torch_geometric
-RUN python3 -m pip install torch-cluster -f https://data.pyg.org/whl/torch-2.1.0+cu118.html
-
-# # # # GEANT
-RUN apt-get -y install libxmu-dev \
-        libgl1-mesa-dev \
-        libxerces-c-dev \
-        libexpat1 \
-        libx11-dev \
-        libglu1-mesa-dev \
-        freeglut3-dev \
-        mesa-common-dev \
-        imagemagick \
-        gv  wget autotools-dev libicu-dev libbz2-dev
-
-
-
-## DAWN FOR VIS
-
-RUN mkdir dawn-source \
-    && wget -q -O - http://geant4.kek.jp/~tanaka/src/dawn_3_91a.tgz | tar xzf - -C "dawn-source" \
-    && export DAWN_PS_PREVIEWER=NONE && cd dawn-source/dawn_3_91a \
-    && make clean && make guiclean && make && make install \
-    && cd - && rm -rf "dawn-source"
-
-## main package — build Geant4 from submodule source
-ADD minicalosim/lib/geant4 /tmp/geant4-src
-
-RUN rm -f /tmp/geant4-src/.git && \
-    cmake \
-        -S /tmp/geant4-src \
-        -B /tmp/geant4-build \
-        -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \
-        -DCMAKE_RULE_MESSAGES=OFF \
-        -DGEANT4_INSTALL_DATA=ON \
-        -DGEANT4_USE_GDML=ON \
-        -DGEANT4_USE_OPENGL_X11=ON \
-        -DGEANT4_BUILD_MULTITHREADED=ON \
-        -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
-        -DGEANT4_USE_RAYTRACER_X11=ON \
-        >/dev/null && \
-    cmake --build /tmp/geant4-build --parallel $(( $(nproc) < 16 ? $(nproc) : 16 )) >/dev/null && \
-    cmake --install /tmp/geant4-build >/dev/null && \
-    rm -rf /tmp/geant4-src /tmp/geant4-build
-
-
-RUN python3 -m pip install geant4-pybind
-
-ENV LD_LIBRARY_PATH="/opt/geant4-v11.1.2/lib:${LD_LIBRARY_PATH}"
-
-RUN apt-get install -y git
-
-RUN python3 -m pip install ipython
-RUN apt-get install -y tk # for dawn
-
-# add jupyter packages for UC2 on top so they don't need to be installed every time
-RUN python3 -m pip install jupyterlab jupyterhub==4.1.5 batchspawner
-RUN ln -s /usr/bin/python3 /usr/bin/python
-
-
-RUN python3 -m pip install torch-scatter -f https://data.pyg.org/whl/torch-2.1.0+cu118.html
-
-#finally the package; use the commit hash to check out the correct version and only get them here, such that the rest can be cached
-ARG BUILD_DATE
-LABEL org.label-schema.build-date=$BUILD_DATE
-ARG COMMIT
-ARG USER
-
-# copy minicalosim and checkout the correct commit
-ADD minicalosim /root/minicalosim
-
-RUN cd  /root/minicalosim && git checkout $COMMIT && \
-    git submodule update --init lib/pybind11 && \
-    mkdir -p build && cd build && rm -rf * && cmake ../ && make -j$(( $(nproc) < 16 ? $(nproc) : 16 )) &&\
-    echo "commit = '${COMMIT}'" > ../bind/minicalo_version.py && \
-    cp minicalo* ../bind/G4Calo.py ../bind/minicalo_version.py /usr/local/lib/python3.8/dist-packages/
-
-
-
-RUN cp /root/minicalosim/docker/start-notebook.py /usr/local/bin/
-RUN cp /root/minicalosim/docker/start-notebook.sh /usr/local/bin/
-RUN cp /root/minicalosim/docker/start-singleuser.py /usr/local/bin/
-RUN cp /root/minicalosim/docker/start-singleuser.sh /usr/local/bin/
-RUN cp /root/minicalosim/docker/fix-permissions /usr/local/bin/
-RUN cp /root/minicalosim/docker/check_cuda_torch.py /usr/local/bin/
-
-ARG NB_USER="jovyan"
-ARG NB_UID="1000"
-ARG NB_GID="100"
-
-USER root
-
-#RUN groupadd -g ${NB_GID} ${NB_USER} && \
-RUN    useradd -m -s /bin/bash -N -u ${NB_UID} -g ${NB_GID} ${NB_USER}
-
-RUN mkdir /etc/jupyter
-RUN fix-permissions /etc/jupyter/
-
-
-# clean up
-RUN rm -rf /root/minicalosim
-
-USER ${NB_UID}
-CMD ["start-notebook.sh"]
-
diff --git a/docker/build.sh b/docker/build.sh
deleted file mode 100755
index 2aa89fb..0000000
--- a/docker/build.sh
+++ /dev/null
@@ -1,95 +0,0 @@
-#!/usr/bin/bash
-
-# a simple parser for the args <commit> and --no-cache
-# if no commit is given, the latest commit is used
-# if --no-cache is given, the --no-cache flag is passed to the docker build command
-# if only --no-cache is given, the latest commit is used
-
-# check if commit is given as argument, if not use the latest commit
-# check if an argument is given at all
-
-
-if [ -n "$1" ]; then
-    #check if the first arg is --no-cache
-    if [ "$1" == "--no-cache" ]; then
-        FORCE_NO_CACHE="--no-cache"
-        COMMIT=$(git rev-parse --short HEAD)
-    else
-        COMMIT=$1
-        #check if this is a valid commit
-        if ! git cat-file -e $COMMIT^{commit} 2>/dev/null; then
-            echo "ERROR: Commit $COMMIT not found in local repository."
-            exit 1
-        fi
-    fi
-else #default to last commit
-    COMMIT=$(git rev-parse --short HEAD)
-fi
-
-
-# COMMIT is a valid commit at this point. If COMMIT is the last commit and changes are not commited, the user is warned.
-
-#check if the commit is the last commit
-if [ "$COMMIT" == "$(git rev-parse --short HEAD)" ]; then
-    # check if we have uncommitted changes and if so warn the user.
-    if [ -n "$(git status --porcelain)" ]; then
-        echo "WARNING: You are building the latest commit ${COMMIT}, but you have uncommitted changes."
-        echo "         This means that the image will not be reproducible."
-        echo "         If you want to build the latest commit, please commit your changes first."
-        read -p "Do you want to continue anyway? [y/N] " -n 1 -r
-        echo
-        if [[ ! $REPLY =~ ^[Yy]$ ]]; then
-            exit 1
-        fi
-    fi
-fi
-
-check_remote_commit_exists() {
-    # Usage: check_remote_commit_exists <repo-url> <commit-sha>
-    local url="$1"
-    local commit="$2"
-
-    # Create a temporary directory for a shallow fetch
-    local tmpdir
-    tmpdir="$(mktemp -d)"
-    trap 'rm -rf "$tmpdir"' RETURN  # auto-cleanup on function exit
-
-    git -C "$tmpdir" init -q
-    git -C "$tmpdir" remote add origin "$url"
-
-    if git -C "$tmpdir" fetch --quiet --depth=1 origin "$commit" 2>/dev/null; then
-        echo "✅ Commit $commit exists on remote."
-        return 0
-    else
-        echo "❌ ERROR: Commit $commit not found on remote."
-        echo "Refs currently visible on remote:"
-        git ls-remote --heads --tags "$url"
-        return 1
-    fi
-}
-
-# check if the commit has been pushed
-if ! check_remote_commit_exists https://github.com/jkiesele/minicalosim $COMMIT; then
-    echo "ERROR: Commit $COMMIT not found in remote repository."
-fi
-
-# check if no-cache is given as second argument
-if [ "$2" == "--no-cache" ]; then
-    FORCE_NO_CACHE="--no-cache"
-fi
-
-#switch to directory this script is located in
-cd "$(dirname "$0")"
-cd ../../ #switch to the root directory of the project
-echo "Building minicalosim:$COMMIT"
-
-#print the current working directory
-echo "Current working directory: $(pwd)"
-
-docker build $FORCE_NO_CACHE -t jkiesele/minicalosim:$COMMIT --build-arg USER=$USER --build-arg BUILD_DATE="$(date)" --build-arg COMMIT=$COMMIT -f minicalosim/docker/Dockerfile .
-
-echo "sucessfully built container jkiesele/minicalosim:${COMMIT}"
-
-docker tag jkiesele/minicalosim:$COMMIT jkiesele/minicalosim:latest
-
-echo "also tagged as jkiesele/minicalosim:latest"
\ No newline at end of file
diff --git a/docker/build_cpu.sh b/docker/build_cpu.sh
deleted file mode 100755
index d751096..0000000
--- a/docker/build_cpu.sh
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/usr/bin/bash
-
-# a simple parser for the args <commit> and --no-cache
-# if no commit is given, the latest commit is used
-# if --no-cache is given, the --no-cache flag is passed to the docker build command
-# if only --no-cache is given, the latest commit is used
-
-# check if commit is given as argument, if not use the latest commit
-# check if an argument is given at all
-
-
-if [ -n "$1" ]; then
-    #check if the first arg is --no-cache
-    if [ "$1" == "--no-cache" ]; then
-        FORCE_NO_CACHE="--no-cache"
-        COMMIT=$(git rev-parse --short HEAD)
-    else
-        COMMIT=$1
-        #check if this is a valid commit
-        if ! git cat-file -e $COMMIT^{commit} 2>/dev/null; then
-            echo "ERROR: Commit $COMMIT not found in local repository."
-            exit 1
-        fi
-    fi
-else #default to last commit
-    COMMIT=$(git rev-parse --short HEAD)
-fi
-
-
-# COMMIT is a valid commit at this point. If COMMIT is the last commit and changes are not commited, the user is warned.
-
-#check if the commit is the last commit
-if [ "$COMMIT" == "$(git rev-parse --short HEAD)" ]; then
-    # check if we have uncommitted changes and if so warn the user.
-    if [ -n "$(git status --porcelain)" ]; then
-        echo "WARNING: You are building the latest commit ${COMMIT}, but you have uncommitted changes."
-        echo "         This means that the image will not be reproducible."
-        echo "         If you want to build the latest commit, please commit your changes first."
-        read -p "Do you want to continue anyway? [y/N] " -n 1 -r
-        echo
-        if [[ ! $REPLY =~ ^[Yy]$ ]]; then
-            exit 1
-        fi
-    fi
-fi
-
-# check if the commit has been pushed 
-REMOTE_COMMIT=$(git ls-remote https://gitlab.etp.kit.edu/jkiesele/minicalosim.git | grep $COMMIT)
-if [ -z "$REMOTE_COMMIT" ]; then
-       echo "ERROR: Commit $COMMIT not found in remote repository."
-       exit 1
-fi
-
-# check if no-cache is given as second argument
-if [ "$2" == "--no-cache" ]; then
-    FORCE_NO_CACHE="--no-cache"
-fi
-
-#switch to directory this script is located in
-cd "$(dirname "$0")"
-cd ../../ #switch to the root directory of the project
-echo "Building minicalosim_cpu:$COMMIT"
-
-#print the current working directory
-echo "Current working directory: $(pwd)"
-
-docker build $FORCE_NO_CACHE -t jkiesele/minicalosim_cpu:$COMMIT --build-arg USER=$USER --build-arg BUILD_DATE="$(date)" --build-arg COMMIT=$COMMIT -f minicalosim/docker/Dockerfile-cpu .
-
-echo "sucessfully built container jkiesele/minicalosim_cpu:${COMMIT}"
-
-docker tag jkiesele/minicalosim_cpu:$COMMIT jkiesele/minicalosim_cpu:latest
-
-echo "also tagged as jkiesele/minicalosim_cpu:latest"
\ No newline at end of file
diff --git a/docker/build_mini.sh b/docker/build_mini.sh
deleted file mode 100755
index 3cd5f08..0000000
--- a/docker/build_mini.sh
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/usr/bin/bash
-
-if [ -n "$1" ]; then
-    if [ "$1" == "--no-cache" ]; then
-        FORCE_NO_CACHE="--no-cache"
-        COMMIT=$(git rev-parse --short HEAD)
-    else
-        COMMIT=$1
-        if ! git cat-file -e $COMMIT^{commit} 2>/dev/null; then
-            echo "ERROR: Commit $COMMIT not found in local repository."
-            exit 1
-        fi
-    fi
-else
-    COMMIT=$(git rev-parse --short HEAD)
-fi
-
-if [ "$COMMIT" == "$(git rev-parse --short HEAD)" ]; then
-    if [ -n "$(git status --porcelain)" ]; then
-        echo "WARNING: You are building the latest commit ${COMMIT}, but you have uncommitted changes."
-        echo "         This means that the image will not be reproducible."
-        echo "         If you want to build the latest commit, please commit your changes first."
-        read -p "Do you want to continue anyway? [y/N] " -n 1 -r
-        echo
-        if [[ ! $REPLY =~ ^[Yy]$ ]]; then
-            exit 1
-        fi
-    fi
-fi
-
-check_remote_commit_exists() {
-    local url="$1"
-    local commit="$2"
-    local tmpdir
-    tmpdir="$(mktemp -d)"
-    trap 'rm -rf "$tmpdir"' RETURN
-    git -C "$tmpdir" init -q
-    git -C "$tmpdir" remote add origin "$url"
-    if git -C "$tmpdir" fetch --quiet --depth=1 origin "$commit" 2>/dev/null; then
-        echo "✅ Commit $commit exists on remote."
-        return 0
-    else
-        echo "❌ ERROR: Commit $commit not found on remote."
-        echo "Refs currently visible on remote:"
-        git ls-remote --heads --tags "$url"
-        return 1
-    fi
-}
-
-if ! check_remote_commit_exists https://github.com/jkiesele/minicalosim $COMMIT; then
-    echo "WARNING: Commit $COMMIT not found in remote repository."
-fi
-
-if [ "$2" == "--no-cache" ]; then
-    FORCE_NO_CACHE="--no-cache"
-fi
-
-cd "$(dirname "$0")"
-cd ../../
-echo "Building minicalosim-mini:$COMMIT"
-echo "Current working directory: $(pwd)"
-
-docker build $FORCE_NO_CACHE \
-    -t jkiesele/minicalosim-mini:$COMMIT \
-    --build-arg USER=$USER \
-    --build-arg BUILD_DATE="$(date)" \
-    --build-arg COMMIT=$COMMIT \
-    -f minicalosim/docker/Dockerfile-mini .
-
-echo "successfully built container jkiesele/minicalosim-mini:${COMMIT}"
-
-docker tag jkiesele/minicalosim-mini:$COMMIT jkiesele/minicalosim-mini:latest
-
-echo "also tagged as jkiesele/minicalosim-mini:latest"
diff --git a/docker/check_cuda_torch.py b/docker/check_cuda_torch.py
deleted file mode 100755
index 8ef2ce3..0000000
--- a/docker/check_cuda_torch.py
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env python
-'''
-little script to check if cuda is available in pytorch and working
-organised as a check that raises an exception if cuda is not available, and data cannot be moved to the gpu
-'''
-import torch
-import numpy as np
-import os
-
-def check_cuda():
-    if not torch.cuda.is_available():
-        raise Exception("CUDA is not available. Please check if you have installed the correct version of CUDA and the correct version of the NVIDIA driver.")
-    
-    try:
-        a = torch.tensor([1,2,3])
-        a = a.cuda()
-        a = a*a
-    except:
-        raise Exception("Cannot move data to the GPU. Please check if you have installed the correct version of CUDA and the correct version of the NVIDIA driver.")
-    
-    print("CUDA is available and working correctly.")
-
-if __name__ == '__main__':
-    check_cuda()
-    print("All checks passed.")
-    os._exit(0)
\ No newline at end of file
diff --git a/docker/fix-permissions b/docker/fix-permissions
deleted file mode 100755
index d540462..0000000
--- a/docker/fix-permissions
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/bash
-# Set permissions on a directory
-# After any installation, if a directory needs to be (human) user-writable, run this script on it.
-# It will make everything in the directory owned by the group ${NB_GID} and writable by that group.
-# Deployments that want to set a specific user id can preserve permissions
-# by adding the `--group-add users` line to `docker run`.
-
-# Uses find to avoid touching files that already have the right permissions,
-# which would cause a massive image explosion
-
-# Right permissions are:
-# group=${NB_GID}
-# AND permissions include group rwX (directory-execute)
-# AND directories have setuid,setgid bits set
-
-set -e
-
-for d in "$@"; do
-    find "${d}" \
-        ! \( \
-            -group "${NB_GID}" \
-            -a -perm -g+rwX \
-        \) \
-        -exec chgrp "${NB_GID}" -- {} \+ \
-        -exec chmod g+rwX -- {} \+
-    # setuid, setgid *on directories only*
-    find "${d}" \
-        \( \
-            -type d \
-            -a ! -perm -6000 \
-        \) \
-        -exec chmod +6000 -- {} \+
-done
\ No newline at end of file
diff --git a/docker/start-notebook.py b/docker/start-notebook.py
deleted file mode 100755
index 973da5a..0000000
--- a/docker/start-notebook.py
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env python
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-import os
-import shlex
-import sys
-
-# If we are in a JupyterHub, we pass on to `start-singleuser.py` instead so it does the right thing
-if "JUPYTERHUB_API_TOKEN" in os.environ:
-    print(
-        "WARNING: using start-singleuser.py instead of start-notebook.py to start a server associated with JupyterHub."
-    )
-    command = ["/usr/local/bin/start-singleuser.py"] + sys.argv[1:]
-    os.execvp(command[0], command)
-
-
-# Entrypoint is start.sh
-command = []
-
-# If we want to survive restarts, launch the command using `run-one-constantly`
-if os.environ.get("RESTARTABLE") == "yes":
-    command.append("run-one-constantly")
-
-# We always launch a jupyter subcommand from this script
-command.append("jupyter")
-
-# Launch the configured subcommand.
-# Note that this should be a single string, so we don't split it.
-# We default to `lab`.
-jupyter_command = os.environ.get("DOCKER_STACKS_JUPYTER_CMD", "lab")
-command.append(jupyter_command)
-
-# Append any optional NOTEBOOK_ARGS we were passed in.
-# This is supposed to be multiple args passed on to the notebook command,
-# so we split it correctly with shlex
-if "NOTEBOOK_ARGS" in os.environ:
-    command += shlex.split(os.environ["NOTEBOOK_ARGS"])
-
-# Pass through any other args we were passed on the command line
-command += sys.argv[1:]
-
-# Execute the command!
-print("Executing: " + " ".join(command))
-os.execvp(command[0], command)
diff --git a/docker/start-notebook.sh b/docker/start-notebook.sh
deleted file mode 100755
index 41db342..0000000
--- a/docker/start-notebook.sh
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/bin/bash
-# Shim to emit warning and call start-notebook.py
-echo "WARNING: Use start-notebook.py instead"
-
-if id jovyan &> /dev/null; then
-        if ! usermod --home "/home/${NB_USER}" --login "${NB_USER}" jovyan 2>&1 | grep "no changes" > /dev/null; then
-            echo "Updated the jovyan user:"
-            echo "- username: jovyan       -> ${NB_USER}"
-            echo "- home dir: /home/jovyan -> /home/${NB_USER}"
-        fi
-elif ! id -u "${NB_USER}" &> /dev/null; then
-        echo "ERROR: Neither the jovyan user nor '${NB_USER}' exists. This could be the result of stopping and starting, the container with a different NB_USER environment variable."
-        exit 1
-fi
-# Ensure the desired user (NB_USER) gets its desired user id (NB_UID) and is
-# a member of the desired group (NB_GROUP, NB_GID)
-if [ "${NB_UID}" != "$(id -u "${NB_USER}")" ] || [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
-        echo "Update ${NB_USER}'s UID:GID to ${NB_UID}:${NB_GID}"
-        # Ensure the desired group's existence
-        if [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
-            groupadd --force --gid "${NB_GID}" --non-unique "${NB_GROUP:-${NB_USER}}"
-        fi
-        # Recreate the desired user as we want it
-        userdel "${NB_USER}"
-        useradd --no-log-init --home "/home/${NB_USER}" --shell /bin/bash --uid "${NB_UID}" --gid "${NB_GID}" --groups 100 "${NB_USER}"
-fi
-
-
-# if root change user to jovyan
-if [ "$EUID" -eq 0 ]; then
-    echo "WARNING: Running as root. Use start-notebook.py to run as ${NB_USER} user"
-    exec su ${NB_USER} -c "exec /usr/local/bin/start-notebook.py $@"
-else
-    exec /usr/local/bin/start-notebook.py "$@"
-fi
diff --git a/docker/start-singleuser.py b/docker/start-singleuser.py
deleted file mode 100755
index c80339f..0000000
--- a/docker/start-singleuser.py
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env python
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-import os
-import shlex
-import sys
-
-# Entrypoint is start.sh
-command = ["jupyterhub-singleuser"]
-
-# set default ip to 0.0.0.0
-if "--ip=" not in os.environ.get("NOTEBOOK_ARGS", ""):
-    command.append("--ip=0.0.0.0")
-
-# Append any optional NOTEBOOK_ARGS we were passed in.
-# This is supposed to be multiple args passed on to the notebook command,
-# so we split it correctly with shlex
-if "NOTEBOOK_ARGS" in os.environ:
-    command += shlex.split(os.environ["NOTEBOOK_ARGS"])
-
-# Pass any other args we have been passed through
-command += sys.argv[1:]
-
-# Execute the command!
-print("Executing: " + " ".join(command))
-os.execvp(command[0], command)
diff --git a/docker/start-singleuser.sh b/docker/start-singleuser.sh
deleted file mode 100755
index ecf0e06..0000000
--- a/docker/start-singleuser.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/bash
-# Shim to emit warning and call start-singleuser.py
-echo "WARNING: Use start-singleuser.py instead"
-
-exec /usr/local/bin/start-singleuser.py "$@"
diff --git a/exampleB4.in b/exampleB4.in
deleted file mode 100644
index 02052f0..0000000
--- a/exampleB4.in
+++ /dev/null
@@ -1,23 +0,0 @@
-# Macro file for example B4 test
-
-/run/initialize
-
-# e+ 300MeV 
-/gun/particle e+
-/gun/energy 300 MeV
-/run/beamOn 1
-#
-# list the existing physics processes
-/process/list
-#
-# switch off MultipleScattering
-/process/inactivate msc
-/run/beamOn 1
-#
-# switch on MultipleScattering
-/process/activate msc 
-#
-# change detector parameter
-/gun/particle gamma
-/gun/energy 500 MeV
-/run/beamOn 1
diff --git a/exampleB4a.cc b/exampleB4a.cc
deleted file mode 100644
index 55351f9..0000000
--- a/exampleB4a.cc
+++ /dev/null
@@ -1,285 +0,0 @@
-//
-// ********************************************************************
-// * License and Disclaimer                                           *
-// *                                                                  *
-// * The  Geant4 software  is  copyright of the Copyright Holders  of *
-// * the Geant4 Collaboration.  It is provided  under  the terms  and *
-// * conditions of the Geant4 Software License,  included in the file *
-// * LICENSE and available at  http://cern.ch/geant4/license .  These *
-// * include a list of copyright holders.                             *
-// *                                                                  *
-// * Neither the authors of this software system, nor their employing *
-// * institutes,nor the agencies providing financial support for this *
-// * work  make  any representation or  warranty, express or implied, *
-// * regarding  this  software system or assume any liability for its *
-// * use.  Please see the license in the file  LICENSE  and URL above *
-// * for the full disclaimer and the limitation of liability.         *
-// *                                                                  *
-// * This  code  implementation is the result of  the  scientific and *
-// * technical work of the GEANT4 collaboration.                      *
-// * By using,  copying,  modifying or  distributing the software (or *
-// * any work based  on the software)  you  agree  to acknowledge its *
-// * use  in  resulting  scientific  publications,  and indicate your *
-// * acceptance of all terms of the Geant4 Software license.          *
-// ********************************************************************
-//
-//
-/// \file exampleB4a.cc
-/// \brief Main program of the B4a example
-
-#include "DetectorConstruction.hh"
-#include "ActionInitialization.hh"
-
-#include "G4RunManagerFactory.hh"
-#include "G4SteppingVerbose.hh"
-#include "G4UIcommand.hh"
-#include "G4UImanager.hh"
-#include "G4UIExecutive.hh"
-#include "G4VisExecutive.hh"
-#include "FTFP_BERT.hh"
-#include "Randomize.hh"
-
-#include "GeometryDescriptor.hh"
-
-#include "G4System.hh"
-
-//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
-
-
-
-
-
-
-namespace {
-  void PrintUsage() {
-    G4cerr << " Usage: " << G4endl;
-    G4cerr << " exampleB4a [-m macro ] [-u UIsession] [-t nThreads] [-vDefault]"
-           << G4endl;
-    G4cerr << "   note: -t option is available only for multi-threaded mode."
-           << G4endl;
-  }
-}
-
-//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
-
-int main2(int argc,char** argv)
-{
-  // Evaluate arguments
-  //
-  if ( argc > 7 ) {
-    PrintUsage();
-    return 1;
-  }
-
-  G4String macro;
-  G4String session;
-  G4bool verboseBestUnits = true;
-#ifdef G4MULTITHREADED
-  G4int nThreads = 0;
-#endif
-  for ( G4int i=1; i<argc; i=i+2 ) {
-    if      ( G4String(argv[i]) == "-m" ) macro = argv[i+1];
-    else if ( G4String(argv[i]) == "-u" ) session = argv[i+1];
-#ifdef G4MULTITHREADED
-    else if ( G4String(argv[i]) == "-t" ) {
-      nThreads = G4UIcommand::ConvertToInt(argv[i+1]);
-    }
-#endif
-    else if ( G4String(argv[i]) == "-vDefault" ) {
-      verboseBestUnits = false;
-      --i;  // this option is not followed with a parameter
-    }
-    else {
-      PrintUsage();
-      return 1;
-    }
-  }
-
-  // Detect interactive mode (if no macro provided) and define UI session
-  //
-  G4UIExecutive* ui = nullptr;
-  if ( ! macro.size() ) {
-    ui = new G4UIExecutive(argc, argv, session);
-  }
-
-  // Optionally: choose a different Random engine...
-  // G4Random::setTheEngine(new CLHEP::MTwistEngine);
-
-  // Use G4SteppingVerboseWithUnits
-  if ( verboseBestUnits ) {
-    G4int precision = 4;
-    G4SteppingVerbose::UseBestUnit(precision);
-  }
-
-  // Construct the default run manager
-  //
-  auto* runManager =
-    G4RunManagerFactory::CreateRunManager(G4RunManagerType::Default);
-#ifdef G4MULTITHREADED
-  if ( nThreads > 0 ) {
-    runManager->SetNumberOfThreads(nThreads);
-  }
-#endif
-
-  GeometryDescriptor * cw = new GeometryDescriptor();
-  cw->addLayer(1, "G4_Pb", false);
-  cw->addLayer(10, "G4_Si", true, 9);
-  cw->addLayer(1, "G4_Pb", false);
-  cw->addLayer(20, "G4_Si", true, 15);
-  cw->addLayer(4, "G4_Pb", false);
-  cw->addLayer(3, "G4_Si", true,  23);
-
-
-  // Set mandatory initialization classes
-  //
-  auto detConstruction = new B4::DetectorConstruction(cw);
-
-  runManager->SetUserInitialization(detConstruction);
-
-  auto physicsList = new FTFP_BERT;
-  runManager->SetUserInitialization(physicsList);
-
-  auto actionInitialization = new B4a::ActionInitialization(detConstruction);
-  runManager->SetUserInitialization(actionInitialization);
-
-  actionInitialization->setGeneratorProperties(100, 1000, "e-");
-
-  // Initialize visualization
-  //
-  auto visManager = new G4VisExecutive;
-  // G4VisExecutive can take a verbosity argument - see /vis/verbose guidance.
-  // G4VisManager* visManager = new G4VisExecutive("Quiet");
-  visManager->Initialize();
-
-  // Get the pointer to the User Interface manager
-  auto UImanager = G4UImanager::GetUIpointer();
-
-  // Process macro or start UI session
-  //
-  if ( macro.size() ) {
-    // batch mode
-    G4String command = "/control/execute ";
-    UImanager->ApplyCommand(command+macro);
-  }
-  else  {
-    // interactive mode : define UI session
-    UImanager->ApplyCommand("/control/execute init_vis.mac");
-    if (ui->IsGUI()) {
-      UImanager->ApplyCommand("/control/execute gui.mac");
-    }
-    ui->SessionStart();
-    delete ui;
-  }
-
-  // Job termination
-  // Free the store: user actions, physics_list and detector_description are
-  // owned and deleted by the run manager, so they should not be deleted
-  // in the main() program !
-
-  delete visManager;
-  delete runManager;
-  delete cw;
-  return 0;
-}
-
-//later
-//class Runner {
-//public:
-//  void initialize(GeometryDescriptor CW, bool gui=false);
-//  void run(int nEvents, std::string partSpecies, double minEnergy, double maxEnergy);
-//}
-
-void run(GeometryDescriptor CW, int nEvents, std::string partSpecies, double minEnergy, double maxEnergy, bool gui=false){
-
-  char* argv[]={(char*)"dummy"};
-
-  // Construct the default run manager
-  //
-  auto* runManager =
-    G4RunManagerFactory::CreateRunManager(G4RunManagerType::Default);
-  runManager->SetNumberOfThreads(1);
-
-  GeometryDescriptor * cw = &CW;
-  G4String session;
-  G4UIExecutive* ui = nullptr;
-  if ( gui ) {
-    ui = new G4UIExecutive((int)1, argv, session);
-  }
-
-  // Set mandatory initialization classes
-  //
-  auto detConstruction = new B4::DetectorConstruction(cw);
-
-  runManager->SetUserInitialization(detConstruction);
-
-  auto physicsList = new FTFP_BERT;
-  runManager->SetUserInitialization(physicsList);
-
-  auto actionInitialization = new B4a::ActionInitialization(detConstruction);
-  runManager->SetUserInitialization(actionInitialization);
-
-  actionInitialization->setGeneratorProperties(minEnergy, maxEnergy, partSpecies);
-
-  // Initialize visualization
-  //
-  auto visManager = new G4VisExecutive;
-  // G4VisExecutive can take a verbosity argument - see /vis/verbose guidance.
-  // G4VisManager* visManager = new G4VisExecutive("Quiet");
-  visManager->Initialize();
-
-  // Get the pointer to the User Interface manager
-  auto UImanager = G4UImanager::GetUIpointer();
-
-  // Process macro or start UI session
-  //
-
-
-  if ( gui ) {
-    // interactive mode : define UI session
-    UImanager->ApplyCommand("/control/execute init_vis.mac");
-    if (ui->IsGUI()) {
-      UImanager->ApplyCommand("/control/execute gui.mac");
-    }
-    ui->SessionStart();
-    delete ui;
-  }
-  else  {
-    G4String command  = "/control/execute run1.mac";
-  UImanager->ApplyCommand("/run/initialize");
-  UImanager->ApplyCommand("/run/beamOn "+ std::to_string(nEvents));
-  }
-
- 
-  // Job termination
-  // Free the store: user actions, physics_list and detector_description are
-  // owned and deleted by the run manager, so they should not be deleted
-  // in the main() program !
-  delete visManager;
-  delete runManager;
-
-}
-
-int main(){
-
-  GeometryDescriptor cw;
-  //to be moved
-  cw.addLayer(1, "G4_Pb", false);
-  cw.addLayer(10, "G4_Si", true, 9);
-  cw.addLayer(1, "G4_Pb", false);
-  cw.addLayer(20, "G4_Si", true, 15);
-  cw.addLayer(4, "G4_Pb", false);
-  cw.addLayer(3, "G4_Si", true,  23);
-
-  G4System builder(true);
-  builder.init(cw);
-  //builder.run_gui();
-  std::vector<std::string> parts = {"e-"};
-  builder.run_batch(10000,parts , 1, 100);
-
-  //run(cw, 1000, "e-", 1, 100, true);
-
-  return 0;
-}
-
-//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
-
diff --git a/exampleB4a.out b/exampleB4a.out
deleted file mode 100644
index 2c978fa..0000000
--- a/exampleB4a.out
+++ /dev/null
@@ -1,1111 +0,0 @@
-Environment variable "G4FORCE_RUN_MANAGER_TYPE" enabled with value == Serial. Forcing G4RunManager type...
-
-        ############################################
-        !!! WARNING - FPE detection is activated !!!
-        ############################################
-
-
-          ################################
-          !!! G4Backtrace is activated !!!
-          ################################
-
-
-**************************************************************
- Geant4 version Name: geant4-11-01-patch-02    (15-June-2023)
-                       Copyright : Geant4 Collaboration
-                      References : NIM A 506 (2003), 250-303
-                                 : IEEE-TNS 53 (2006), 270-278
-                                 : NIM A 835 (2016), 186-225
-                             WWW : http://geant4.org/
-**************************************************************
-
-<<< Geant4 Physics List simulation engine: FTFP_BERT
-
-Visualization Manager instantiating with verbosity "warnings (3)"...
-Visualization Manager initialising...
-Registering graphics systems...
-
-You have successfully registered the following graphics systems.
-Registered graphics systems are:
-  ASCIITree (ATree)
-  DAWNFILE (DAWNFILE)
-  G4HepRepFile (HepRepFile)
-  RayTracer (RayTracer)
-  VRML2FILE (VRML2FILE)
-  gMocrenFile (gMocrenFile)
-  TOOLSSG_OFFSCREEN (TSG_OFFSCREEN)
-  TOOLSSG_OFFSCREEN (TSG_OFFSCREEN, TSG_FILE)
-  OpenGLImmediateQt (OGLIQt, OGLI)
-  OpenGLStoredQt (OGLSQt, OGL, OGLS)
-  OpenGLImmediateXm (OGLIXm, OGLIQt_FALLBACK)
-  OpenGLStoredXm (OGLSXm, OGLSQt_FALLBACK)
-  OpenGLImmediateX (OGLIX, OGLIQt_FALLBACK, OGLIXm_FALLBACK)
-  OpenGLStoredX (OGLSX, OGLSQt_FALLBACK, OGLSXm_FALLBACK)
-  RayTracerX (RayTracerX)
-  Qt3D (Qt3D)
-  TOOLSSG_X11_GLES (TSG_X11_GLES, TSGX11, TSG_XT_GLES_FALLBACK)
-  TOOLSSG_XT_GLES (TSG_XT_GLES, TSGXt, TSG_QT_GLES_FALLBACK)
-  TOOLSSG_QT_GLES (TSG_QT_GLES, TSGQt, TSG)
-
-Registering model factories...
-
-You have successfully registered the following model factories.
-Registered model factories:
-  generic
-  drawByAttribute
-  drawByCharge
-  drawByOriginVolume
-  drawByParticleID
-  drawByEncounteredVolume
-
-Registered models:
-  None
-
-Registered filter factories:
-  attributeFilter
-  chargeFilter
-  originVolumeFilter
-  particleFilter
-  encounteredVolumeFilter
-
-Registered filters:
-  None
-
-You have successfully registered the following user vis actions.
-Run Duration User Vis Actions: none
-End of Event User Vis Actions: none
-End of Run User Vis Actions: none
-
-Some /vis commands (optionally) take a string to specify colour.
-"/vis/list" to see available colours.
-
-***** Table : Nb of materials = 3 *****
-
- Material:    G4_Pb    density: 11.350 g/cm3   RadL:   5.613 mm   Nucl.Int.Length:  18.248 cm 
-                       Imean: 823.000 eV   temperature: 293.15 K  pressure:   1.00 atm
-
-   --->  Element: Pb (Pb)   Z = 82.0   N =   207   A = 207.217 g/mole
-         --->  Isotope: Pb204   Z = 82   N = 204   A = 203.97 g/mole   abundance:  1.400 %
-         --->  Isotope: Pb206   Z = 82   N = 206   A = 205.97 g/mole   abundance: 24.100 %
-         --->  Isotope: Pb207   Z = 82   N = 207   A = 206.98 g/mole   abundance: 22.100 %
-         --->  Isotope: Pb208   Z = 82   N = 208   A = 207.98 g/mole   abundance: 52.400 %
-          ElmMassFraction: 100.00 %  ElmAbundance 100.00 % 
-
-
- Material: liquidArgon    density:  1.390 g/cm3   RadL:  14.064 cm   Nucl.Int.Length:  86.076 cm 
-                       Imean: 188.000 eV   temperature: 293.15 K  pressure:   1.00 atm
-
-   --->  Element: Ar (Ar)   Z = 18.0   N =    40   A = 39.948 g/mole
-         --->  Isotope:  Ar36   Z = 18   N =  36   A =  35.97 g/mole   abundance:  0.337 %
-         --->  Isotope:  Ar38   Z = 18   N =  38   A =  37.96 g/mole   abundance:  0.063 %
-         --->  Isotope:  Ar40   Z = 18   N =  40   A =  39.96 g/mole   abundance: 99.600 %
-          ElmMassFraction: 100.00 %  ElmAbundance 100.00 % 
-
-
- Material: Galactic    density:  0.000 mg/cm3  RadL: 204310098.490 pc   Nucl.Int.Length: 113427284.261 pc 
-                       Imean:  19.200 eV   temperature:   2.73 K  pressure:   0.00 atm
-
-   --->  Element: H (H)   Z =  1.0   N =     1   A =  1.008 g/mole
-         --->  Isotope:    H1   Z =  1   N =   1   A =   1.01 g/mole   abundance: 99.989 %
-         --->  Isotope:    H2   Z =  1   N =   2   A =   2.01 g/mole   abundance:  0.011 %
-          ElmMassFraction: 100.00 %  ElmAbundance 100.00 % 
-
-
-
-Checking overlaps for volume Calorimeter:0 (G4Box) ... OK! 
-Checking overlaps for volume Abso:0 (G4Box) ... OK! 
-Checking overlaps for volume Gap:0 (G4Box) ... OK! 
-
-------------------------------------------------------------
----> The calorimeter is 10 layers of: [ 10mm of G4_Pb + 5mm of liquidArgon ] 
-------------------------------------------------------------
-
- hInelastic FTFP_BERT : threshold between BERT and FTFP is over the interval 
- for pions :   3 to 6 GeV
- for kaons :   3 to 6 GeV
- for proton :  3 to 6 GeV
- for neutron : 3 to 6 GeV
-
-### Adding tracking cuts for neutron  TimeCut(ns)= 10000  KinEnergyCut(MeV)= 0
-=======================================================================
-======                 Electromagnetic Physics Parameters      ========
-=======================================================================
-LPM effect enabled                                 1
-Enable creation and use of sampling tables         0
-Apply cuts on all EM processes                     0
-Use combined TransportationWithMsc                 Disabled
-Use general process                                1
-Enable linear polarisation for gamma               0
-Enable photoeffect sampling below K-shell          1
-Enable sampling of quantum entanglement            0
-X-section factor for integral approach             0.8
-Min kinetic energy for tables                      100 eV 
-Max kinetic energy for tables                      100 TeV
-Number of bins per decade of a table               7
-Verbose level                                      1
-Verbose level for worker thread                    0
-Bremsstrahlung energy threshold above which 
-  primary e+- is added to the list of secondary    100 TeV
-Bremsstrahlung energy threshold above which primary
-  muon/hadron is added to the list of secondary    100 TeV
-Lowest triplet kinetic energy                      1 MeV
-Enable sampling of gamma linear polarisation       0
-5D gamma conversion model type                     0
-5D gamma conversion model on isolated ion          0
-Livermore data directory                           epics_2017
-=======================================================================
-======                 Ionisation Parameters                   ========
-=======================================================================
-Step function for e+-                              (0.2, 1 mm)
-Step function for muons/hadrons                    (0.2, 0.1 mm)
-Step function for light ions                       (0.2, 0.1 mm)
-Step function for general ions                     (0.2, 0.1 mm)
-Lowest e+e- kinetic energy                         1 keV
-Lowest muon/hadron kinetic energy                  1 keV
-Use ICRU90 data                                    0
-Fluctuations of dE/dx are enabled                  1
-Type of fluctuation model for leptons and hadrons  Urban
-Use built-in Birks satuaration                     0
-Build CSDA range enabled                           0
-Use cut as a final range enabled                   0
-Enable angular generator interface                 0
-Max kinetic energy for CSDA tables                 1 GeV
-Max kinetic energy for NIEL computation            0 eV 
-Linear loss limit                                  0.01
-Read data from file for e+e- pair production by mu 0
-=======================================================================
-======                 Multiple Scattering Parameters          ========
-=======================================================================
-Type of msc step limit algorithm for e+-           1
-Type of msc step limit algorithm for muons/hadrons 0
-Msc lateral displacement for e+- enabled           1
-Msc lateral displacement for muons and hadrons     0
-Urban msc model lateral displacement alg96         1
-Range factor for msc step limit for e+-            0.04
-Range factor for msc step limit for muons/hadrons  0.2
-Geometry factor for msc step limitation of e+-     2.5
-Safety factor for msc step limit for e+-           0.6
-Skin parameter for msc step limitation of e+-      1
-Lambda limit for msc step limit for e+-            1 mm
-Use Mott correction for e- scattering              0
-Factor used for dynamic computation of angular 
-  limit between single and multiple scattering     1
-Fixed angular limit between single 
-  and multiple scattering                          3.1416 rad
-Upper energy limit for e+- multiple scattering     100 MeV
-Type of electron single scattering model           0
-Type of nuclear form-factor                        1
-Screening factor                                   1
-=======================================================================
-
-phot:  for gamma SubType=12 BuildTable=0
-      LambdaPrime table from 200 keV to 100 TeV in 61 bins 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
- LivermorePhElectric : Emin=    0 eV  Emax=  100 TeV  SauterGavrila Fluo
-
-compt:  for gamma SubType=13 BuildTable=1
-      Lambda table from 100 eV  to 1 MeV, 7 bins/decade, spline: 1
-      LambdaPrime table from 1 MeV to 100 TeV in 56 bins 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-       Klein-Nishina : Emin=    0 eV  Emax=  100 TeV
-
-conv:  for gamma SubType=14 BuildTable=1
-      Lambda table from 1.022 MeV to 100 TeV, 18 bins/decade, spline: 1
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-     BetheHeitlerLPM : Emin=    0 eV  Emax=  100 TeV  ModifiedTsai
-
-Rayl:  for gamma SubType=11 BuildTable=1
-      Lambda table from 100 eV  to 150 keV, 7 bins/decade, spline: 0
-      LambdaPrime table from 150 keV to 100 TeV in 62 bins 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-   LivermoreRayleigh : Emin=    0 eV  Emax=  100 TeV  CullenGenerator
-
-msc:  for e-  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            UrbanMsc : Emin=    0 eV  Emax=  100 MeV Nbins=42 100 eV  - 100 MeV
-          StepLim=UseSafety Rfact=0.04 Gfact=2.5 Sfact=0.6 DispFlag:1 Skin=1 Llim=1 mm
-        WentzelVIUni : Emin=  100 MeV Emax=  100 TeV Nbins=42 100 MeV - 100 TeV
-          StepLim=UseSafety Rfact=0.04 Gfact=2.5 Sfact=0.6 DispFlag:1 Skin=1 Llim=1 mm
-
-eIoni:  for e-  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        MollerBhabha : Emin=    0 eV  Emax=  100 TeV
-
-eBrem:  for e-  XStype:4  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      LPM flag: 1 for E > 1 GeV,  VertexHighEnergyTh(GeV)= 100000
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-             eBremSB : Emin=    0 eV  Emax=    1 GeV  ModifiedTsai
-            eBremLPM : Emin=    1 GeV Emax=  100 TeV  ModifiedTsai
-
-CoulombScat:  for e- XStype:1 SubType=1 BuildTable=1
-      Lambda table from 100 MeV to 100 TeV, 7 bins/decade, spline: 0
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=  100 MeV Emax=  100 TeV
-
-msc:  for e+  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            UrbanMsc : Emin=    0 eV  Emax=  100 MeV Nbins=42 100 eV  - 100 MeV
-          StepLim=UseSafety Rfact=0.04 Gfact=2.5 Sfact=0.6 DispFlag:1 Skin=1 Llim=1 mm
-        WentzelVIUni : Emin=  100 MeV Emax=  100 TeV Nbins=42 100 MeV - 100 TeV
-          StepLim=UseSafety Rfact=0.04 Gfact=2.5 Sfact=0.6 DispFlag:1 Skin=1 Llim=1 mm
-
-eIoni:  for e+  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        MollerBhabha : Emin=    0 eV  Emax=  100 TeV
-
-eBrem:  for e+  XStype:4  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      LPM flag: 1 for E > 1 GeV,  VertexHighEnergyTh(GeV)= 100000
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-             eBremSB : Emin=    0 eV  Emax=    1 GeV  ModifiedTsai
-            eBremLPM : Emin=    1 GeV Emax=  100 TeV  ModifiedTsai
-
-annihil:  for e+ XStype:2 SubType=5 BuildTable=0
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            eplus2gg : Emin=    0 eV  Emax=  100 TeV
-
-CoulombScat:  for e+ XStype:1 SubType=1 BuildTable=1
-      Lambda table from 100 MeV to 100 TeV, 7 bins/decade, spline: 0
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=  100 MeV Emax=  100 TeV
-
-msc:  for proton  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        WentzelVIUni : Emin=    0 eV  Emax=  100 TeV Nbins=84 100 eV  - 100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-hIoni:  for proton  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               Bragg : Emin=    0 eV  Emax=    2 MeV
-          BetheBloch : Emin=    2 MeV Emax=  100 TeV
-
-hBrems:  for proton  XStype:1  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               hBrem : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-hPairProd:  for proton  XStype:1  SubType=4
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      Sampling table 17x1001 from 7.50618 GeV to 100 TeV 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-           hPairProd : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-CoulombScat:  for proton XStype:1 SubType=1 BuildTable=1
-      Lambda table from threshold  to 100 TeV, 7 bins/decade, spline: 0
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=    0 eV  Emax=  100 TeV
-
-msc:  for GenericIon  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            UrbanMsc : Emin=    0 eV  Emax=  100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-ionIoni:  for GenericIon  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.02
-      Stopping Power data for 17 ion/material pairs
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            BraggIon : Emin=    0 eV  Emax=    2 MeV
-          BetheBloch : Emin=    2 MeV Emax=  100 TeV
-
-msc:  for alpha  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            UrbanMsc : Emin=    0 eV  Emax=  100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-ionIoni:  for alpha  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.02
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            BraggIon : Emin=    0 eV  Emax=7.9452 MeV
-          BetheBloch : Emin=7.9452 MeV Emax=  100 TeV
-
-msc:  for anti_proton  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        WentzelVIUni : Emin=    0 eV  Emax=  100 TeV Nbins=84 100 eV  - 100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-hIoni:  for anti_proton  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            ICRU73QO : Emin=    0 eV  Emax=    2 MeV
-          BetheBloch : Emin=    2 MeV Emax=  100 TeV
-
-hBrems:  for anti_proton  XStype:1  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               hBrem : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-hPairProd:  for anti_proton  XStype:1  SubType=4
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      Sampling table 17x1001 from 7.50618 GeV to 100 TeV 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-           hPairProd : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-CoulombScat:  for anti_proton XStype:1 SubType=1 BuildTable=1
-      Lambda table from threshold  to 100 TeV, 7 bins/decade, spline: 0
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=    0 eV  Emax=  100 TeV
-
-msc:  for kaon+  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        WentzelVIUni : Emin=    0 eV  Emax=  100 TeV Nbins=84 100 eV  - 100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-hIoni:  for kaon+  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               Bragg : Emin=    0 eV  Emax=1.05231 MeV
-          BetheBloch : Emin=1.05231 MeV Emax=  100 TeV
-
-hBrems:  for kaon+  XStype:1  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               hBrem : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-hPairProd:  for kaon+  XStype:1  SubType=4
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      Sampling table 18x1001 from 3.94942 GeV to 100 TeV 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-           hPairProd : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-CoulombScat:  for kaon+ XStype:1 SubType=1 BuildTable=1
-      Lambda table from threshold  to 100 TeV, 7 bins/decade, spline: 0
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=    0 eV  Emax=  100 TeV
-
-msc:  for kaon-  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        WentzelVIUni : Emin=    0 eV  Emax=  100 TeV Nbins=84 100 eV  - 100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-hIoni:  for kaon-  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            ICRU73QO : Emin=    0 eV  Emax=1.05231 MeV
-          BetheBloch : Emin=1.05231 MeV Emax=  100 TeV
-
-hBrems:  for kaon-  XStype:1  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               hBrem : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-hPairProd:  for kaon-  XStype:1  SubType=4
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      Sampling table 18x1001 from 3.94942 GeV to 100 TeV 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-           hPairProd : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-CoulombScat:  for kaon- XStype:1 SubType=1 BuildTable=1
-      Used Lambda table of kaon+
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=    0 eV  Emax=  100 TeV
-
-msc:  for mu+  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        WentzelVIUni : Emin=    0 eV  Emax=  100 TeV Nbins=84 100 eV  - 100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-muIoni:  for mu+  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               Bragg : Emin=    0 eV  Emax=  200 keV
-        MuBetheBloch : Emin=  200 keV Emax=  100 TeV
-
-muBrems:  for mu+  XStype:1  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-              MuBrem : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-muPairProd:  for mu+  XStype:1  SubType=4
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      Sampling table 21x1001 from 0.85 GeV to 100 TeV 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-          muPairProd : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-CoulombScat:  for mu+ XStype:1 SubType=1 BuildTable=1
-      Lambda table from threshold  to 100 TeV, 7 bins/decade, spline: 0
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=    0 eV  Emax=  100 TeV
-
-msc:  for mu-  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        WentzelVIUni : Emin=    0 eV  Emax=  100 TeV Nbins=84 100 eV  - 100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-muIoni:  for mu-  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            ICRU73QO : Emin=    0 eV  Emax=  200 keV
-        MuBetheBloch : Emin=  200 keV Emax=  100 TeV
-
-muBrems:  for mu-  XStype:1  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-              MuBrem : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-muPairProd:  for mu-  XStype:1  SubType=4
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      Sampling table 21x1001 from 0.85 GeV to 100 TeV 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-          muPairProd : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-CoulombScat:  for mu- XStype:1 SubType=1 BuildTable=1
-      Used Lambda table of mu+
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=    0 eV  Emax=  100 TeV
-
-msc:  for pi+  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        WentzelVIUni : Emin=    0 eV  Emax=  100 TeV Nbins=84 100 eV  - 100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-hIoni:  for pi+  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               Bragg : Emin=    0 eV  Emax=297.505 keV
-          BetheBloch : Emin=297.505 keV Emax=  100 TeV
-
-hBrems:  for pi+  XStype:1  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               hBrem : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-hPairProd:  for pi+  XStype:1  SubType=4
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      Sampling table 20x1001 from 1.11656 GeV to 100 TeV 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-           hPairProd : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-CoulombScat:  for pi+ XStype:1 SubType=1 BuildTable=1
-      Lambda table from threshold  to 100 TeV, 7 bins/decade, spline: 0
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=    0 eV  Emax=  100 TeV
-
-msc:  for pi-  SubType= 10
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-        WentzelVIUni : Emin=    0 eV  Emax=  100 TeV Nbins=84 100 eV  - 100 TeV
-          StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:0 Skin=1 Llim=1 mm
-
-hIoni:  for pi-  XStype:3  SubType=2
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      StepFunction=(0.2, 0.1 mm), integ: 3, fluct: 1, linLossLim= 0.01
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-            ICRU73QO : Emin=    0 eV  Emax=297.505 keV
-          BetheBloch : Emin=297.505 keV Emax=  100 TeV
-
-hBrems:  for pi-  XStype:1  SubType=3
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-               hBrem : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-hPairProd:  for pi-  XStype:1  SubType=4
-      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
-      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
-      Sampling table 20x1001 from 1.11656 GeV to 100 TeV 
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-           hPairProd : Emin=    0 eV  Emax=  100 TeV  ModifiedMephi
-
-CoulombScat:  for pi- XStype:1 SubType=1 BuildTable=1
-      Used Lambda table of pi+
-      ThetaMin(p) < Theta(degree) < 180 pLimit(GeV^1)= 0.139531
-      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
-  eCoulombScattering : Emin=    0 eV  Emax=  100 TeV
-
-====================================================================
-                  HADRONIC PROCESSES SUMMARY (verbose level 1)
-
----------------------------------------------------
-                           Hadronic Processes for neutron
-
-  Process: hadElastic
-        Model:             hElasticCHIPS: 0 eV  ---> 100 TeV
-     Cr_sctns:        G4NeutronElasticXS: 0 eV  ---> 100 TeV
-
-
-  Process: neutronInelastic
-        Model:                      FTFP: 3 GeV ---> 100 TeV
-        Model:            BertiniCascade: 0 eV  ---> 6 GeV
-     Cr_sctns:      G4NeutronInelasticXS: 0 eV  ---> 100 TeV
-
-
-  Process: nCapture
-        Model:               nRadCapture: 0 eV  ---> 100 TeV
-     Cr_sctns:        G4NeutronCaptureXS: 0 eV  ---> 100 TeV
-
-
-  Process: nKiller
-
----------------------------------------------------
-                           Hadronic Processes for B-
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: B-Inelastic
-        Model:                      FTFP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for D-
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: D-Inelastic
-        Model:                      FTFP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for GenericIon
-
-  Process: ionInelastic
-        Model:  Binary Light Ion Cascade: 0 eV /n ---> 6 GeV/n
-        Model:                      FTFP: 3 GeV/n ---> 100 TeV/n
-     Cr_sctns:  Glauber-Gribov Nucl-nucl: 0 eV  ---> 25.6 PeV
-
-
----------------------------------------------------
-                           Hadronic Processes for He3
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV /n ---> 100 TeV/n
-     Cr_sctns:  Glauber-Gribov Nucl-nucl: 0 eV  ---> 25.6 PeV
-
-
-  Process: He3Inelastic
-        Model:  Binary Light Ion Cascade: 0 eV /n ---> 6 GeV/n
-        Model:                      FTFP: 3 GeV/n ---> 100 TeV/n
-     Cr_sctns:  Glauber-Gribov Nucl-nucl: 0 eV  ---> 25.6 PeV
-
-
----------------------------------------------------
-                           Hadronic Processes for alpha
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV /n ---> 100 TeV/n
-     Cr_sctns:  Glauber-Gribov Nucl-nucl: 0 eV  ---> 25.6 PeV
-
-
-  Process: alphaInelastic
-        Model:  Binary Light Ion Cascade: 0 eV /n ---> 6 GeV/n
-        Model:                      FTFP: 3 GeV/n ---> 100 TeV/n
-     Cr_sctns:  Glauber-Gribov Nucl-nucl: 0 eV  ---> 25.6 PeV
-
-
----------------------------------------------------
-                           Hadronic Processes for anti_He3
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV /n ---> 100.1 MeV/n
-        Model:              AntiAElastic: 100 MeV/n ---> 100 TeV/n
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: anti_He3Inelastic
-        Model:                      FTFP: 0 eV /n ---> 100 TeV/n
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: hFritiofCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for anti_alpha
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV /n ---> 100.1 MeV/n
-        Model:              AntiAElastic: 100 MeV/n ---> 100 TeV/n
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: anti_alphaInelastic
-        Model:                      FTFP: 0 eV /n ---> 100 TeV/n
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: hFritiofCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for anti_deuteron
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV /n ---> 100.1 MeV/n
-        Model:              AntiAElastic: 100 MeV/n ---> 100 TeV/n
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: anti_deuteronInelastic
-        Model:                      FTFP: 0 eV /n ---> 100 TeV/n
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: hFritiofCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for anti_hypertriton
-
-  Process: hFritiofCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for anti_lambda
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: anti_lambdaInelastic
-        Model:                      FTFP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: hFritiofCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for anti_neutron
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV  ---> 100.1 MeV
-        Model:              AntiAElastic: 100 MeV ---> 100 TeV
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: anti_neutronInelastic
-        Model:                      FTFP: 0 eV  ---> 100 TeV
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: hFritiofCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for anti_proton
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV  ---> 100.1 MeV
-        Model:              AntiAElastic: 100 MeV ---> 100 TeV
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: anti_protonInelastic
-        Model:                      FTFP: 0 eV  ---> 100 TeV
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: hFritiofCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for anti_triton
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV /n ---> 100.1 MeV/n
-        Model:              AntiAElastic: 100 MeV/n ---> 100 TeV/n
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: anti_tritonInelastic
-        Model:                      FTFP: 0 eV /n ---> 100 TeV/n
-     Cr_sctns:              AntiAGlauber: 0 eV  ---> 25.6 PeV
-
-
-  Process: hFritiofCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for deuteron
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV /n ---> 100 TeV/n
-     Cr_sctns:  Glauber-Gribov Nucl-nucl: 0 eV  ---> 25.6 PeV
-
-
-  Process: dInelastic
-        Model:  Binary Light Ion Cascade: 0 eV /n ---> 6 GeV/n
-        Model:                      FTFP: 3 GeV/n ---> 100 TeV/n
-     Cr_sctns:  Glauber-Gribov Nucl-nucl: 0 eV  ---> 25.6 PeV
-
-
----------------------------------------------------
-                           Hadronic Processes for e+
-
-  Process: positronNuclear
-        Model:   G4ElectroVDNuclearModel: 0 eV  ---> 1 PeV
-     Cr_sctns:          ElectroNuclearXS: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for e-
-
-  Process: electronNuclear
-        Model:   G4ElectroVDNuclearModel: 0 eV  ---> 1 PeV
-     Cr_sctns:          ElectroNuclearXS: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for gamma
-
-  Process: photonNuclear
-        Model:               GammaNPreco: 0 eV  ---> 200 MeV
-        Model:            BertiniCascade: 199 MeV ---> 6 GeV
-        Model:           TheoFSGenerator: 3 GeV ---> 100 TeV
-     Cr_sctns:            GammaNuclearXS: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for kaon+
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: kaon+Inelastic
-        Model:                      FTFP: 3 GeV ---> 100 TeV
-        Model:            BertiniCascade: 0 eV  ---> 6 GeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for kaon-
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: kaon-Inelastic
-        Model:                      FTFP: 3 GeV ---> 100 TeV
-        Model:            BertiniCascade: 0 eV  ---> 6 GeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: hBertiniCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for lambda
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: lambdaInelastic
-        Model:                      FTFP: 3 GeV ---> 100 TeV
-        Model:            BertiniCascade: 0 eV  ---> 6 GeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for mu+
-
-  Process: muonNuclear
-        Model:      G4MuonVDNuclearModel: 0 eV  ---> 1 PeV
-     Cr_sctns:     KokoulinMuonNuclearXS: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for mu-
-
-  Process: muonNuclear
-        Model:      G4MuonVDNuclearModel: 0 eV  ---> 1 PeV
-     Cr_sctns:     KokoulinMuonNuclearXS: 0 eV  ---> 100 TeV
-
-
-  Process: muMinusCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for pi+
-
-  Process: hadElastic
-        Model:           hElasticGlauber: 0 eV  ---> 100 TeV
-     Cr_sctns:  BarashenkovGlauberGribov: 0 eV  ---> 100 TeV
-
-
-  Process: pi+Inelastic
-        Model:                      FTFP: 3 GeV ---> 100 TeV
-        Model:            BertiniCascade: 0 eV  ---> 6 GeV
-     Cr_sctns:  BarashenkovGlauberGribov: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for pi-
-
-  Process: hadElastic
-        Model:           hElasticGlauber: 0 eV  ---> 100 TeV
-     Cr_sctns:  BarashenkovGlauberGribov: 0 eV  ---> 100 TeV
-
-
-  Process: pi-Inelastic
-        Model:                      FTFP: 3 GeV ---> 100 TeV
-        Model:            BertiniCascade: 0 eV  ---> 6 GeV
-     Cr_sctns:  BarashenkovGlauberGribov: 0 eV  ---> 100 TeV
-
-
-  Process: hBertiniCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for proton
-
-  Process: hadElastic
-        Model:             hElasticCHIPS: 0 eV  ---> 100 TeV
-     Cr_sctns:  BarashenkovGlauberGribov: 0 eV  ---> 100 TeV
-
-
-  Process: protonInelastic
-        Model:                      FTFP: 3 GeV ---> 100 TeV
-        Model:            BertiniCascade: 0 eV  ---> 6 GeV
-     Cr_sctns:  BarashenkovGlauberGribov: 0 eV  ---> 100 TeV
-
-
----------------------------------------------------
-                           Hadronic Processes for sigma-
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV  ---> 100 TeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: sigma-Inelastic
-        Model:                      FTFP: 3 GeV ---> 100 TeV
-        Model:            BertiniCascade: 0 eV  ---> 6 GeV
-     Cr_sctns:            Glauber-Gribov: 0 eV  ---> 100 TeV
-
-
-  Process: hBertiniCaptureAtRest
-
----------------------------------------------------
-                           Hadronic Processes for triton
-
-  Process: hadElastic
-        Model:              hElasticLHEP: 0 eV /n ---> 100 TeV/n
-     Cr_sctns:  Glauber-Gribov Nucl-nucl: 0 eV  ---> 25.6 PeV
-
-
-  Process: tInelastic
-        Model:  Binary Light Ion Cascade: 0 eV /n ---> 6 GeV/n
-        Model:                      FTFP: 3 GeV/n ---> 100 TeV/n
-     Cr_sctns:  Glauber-Gribov Nucl-nucl: 0 eV  ---> 25.6 PeV
-
-
-================================================================
-=======================================================================
-======       Pre-compound/De-excitation Physics Parameters     ========
-=======================================================================
-Type of pre-compound inverse x-section              3
-Pre-compound model active                           1
-Pre-compound excitation low energy                  100 keV
-Pre-compound excitation high energy                 30 MeV
-Type of de-excitation inverse x-section             3
-Type of de-excitation factory                       Evaporation+GEM
-Number of de-excitation channels                    68
-Min excitation energy                               10 eV 
-Min energy per nucleon for multifragmentation       200 GeV
-Limit excitation energy for Fermi BreakUp           20 MeV
-Level density (1/MeV)                               0.075
-Use simple level density model                      1
-Use discrete excitation energy of the residual      1
-Time limit for long lived isomeres                  1 ns 
-Isomer production flag                              1
-Internal e- conversion flag                         1
-Store e- internal conversion data                   0
-Correlated gamma emission flag                      0
-Max 2J for sampling of angular correlations         10
-=======================================================================
-G4VisManager: Using G4TrajectoryDrawByCharge as fallback trajectory model.
-See commands in /vis/modeling/trajectories/ for other options.
-### Run 0 starts.
-
--------- WWWW ------- G4Exception-START -------- WWWW -------
-*** G4Exception : Analysis_W001
-      issued by : G4RootNtupleFileManager::SetNtupleMergingMode
-Merging ntuples is not applicable in sequential application.
-Setting was ignored.
-*** This is just a warning message. ***
--------- WWWW -------- G4Exception-END --------- WWWW -------
-
-... set ntuple merging row mode : row-wise - done
-... create file : B4.root - done
-... open analysis file : B4.root - done
-... open analysis file : B4.root - done
-Using 
---> Event 0 starts.
----> End of event: 0
-   Absorber: total energy: 259.894 MeV       total track length: 18.9569 cm 
-        Gap: total energy: 17.4244 MeV       total track length: 8.74398 cm 
-
- ----> print histograms statistic for the entire run 
-
- EAbs : mean = 259.894 MeV rms = 0 eV 
- EGap : mean = 17.4244 MeV rms = 0 eV 
- LAbs : mean = 18.9569 cm  rms = 0 fm 
- LGap : mean = 8.74398 cm  rms = 0 fm 
-... write file : B4.root - done
-... close file : B4.root - done
-There are 4 h1 histograms
-  0 with      0 entries: Edep in absorber
-  1 with      0 entries: Edep in gap
-  2 with      0 entries: trackL in absorber
-  3 with      0 entries: trackL in gap
-List them with "/analysis/list".
-View them with "/vis/plot" or "/vis/reviewPlots".
-     Transportation,   GammaGeneralProc,                msc,              eIoni
-              eBrem,        CoulombScat,                msc,              eIoni
-              eBrem,            annihil,        CoulombScat,                msc
-            ionIoni,                msc,             muIoni,            muBrems
-         muPairProd,        CoulombScat,             muIoni,                msc
-              hIoni,             hBrems,          hPairProd,        CoulombScat
-              hIoni,                msc,              hIoni,             hBrems
-          hPairProd,        CoulombScat,              hIoni,                msc
-              hIoni,             hBrems,          hPairProd,        CoulombScat
-                msc,              hIoni,        CoulombScat,              hIoni
-              hIoni,                msc,            ionIoni,                msc
-            ionIoni,              hIoni,              hIoni,              hIoni
-              hIoni,              hIoni,              hIoni,              hIoni
-              hIoni,              hIoni,              hIoni,              hIoni
-              hIoni,              hIoni,              hIoni,              hIoni
-              hIoni,              hIoni,              hIoni,              hIoni
-              hIoni,              hIoni,              hIoni,              hIoni
-              hIoni,              hIoni,              hIoni,              hIoni
-              hIoni,              hIoni,              hIoni,              hIoni
-              hIoni,              hIoni,              hIoni,              hIoni
-              hIoni,              hIoni,              hIoni,    electronNuclear
-    positronNuclear,        muonNuclear,              Decay,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,         hadElastic
-         hadElastic,         hadElastic,         hadElastic,   neutronInelastic
-           nCapture,    protonInelastic,       pi+Inelastic,       pi-Inelastic
-     kaon+Inelastic,     kaon-Inelastic,    kaon0LInelastic,    kaon0SInelastic
-anti_protonInelastic,anti_neutronInelastic,anti_deuteronInelastic,anti_tritonInelastic
-  anti_He3Inelastic,anti_alphaInelastic,    lambdaInelastic,    sigma+Inelastic
-    sigma-Inelastic,       xi0Inelastic,       xi-Inelastic,    omega-Inelastic
-anti_lambdaInelastic,anti_sigma+Inelastic,anti_sigma-Inelastic,  anti_xi0Inelastic
-  anti_xi-Inelastic,anti_omega-Inelastic,        D+Inelastic,        D0Inelastic
-        D-Inelastic,   anti_D0Inelastic,       Ds+Inelastic,       Ds-Inelastic
-        B+Inelastic,        B0Inelastic,        B-Inelastic,   anti_B0Inelastic
-       Bs0Inelastic,  anti_Bs0Inelastic,       Bc+Inelastic,       Bc-Inelastic
- lambda_c+Inelastic,     xi_c+Inelastic,     xi_c0Inelastic,  omega_c0Inelastic
-  lambda_bInelastic,     xi_b0Inelastic,     xi_b-Inelastic,  omega_b-Inelastic
-anti_lambda_c+Inelastic,anti_xi_c+Inelastic,anti_xi_c0Inelastic,anti_omega_c0Inelastic
-anti_lambda_bInelastic,anti_xi_b0Inelastic,anti_xi_b-Inelastic,anti_omega_b-Inelastic
-hFritiofCaptureAtRest,hBertiniCaptureAtRest,muMinusCaptureAtRest,         dInelastic
-         tInelastic,       He3Inelastic,     alphaInelastic,       ionInelastic
-            nKiller
-### Run 1 starts.
-... create file : B4.root - done
-... open analysis file : B4.root - done
-... open analysis file : B4.root - done
-Using 
---> Event 0 starts.
----> End of event: 0
-   Absorber: total energy: 278.136 MeV       total track length: 20.1737 cm 
-        Gap: total energy: 19.9095 MeV       total track length: 10.0917 cm 
-
- ----> print histograms statistic for the entire run 
-
- EAbs : mean = 278.136 MeV rms = 0 eV 
- EGap : mean = 19.9095 MeV rms = 0 eV 
- LAbs : mean = 20.1737 cm  rms = 0 fm 
- LGap : mean = 10.0917 cm  rms = 0 fm 
-... write file : B4.root - done
-... close file : B4.root - done
-There are 4 h1 histograms
-  0 with      0 entries: Edep in absorber
-  1 with      0 entries: Edep in gap
-  2 with      0 entries: trackL in absorber
-  3 with      0 entries: trackL in gap
-List them with "/analysis/list".
-View them with "/vis/plot" or "/vis/reviewPlots".
-### Run 2 starts.
-... create file : B4.root - done
-... open analysis file : B4.root - done
-... open analysis file : B4.root - done
-Using 
---> Event 0 starts.
----> End of event: 0
-   Absorber: total energy: 435.043 MeV       total track length: 31.1955 cm 
-        Gap: total energy: 37.3961 MeV       total track length: 18.5223 cm 
-
- ----> print histograms statistic for the entire run 
-
- EAbs : mean = 435.043 MeV rms = 0 eV 
- EGap : mean = 37.3961 MeV rms = 0 eV 
- LAbs : mean = 31.1955 cm  rms = 0 fm 
- LGap : mean = 18.5223 cm  rms = 0 fm 
-... write file : B4.root - done
-... close file : B4.root - done
-There are 4 h1 histograms
-  0 with      0 entries: Edep in absorber
-  1 with      0 entries: Edep in gap
-  2 with      0 entries: trackL in absorber
-  3 with      0 entries: trackL in gap
-List them with "/analysis/list".
-View them with "/vis/plot" or "/vis/reviewPlots".
-Graphics systems deleted.
-Visualization Manager deleting...
diff --git a/gui.mac b/gui.mac
deleted file mode 100644
index d7bb656..0000000
--- a/gui.mac
+++ /dev/null
@@ -1,37 +0,0 @@
-#
-# This file permits to customize, with commands,
-# the menu bar of the G4UIXm, G4UIQt, G4UIWin32 sessions.
-# It has no effect with G4UIterminal.
-#
-# File menu :
-/gui/addMenu file File
-/gui/addButton file Quit exit
-#
-# Run menu :
-/gui/addMenu run Run
-/gui/addButton run "beamOn 1" "/run/beamOn 1"
-/gui/addButton run run1 "/control/execute run1.mac"
-#
-# Gun menu :
-/gui/addMenu gun Gun
-/gui/addButton gun "50 MeV"  "/gun/energy 50 MeV"
-/gui/addButton gun "1 GeV"   "/gun/energy 1 GeV"
-/gui/addButton gun "10 GeV"  "/gun/energy 10 GeV"
-/gui/addButton gun "e-"      "/gun/particle e-"
-/gui/addButton gun "pi0"     "/gun/particle pi0"
-/gui/addButton gun "pi+"     "/gun/particle pi+"
-/gui/addButton gun "neutron" "/gun/particle neutron"
-/gui/addButton gun "proton"  "/gun/particle proton"
-#
-# Viewer menu :
-/gui/addMenu viewer Viewer
-/gui/addButton viewer "Set style surface" "/vis/viewer/set/style surface"
-/gui/addButton viewer "Set style wireframe" "/vis/viewer/set/style wireframe"
-/gui/addButton viewer "Refresh viewer" "/vis/viewer/refresh"
-/gui/addButton viewer "Update viewer (interaction or end-of-file)" "/vis/viewer/update"
-/gui/addButton viewer "Flush viewer (= refresh + update)" "/vis/viewer/flush"
-/gui/addButton viewer "Update scene" "/vis/scene/notifyHandlers"
-#
-# To limit the output flow in the "dump" widget :
-/run/printProgress 100
-#
diff --git a/init_vis.mac b/init_vis.mac
deleted file mode 100644
index bcf4ae0..0000000
--- a/init_vis.mac
+++ /dev/null
@@ -1,17 +0,0 @@
-# Macro file for the initialization of example B4
-# in interactive session
-#
-# Set some default verbose
-#
-/control/verbose 2
-/control/saveHistory
-/run/verbose 2
-#
-# Change the default number of threads (in multi-threaded mode)
-#/run/numberOfThreads 4
-#
-# Initialize kernel
-/run/initialize
-#
-# Visualization setting
-/control/execute vis.mac
diff --git a/plotHisto.C b/plotHisto.C
deleted file mode 100644
index 868a742..0000000
--- a/plotHisto.C
+++ /dev/null
@@ -1,43 +0,0 @@
-// ROOT macro file for plotting example B4 histograms
-//
-// Can be run from ROOT session:
-// root[0] .x plotHisto.C
-
-{
-  gROOT->Reset();
-  gROOT->SetStyle("Plain");
-
-  // Draw histos filled by Geant4 simulation
-  //
-
-  // Open file filled by Geant4 simulation
-  TFile f("B4.root");
-
-  // Create a canvas and divide it into 2x2 pads
-  TCanvas* c1 = new TCanvas("c1", "", 20, 20, 1000, 1000);
-  c1->Divide(2,2);
-
-  // Draw Eabs histogram in the pad 1
-  c1->cd(1);
-  TH1D* hist1 = (TH1D*)f.Get("Eabs");
-  hist1->Draw("HIST");
-
-  // Draw Labs histogram in the pad 2
-  c1->cd(2);
-  TH1D* hist2 = (TH1D*)f.Get("Labs");
-  hist2->Draw("HIST");
-
-  // Draw Egap histogram in the pad 3
-  // with logaritmic scale for y
-  TH1D* hist3 = (TH1D*)f.Get("Egap");
-  c1->cd(3);
-  gPad->SetLogy(1);
-  hist3->Draw("HIST");
-
-  // Draw Lgap histogram in the pad 4
-  // with logaritmic scale for y
-  c1->cd(4);
-  gPad->SetLogy(1);
-  TH1D* hist4 = (TH1D*)f.Get("Lgap");
-  hist4->Draw("HIST");
-}
diff --git a/plotNtuple.C b/plotNtuple.C
deleted file mode 100644
index 086bbd4..0000000
--- a/plotNtuple.C
+++ /dev/null
@@ -1,42 +0,0 @@
-// ROOT macro file for plotting example B4 ntuple
-//
-// Can be run from ROOT session:
-// root[0] .x plotNtuple.C
-
-{
-  gROOT->Reset();
-  gROOT->SetStyle("Plain");
-
-  // Draw histos filled by Geant4 simulation
-  //
-
-  // Open file filled by Geant4 simulation
-  TFile f("B4.root");
-
-  // Create a canvas and divide it into 2x2 pads
-  TCanvas* c1 = new TCanvas("c1", "", 20, 20, 1000, 1000);
-  c1->Divide(2,2);
-
-  // Get ntuple
-  TNtuple* ntuple = (TNtuple*)f.Get("B4");
-
-  // Draw Eabs histogram in the pad 1
-  c1->cd(1);
-  ntuple->Draw("Eabs");
-
-  // Draw Labs histogram in the pad 2
-  c1->cd(2);
-  ntuple->Draw("Labs");
-
-  // Draw Egap histogram in the pad 3
-  // with logaritmic scale for y  ?? how to do this?
-  c1->cd(3);
-  gPad->SetLogy(1);
-  ntuple->Draw("Egap");
-
-  // Draw Lgap histogram in the pad 4
-  // with logaritmic scale for y  ?? how to do this?
-  c1->cd(4);
-  gPad->SetLogy(1);
-  ntuple->Draw("Egap");
-}
diff --git a/run1.mac b/run1.mac
deleted file mode 100644
index 1898371..0000000
--- a/run1.mac
+++ /dev/null
@@ -1,44 +0,0 @@
-# Macro file for example B4
-# 
-# Can be run in batch, without graphic
-# or interactively: Idle> /control/execute run1.mac
-#
-# Change the default number of workers (in multi-threading mode) 
-#/run/numberOfThreads 4
-#
-# Initialize kernel
-/run/initialize
-#
-# Default kinematics: 
-# electron 50 MeV in direction (0.,0.,1.)
-# 1 event with tracking/verbose
-#
-/tracking/verbose 1
-/run/beamOn 1
-#
-#
-# muon 300 MeV in direction (0.,0.,1.)
-# 3 events
-#
-/gun/particle mu+
-/gun/energy 3 MeV
-/run/beamOn 3
-#
-# 20 events
-#
-/tracking/verbose 0
-/run/printProgress 5
-/run/beamOn 20
-#
-# Magnetic field
-# 
-/globalField/setValue 0.2 0 0 tesla
-/run/beamOn 3
-#
-# Activate/inactivate physics processes
-#
-/process/list
-/process/inactivate eBrem
-#
-/run/beamOn 20
-#
diff --git a/run2.mac b/run2.mac
deleted file mode 100644
index 35e16a6..0000000
--- a/run2.mac
+++ /dev/null
@@ -1,17 +0,0 @@
-# Macro file for example B4
-# 
-# To be run preferably in batch, without graphics:
-# % exampleB4[a,b,c,d] run2.mac
-#
-#/run/numberOfThreads 4
-#/control/cout/ignoreThreadsExcept 0
-#
-/run/initialize
-#
-# Default kinemtics: 
-# electron 50 MeV in direction (0.,0.,1.)
-# 1000 events
-#
-/run/printProgress 100
-/run/beamOn 1000
-
diff --git a/vis.mac b/vis.mac
deleted file mode 100644
index a4df708..0000000
--- a/vis.mac
+++ /dev/null
@@ -1,82 +0,0 @@
-# Macro file for the visualization setting for the initialization phase 
-# of the B4 example when running in interactive mode
-#
-
-# Use these open statements to open selected visualization
-#
-# Use this open statement to create an OpenGL view:
-/vis/open OGL 600x600-0+0
-#
-# Use this open statement to create an OpenInventor view:
-#/vis/open OIX
-#
-# Use this open statement to create a .prim file suitable for
-# viewing in DAWN:
-#/vis/open DAWNFILE
-#
-# Use this open statement to create a .heprep file suitable for
-# viewing in HepRApp:
-#/vis/open HepRepFile
-#
-# Use this open statement to create a .wrl file suitable for
-# viewing in a VRML viewer:
-#/vis/open VRML2FILE
-#
-# Disable auto refresh and quieten vis messages whilst scene and
-# trajectories are established:
-/vis/viewer/set/autoRefresh false
-/vis/verbose errors
-#
-# Draw geometry:
-/vis/drawVolume
-#
-# Specify view angle:
-/vis/viewer/set/viewpointThetaPhi 90. 180.
-#
-# Specify zoom value:
-#/vis/viewer/zoom 2.
-#
-# Specify style (surface, wireframe, auxiliary edges,...)
-#/vis/viewer/set/style wireframe
-#/vis/viewer/set/auxiliaryEdge true
-#/vis/viewer/set/lineSegmentsPerCircle 100
-#
-# Draw coordinate axes:
-#/vis/scene/add/axes 0 0 0 1 m
-#
-# Draw smooth trajectories at end of event, showing trajectory points
-# as markers 2 pixels wide:
-/vis/scene/add/trajectories smooth
-/vis/modeling/trajectories/create/drawByCharge
-/vis/modeling/trajectories/drawByCharge-0/default/setDrawStepPts true
-/vis/modeling/trajectories/drawByCharge-0/default/setStepPtsSize 1
-# (if too many tracks cause core dump => /tracking/storeTrajectory 0)
-#
-# Draw hits at end of event:
-#/vis/scene/add/hits
-#
-# To draw only gammas:
-#/vis/filtering/trajectories/create/particleFilter
-#/vis/filtering/trajectories/particleFilter-0/add gamma
-#
-# To invert the above, drawing all particles except gammas,
-# keep the above two lines but also add:
-#/vis/filtering/trajectories/particleFilter-0/invert true
-#
-# Many other options are available with /vis/modeling and /vis/filtering.
-# For example, to select colour by particle ID:
-#/vis/modeling/trajectories/create/drawByParticleID
-#/vis/modeling/trajectories/drawByParticleID-0/default/setDrawStepPts true
-# To select or override default colours (note: e+ is blue by default):
-#/vis/modeling/trajectories/list
-#/vis/modeling/trajectories/drawByParticleID-0/set e+ yellow
-#
-# To superimpose all of the events from a given run:
-/vis/scene/endOfEventAction accumulate
-#
-# Re-establish auto refreshing and verbosity:
-/vis/viewer/set/autoRefresh true
-/vis/verbose warnings
-#
-# For file-based drivers, use this to create an empty detector view:
-#/vis/viewer/flush

From c11ecf51de45cc2bc24a12f9cb238234cd07f100 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 11 Jun 2026 11:07:58 +0200
Subject: [PATCH 22/33] update geant4 submodule: fix circular dep in track ID
 pre-assignment

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 lib/geant4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/geant4 b/lib/geant4
index e7827c9..71c7582 160000
--- a/lib/geant4
+++ b/lib/geant4
@@ -1 +1 @@
-Subproject commit e7827c9b07aa6788f37e70658302945d6f129c70
+Subproject commit 71c7582c45c8b7624ef7be16288349c056b1a6dd

From 38a0273087b38fdda2e7dbe8b61007dcc6688628 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 11 Jun 2026 11:10:44 +0200
Subject: [PATCH 23/33] link run_pbwo4 to build root in both build modes

Superbuild: install step creates build/run_pbwo4 symlink pointing at
the executable in build/minicalosim-build/.
Regular build: CMAKE_RUNTIME_OUTPUT_DIRECTORY ensures the executable
lands in build/ regardless of generator.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 CMakeLists.txt            | 2 ++
 superbuild/CMakeLists.txt | 4 +++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b0133e5..381d34d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -55,6 +55,8 @@ target_link_libraries(minicalo PUBLIC ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
 #----------------------------------------------------------------------------
 # Add the executable, and link it to the Geant4 and Python libraries
 #
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+
 add_executable(run_pbwo4 run_pbwo4.cc ${sources} ${headers})
 target_link_libraries(run_pbwo4 ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
 
diff --git a/superbuild/CMakeLists.txt b/superbuild/CMakeLists.txt
index 4a64abe..20b8514 100644
--- a/superbuild/CMakeLists.txt
+++ b/superbuild/CMakeLists.txt
@@ -43,6 +43,8 @@ ExternalProject_Add(run_pbwo4
     -DCMAKE_PREFIX_PATH=${G4_INSTALL}
     -DWITH_GEANT4_UIVIS=OFF
   BUILD_COMMAND   cmake --build <BINARY_DIR> --target run_pbwo4 --parallel ${NPROC}
-  INSTALL_COMMAND ""
+  INSTALL_COMMAND ${CMAKE_COMMAND} -E create_symlink
+    ${CMAKE_BINARY_DIR}/minicalosim-build/run_pbwo4
+    ${CMAKE_BINARY_DIR}/run_pbwo4
   DEPENDS geant4
 )

From 2f74ee0637bf57c72e1ddb7e26fb9d0b8dae8f43 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 11 Jun 2026 11:15:11 +0200
Subject: [PATCH 24/33] rewrite README with full project and Geant4
 modification docs

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 README.md | 292 ++++++++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 273 insertions(+), 19 deletions(-)

diff --git a/README.md b/README.md
index a3e64bb..a887aad 100644
--- a/README.md
+++ b/README.md
@@ -1,31 +1,285 @@
 # miniCaloSim
 
+A Geant4-based calorimeter simulator for teaching and research. Supports arbitrary sampling or homogeneous calorimeter geometries, runs batches of particle showers, and writes ROOT output for analysis.
 
+---
 
-## Getting started
+## Contents
 
+- [Overview](#overview)
+- [Repository layout](#repository-layout)
+- [Build](#build)
+  - [Option A — system Geant4](#option-a--system-geant4)
+  - [Option B — build Geant4 from submodule](#option-b--build-geant4-from-submodule)
+- [Running](#running)
+- [ROOT output format](#root-output-format)
+  - [Hits tree](#hits-tree)
+  - [Steps tree](#steps-tree)
+  - [Spawning tree](#spawning-tree)
+- [Calorimeter materials](#calorimeter-materials)
+- [Docker](#docker)
+- [Geant4 modifications](#geant4-modifications)
 
-### Materials
+---
 
-Below are some useful material choices. Not all information is provided, but can be found on the internet ;)
+## Overview
 
-## Scintillator materials:
+miniCaloSim wraps the standard Geant4 B4a example into a configurable geometry driven by a `GeometryDescriptor` object. A geometry is a stack of layers; each layer is a slab of named NIST material with an optional sensor grid that accumulates deposited energy. The primary particle type and energy are configurable at run time.
 
- *  G4_POLYSTYRENE: a polymer of styrene with a density of 1.06 g/cm3 and a refractive index of 1.57. Cost: basically nothing.
- *  G4_PLASTIC_SC_VINYLTOLUENE: a plastic scintillator based on vinyltoluene with a density of 1.032 g/cm3 and a refractive index of 1.58. Cost: basically nothing.
- *  G4_BGO: bismuth germanate, an inorganic crystal scintillator with a density of 7.13 g/cm3 and a refractive index of 2.15. Cost 0.8 CHF/cm3
- *  G4_LSO: lutetium oxyorthosilicate, an inorganic crystal scintillator with a density of 7.4 g/cm3 and a refractive index of 1.82. Cost: 6 CHF/cm3
- *  G4_LYSO: lutetium yttrium oxyorthosilicate, an inorganic crystal scintillator with a density of 7.1 g/cm3 and a refractive index of 1.81. 30CHF / cm3
+The default executable `run_pbwo4` simulates electron showers in a 20 cm PbWO₄ crystal with a 10×10 sensor grid and writes a ROOT file.
 
-## Absorber materials
- 
- * G4_Pb: lead, a high-density and high-Z material that is commonly used as an absorber for electromagnetic calorimeters. It has a density of 11.35 g/cm3 and a radiation length of 0.56 cm. Cost: 0.03 CHF/cm3.
- * G4_Fe: iron, a medium-density and medium-Z material that is often used as an absorber for hadronic calorimeters. It has a density of 7.87 g/cm3 and an interaction length of 16.77 cm. Cost: 0.005 CHF/cm3.
- * G4_W: tungsten, a very high-density and very high-Z material that is suitable for compact and high-resolution electromagnetic calorimeters. It has a density of 19.3 g/cm3 and a radiation length of 0.35 cm. 0.6 CHF/cm3.
- * G4_Cu: copper, a high-density and high-Z material that is also used as an absorber for electromagnetic calorimeters. It has a density of 8.96 g/cm3 and a radiation length of 1.43 cm. 0.08 CHF/cm3
- * G4_BRASS: It has a density of 8.53 g/cm3 and a composition of 70% copper and 30% zinc by mass. It has a radiation length of 1.46 cm and an interaction length of 16.95 cm. Cost: 0.02 CHF/cm3
+---
 
-## For homogenous calorimeters
+## Repository layout
 
- *  G4_CESIUM_IODIDE: cesium iodide, an inorganic crystal scintillator with a density of 4.51 g/cm3 and a refractive index of 1.79. radiation length about 1.9 cm. Cost: about 2 CHF/cm3
- * G4_PbWO4: lead tungstate crystal (CMS ECAL). Lead tungstate has a very high density of 19.3 g/cm3 and a very short radiation length of 0.89 cm, which makes it suitable for compact and high-resolution electromagnetic calorimeters. Cost: about 3 CHF/cm3
+```
+run_pbwo4.cc          main executable entry point
+src/                  Geant4 application sources
+  ActionInitialization.cc
+  DetectorConstruction.cc   reads GeometryDescriptor, builds Geant4 volumes
+  EventAction.cc            fills the Hits ntuple at end of each event
+  SteppingAction.cc         fills Steps and Spawning ntuples per step
+  RunAction.cc              creates all three ROOT ntuples
+  G4System.cc               owns the Geant4 run manager lifetime
+  GeometryDescriptor.cc     geometry data model (layers + sensors)
+  PrimaryGeneratorAction.cc
+include/              corresponding headers
+bind/                 Python bindings (pybind11 + pure-Python helpers)
+  bindings.cpp        exposes Sensor, Layer, GeometryDescriptor, G4System
+  G4Calo.py           high-level Python API (run_batch, display_event)
+  G4Calo_exec.py      worker subprocess entry point
+  minicalo_tools.py   TempFileManager for subprocess IPC via /dev/shm
+  minipandas.py       MiniFrame: minimal NumPy-backed dataframe
+lib/
+  geant4/             Geant4 source submodule (fork with modifications)
+  pybind11/           pybind11 submodule
+superbuild/           CMake superbuild to compile Geant4 from source
+docker/               Dockerfile-mini
+docs/                 design documents
+```
+
+---
+
+## Build
+
+### Option A — system Geant4
+
+Requires a Geant4 ≥ 11 installation visible to CMake (e.g. via `Geant4_DIR` or `CMAKE_PREFIX_PATH`), plus pybind11 (submodule) and Python 3 development headers.
+
+```bash
+cmake -B build -S .
+cmake --build build --parallel $(nproc)
+# executable: build/run_pbwo4
+```
+
+### Option B — build Geant4 from submodule
+
+The superbuild compiles Geant4 from `lib/geant4` into `build/geant4-install`, then builds minicalosim against it. Three targets are available:
+
+```bash
+cmake -B build -S superbuild/            # configure once
+
+cmake --build build --target geant4      # compile Geant4 (~30–60 min)
+cmake --build build --target run_pbwo4   # compile minicalosim
+cmake --build build                      # both
+```
+
+After the build, the executable is at `build/run_pbwo4` (symlink in the superbuild case).
+
+**Options:**
+
+| CMake option | Default | Meaning |
+|---|---|---|
+| `GEANT4_INSTALL_DATA` | `ON` | Download Geant4 physics data tables (~2 GB) |
+
+The superbuild caps parallelism at `min(nproc, 16)` to avoid memory exhaustion.
+
+---
+
+## Running
+
+```bash
+# default: 10 events, writes pbwo4_10events_hits.root
+build/run_pbwo4
+
+# custom number of events
+build/run_pbwo4 500
+```
+
+Output file name: `pbwo4_<nEvents>events_hits.root`.
+
+The geometry is hardcoded in `run_pbwo4.cc`: a single 20 cm PbWO₄ layer with a 10×10 sensor grid, bombarded with 1 GeV electrons.
+
+---
+
+## ROOT output format
+
+Each run produces a ROOT file with three TTrees.
+
+### Hits tree
+
+One row per simulated event. Contains integrated quantities over the whole calorimeter.
+
+| Column | Type | Description |
+|---|---|---|
+| `true_energy` | `double` | Primary particle energy [MeV] |
+| `total_dep_energy` | `double` | Total energy deposited in all sensors [MeV] |
+| `N_layers` | `int` | Number of layers |
+| `N_active_layers` | `int` | Number of active (sensitive) layers |
+| `N_sensors` | `int` | Total number of sensors |
+| `sensor_energy[N]` | `double[]` | Deposited energy per sensor [MeV] |
+| `sensor_x/y/z[N]` | `double[]` | Sensor centre position [mm] |
+| `sensor_dx/dy/dz[N]` | `double[]` | Sensor half-size [mm] |
+| `sensor_layer[N]` | `int[]` | Layer index of each sensor |
+| `sensor_copy_number[N]` | `int[]` | Copy number within its layer |
+
+### Steps tree
+
+One row per Geant4 step. Every step of every track of every event is recorded.
+
+| Column | Type | Description |
+|---|---|---|
+| `event_id` | `int` | Event index within the run |
+| `track_id` | `int` | Track ID (1 = primary, ≥2 = secondaries) |
+| `step_no` | `int` | Step number within this track (starts at 1) |
+| `pdg` | `int` | PDG encoding of the particle |
+| `pre_x/y/z` | `double` | Pre-step position [mm] |
+| `pre_E` | `double` | Kinetic energy at step start [MeV] |
+| `post_x/y/z` | `double` | Post-step position [mm] |
+| `post_E` | `double` | Kinetic energy at step end [MeV] |
+| `edep` | `double` | Energy deposited in medium at this step [MeV] |
+| `step_length` | `double` | Geometric step length [mm] |
+| `process` | `string` | Physics process that ended this step |
+| `layer_id` | `int` | Layer index at the pre-step point (-1 = outside all layers) |
+| `material` | `string` | Material name at the pre-step point |
+| `pre_dx/dy/dz` | `double` | Pre-step momentum unit direction |
+| `Bx/By/Bz` | `double` | Magnetic field at pre-step position [T] |
+| `Ex/Ey/Ez` | `double` | Electric field at pre-step position [V/m] |
+| `child_track_ids` | `int[]` | Track IDs of all secondaries spawned during this step (empty if none) |
+
+**Track IDs** are assigned sequentially per event starting from 1. The primary particle is always track 1. Within an event, `track_id` uniquely identifies a particle. See also the Spawning tree.
+
+### Spawning tree
+
+One row per secondary particle birth. Enables direct shower-tree reconstruction without position joins.
+
+| Column | Type | Description |
+|---|---|---|
+| `event_id` | `int` | Event index |
+| `parent_track_id` | `int` | Track ID of the parent particle |
+| `parent_step_no` | `int` | Step number of the parent at which this secondary was created |
+| `child_track_id` | `int` | Track ID of the newly born secondary |
+
+**Example join:** to find all secondaries born at step 5 of track 3 in event 0:
+```python
+spawning[(spawning.event_id == 0) &
+         (spawning.parent_track_id == 3) &
+         (spawning.parent_step_no == 5)]
+```
+
+The same information is available in the Steps tree via the `child_track_ids` array column on the parent's row.
+
+---
+
+## Calorimeter materials
+
+A few material choices available via NIST names:
+
+### Scintillators (active layers)
+
+| NIST name | Density | Notes |
+|---|---|---|
+| `G4_POLYSTYRENE` | 1.06 g/cm³ | cheap plastic scintillator |
+| `G4_PLASTIC_SC_VINYLTOLUENE` | 1.032 g/cm³ | plastic scintillator |
+| `G4_BGO` | 7.13 g/cm³ | inorganic crystal, ~0.8 CHF/cm³ |
+| `G4_LSO` | 7.4 g/cm³ | inorganic crystal, ~6 CHF/cm³ |
+| `G4_LYSO` | 7.1 g/cm³ | inorganic crystal, ~30 CHF/cm³ |
+
+### Absorbers (passive layers)
+
+| NIST name | Density | X₀ | Notes |
+|---|---|---|---|
+| `G4_Pb` | 11.35 g/cm³ | 0.56 cm | standard EM calorimeter absorber |
+| `G4_Fe` | 7.87 g/cm³ | — | hadronic calorimeter absorber |
+| `G4_W` | 19.3 g/cm³ | 0.35 cm | compact high-resolution EM |
+| `G4_Cu` | 8.96 g/cm³ | 1.43 cm | EM calorimeter absorber |
+| `G4_BRASS` | 8.53 g/cm³ | 1.46 cm | 70% Cu / 30% Zn |
+
+### Homogeneous calorimeters
+
+| NIST name | Density | X₀ | Notes |
+|---|---|---|---|
+| `G4_CESIUM_IODIDE` | 4.51 g/cm³ | ~1.9 cm | inorganic crystal |
+| `G4_PbWO4` | 8.28 g/cm³ | 0.89 cm | lead tungstate (CMS ECAL) |
+
+---
+
+## Docker
+
+`docker/Dockerfile-mini` builds a minimal Ubuntu 22.04 image with:
+- Geant4 compiled from the `lib/geant4` submodule (batch mode, no vis, no multithreading)
+- The `minicalo` Python package installed system-wide
+- Python dependencies: numpy, pandas, uproot, awkward, plotly
+
+Build (from the repo root, passing `COMMIT` to pin the source):
+```bash
+docker build \
+  --build-arg COMMIT=$(git rev-parse HEAD) \
+  --build-arg BUILD_DATE=$(date -u +"%Y-%m-%dT%H:%M:%SZ") \
+  -f docker/Dockerfile-mini \
+  -t minicalosim:latest \
+  --build-context minicalosim=. \
+  .
+```
+
+---
+
+## Geant4 modifications
+
+The `lib/geant4` submodule is a fork of Geant4 with three small changes to enable pre-assigning track IDs to secondary particles at the moment they are created, so that `UserSteppingAction` can record which child track IDs a step spawned (the `child_track_ids` column and the Spawning tree).
+
+### Background
+
+In unmodified Geant4, track IDs are assigned in `G4EventManager::StackTracks()`, which is called only after the parent track has finished all its steps. At the time `UserSteppingAction` fires, the secondaries visible via `G4Step::GetSecondaryInCurrentStep()` have not yet received their IDs.
+
+### Changes
+
+All changes are on the `minicalosim-spawning` branch of `git@gitlab.etp.kit.edu:lbogner/geant4.git`.
+
+**`source/tracking/include/G4SteppingManager.hh`**
+
+Adds a `G4int* fTrackIDCounter` member and a `SetTrackIDCounter(G4int*)` setter. The pointer is set by `G4EventManager` (via `G4TrackingManager`) at the start of each event and points directly into `G4EventManager::trackIDCounter`.
+
+**`source/tracking/include/G4TrackingManager.hh`**
+
+Adds a `SetTrackIDCounter(G4int*)` pass-through that forwards the pointer into `G4SteppingManager`.
+
+**`source/tracking/src/G4SteppingManager.cc`**
+
+In `ProcessSecondariesFromParticleChange()`, after `SetParentID` and `SetCreatorProcess`, immediately assigns a track ID to each secondary by incrementing through the pointer:
+
+```cpp
+if (fTrackIDCounter) {
+    tempSecondaryTrack->SetTrackID(++(*fTrackIDCounter));
+}
+```
+
+**`source/event/src/G4EventManager.cc`**
+
+- Calls `trackManager->SetTrackIDCounter(&trackIDCounter)` once before the event's tracking loop.
+- `StackTracks()` is updated to skip counter increment and ID assignment for tracks that already have a non-zero ID (i.e. were pre-assigned above):
+
+```cpp
+if (IDhasAlreadySet) {
+    ++trackIDCounter;          // advance for primaries (ID set externally)
+} else if (newTrack->GetTrackID() == 0) {
+    ++trackIDCounter;          // normal secondary: assign as before
+    newTrack->SetTrackID(trackIDCounter);
+    ...
+}
+// else: pre-assigned secondary — counter already incremented, skip
+```
+
+### Why not include `G4EventManager.hh` in `G4SteppingManager.cc`?
+
+`G4event` already depends on `G4tracking` (`G4EventManager` uses `G4TrackingManager`), so including `G4EventManager.hh` in the tracking module would create a circular dependency. The pointer approach avoids any new include: `G4SteppingManager` only needs a `G4int*`, which requires no additional header.

From 26821af188e3102ff9bbb26c6cdcb0a8993a1a50 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Fri, 12 Jun 2026 13:06:51 +0200
Subject: [PATCH 25/33] replace Dockerfile-mini with new superbuild-based
 Dockerfile

Switches from the old per-component Dockerfile-mini to a unified
Dockerfile that uses the superbuild CMake setup, Ubuntu 24.04, uv for
Python dependency management, and pyproject.toml for the Python
environment.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 docker/Dockerfile      | 68 ++++++++++++++++++++++++++++++++++++++++++
 docker/Dockerfile-mini | 68 ------------------------------------------
 docker/pyproject.toml  | 21 +++++++++++++
 3 files changed, 89 insertions(+), 68 deletions(-)
 create mode 100644 docker/Dockerfile
 delete mode 100644 docker/Dockerfile-mini
 create mode 100644 docker/pyproject.toml

diff --git a/docker/Dockerfile b/docker/Dockerfile
new file mode 100644
index 0000000..756d9b4
--- /dev/null
+++ b/docker/Dockerfile
@@ -0,0 +1,68 @@
+FROM ubuntu:24.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+# ---------------------------------------------------------------------------
+# System dependencies (dnf instead of apt)
+# ---------------------------------------------------------------------------
+RUN apt-get update && apt-get install -y \
+    gcc \
+    g++ \
+    make \
+    cmake \
+    ninja-build \
+    libxerces-c-dev \
+    git \
+    curl \
+    ca-certificates \
+    python3 \
+    python3-dev \
+    python3-pip \
+    python3-venv \
+    && rm -rf /var/lib/apt/lists/*
+# ---------------------------------------------------------------------------
+# uv
+# ---------------------------------------------------------------------------
+RUN curl -LsSf https://astral.sh/uv/install.sh | sh
+ENV PATH="/root/.local/bin:${PATH}"
+
+WORKDIR /src
+
+# ---------------------------------------------------------------------------
+# Copy only files needed for the C++ build
+# ---------------------------------------------------------------------------
+COPY CMakeLists.txt .
+COPY superbuild/ superbuild/
+COPY src/ src/
+COPY include/ include/
+COPY bind/ bind/
+COPY lib/ lib/
+COPY run_pbwo4.cc .
+
+# lib/geant4/.git is a submodule pointer to the host's .git/modules dir, which
+# is not copied into the image. Replace it with a fresh repo so Geant4's cmake
+# git status calls succeed.
+RUN rm lib/geant4/.git && git init lib/geant4
+
+# ---------------------------------------------------------------------------
+# Build Geant4 + miniCaloSim
+# ---------------------------------------------------------------------------
+RUN cmake -S superbuild -B build -G Ninja \
+      -DGEANT4_INSTALL_DATA=ON
+
+RUN cmake --build build --parallel
+
+# ---------------------------------------------------------------------------
+# Python environment (uv)
+# ---------------------------------------------------------------------------
+RUN uv venv /opt/venv
+
+ENV PATH="/opt/venv/bin:${PATH}"
+
+ADD docker/pyproject.toml pyproject.toml
+
+RUN uv sync
+
+WORKDIR /workspace
+
+ENTRYPOINT ["/bin/bash", "-l"]
\ No newline at end of file
diff --git a/docker/Dockerfile-mini b/docker/Dockerfile-mini
deleted file mode 100644
index 7a45b7c..0000000
--- a/docker/Dockerfile-mini
+++ /dev/null
@@ -1,68 +0,0 @@
-FROM ubuntu:22.04
-
-SHELL ["/bin/bash", "-c"]
-
-USER root
-ENV DEBIAN_FRONTEND=noninteractive
-
-# Build tools + minimal Python
-RUN apt-get update -y && apt-get install -y \
-    python3 python3-dev python3-pip \
-    cmake g++ gcc binutils \
-    libssl-dev wget git \
-    && rm -rf /var/lib/apt/lists/*
-
-RUN python3 -m pip install --upgrade pip && \
-    python3 -m pip install numpy pandas uproot awkward plotly ipython && \
-    ln -sf /usr/bin/python3 /usr/bin/python
-
-# Geant4 — build from submodule source (batch mode only, no visualization, no multithreading)
-ADD minicalosim/lib/geant4 /tmp/geant4-src
-
-RUN rm -f /tmp/geant4-src/.git && \
-    cmake \
-        -S /tmp/geant4-src \
-        -B /tmp/geant4-build \
-        -DCMAKE_INSTALL_PREFIX=/opt/geant4-v11.1.2 \
-        -DCMAKE_RULE_MESSAGES=OFF \
-        -DGEANT4_INSTALL_DATA=ON \
-        -DGEANT4_BUILD_MULTITHREADED=OFF \
-        -DGEANT4_BUILD_TLS_MODEL=global-dynamic \
-        > /dev/null && \
-    cmake --build /tmp/geant4-build --parallel $(( $(nproc) < 16 ? $(nproc) : 16 )) > /dev/null && \
-    cmake --install /tmp/geant4-build > /dev/null && \
-    rm -rf /tmp/geant4-src /tmp/geant4-build
-
-ENV LD_LIBRARY_PATH="/opt/geant4-v11.1.2/lib"
-
-# Build minicalo
-ARG BUILD_DATE
-ARG COMMIT
-ARG USER
-LABEL org.label-schema.build-date=$BUILD_DATE
-
-ADD minicalosim /root/minicalosim
-
-RUN cd /root/minicalosim && git checkout $COMMIT && \
-    git submodule update --init lib/pybind11 && \
-    cmake \
-        -S . -B build \
-        -DWITH_GEANT4_UIVIS=OFF \
-        > /dev/null && \
-    cmake --build build --parallel $(( $(nproc) < 16 ? $(nproc) : 16 )) && \
-    cp build/minicalo*.so /usr/local/lib/python3.10/dist-packages/
-
-RUN echo "commit = '${COMMIT}'" > /root/minicalosim/bind/minicalo_version.py && \
-    cp /root/minicalosim/bind/G4Calo.py \
-       /root/minicalosim/bind/minicalo_tools.py \
-       /root/minicalosim/bind/minipandas.py \
-       /root/minicalosim/bind/minicalo_version.py \
-       /usr/local/lib/python3.10/dist-packages/ && \
-    install -m 755 /root/minicalosim/bind/G4Calo_exec.py /usr/local/bin/G4Calo_exec.py
-
-# Copy examples
-RUN cp -r /root/minicalosim/bind /examples && \
-    rm -rf /root/minicalosim
-
-WORKDIR /examples
-CMD ["bash"]
diff --git a/docker/pyproject.toml b/docker/pyproject.toml
new file mode 100644
index 0000000..89a6ab0
--- /dev/null
+++ b/docker/pyproject.toml
@@ -0,0 +1,21 @@
+[project]
+name = "minicalosim"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.14"
+dependencies = [
+    "awkward>=2.9.1",
+    "awkward-pandas>=2023.8.0",
+    "hist>=2.10.1",
+    "jupyter>=1.1.1",
+    "matplotlib>=3.10.9",
+    "mplhep>=1.2.0",
+    "networkx>=3.6.1",
+    "numpy>=2.4.6",
+    "pandas>=3.0.3",
+    "plotly>=6.8.0",
+    "polars>=1.41.2",
+    "seaborn>=0.13.2",
+    "uproot>=5.7.4",
+]

From 0adc896bce498b64e83c2f0b543a742b740ae7de Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Wed, 17 Jun 2026 14:40:05 +0200
Subject: [PATCH 26/33] add post-step momentum direction to Steps ntuple

Pre-step direction was already recorded; post_dx/dy/dz lets students
compare momentum direction before and after each step.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 README.md             | 1 +
 src/RunAction.cc      | 3 +++
 src/SteppingAction.cc | 6 ++++++
 3 files changed, 10 insertions(+)

diff --git a/README.md b/README.md
index a887aad..8d2f147 100644
--- a/README.md
+++ b/README.md
@@ -153,6 +153,7 @@ One row per Geant4 step. Every step of every track of every event is recorded.
 | `layer_id` | `int` | Layer index at the pre-step point (-1 = outside all layers) |
 | `material` | `string` | Material name at the pre-step point |
 | `pre_dx/dy/dz` | `double` | Pre-step momentum unit direction |
+| `post_dx/dy/dz` | `double` | Post-step momentum unit direction |
 | `Bx/By/Bz` | `double` | Magnetic field at pre-step position [T] |
 | `Ex/Ey/Ez` | `double` | Electric field at pre-step position [V/m] |
 | `child_track_ids` | `int[]` | Track IDs of all secondaries spawned during this step (empty if none) |
diff --git a/src/RunAction.cc b/src/RunAction.cc
index 2d7507f..4e00ef5 100644
--- a/src/RunAction.cc
+++ b/src/RunAction.cc
@@ -111,6 +111,9 @@ RunAction::RunAction()
   analysisManager->CreateNtupleDColumn("Ey");          // col 24 [V/m]
   analysisManager->CreateNtupleDColumn("Ez");          // col 25 [V/m]
   analysisManager->CreateNtupleIColumn("child_track_ids", stepChildIds); // col 26 (variable-length array)
+  analysisManager->CreateNtupleDColumn("post_dx");     // col 27
+  analysisManager->CreateNtupleDColumn("post_dy");     // col 28
+  analysisManager->CreateNtupleDColumn("post_dz");     // col 29
   analysisManager->FinishNtuple();
 
   // Spawning ntuple (one row per secondary born, ntuple id=2)
diff --git a/src/SteppingAction.cc b/src/SteppingAction.cc
index cb4146f..a40b6c4 100644
--- a/src/SteppingAction.cc
+++ b/src/SteppingAction.cc
@@ -143,6 +143,12 @@ void SteppingAction::UserSteppingAction(const G4Step* step)
   analysisManager->FillNtupleDColumn(1, 18, dir.y());
   analysisManager->FillNtupleDColumn(1, 19, dir.z());
 
+  // G: post-step momentum direction (unit vector)
+  const auto postDir = post->GetMomentumDirection();
+  analysisManager->FillNtupleDColumn(1, 27, postDir.x());
+  analysisManager->FillNtupleDColumn(1, 28, postDir.y());
+  analysisManager->FillNtupleDColumn(1, 29, postDir.z());
+
   // Field: B [T] and E [V/m] at pre-step position; zero if no field is registered
   G4double Bx=0, By=0, Bz=0, Ex=0, Ey=0, Ez=0;
   const auto* fm = G4TransportationManager::GetTransportationManager()->GetFieldManager();

From 942130c667c3c0e736d782cff4cae373db095831 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Wed, 17 Jun 2026 14:50:34 +0200
Subject: [PATCH 27/33] add run-at-etp.sh for batch pbwo4 production runs

Builds and runs run_pbwo4 ten times with 10k events each, then moves
the renamed outputs to /ceph/lbogner/geant_steps/.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 run-at-etp.sh | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100755 run-at-etp.sh

diff --git a/run-at-etp.sh b/run-at-etp.sh
new file mode 100755
index 0000000..ff264e4
--- /dev/null
+++ b/run-at-etp.sh
@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+cd "$(dirname "${BASH_SOURCE[0]}")"
+
+cmake -B build -S .
+cmake --build build --parallel 8
+
+for i in $(seq 0 9); do
+    build/run_pbwo4 10000
+    mv pbwo4_10000events_hits.root "pbwo4_10k_${i}.root"
+done
+
+mv pbwo4_10k_*.root /ceph/lbogner/geant_steps/

From 11d01d701501aac0a6fc59670e6f7bbe86499b08 Mon Sep 17 00:00:00 2001
From: Lars Bogner <ich@larsbogner.de>
Date: Wed, 24 Jun 2026 09:45:31 +0200
Subject: [PATCH 28/33] Add run_sampling executable for sampling calorimeter
 geometries

Mirrors run_pbwo4 but alternates thin absorber and active layers,
with four selectable configs (by name or 1-based index): pb_scint,
fe_scint, w_scint_ecal (homogeneous ECAL-like preshower + W/scint
sampling section), and pb_lar. Each is sized to reach ~20-25 X0 of
absorber despite the dilution from inactive gaps. Wired into the
top-level CMakeLists, superbuild, and Dockerfile alongside run_pbwo4.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 CMakeLists.txt            |   3 +
 README.md                 |  45 +++++++++++---
 docker/Dockerfile         |   1 +
 run_sampling.cc           | 124 ++++++++++++++++++++++++++++++++++++++
 superbuild/CMakeLists.txt |  16 +++++
 5 files changed, 180 insertions(+), 9 deletions(-)
 create mode 100644 run_sampling.cc

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 381d34d..b6ce8ad 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -60,6 +60,9 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 add_executable(run_pbwo4 run_pbwo4.cc ${sources} ${headers})
 target_link_libraries(run_pbwo4 ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
 
+add_executable(run_sampling run_sampling.cc ${sources} ${headers})
+target_link_libraries(run_sampling ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
+
 #----------------------------------------------------------------------------
 # Install the executable to 'bin' directory under CMAKE_INSTALL_PREFIX
 #
diff --git a/README.md b/README.md
index 8d2f147..0634da7 100644
--- a/README.md
+++ b/README.md
@@ -26,14 +26,15 @@ A Geant4-based calorimeter simulator for teaching and research. Supports arbitra
 
 miniCaloSim wraps the standard Geant4 B4a example into a configurable geometry driven by a `GeometryDescriptor` object. A geometry is a stack of layers; each layer is a slab of named NIST material with an optional sensor grid that accumulates deposited energy. The primary particle type and energy are configurable at run time.
 
-The default executable `run_pbwo4` simulates electron showers in a 20 cm PbWO₄ crystal with a 10×10 sensor grid and writes a ROOT file.
+The default executable `run_pbwo4` simulates electron showers in a 20 cm PbWO₄ crystal with a 10×10 sensor grid and writes a ROOT file. A second executable, `run_sampling`, simulates the same kind of showers in a sampling calorimeter (alternating thin absorber and active layers); the layer configuration is selected by name at run time.
 
 ---
 
 ## Repository layout
 
 ```
-run_pbwo4.cc          main executable entry point
+run_pbwo4.cc          homogeneous PbWO4 crystal executable entry point
+run_sampling.cc       sampling calorimeter executable entry point (selectable layer configs)
 src/                  Geant4 application sources
   ActionInitialization.cc
   DetectorConstruction.cc   reads GeometryDescriptor, builds Geant4 volumes
@@ -69,22 +70,23 @@ Requires a Geant4 ≥ 11 installation visible to CMake (e.g. via `Geant4_DIR` or
 ```bash
 cmake -B build -S .
 cmake --build build --parallel $(nproc)
-# executable: build/run_pbwo4
+# executables: build/run_pbwo4, build/run_sampling
 ```
 
 ### Option B — build Geant4 from submodule
 
-The superbuild compiles Geant4 from `lib/geant4` into `build/geant4-install`, then builds minicalosim against it. Three targets are available:
+The superbuild compiles Geant4 from `lib/geant4` into `build/geant4-install`, then builds minicalosim against it. Four targets are available:
 
 ```bash
-cmake -B build -S superbuild/            # configure once
+cmake -B build -S superbuild/              # configure once
 
-cmake --build build --target geant4      # compile Geant4 (~30–60 min)
-cmake --build build --target run_pbwo4   # compile minicalosim
-cmake --build build                      # both
+cmake --build build --target geant4        # compile Geant4 (~30–60 min)
+cmake --build build --target run_pbwo4     # compile run_pbwo4
+cmake --build build --target run_sampling  # compile run_sampling
+cmake --build build                        # all
 ```
 
-After the build, the executable is at `build/run_pbwo4` (symlink in the superbuild case).
+After the build, the executables are at `build/run_pbwo4` and `build/run_sampling` (symlinks in the superbuild case).
 
 **Options:**
 
@@ -110,6 +112,30 @@ Output file name: `pbwo4_<nEvents>events_hits.root`.
 
 The geometry is hardcoded in `run_pbwo4.cc`: a single 20 cm PbWO₄ layer with a 10×10 sensor grid, bombarded with 1 GeV electrons.
 
+### Sampling calorimeter (`run_sampling`)
+
+```bash
+# default config (pb_scint), 10 events, writes sampling_pb_scint_10events_hits.root
+build/run_sampling
+
+# pick a config by name, default event count
+build/run_sampling fe_scint
+
+# pick a config by 1-based index, and a number of events
+build/run_sampling 3 500
+```
+
+The config can be given either by name or by its 1-based index (`run_sampling --help`-style usage, including the index list, is printed on an invalid selection). Output file name: `sampling_<configName>_<nEvents>events_hits.root` (always uses the resolved name, even when selected by index).
+
+All configs use a 10×10 sensor grid per active layer and are sized to reach ~20–25 X₀ of absorber, comparable to `run_pbwo4`'s 20 cm PbWO₄ block. Because a sampling stack dilutes the absorber with inactive gaps, the lower the absorber's Z the physically deeper the stack has to be to reach the same number of radiation lengths — `fe_scint` is twice as deep as `pb_scint` for this reason. Configs, defined in `run_sampling.cc`:
+
+| # | Config name | Layers | Total depth | ~X₀ | Notes |
+|---|---|---|---|---|---|
+| 1 | `pb_scint` | 60× (0.2 cm `G4_Pb` + 0.3 cm scint) | 30 cm | 21 | classic fine-sampling EM calo |
+| 2 | `fe_scint` | 40× (1.0 cm `G4_Fe` + 0.5 cm scint) | 60 cm | 23 | coarse sampling, Tile-cal-like |
+| 3 | `w_scint_ecal` | 1× 2.0 cm homogeneous scint, then 75× (0.1 cm `G4_W` + 0.2 cm scint) | 24.5 cm | 21 | thin homogeneous ECAL-like preshower (~0.05 X₀, sees MIPs/shower-start only) followed by a compact W/scint HCAL-like sampling section |
+| 4 | `pb_lar` | 70× (0.2 cm `G4_Pb` + 0.4 cm `G4_lAr`) | 42 cm | 25 | same absorber as `pb_scint`, liquid argon active medium |
+
 ---
 
 ## ROOT output format
@@ -195,6 +221,7 @@ A few material choices available via NIST names:
 | `G4_BGO` | 7.13 g/cm³ | inorganic crystal, ~0.8 CHF/cm³ |
 | `G4_LSO` | 7.4 g/cm³ | inorganic crystal, ~6 CHF/cm³ |
 | `G4_LYSO` | 7.1 g/cm³ | inorganic crystal, ~30 CHF/cm³ |
+| `G4_lAr` | 1.40 g/cm³ | liquid argon, cryogenic (ATLAS EM calo-style) |
 
 ### Absorbers (passive layers)
 
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 756d9b4..f34f7c3 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -38,6 +38,7 @@ COPY include/ include/
 COPY bind/ bind/
 COPY lib/ lib/
 COPY run_pbwo4.cc .
+COPY run_sampling.cc .
 
 # lib/geant4/.git is a submodule pointer to the host's .git/modules dir, which
 # is not copied into the image. Replace it with a fresh repo so Geant4's cmake
diff --git a/run_sampling.cc b/run_sampling.cc
new file mode 100644
index 0000000..1f329c6
--- /dev/null
+++ b/run_sampling.cc
@@ -0,0 +1,124 @@
+#include "GeometryDescriptor.hh"
+#include "G4System.hh"
+
+#include <iostream>
+#include <stdexcept>
+#include <string>
+#include <utility>
+#include <vector>
+
+namespace {
+
+GeometryDescriptor buildPbScint() {
+    GeometryDescriptor gd;
+    for (int i = 0; i < 60; ++i) {
+        gd.addLayer(0.2, "G4_Pb", false);
+        gd.addLayer(0.3, "G4_PLASTIC_SC_VINYLTOLUENE", true, 10, 10);
+    }
+    return gd;
+}
+
+GeometryDescriptor buildFeScint() {
+    GeometryDescriptor gd;
+    for (int i = 0; i < 40; ++i) {
+        gd.addLayer(1.0, "G4_Fe", false);
+        gd.addLayer(0.5, "G4_PLASTIC_SC_VINYLTOLUENE", true, 10, 10);
+    }
+    return gd;
+}
+
+GeometryDescriptor buildWScintEcal() {
+    GeometryDescriptor gd;
+    // Thin homogeneous preshower: ~0.05 X0, sees MIPs/shower-start, not containment.
+    gd.addLayer(2.0, "G4_PLASTIC_SC_VINYLTOLUENE", true, 10, 10);
+    for (int i = 0; i < 75; ++i) {
+        gd.addLayer(0.1, "G4_W", false);
+        gd.addLayer(0.2, "G4_PLASTIC_SC_VINYLTOLUENE", true, 10, 10);
+    }
+    return gd;
+}
+
+GeometryDescriptor buildPbLAr() {
+    GeometryDescriptor gd;
+    for (int i = 0; i < 70; ++i) {
+        gd.addLayer(0.2, "G4_Pb", false);
+        gd.addLayer(0.4, "G4_lAr", true, 10, 10);
+    }
+    return gd;
+}
+
+// Ordered (not alphabetical) so configs can also be selected by 1-based index.
+const std::vector<std::pair<std::string, GeometryDescriptor (*)()>> kConfigs = {
+    {"pb_scint", buildPbScint},
+    {"fe_scint", buildFeScint},
+    {"w_scint_ecal", buildWScintEcal},
+    {"pb_lar", buildPbLAr},
+};
+
+void printUsage() {
+    std::cerr << "Usage: run_sampling [configName|configIndex] [nEvents]" << std::endl;
+    std::cerr << "Available configs:" << std::endl;
+    for (std::size_t i = 0; i < kConfigs.size(); ++i) {
+        std::cerr << "  " << (i + 1) << ": " << kConfigs[i].first << std::endl;
+    }
+}
+
+}  // namespace
+
+int main(int argc, char** argv) {
+    std::string configName = kConfigs.front().first;
+    int nEvents = 10;
+
+    if (argc > 3) {
+        printUsage();
+        return 1;
+    }
+    if (argc >= 2) {
+        configName = argv[1];
+    }
+    if (argc == 3) {
+        try {
+            nEvents = std::stoi(argv[2]);
+            if (nEvents <= 0) throw std::invalid_argument("must be positive");
+        } catch (const std::exception& e) {
+            std::cerr << "Invalid nEvents '" << argv[2] << "': " << e.what() << std::endl;
+            return 1;
+        }
+    }
+
+    GeometryDescriptor (*builder)() = nullptr;
+    try {
+        std::size_t pos = 0;
+        int index = std::stoi(configName, &pos);
+        if (pos == configName.size() && index >= 1 && index <= static_cast<int>(kConfigs.size())) {
+            configName = kConfigs[index - 1].first;
+            builder = kConfigs[index - 1].second;
+        }
+    } catch (const std::exception&) {
+        // Not a valid index; fall through to name lookup below.
+    }
+    if (builder == nullptr) {
+        for (const auto& kv : kConfigs) {
+            if (kv.first == configName) {
+                builder = kv.second;
+                break;
+            }
+        }
+    }
+    if (builder == nullptr) {
+        std::cerr << "Unknown config '" << configName << "'." << std::endl;
+        printUsage();
+        return 1;
+    }
+
+    GeometryDescriptor gd = builder();
+
+    std::string outfile = "sampling_" + configName + "_" + std::to_string(nEvents) + "events_hits.root";
+
+    G4System g4;
+    g4.init(gd, -1);
+    g4.run_batch(nEvents, {"e-"}, 1.0, 1.0, outfile);
+
+    std::cout << "Saved " << nEvents << " events to " << outfile << std::endl;
+    return 0;
+}
diff --git a/superbuild/CMakeLists.txt b/superbuild/CMakeLists.txt
index 20b8514..4d58e14 100644
--- a/superbuild/CMakeLists.txt
+++ b/superbuild/CMakeLists.txt
@@ -48,3 +48,19 @@ ExternalProject_Add(run_pbwo4
     ${CMAKE_BINARY_DIR}/run_pbwo4
   DEPENDS geant4
 )
+
+# ── minicalosim (run_sampling) ─────────────────────────────────────────────
+# Shares run_pbwo4's BINARY_DIR (already configured against G4_INSTALL) and
+# depends on it so the two ExternalProjects don't reconfigure that dir concurrently.
+ExternalProject_Add(run_sampling
+  SOURCE_DIR  ${MINI_SRC}
+  BINARY_DIR  ${CMAKE_BINARY_DIR}/minicalosim-build
+  CMAKE_ARGS
+    -DCMAKE_PREFIX_PATH=${G4_INSTALL}
+    -DWITH_GEANT4_UIVIS=OFF
+  BUILD_COMMAND   cmake --build <BINARY_DIR> --target run_sampling --parallel ${NPROC}
+  INSTALL_COMMAND ${CMAKE_COMMAND} -E create_symlink
+    ${CMAKE_BINARY_DIR}/minicalosim-build/run_sampling
+    ${CMAKE_BINARY_DIR}/run_sampling
+  DEPENDS run_pbwo4
+)

From 2715bc8d0dd098732e39c39307eb6318829d6539 Mon Sep 17 00:00:00 2001
From: Lars Bogner <ich@larsbogner.de>
Date: Wed, 24 Jun 2026 19:24:35 +0200
Subject: [PATCH 29/33] Add next_volume/next_material columns and sampling
 batch script

Records the volume and material a track is about to enter when a step
ends at a geometric boundary, since post-step's physical volume still
refers to the volume the step occurred in. Also adds
run-sampling-batch.sh to run all run_sampling configs in parallel from
isolated directories, avoiding output filename collisions.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 run-sampling-batch.sh | 40 ++++++++++++++++++++++++++++++++++++++++
 src/RunAction.cc      |  2 ++
 src/SteppingAction.cc | 16 ++++++++++++++++
 3 files changed, 58 insertions(+)
 create mode 100755 run-sampling-batch.sh

diff --git a/run-sampling-batch.sh b/run-sampling-batch.sh
new file mode 100755
index 0000000..12def56
--- /dev/null
+++ b/run-sampling-batch.sh
@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+cd "$(dirname "${BASH_SOURCE[0]}")"
+
+CONFIGS=(pb_scint fe_scint w_scint_ecal pb_lar)
+RUNS_PER_CONFIG=4
+NEVENTS=10000
+MAX_PARALLEL=16
+
+EXE="$(pwd)/build/run_sampling"
+OUTDIR="$(pwd)/sampling_batch_output"
+WORKROOT="$OUTDIR/.work"
+
+mkdir -p "$WORKROOT"
+
+run_one() {
+    local config="$1" idx="$2"
+    local workdir="$WORKROOT/${config}_${idx}"
+    mkdir -p "$workdir"
+    (
+        cd "$workdir"
+        "$EXE" "$config" "$NEVENTS"
+        mv "sampling_${config}_${NEVENTS}events_hits.root" "$OUTDIR/sampling_${config}_10k_${idx}.root"
+    )
+    rmdir "$workdir"
+}
+export -f run_one
+export EXE NEVENTS OUTDIR WORKROOT
+
+jobs=()
+for config in "${CONFIGS[@]}"; do
+    for idx in $(seq 0 $((RUNS_PER_CONFIG - 1))); do
+        jobs+=("$config $idx")
+    done
+done
+
+printf '%s\n' "${jobs[@]}" | xargs -P "$MAX_PARALLEL" -L 1 bash -c 'run_one "$1" "$2"' _
+
+rmdir "$WORKROOT"
diff --git a/src/RunAction.cc b/src/RunAction.cc
index 4e00ef5..ac7eb5f 100644
--- a/src/RunAction.cc
+++ b/src/RunAction.cc
@@ -114,6 +114,8 @@ RunAction::RunAction()
   analysisManager->CreateNtupleDColumn("post_dx");     // col 27
   analysisManager->CreateNtupleDColumn("post_dy");     // col 28
   analysisManager->CreateNtupleDColumn("post_dz");     // col 29
+  analysisManager->CreateNtupleSColumn("next_volume");   // col 30 (volume entered if step ended at a boundary, else "")
+  analysisManager->CreateNtupleSColumn("next_material"); // col 31 (material entered if step ended at a boundary, else "")
   analysisManager->FinishNtuple();
 
   // Spawning ntuple (one row per secondary born, ntuple id=2)
diff --git a/src/SteppingAction.cc b/src/SteppingAction.cc
index a40b6c4..c395a7f 100644
--- a/src/SteppingAction.cc
+++ b/src/SteppingAction.cc
@@ -149,6 +149,22 @@ void SteppingAction::UserSteppingAction(const G4Step* step)
   analysisManager->FillNtupleDColumn(1, 28, postDir.y());
   analysisManager->FillNtupleDColumn(1, 29, postDir.z());
 
+  // H: volume/material the track is about to enter, if this step ended at a
+  // geometric boundary. post->GetPhysicalVolume() still refers to the volume
+  // the step occurred in, not the one being entered, so use track->GetNextVolume().
+  G4String nextVolumeName = "";
+  G4String nextMaterialName = "";
+  if (post->GetStepStatus() == fGeomBoundary) {
+    auto nextVolume = track->GetNextVolume();
+    if (nextVolume) {
+      nextVolumeName = nextVolume->GetName();
+      auto nextMaterial = nextVolume->GetLogicalVolume()->GetMaterial();
+      if (nextMaterial) nextMaterialName = nextMaterial->GetName();
+    }
+  }
+  analysisManager->FillNtupleSColumn(1, 30, nextVolumeName);
+  analysisManager->FillNtupleSColumn(1, 31, nextMaterialName);
+
   // Field: B [T] and E [V/m] at pre-step position; zero if no field is registered
   G4double Bx=0, By=0, Bz=0, Ex=0, Ey=0, Ez=0;
   const auto* fm = G4TransportationManager::GetTransportationManager()->GetFieldManager();

From 62945c95c453a2e24525d5370bdd0a2a62531a34 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Thu, 25 Jun 2026 16:53:23 +0200
Subject: [PATCH 30/33] Add export_xsec executable for PbWO4 gamma attenuation
 coefficients

Builds a minimal PbWO4 geometry, forces EM physics tables via a
zero-event run, then sweeps photon energy 1 eV-10 MeV with
G4EmCalculator to dump per-process mass attenuation coefficients to CSV.
---
 CMakeLists.txt |  3 ++
 export_xsec.cc | 86 ++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 89 insertions(+)
 create mode 100644 export_xsec.cc

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b6ce8ad..bbe7a56 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -63,6 +63,9 @@ target_link_libraries(run_pbwo4 ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
 add_executable(run_sampling run_sampling.cc ${sources} ${headers})
 target_link_libraries(run_sampling ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
 
+add_executable(export_xsec export_xsec.cc ${sources} ${headers})
+target_link_libraries(export_xsec ${Geant4_LIBRARIES} ${Python3_LIBRARIES})
+
 #----------------------------------------------------------------------------
 # Install the executable to 'bin' directory under CMAKE_INSTALL_PREFIX
 #
diff --git a/export_xsec.cc b/export_xsec.cc
new file mode 100644
index 0000000..3b45fbf
--- /dev/null
+++ b/export_xsec.cc
@@ -0,0 +1,86 @@
+// Export material-specific gamma cross sections for PbWO4 using G4EmCalculator.
+//
+// Builds a minimal geometry, initialises FTFP_BERT, forces the EM physics
+// tables to be built (via a fakeRun "/run/beamOn 0"), then sweeps photon
+// energy from 1 eV to 1e5 eV and writes a CSV of the mass attenuation
+// coefficients (cm^2/g) for each gamma process plus the total.
+
+#include "GeometryDescriptor.hh"
+#include "G4System.hh"
+
+#include "G4EmCalculator.hh"
+#include "G4Material.hh"
+#include "G4NistManager.hh"
+#include "G4Gamma.hh"
+#include "G4SystemOfUnits.hh"
+
+#include <cmath>
+#include <fstream>
+#include <iostream>
+#include <vector>
+
+int main(int argc, char** argv) {
+    const std::string materialName = "G4_PbWO4";
+    const std::string outfile = (argc > 1) ? argv[1] : "pbwo4_xsec.csv";
+
+    // Log-spaced energy grid: 1 eV -> 1e5 eV, points per decade (small steps).
+    const double eMin = 1.0 * eV;
+    const double eMax = 1.0e7 * eV;  // 10 MeV
+    const int pointsPerDecade = 200;
+    const int nDecades = 7;  // 1e0 .. 1e7 eV
+    const int nPoints = pointsPerDecade * nDecades + 1;
+
+    // Gamma processes registered by the EM standard physics in FTFP_BERT.
+    const std::vector<std::string> processes = {"phot", "compt", "conv", "Rayl"};
+
+    // Minimal valid geometry: one active PbWO4 layer so init() has something to build.
+    GeometryDescriptor gd;
+    gd.addLayer(2.0, materialName, true, 1, 1);
+
+    G4System g4;
+    g4.init(gd, -1);
+    // fakeRun: builds EM physics tables without invoking RunAction (no ROOT file).
+    g4.applyUICommand("/run/beamOn 0");
+
+    const G4Material* mat = G4NistManager::Instance()->FindOrBuildMaterial(materialName);
+    if (mat == nullptr) {
+        std::cerr << "Could not build material " << materialName << std::endl;
+        return 1;
+    }
+    const double density_g_cm3 = mat->GetDensity() / (g / cm3);
+
+    G4EmCalculator calc;
+    const G4ParticleDefinition* gamma = G4Gamma::Gamma();
+
+    std::ofstream out(outfile);
+    out << "# material=" << materialName
+        << " density_g_per_cm3=" << density_g_cm3 << "\n";
+    out << "# mass attenuation coefficients mu/rho in cm^2/g\n";
+    out << "energy_eV,phot,compt,conv,rayl,total\n";
+    out.setf(std::ios::scientific);
+    out.precision(6);
+
+    const double logStep = (std::log10(eMax) - std::log10(eMin)) / (nPoints - 1);
+    for (int i = 0; i < nPoints; ++i) {
+        const double energy = std::pow(10.0, std::log10(eMin) + i * logStep);
+
+        double total_lin = 0.0;  // linear attenuation, G4 units (1/mm)
+        std::vector<double> mu;  // per-process mass attenuation (cm^2/g)
+        mu.reserve(processes.size());
+        for (const auto& proc : processes) {
+            // Macroscopic cross section Sigma [1/mm] = material-specific cross section.
+            const double sigmaVol = calc.ComputeCrossSectionPerVolume(energy, gamma, proc, mat);
+            total_lin += sigmaVol;
+            // Convert to mass attenuation coefficient: (Sigma in 1/cm) / density.
+            mu.push_back((sigmaVol * cm) / density_g_cm3);
+        }
+        const double total_mu = (total_lin * cm) / density_g_cm3;
+
+        out << energy / eV << "," << mu[0] << "," << mu[1] << ","
+            << mu[2] << "," << mu[3] << "," << total_mu << "\n";
+    }
+
+    std::cout << "Wrote " << nPoints << " energy points for " << materialName
+              << " to " << outfile << std::endl;
+    return 0;
+}

From 6a3aabf772cd6f8b0c9d6bbdf2d0e071e7a94f6e Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Wed, 1 Jul 2026 12:48:54 +0200
Subject: [PATCH 31/33] Allow disabling of GDML so there is no dependency on
 xerces-c

---
 README.md                 | 1 +
 superbuild/CMakeLists.txt | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 0634da7..dfdafa0 100644
--- a/README.md
+++ b/README.md
@@ -93,6 +93,7 @@ After the build, the executables are at `build/run_pbwo4` and `build/run_samplin
 | CMake option | Default | Meaning |
 |---|---|---|
 | `GEANT4_INSTALL_DATA` | `ON` | Download Geant4 physics data tables (~2 GB) |
+| `GEANT4_USE_GDML` | `ON` | Build Geant4 with GDML support (requires Xerces-C); set `OFF` to build without Xerces-C |
 
 The superbuild caps parallelism at `min(nproc, 16)` to avoid memory exhaustion.
 
diff --git a/superbuild/CMakeLists.txt b/superbuild/CMakeLists.txt
index 4d58e14..5454a5d 100644
--- a/superbuild/CMakeLists.txt
+++ b/superbuild/CMakeLists.txt
@@ -18,6 +18,7 @@ set(G4_SRC     ${CMAKE_SOURCE_DIR}/../lib/geant4)
 set(MINI_SRC   ${CMAKE_SOURCE_DIR}/..)
 
 option(GEANT4_INSTALL_DATA "Download Geant4 physics data files (~2 GB)" ON)
+option(GEANT4_USE_GDML "Build Geant4 with GDML support (requires Xerces-C)" ON)
 
 # ── Geant4 ────────────────────────────────────────────────────────────────────
 ExternalProject_Add(geant4
@@ -28,7 +29,7 @@ ExternalProject_Add(geant4
     -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
     -DCMAKE_BUILD_TYPE=Release
     -DGEANT4_INSTALL_DATA=${GEANT4_INSTALL_DATA}
-    -DGEANT4_USE_GDML=ON
+    -DGEANT4_USE_GDML=${GEANT4_USE_GDML}
     -DGEANT4_BUILD_MULTITHREADED=OFF
     -DGEANT4_BUILD_TLS_MODEL=global-dynamic
   BUILD_COMMAND   cmake --build <BINARY_DIR> --parallel ${NPROC}

From 068cf93604d5866000e16b44e5ab50ea13df64a0 Mon Sep 17 00:00:00 2001
From: Lars Bogner <ich@larsbogner.de>
Date: Thu, 9 Jul 2026 10:04:47 +0200
Subject: [PATCH 32/33] Allow MINICALOSIM_SEED env var to override RNG seed in
 run_pbwo4/run_sampling

Concurrent job launches can land in the same wall-clock second, causing
G4System::init's time-based seed (seed=-1) to collide and produce
byte-identical physics across separately-named shards. Falls back to
the existing time-based seed if the variable is unset, empty, or invalid.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
---
 run_pbwo4.cc    | 15 ++++++++++++++-
 run_sampling.cc | 15 ++++++++++++++-
 2 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/run_pbwo4.cc b/run_pbwo4.cc
index 1754eb1..22e3895 100644
--- a/run_pbwo4.cc
+++ b/run_pbwo4.cc
@@ -1,6 +1,7 @@
 #include "GeometryDescriptor.hh"
 #include "G4System.hh"
 
+#include <cstdlib>
 #include <iostream>
 #include <string>
 #include <vector>
@@ -8,6 +9,18 @@
 int main(int argc, char** argv) {
     int nEvents = 10;
 
+    int seed = -1;
+    if (const char* seedEnv = std::getenv("MINICALOSIM_SEED")) {
+        try {
+            std::size_t pos = 0;
+            std::string seedStr(seedEnv);
+            int parsed = std::stoi(seedStr, &pos);
+            if (pos == seedStr.size()) seed = parsed;
+        } catch (const std::exception&) {
+            // Not a valid integer; fall back to time-based seed.
+        }
+    }
+
     if (argc > 2) {
         std::cerr << "Usage: run_pbwo4 [nEvents]" << std::endl;
         return 1;
@@ -28,7 +41,7 @@ int main(int argc, char** argv) {
     gd.addLayer(20.0, "G4_PbWO4", true, 10, 10);
 
     G4System g4;
-    g4.init(gd, -1);
+    g4.init(gd, seed);
     g4.run_batch(nEvents, {"e-"}, 1.0, 1.0, outfile);
 
     std::cout << "Saved " << nEvents << " events to " << outfile << std::endl;
diff --git a/run_sampling.cc b/run_sampling.cc
index 1f329c6..b2da2b1 100644
--- a/run_sampling.cc
+++ b/run_sampling.cc
@@ -1,6 +1,7 @@
 #include "GeometryDescriptor.hh"
 #include "G4System.hh"
 
+#include <cstdlib>
 #include <iostream>
 #include <stdexcept>
 #include <string>
@@ -111,12 +112,24 @@ int main(int argc, char** argv) {
         return 1;
     }
 
+    int seed = -1;
+    if (const char* seedEnv = std::getenv("MINICALOSIM_SEED")) {
+        try {
+            std::size_t pos = 0;
+            std::string seedStr(seedEnv);
+            int parsed = std::stoi(seedStr, &pos);
+            if (pos == seedStr.size()) seed = parsed;
+        } catch (const std::exception&) {
+            // Not a valid integer; fall back to time-based seed.
+        }
+    }
+
     GeometryDescriptor gd = builder();
 
     std::string outfile = "sampling_" + configName + "_" + std::to_string(nEvents) + "events_hits.root";
 
     G4System g4;
-    g4.init(gd, -1);
+    g4.init(gd, seed);
     g4.run_batch(nEvents, {"e-"}, 1.0, 1.0, outfile);
 
     std::cout << "Saved " << nEvents << " events to " << outfile << std::endl;

From 14cfc18369c7606f79309eb4997f2866c3059fd7 Mon Sep 17 00:00:00 2001
From: Lars Bogner <upyxo@student.kit.edu>
Date: Mon, 13 Jul 2026 13:58:54 +0200
Subject: [PATCH 33/33] Add optional primary particle energy argument to
 dataset scripts

run_pbwo4 and run_sampling previously hardcoded 1 GeV mono-energetic
e- primaries. Both now accept a trailing energy_GeV CLI argument
(default 1.0, unchanged) so datasets at other energies can be
produced without recompiling.
---
 run_pbwo4.cc    | 18 ++++++++++++++----
 run_sampling.cc | 18 ++++++++++++++----
 2 files changed, 28 insertions(+), 8 deletions(-)

diff --git a/run_pbwo4.cc b/run_pbwo4.cc
index 22e3895..c6b11e6 100644
--- a/run_pbwo4.cc
+++ b/run_pbwo4.cc
@@ -8,6 +8,7 @@
 
 int main(int argc, char** argv) {
     int nEvents = 10;
+    double energy_GeV = 1.0;
 
     int seed = -1;
     if (const char* seedEnv = std::getenv("MINICALOSIM_SEED")) {
@@ -21,11 +22,11 @@ int main(int argc, char** argv) {
         }
     }
 
-    if (argc > 2) {
-        std::cerr << "Usage: run_pbwo4 [nEvents]" << std::endl;
+    if (argc > 3) {
+        std::cerr << "Usage: run_pbwo4 [nEvents] [energy_GeV]" << std::endl;
         return 1;
     }
-    if (argc == 2) {
+    if (argc >= 2) {
         try {
             nEvents = std::stoi(argv[1]);
             if (nEvents <= 0) throw std::invalid_argument("must be positive");
@@ -34,6 +35,15 @@ int main(int argc, char** argv) {
             return 1;
         }
     }
+    if (argc == 3) {
+        try {
+            energy_GeV = std::stod(argv[2]);
+            if (energy_GeV <= 0) throw std::invalid_argument("must be positive");
+        } catch (const std::exception& e) {
+            std::cerr << "Invalid energy_GeV '" << argv[2] << "': " << e.what() << std::endl;
+            return 1;
+        }
+    }
 
     std::string outfile = "pbwo4_" + std::to_string(nEvents) + "events_hits.root";
 
@@ -42,7 +52,7 @@ int main(int argc, char** argv) {
 
     G4System g4;
     g4.init(gd, seed);
-    g4.run_batch(nEvents, {"e-"}, 1.0, 1.0, outfile);
+    g4.run_batch(nEvents, {"e-"}, energy_GeV, energy_GeV, outfile);
 
     std::cout << "Saved " << nEvents << " events to " << outfile << std::endl;
     return 0;
diff --git a/run_sampling.cc b/run_sampling.cc
index b2da2b1..53c1c7b 100644
--- a/run_sampling.cc
+++ b/run_sampling.cc
@@ -57,7 +57,7 @@ const std::vector<std::pair<std::string, GeometryDescriptor (*)()>> kConfigs = {
 };
 
 void printUsage() {
-    std::cerr << "Usage: run_sampling [configName|configIndex] [nEvents]" << std::endl;
+    std::cerr << "Usage: run_sampling [configName|configIndex] [nEvents] [energy_GeV]" << std::endl;
     std::cerr << "Available configs:" << std::endl;
     for (std::size_t i = 0; i < kConfigs.size(); ++i) {
         std::cerr << "  " << (i + 1) << ": " << kConfigs[i].first << std::endl;
@@ -69,15 +69,16 @@ void printUsage() {
 int main(int argc, char** argv) {
     std::string configName = kConfigs.front().first;
     int nEvents = 10;
+    double energy_GeV = 1.0;
 
-    if (argc > 3) {
+    if (argc > 4) {
         printUsage();
         return 1;
     }
     if (argc >= 2) {
         configName = argv[1];
     }
-    if (argc == 3) {
+    if (argc >= 3) {
         try {
             nEvents = std::stoi(argv[2]);
             if (nEvents <= 0) throw std::invalid_argument("must be positive");
@@ -86,6 +87,15 @@ int main(int argc, char** argv) {
             return 1;
         }
     }
+    if (argc == 4) {
+        try {
+            energy_GeV = std::stod(argv[3]);
+            if (energy_GeV <= 0) throw std::invalid_argument("must be positive");
+        } catch (const std::exception& e) {
+            std::cerr << "Invalid energy_GeV '" << argv[3] << "': " << e.what() << std::endl;
+            return 1;
+        }
+    }
 
     GeometryDescriptor (*builder)() = nullptr;
     try {
@@ -130,7 +140,7 @@ int main(int argc, char** argv) {
 
     G4System g4;
     g4.init(gd, seed);
-    g4.run_batch(nEvents, {"e-"}, 1.0, 1.0, outfile);
+    g4.run_batch(nEvents, {"e-"}, energy_GeV, energy_GeV, outfile);
 
     std::cout << "Saved " << nEvents << " events to " << outfile << std::endl;
     return 0;