Basic Tutorial¶

In this tutorial we are going to demonstrate the basic functionality of remage by simulating a series of particle physics processes in a simple setup.

Experimental geometry¶

We need to develop a geometry, and we will be using the pyg4ometry library for this purpose. This library is well-suited for creating geometries that are compatible with the Geant4 framework, as it closely mirrors the Geant4 interface, making it easy for those familiar with Geant4 to use. Importantly, pyg4ometry is independent of Geant4 itself, meaning it doesn’t require Geant4 as a dependency. Additionally, it offers the flexibility to export the developed geometry in GDML format, which is widely compatible for simulations and analyses in high-energy physics applications.

The geometry consist in two high-purity germanium detectors (HPGes) immersed in a liquid argon balloon. The legend-pygeom-hpges package will help us creating the HPGe volumes. Let’s start by importing the Python packages, declaring a geometry registry and specifying the dimensions and types of the two detectors as dictionaries:

import pygeomhpges as hpges
import pyg4ometry as pg4
from numpy import pi
import pygeomtools


reg = pg4.geant4.Registry()

bege_meta = {
    "name": "B00000B",
    "type": "bege",
    "production": {
        "enrichment": {"val": 0.874, "unc": 0.003},
        "mass_in_g": 697.0,
    },
    "geometry": {
        "height_in_mm": 29.46,
        "radius_in_mm": 36.98,
        "groove": {"depth_in_mm": 2.0, "radius_in_mm": {"outer": 10.5, "inner": 7.5}},
        "pp_contact": {"radius_in_mm": 7.5, "depth_in_mm": 0},
        "taper": {
            "top": {"angle_in_deg": 0.0, "height_in_mm": 0.0},
            "bottom": {"angle_in_deg": 0.0, "height_in_mm": 0.0},
        },
    },
}

coax_meta = {
    "name": "C000RG1",
    "type": "coax",
    "production": {
        "enrichment": {"val": 0.855, "unc": 0.015},
    },
    "geometry": {
        "height_in_mm": 84,
        "radius_in_mm": 38.25,
        "borehole": {"radius_in_mm": 6.75, "depth_in_mm": 73},
        "groove": {"depth_in_mm": 2, "radius_in_mm": {"outer": 20, "inner": 17}},
        "pp_contact": {"radius_in_mm": 17, "depth_in_mm": 0},
        "taper": {
            "top": {"angle_in_deg": 45, "height_in_mm": 5},
            "bottom": {"angle_in_deg": 45, "height_in_mm": 2},
            "borehole": {"angle_in_deg": 0, "height_in_mm": 0},
        },
    },
}

Now we can build all the logical volumes and place them in the world volume:

# create logical volumes for the two HPGe detectors
bege_l = hpges.make_hpge(bege_meta, name="BEGe_L", registry=reg)
coax_l = hpges.make_hpge(coax_meta, name="Coax_L", registry=reg)

# create a world volume
world_s = pg4.geant4.solid.Orb("World_s", 20, registry=reg, lunit="cm")
world_l = pg4.geant4.LogicalVolume(world_s, "G4_Galactic", "World", registry=reg)
reg.setWorld(world_l)

# let's make a liquid argon balloon
lar_s = pg4.geant4.solid.Orb("LAr_s", 15, registry=reg, lunit="cm")
lar_l = pg4.geant4.LogicalVolume(lar_s, "G4_lAr", "LAr_l", registry=reg)
pg4.geant4.PhysicalVolume([0, 0, 0], [0, 0, 0], lar_l, "LAr", world_l, registry=reg)

# now place the two HPGe detectors in the argon
bege_pv = pg4.geant4.PhysicalVolume(
    [0, 0, 0], [5, 0, -3, "cm"], bege_l, "BEGe", lar_l, registry=reg
)
coax_pv = pg4.geant4.PhysicalVolume(
    [0, 0, 0], [-5, 0, -3, "cm"], coax_l, "Coax", lar_l, registry=reg
)

# register them as sensitive in remage
# this also saves the metadata into the files for later use
bege_pv.set_pygeom_active_detector(
    pygeomtools.RemageDetectorInfo("germanium", 1, bege_meta)
)
coax_pv.set_pygeom_active_detector(
    pygeomtools.RemageDetectorInfo("germanium", 2, coax_meta)
)

# finally create a small radioactive source
source_s = pg4.geant4.solid.Tubs("Source_s", 0, 1, 1, 0, 2 * pi, registry=reg)
source_l = pg4.geant4.LogicalVolume(source_s, "G4_BRAIN_ICRP", "Source_L", registry=reg)
pg4.geant4.PhysicalVolume(
    [0, 0, 0], [0, 5, 0, "cm"], source_l, "Source", lar_l, registry=reg
)

Note how we also created a small cylinder to represent a radioactive source later in the simulation.

Now we can quickly visualize the result, still with pyg4ometry:

# start an interactive VTK viewer instance
lar_l.pygeom_color_rgba = (0, 0, 1, 0.1)
pygeomtools.viewer.visualize(reg)

Geometry visualization

We can also easily save the geometry as a geometry description markup language (GDML) file. This format allows us to input the geometry to remage.

pygeomtools.write_pygeom(reg, "geometry.gdml")

Visualizing a simple simulation¶

By following instructions in the installation section, you should have access to the remage executable. We are now ready to simulate some particle physics with it.

Like any other Geant4-based application, we need to configure the simulation with a macro file. Standard Geant4 commands as well as custom commands (see the command interface) are available.

At the beginning of the file, we can set some global application options, like the verbosity. Let’s increase it a bit (compared to the default summary) to be more informed on what’s going on by remage:

/RMG/Manager/Logging/LogLevel detail

Then we have to register the “sensitive detectors” (in our simple case, the two HPGes and the LAr). remage offers several types of predefined detectors, targeting different physical quantities of the particles that interact with them. HPGes are of type Germanium, while the LAr is of type Scintillator. Their difference in terms of simulation output will be clear later, while inspecting it. As per specification of the /RMG/Geometry/RegisterDetector command, we need to provide a unique numeric identifier that will be used to label the detector data in the simulation output:

/RMG/Geometry/RegisterDetector Germanium BEGe 001
/RMG/Geometry/RegisterDetector Germanium Coax 002
/RMG/Geometry/RegisterDetector Scintillator LAr 003

Now we can initialize the simulation. Additionally, let’s setup some Geant4 visualization to look at the tracks:

/run/initialize

# create a scene
/vis/open OI
/vis/scene/create
/vis/sceneHandler/attach

# draw the geometry
/vis/drawVolume

# setup better colors
/vis/viewer/set/defaultColour black
/vis/viewer/set/background white

# and also show trajectories and particle hits
/vis/scene/add/trajectories smooth
/vis/scene/add/hits
/vis/scene/endOfEventAction accumulate

Now with the actual physics. We want to start ten 1 MeV gammas from the radioactive source:

/RMG/Generator/Confine Volume
/RMG/Generator/Confinement/Physical/AddVolume Source

/RMG/Generator/Select GPS
/gps/particle gamma
/gps/ang/type iso
/gps/energy 1000 keV

/run/beamOn 50

The macro commands should be placed in a plain text file (conventionally ended with the .mac suffix). For example the complete macro file is shown below.

Complete macro file (vis-gammas.mac)

/RMG/Manager/Logging/LogLevel detail

/RMG/Geometry/RegisterDetector Germanium BEGe 001
/RMG/Geometry/RegisterDetector Germanium Coax 002
/RMG/Geometry/RegisterDetector Scintillator LAr 003

/run/initialize

/vis/open OI
/vis/scene/create
/vis/sceneHandler/attach

/vis/drawVolume

/vis/viewer/set/defaultColour black
/vis/viewer/set/background white

/vis/scene/add/trajectories smooth
/vis/scene/add/hits
/vis/scene/endOfEventAction accumulate

/RMG/Generator/Confine Volume
/RMG/Generator/Confinement/Physical/AddVolume Source

/RMG/Generator/Select GPS
/gps/particle gamma
/gps/ang/type iso
/gps/energy 1000 keV

/run/beamOn 10

We can finally pass the GDML geometry and the macro to the remage executable and look at the result!

$ remage --interactive --gdml-files geometry.gdml -- vis-gammas.mac
  _ __ ___ _ __ ___   __ _  __ _  ___
 | '__/ _ \ '_ ` _ \ / _` |/ _` |/ _ \
 | | |  __/ | | | | | (_| | (_| |  __/ v0.19.5
 |_|  \___|_| |_| |_|\__,_|\__, |\___| using geant4-11-03-patch-02 [MT]
                           |___/

[Summary -> CLHEP::HepRandom seed changed to: 1366165609 (from system entropy)
[Summary -> Entering interactive mode
...

Note

Interactive visualization requires passing --interactive to the remage executable.

Interactions in HPGes and in LAr are marked in red and blue, respectively.

Simulation visualization

Tip

With Apptainer, additional tweaks are required in order to allow for graphics to be displayed, e.g.

$ apptainer run \
    --env DISPLAY=$DISPLAY \
    --env XDG_RUNTIME_DIR=$XDG_RUNTIME_DIR \
    --env XAUTHORITY=$XAUTHORITY \
    -B $XDG_RUNTIME_DIR \
    path/to/remage_latest.sif --interactive [...]

and similarly with Docker.

If remage from the Apptainer image refuses to run simulations, this might be due to some of your environment variables from outside the container. Give --cleanenv a try.

Storing simulated data on disk¶

Let’s now simulate more events in batch mode and store Geant4 step information in an output file. Using the same macro as before, without the visualization commands:

/RMG/Manager/Logging/LogLevel detail

/RMG/Geometry/RegisterDetector Germanium BEGe 001
/RMG/Geometry/RegisterDetector Germanium Coax 002
/RMG/Geometry/RegisterDetector Scintillator LAr 003

/RMG/Output/NtupleUseVolumeName true

/run/initialize

/RMG/Generator/Confine Volume
/RMG/Generator/Confinement/Physical/AddVolume Source

/RMG/Generator/Select GPS
/gps/particle gamma
/gps/ang/type iso
/gps/energy 1000 keV

/run/beamOn 100000

We will simulate 10^5 events. Profiting from Geant4’s multithreading capabilities, we can speed up the simulation but running it on several threads in parallel. The number of threads is specified with the --threads command line option.

Now we only need to tell remage which file name to use for the output. remage supports multiple file formats, including LEGEND’s HDF5. We are going to select the latter by supplying a file name with .lh5 extension:

$ remage --threads 8 --gdml-files geometry.gdml --output-file output.lh5 --merge-output-files -- gammas.mac

We’ll use the legend-pydataobj Python package to read the data from disk. Let’s first have a look at the data layout with the lh5ls utility:

$ lh5ls -d3 -a output.lh5
/
├── detector_origins · struct{BEGe,Coax}
│   ├── BEGe · struct{xloc,yloc,zloc}
│   │   ├── xloc · real
│   │   ├── yloc · real
│   │   └── zloc · real
│   └── Coax · struct{xloc,yloc,zloc}
│       ├── xloc · real
│       ├── yloc · real
│       └── zloc · real
├── stp · struct{BEGe,Coax,LAr}
│   ├── BEGe · table{dist_to_surf,edep,evtid,particle,t0,time,xloc,yloc,zloc}
│   │   ├── dist_to_surf · array<1>{array<1>{real}}
│   │   ├── edep · array<1>{array<1>{real}}
│   │   ├── evtid · array<1>{real}
│   │   ├── particle · array<1>{array<1>{real}}
│   │   ├── t0 · array<1>{real} ── {'units': 'ns'}
│   │   ├── time · array<1>{array<1>{real}}
│   │   ├── xloc · array<1>{array<1>{real}}
│   │   ├── yloc · array<1>{array<1>{real}}
│   │   └── zloc · array<1>{array<1>{real}}
│   ├── Coax · table{dist_to_surf,edep,evtid,particle,t0,time,xloc,yloc,zloc}
│   │   ├── dist_to_surf · array<1>{array<1>{real}}
│   │   ├── edep · array<1>{array<1>{real}}
│   │   ├── evtid · array<1>{real}
│   │   ├── particle · array<1>{array<1>{real}}
│   │   ├── t0 · array<1>{real} ── {'units': 'ns'}
│   │   ├── time · array<1>{array<1>{real}}
│   │   ├── xloc · array<1>{array<1>{real}}
│   │   ├── yloc · array<1>{array<1>{real}}
│   │   └── zloc · array<1>{array<1>{real}}
│   ├── LAr · table{edep,evtid,particle,t0,time,xloc,yloc,zloc}
│   │   ├── edep · array<1>{array<1>{real}}
│   │   ├── evtid · array<1>{real}
│   │   ├── particle · array<1>{array<1>{real}}
│   │   ├── t0 · array<1>{real} ── {'units': 'ns'}
│   │   ├── time · array<1>{array<1>{real}}
│   │   ├── xloc · array<1>{array<1>{real}}
│   │   ├── yloc · array<1>{array<1>{real}}
│   │   └── zloc · array<1>{array<1>{real}}
│   └── __by_uid__ · struct{det001,det002,det003}
│       ├── det001 -> /stp/BEGe
│       ├── det002 -> /stp/Coax
│       └── det003 -> /stp/LAr
├── tcm · table{row_in_table,table_key} ── {'hash_func': '(?<=stp/__by_uid__/det)\\d+', 'tables': "['stp/__by_uid__/det001', 'stp/__by_uid__/det002', 'stp/__by_uid__/det003']"}
│   ├── row_in_table · array<1>{array<1>{real}}
│   │   ├── cumulative_length · array<1>{real}
│   │   └── flattened_data · array<1>{real}
│   └── table_key · array<1>{array<1>{real}}
│       ├── cumulative_length · array<1>{real}
│       └── flattened_data · array<1>{real}
└── vtx · table{evtid,n_part,time,xloc,yloc,zloc}
    ├── evtid · array<1>{real}
    ├── n_part · array<1>{real}
    ├── time · array<1>{real} ── {'units': 'ns'}
    ├── xloc · array<1>{real} ── {'units': 'm'}
    ├── yloc · array<1>{real} ── {'units': 'm'}
    └── zloc · array<1>{real} ── {'units': 'm'}

Note

The units on the time/xloc/yloc/zloc fields are present (nanoseconds and meter), but not shown by above output of the lh5ls tool.

The step information is organized into data tables, one per sensitive detector. The table format is specified by the detector type (Germanium or Scintillator in this example). Event vertex information is stored in a separate table, vtx. Note the physical units specified as attributes, as per LH5 specification.

Let’s make an histogram of the total energy deposited in the HPGe detectors in each event. Check out the legend-pydataobj documentation for more details.

from lgdo import lh5
import awkward as ak
import glob
import hist
import matplotlib.pyplot as plt

plt.rcParams["figure.figsize"] = (9, 3)


def plot_edep(detid):
    # read the data from detector "detid". pass all 8 files to concatenate them
    # in addition, view it as and Awkward Array
    data = lh5.read_as(f"stp/{detid}", "output.lh5", "ak")

    # make and plot an histogram
    hist.new.Reg(551, 0, 1005, name="energy [keV]").Double().fill(
        ak.sum(data.edep, axis=-1)
    ).plot(yerr=False, label=detid)


plot_edep("BEGe")
plot_edep("Coax")
plt.ylabel("counts / 5 keV")
plt.yscale("log")
plt.legend()

plot

The expected spectrum, composed by full-energy peak at 1 MeV and Compton shoulder. We can also plot the interaction points:

def plot_hits(detid):
    data = lh5.read_as(f"stp/{detid}", "output.lh5", "ak")[:1_000]
    plt.scatter(
        ak.flatten(data.xloc), ak.flatten(data.yloc), marker="o", s=1, label=detid
    )


plot_hits("BEGe")
plot_hits("Coax")
plt.xlabel("[m]")
plt.ylabel("[m]")
plt.legend()
plt.axis("equal")

plot

Advanced usage¶

remage can do much more than this! While we prepare more documentation, be aware that a lot of the simulation and the output can be customized:

commands below /RMG/Output are available to filter steps, isotopes, store all steps in a single table etc.
physics list settings can be adjusted
the randomization can be controlled
advanced vertex confinement modes are implemented
many interesting event generators, related to germanium detector experiments are available
vertex coordinates can be read from an input file
the simulation of optical physics can be optimized

And much more! Have a look at the API reference and the macro command reference.

For advanced simulation output analysis, refer to Analyzing simulation output.

Finally, Don’t miss remage’s Related projects and in particular reboost for advanced remage output analysis and post-processing.