TOPAS-nBio

This is the TOPAS-nBio extension repository, a Monte Carlo simulation framework for (sub-) cellular radiobiology.

TOPAS-nBio is described here: https://topas-nbio.readthedocs.io/. This page includes a class documentation and the license.

TOPAS-nBio is an extension of OpenTOPAS (TOol for PArticle Simulations), which can be obtained from https://OpenTOPAS.github.io. The TOPAS documentation can be found at https://opentopas.readthedocs.io/.

The TOPAS-nBio package was described in Schuemann et al., Radiation Research, 2019, 191(2), p.125. This reference should be cited for all work using the TOPAS-nBio package.

We encourage contribution of user-developed extensions that fit within the TOPAS-nBio scheme. If you would like to contribute code, please contact the developers.

---

General information

Note

The main difference in installing for Debian/Ubuntu and MacOS is the installation paths.

Tip

Users can install multiple extensions by either:

• Copy all the Extension directories into a common global directory, or

• Using the \; between directory paths e.g., (and see below):

  -DTOPAS_EXTENSIONS_DIR=/MyProject1Extensions/\;/MyProject2Extensions/

Debian

Follow installation for Debian/Ubuntu procedures after and including step 8.4. Then:

$ cd $HOME/Applications/

Clone the repository:

$ git clone https://github.com/topas-nbio/TOPAS-nBio.git

Return to the OpenTopas-build directory:

$ cd $HOME/Applications/TOPAS/OpenTOPAS-build

Repeat cmake command by including the TOPAS_EXTENSIONS_DIR variable as follows (don't miss the -D):

$ cmake ../OpenTOPAS -DCMAKE_INSTALL_PREFIX=../OpenTOPAS-install -DTOPAS_EXTENSIONS_DIR=$HOME/Applications/TOPAS-nBio

Build:

$ make -j8 install

MacOS

Follow installation for MacOS procedures after and including step 7.4. Then:

$ cd /Applications

Clone the repository:

$ git clone https://github.com/topas-nbio/TOPAS-nBio.git

Return to the OpenTopas-build directory:

$ cd /Applications/TOPAS/OpenTOPAS-build

Repeat cmake command by including the TOPAS_EXTENSIONS_DIR variable as follows (don't miss the -D):

$ cmake ../OpenTOPAS -DCMAKE_INSTALL_PREFIX=../OpenTOPAS-install -DTOPAS_EXTENSIONS_DIR=/Applications/TOPAS-nBio

Build:

$ make -j8 install

---

Run the demos. For some demos, a pause before quit is enabled, then, write exit at the terminal prompt.

Linux:

    $ source rundemos.csh

Mac:

    $ source rundemos.csh

---