OpenTRIM

A C++ Monte-Carlo code for simulating ion transport in materials with an emphasis on calculation of radiation damage.

OpenTRIM offers the following components:

• opentrim-gui: A GUI tool to configure, run and evaluate simulations
• opentrim: A command line program for batch mode
• libopentrim: A C++ library with all the ion transport code, which can be linked to external applications
• libxs_*: A set of C++ libraries for screened Coulomb scattering calculations with various potentials, * = ZBL, Moliere, ...
• libdedx: A C++ library for electronic stopping & straggling calculations

Documentation can be found here: https://ir2-lab.gitlab.io/opentrim

Installation

Binary packages

Binary packages and repositories for a number of Linux distributions (Ubuntu, RHEL, OpenSUSE, etc.) are built on the openSUSE Build Service. Please follow the instructions found there to install OpenTRIM on your system.

On Windows, please download the latest binary distribution release provided as a zip file and extract to some location. To be able to run the program from the windows command line, add the program folder to the user or system path.

Building from source

On Linux the project can be built and installed with cmake.

Tested compilers: GCC 8 and above, Clang 14.

Clone the project using

> git clone [email protected]:ir2-lab/opentrim.git

or download a tarball of the last version.

To build OpenTRIM you will need the following libraries:

• Eigen v3.4.0 for vector operations
• HDF5 v1.10.7 for file storage
• Qt5 or Qt6 for the GUI program
• Qwt v6.x for plotting

They can be installed with

# Ubuntu 22.04 / DEB
sudo apt install libeigen3-dev libhdf5-dev libhdf5-103-1 
# for the GUI component add the following
sudo apt install qtbase5-dev libqt5svg5 libqwt-qt5-dev libqwt-qt5-6

# RHEL 9 / RPM
sudo dnf install eigen3-devel.noarch hdf5.x86_64 hdf5-devel.x86_64

Basic build recipe (run from project directory):

mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
ninja
ninja install

The default install location is $HOME/.local, thus sudo is not required. Override this by setting the option -DCMAKE_INSTALL_PREFIX="/your/install/location" when calling cmake.

On Windows the project can be built with MSYS2. Detailed instructions will be given in the future.

Usage

The GUI application can be invoked from the command line

> opentrim-gui

or by double-clicking the executable. Some simulation examples are included in the program and can be readily used as templates.

The command line program can be invoked by

> opentrim [options] [-f config.json]

The program accepts a JSON-formatted configuration input either directly from a file (with the -f option) or from stdin.

To see all available options run opentrim -h, which prints

Monte-Carlo ion transport simulation
Usage:
  opentrim [OPTION...]

  -n arg            Number of histories to run (overrides config input)
  -j arg            Number of threads (overrides config input)
  -s, --seed arg    random generator seed (overrides config input)
  -i, --input arg   input HDF5 file name
  -f arg            JSON config file
  -o, --output arg  output HDF5 file name (overrides config input)
  -t, --template    print a template JSON config to stdout
  -v, --version     Display version information
  -h, --help        Display short help message

The cli program first checks and validates the configuration input. It then runs the simulation and saves the results into a HDF5 archive.

Testing

The examples contained in the GUI app can be used for testing.

Some benchmarks for comparison to other codes are given in folder test/. The file test/README.md gives a short description of each benchmark.

The folders test/opentrim/b1 to b7 have config files for running the benchmarks with opentrim -f config.json.

The file test/octave/plot_benchmark.m is a MATLAB/OCTAVE script which can be used for plotting benchmark results.

Credits

OpenTRIM draws heavily on SRIM by J.F. Ziegler, one of the first ion simulation programs created in the 80s and still widely used until today. The electronic energy loss data in OpenTRIM have been obtained from the SRIM-2013 distribution using the provided utility SRmodule.exe.

Many ideas, techniques and code were taken from the following open-source ion simulation programs:

• The program iradina written by Ch. Borschel & C. Ronning and extended by J.P. Crocombette & Ch. Van Wambeke.
• The program Corteo by F. Schiettekatte.

The Eigen library by B. Jacob & G. Guennebaud is used for 3D vector math.

The Xoshiro256+ algorithm by D. Blackman and S. Vigna is used for random number generation.

JSON for Modern C++ by N. Lohmann is used for encoding/decoding program options to/from json.

cxxopts by jarro2783 is used for handling cli options.

The HDF5 library with the HighFive C++ interface are used for saving results to the HDF5 archive.

License

OpenTRIM is distributed under the MIT license.