README

All the supplementary data needed for the reproduction of the experiment described in the manuscript are provided on this ZENODO repository. The supplementary data includes the following:

1. 01_palm_source_code.zip contains the source code for the current version of the PALM model used for this experiment

2. 02_inputs-configs.zip which contains:

• static driver files (for cases 01 = full-trees, 02 = half-trees, 03 = no-strees)
• dynamic driver files (for different winds directions W = west, SW = southwest, S = south and stratifications C = convective, N = neutral + stable)
• configuration files for the first PALM run (p3d), and the configuration files for the restart runs (p3dr) for each of the performed simulations
• the files with N02 are apllied for child domain

3. 03_maps-GIS contains maps in gis or png format with one hour averages outputs: 

• the cases are terC/N_W/SW/S_01/02/03 for the stratifications, wind direcrions and trees-scenario (see the legend above)
• abs for absolute values, diff for differences from no-tree scenario, 01h = 1 hour average
• variables are bio_UTCI, kc_PM10 = PM10 concentration in 2m or 10m height, theta = temperature in 2m and wspeed = wind-speed in 10m

4. 04_cuts contains svg and png plots with vertical and horizontal (xy) cuts 

• the cases are terC/N_W_01/02/03 for the stratifications and trees-scenario (see the legend above) and west winds
• jugp-ciirc = the vertical cut for (JugP) street (near the ciirc-CTU building), terr-street = the vertical cut for (Terr) street

PALM MODEL INSTALLATION AND USAGE GUIDE

A. Installation

1. First, make sure to satisfy the Software Requirements. On Debian-based Linux Distributions, this can be achieved by the following command:

sudo apt-get install gfortran g++ make cmake coreutils libopenmpi-dev openmpi-bin libnetcdff-dev netcdf-bin libfftw3-dev python3-pip python3-pyqt5 flex bison ncl-ncarg

2. Also, some additional python dependencies are needed, which can be installed using pip. In case you want to use a virtual environment for these dependencies, please make sure to create one first. Afterwards, you can install the python dependencies by executing the following command:

python3 -m pip install -r requirements.txt

3. Now the PALM model system can be installed with the following commands (please replace  with the desired installation directory):

export install_prefix=""
bash install -p ${install_prefix}
export PATH=${install_prefix}/bin:${PATH}

4. The following optional command permanently adds this installation to your bash environment:

echo "export PATH=${install_prefix}/bin:\${PATH}" >> ~/.bashrc

5. Type bash install -h to get all available options of the install script. During installation, the script calls the respective install script of all packages in this repository and installs them to the chosen  directory. Therefore, it is not necessary to manually install any of the packages.

You can test your installation with the following commands:

palmtest --cases urban_environment_restart --cores 4

B. Usage

After a successful installation, the executables for all packages have been linked into the directory /bin and a default PALM configuration file can be found at /.palm.config.default. In case you have installed the python dependencies inside a virtual environment, that environment needs to be active whenever you wand to use PALM. For usage of each of the packages, please refer to their individual documentation. Next, you need to create your first PALM setup in order to start a simulation. To get a simple preconfigured setup and start your first PALM simulation, please execute the following sequence of commands:

mkdir -p "${install_prefix}/JOBS/example_cbl/INPUT"
cp "packages/palm/model/tests/cases/example_cbl/INPUT/example_cbl_p3d" "${install_prefix}/JOBS/example_cbl/INPUT/"
cd ${install_prefix}
palmrun -r example_cbl -c default -a "d3#" -X 4 -v -z