Getting started

You can download the 3D-PDR code from this GitHub link.

To install 3D-PDR, you must first install SUNDIALS. You will need the gfortran and gcc compilers, as well as CMake.

Before proceeding, create a home directory where the code will be installed, for example:

$ cd
$ mkdir 3D-PDR
$ cd 3D-PDR

Installing CMake

First, check whether cmake is already installed on your system. If it is, you may skip this section.

To install cmake, download it within your ~/3D-PDR/ directory:

$ wget https://github.com/Kitware/CMake/releases/download/v3.23.0/cmake-3.23.0-linux-x86_64.tar.gz

Extract the tarball:

$ tar -xzvf cmake-3.23.0-linux-x86_64.tar.gz

Move the extracted directory to /opt:

$ sudo mv cmake-3.23.0-linux-x86_64 /opt/cmake-3.23.0

Create a symbolic link to make it accessible system-wide:

$ sudo ln -sf /opt/cmake-3.23.0/bin /usr/bin/

Verify that cmake is properly installed:

$ cmake --version

For more information about CMake, visit the CMake official website.

Installing SUNDIALS

Clone the SUNDIALS repository:

$ git clone https://github.com/LLNL/sundials.git sundials

Create and enter a build directory:

$ mkdir sundials/build
$ cd sundials/build

Configure SUNDIALS using cmake:

$ cmake -DCMAKE_INSTALL_PREFIX=/YOUR-HOMEPATH/3D-PDR/sundials ../

Build and install:

$ make
$ make install

Next, edit your shell configuration file (e.g. ~/.bashrc) and add the following lines:

export LD_LIBRARY_PATH=/home/USERNAME/3D-PDR/sundials/lib
export SUNDIALS_DIR=/home/USERNAME/3D-PDR/sundials

Then, reload your shell configuration:

$ source ~/.bashrc

Note

If you are using a different shell, adjust the above commands accordingly.

For further details on SUNDIALS, see the SUNDIALS GitHub repository.

Installing 3D-PDR

Within the directory ~/3D-PDR/, extract the 3D-PDR package:

$ cd ~/3D-PDR/
$ tar xvzf 3DPDR.tgz

Navigate to the source directory:

$ cd 3D-PDR-main/src

Compiling the Code and Running a Test Model

Before compiling, open the file config.mk and ensure that the F90 (Fortran) and CC (C++) compiler paths are correctly set.

Note

For macOS users: Compilation may fail if you have a Conda environment activated. Deactivate Conda before compiling:

$ conda deactivate

To compile 3D-PDR:

$ make

If compilation completes successfully, an executable named 3DPDR will appear in your ~/3D-PDR/ directory.

You can now run a test model to verify that the installation is successful:

$ ./3DPDR

The test run should complete within a few seconds (depending on your system).

To confirm that the run was successful, compare the gas temperature vs. visual extinction results with the provided benchmark model.

Plot columns 3 (visual extinction) and 4 (gas temperature) of your output file sims/test.pdr.fin against those in benchmark/model.pdr.fin.

For example, using gnuplot:

set log
plot 'sims/test.pdr.fin' u 3:4 w l t 'my model', \
     'benchmark/model.pdr.fin' u 3:4 w l t 'benchmark'

If the curves match, your installation is complete and functioning correctly.

—

Congratulations! You are now ready to begin running your own 3D-PDR simulations.