EGS_Mesh
EGS_Mesh is an unstructured tetrahedral mesh library for EGSnrc.
:start geometry:
library = egs_mesh
name = my_mesh
file = # your mesh here
:stop geometry:
If you're new to EGS_Mesh, you can work through a guided example. You can also consult the egsinp syntax reference. If you want to simulate STEP files using EGS_Mesh, check out the STEP file example.
Overview
EGS_Mesh offers modelling flexibility over traditional voxel-based simulations. Instead of building up a geometry using a constructive-solid approach, EGS_Mesh uses tetrahedral mesh files as input. CAD geometries can be meshed and then simulated directly.
Users can generate meshes using the standalone tool Gmsh, or create a mesh file from their data.
Alternatives
Other Monte Carlo codes that support tetrahedral mesh simulations include:
Guided simulation
This guide goes through a complete EGS_Mesh simulation step by step. By the end, you'll be ready to conduct your own simulations. Along the way we'll cover:
- Fundamental EGSnrc and
EGS_Meshconcepts - Gmsh basics
- Running EGSnrc simulations
- Viewing
EGS_Meshsimulation results in Paraview
Prerequisites
To follow along, you'll need the following software:
With that, you're ready to start!
Generate an input mesh
EGS_Mesh simulations have three steps:
- Create an input mesh file for your geometry
- Write an
egsinpfile for your simulation - Run the simulation and view the results
For this example, you're going to simulate a cube of water. The cube will have side lengths of 10cm for a total volume of 1000 cm³.
Creating the geometry using Gmsh
In this example, you'll create the geometry in Gmsh and then mesh it. It's also possible to define your geometry in CAD, export it to STEP, and then use Gmsh to mesh the STEP file.
First, open Gmsh. Create a new script file using File->New called cube.geo. If prompted, use the OpenCASCADE geometry kernel. Create a 10cm cube using:
Geometry->Elementary entities->Add->Box
After adding the box, hit the q key to quit the box dialog. Gmsh is unitless, so a length of 10 could have any unit attached. By default, EGS_Mesh assumes mesh files are given in cm.
Assigning mesh media
You've made a cube. But how will EGSnrc know it's water? You also have to assign EGSnrc media names to each volume. Media names are specified using Gmsh Physical Volumes. Open the Physical Volumes dialog using:
Geometry->Physical groups->Add->Volume
In the Name input, enter H2O for water. Select the volume using the mouse, and the yellow sphere at the center of the cube should turn red. End the selection by pressing the e key, and then hit the q key to exit the volume dialog entirely.
Meshing the geometry
Now, you have a geometry with media names attached. All that's left is to mesh it. Generate a 3D mesh using:
Mesh->3D
After meshing, you can find information like the number of tetrahedrons using Tools->Statistics. The mesh shown here has 1153 elements. Mesh visibility settings are in Tools->Options->Mesh->Visibility.
Write the mesh to disk using:
File->Save Mesh
Only ASCII v4.1 msh files are currently supported in EGS_Mesh. You can open up the file in a text editor to check the details:
$MeshFormat
4.1 0 8
$EndMeshFormat
$PhysicalNames
1
3 1 "H2O"
$EndPhysicalNames
... // continued
Here, the format version is confirmed to be 4.1, and the only media name is H2O. Further on in the file, node coordinates and element nodes are also stored. The msh format is documented here.
With a fresh mesh file in hand, you're ready to write an EGSnrc input file.
Scripting in Gmsh
If GUIs aren't your thing, Gmsh also has a scripting interface. Every action in the GUI is written to a project script file, which can be edited and reloaded on the fly.
The script for this session looks like:
SetFactory("OpenCASCADE");
Box(1) = {0, 0, 0, 10, 10, 10};
Physical Volume("H2O") = {1};
You can edit the script using Geometry->Edit script. After you make changes and save, reload it with Geometry->Reload script. Gmsh also provides language bindings for Python, C++, Julia and C, but this requires installing the Gmsh Software Development Kit.
Going further
-
Try meshing another geometry, like a
Torus. -
There are a few ways to generate a more refined mesh. One way is to adjust the maximum element size (
Tools->Options->Mesh->General->Max element size). Try obtaining a mesh with roughly 50,000 elements by varying the maximum element size. Before remeshing, hit the0key to reset the old mesh. If you need to refine just a few mesh areas, check out the Gmsh documentation on size fields. -
Change the meshing algorithm using
Tools->Options->Mesh->3D algorithmand remesh. Do you observe any difference in the generated mesh? For complex models, sometimes one algorithm succeeds where another fails.
Note: the full mesh file is saved below. You can copy the contents to a file using the copy button on the top right and continue the walkthrough if there were any issues generating the mesh yourself.
cube.msh file
$MeshFormat
4.1 0 8
$EndMeshFormat
$PhysicalNames
1
3 1 "H2O"
$EndPhysicalNames
$Entities
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1 -1.000000002804313e-007 -1.000000002804313e-007 -1.000000002804313e-007 10.0000001 10.0000001 10.0000001 1 1 6 1 2 3 4 5 6
$EndEntities
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$EndElements
$Parametrizations
0 0
$EndParametrizations
Write an egsinp file
Once you have a mesh file, you're ready to write the input file. The three required input file sections are:
- Geometry definition
- Source definition
- Run control
First, define the mesh geometry. An EGS_Mesh geometry block looks like:
:start geometry definition:
:start geometry:
library = egs_mesh
name = my_mesh
file = cube.msh # your mesh here
:stop geometry:
# define a 15x15x15cm vacuum envelope around the mesh
:start geometry:
library = egs_box
name = my_box
box size = 15 15 15
# translate it from the origin to the cube's centre point (5, 5, 5)
:start transformation:
translation = 5 5 5
:stop transformation:
:start media input:
media = vacuum
:stop media input:
:stop geometry:
:start geometry:
library = egs_genvelope
name = my_envelope
base geometry = my_box
inscribed geometries = my_mesh
:stop geometry:
simulation geometry = my_envelope
:stop geometry definition:
For the mesh, the only input you need to adjust is the file. If you're following along, this should be named cube.msh. We also defined a vacuum envelope around the mesh, so that particles exiting the mesh are only discarded when they exit the vacuum too. This probably won't cause a noticable difference for this convex mesh, but defining an envelope is crucial for correctly simulating meshes in general. For your own simulations, make sure to adjust the envelope's size and position to bound the mesh.
Next, the source. Let's define an exterior point source. The meshed box starts at the origin and extends 10cm along x, y and z. So placing the source at (5, 5, -1) means the source will be 1cm away from the box's -z face. For this example, you'll simulate a 10MeV photon monoenergetic point source.
:start source definition:
:start source:
library = egs_point_source
name = my_source
position = 5 5 -1
:start spectrum:
type = monoenergetic
energy = 10
:stop spectrum:
charge = 0
:stop source:
simulation source = my_source
:stop source definition:
And finally, the run control section. Let's run 1 million histories.
:start run control:
ncase = 1e6
:stop run control:
The input file is done, and you're ready to run the simulation.
:start geometry definition:
:start geometry:
library = egs_mesh
name = my_mesh
file = cube.msh # your mesh here
:stop geometry:
# define a 15x15x15cm vacuum envelope around the mesh
:start geometry:
library = egs_box
name = my_box
box size = 15 15 15
# translate it from the origin to the cube's centre point (5, 5, 5)
:start transformation:
translation = 5 5 5
:stop transformation:
:start media input:
media = vacuum
:stop media input:
:stop geometry:
:start geometry:
library = egs_genvelope
name = my_envelope
base geometry = my_box
inscribed geometries = my_mesh
:stop geometry:
simulation geometry = my_envelope
:stop geometry definition:
:start source definition:
:start source:
library = egs_point_source
name = my_source
position = 5 5 -1
:start spectrum:
type = monoenergetic
energy = 10
:stop spectrum:
charge = 0
:stop source:
simulation source = my_source
:stop source definition:
:start run control:
ncase = 1e6
:stop run control:
Run the simulation and view the results
To run the simulation, you'll use the mevegs EGSnrc user code, which outputs the results to a VTK file to be analyzed in Paraview.
As an
egs++geometry,EGS_Meshis technically usable from anyegs++application. ButmevegsconvertsEGS_Meshresults to VTK for quick analysis without any extra steps.
Back when you created the mesh file, you also assigned media names. In this example, the only media was H2O, but simulations can have many different media. For all mesh media, you have to ensure that EGSnrc has the corresponding data loaded. This can either be done by specifying a pegs4dat file using the -p flag on the command line, or defining the media in the input file. Either method is fine, but for this example you'll use a pegs4dat file. The file tutor_data.pegs4dat comes bundled with EGSnrc and has a definition of H2O.
Enter the mevegs directory in egs_home and run the simulation:
mevegs -i cube.egsinp -p tutor_data.pegs4dat
Make sure the cube.msh file is in the same directory you're running the code in.
EGSnrc will print a few screens of information to the console and then report simulation progress until it's done.
Running 1000000 histories
Batch CPU time Result Uncertainty(%)
==========================================================
1 1.09 0.501526 0.31
2 2.44 0.501762 0.22
3 3.70 0.502413 0.18
4 5.22 0.501949 0.16
5 7.25 0.501994 0.14
6 9.19 0.501892 0.13
7 10.92 0.501821 0.12
8 13.03 0.501918 0.11
9 15.42 0.502218 0.10
10 17.25 0.502418 0.10
Finished simulation
Total cpu time for this run: 17.25 (sec.) 0.0048(hours)
Histories per hour: 2.08696e+08
Number of random numbers used: 121444161
Number of electron CH steps: 5.88643e+06
Number of all electron steps: 9.2142e+06
last case = 1000000 Etot = 1e+07
================================================================================
Finished simulation
Elapsed time: 20.5 s ( 0.006 h)
CPU time: 17.8 s ( 0.005 h)
Ratio: 1.152
Afterwards, there should be a new file called cube.vtk. Start Paraview and open this file using File->Open, and Apply in the Properties toolbar. Color the mesh by dose to see the dose results.
And you're done! That's a full EGS_Mesh simulation from start to finish. Color the mesh by uncertainty to see whether these results can be trusted, or if you need to run more histories to be sure.
Going further
-
Refine the mesh and run another simulation. How did the simulation runtime change? Do the results look different? More refined meshes are required to observe accurate dose gradients.
-
After the simulation, the histories per hour is reported. Run a simulation with more histories and check if the histories per hour changes. Given this number, how long would it take you to run one billion histories?
-
Run an
EGS_XYZGeometrysimulation with a similar number of elements and compare the simulation runtimes. Typically,EGS_Meshsimulations are 2 to 3 times slower thanEGS_XYZGeometry. Do you observe this? How do the results compare? -
The dose result is fairly uneven, especially for coarse meshes like this one. Why? Does this persist if you keep refining the mesh?
References
Egsinp syntax
The basic EGS_Mesh input file syntax is:
:start geometry definition:
:start geometry:
library = egs_mesh
name = my_mesh
file = model.msh # your mesh here
:stop geometry:
simulation geometry = my_mesh
:stop geometry definition:
However, most meshes should be simulated in an envelope, otherwise particles exiting the mesh are discarded immediately, even if they would have reentered the mesh later on.
In an envelope
This example embeds a mesh inside an air box.
:start geometry definition:
:start geometry:
library = egs_mesh
name = my_mesh
file = model.msh
:stop geometry:
# define a 50cm air cube at the origin
:start geometry:
library = egs_box
name = my_box
box size = 50 50 50
:start media input:
media = air
:stop media input:
:stop geometry:
# embed the mesh in the air box
:start geometry:
library = egs_genvelope
name = my_envelope
base geometry = my_box
inscribed geometries = my_mesh
:stop geometry:
simulation geometry = my_envelope
:stop geometry definition:
Scaling the mesh
Mesh files are assumed to be in cm. The scale key can be used to scale the
mesh if the file uses different units.
:start geometry definition:
:start geometry:
library = egs_mesh
name = my_mesh
file = model.msh
scale = 0.1 # multiply all node coordinates by 0.1 (e.g. mm to cm)
:stop geometry:
simulation geometry = my_mesh
:stop geometry definition:
STEP file simulation (WIP)
TODO
Mesh file reference (WIP)
Developer reference (WIP)
TODO