Tools for calculating basinwide denudation rates from cosmogenic nuclides

The repository contains the code for calculating denudation rates based on ¹⁰Be and ²⁶Al concentrations measured in stream sediments.

It is the software behind the CAIRN method, as described in Mudd et al., 2016 ESURF.

This code is part of the LSDTopoTools software package.

The versions here are updated on a semi regular basis.

For instructions, go to the LSDTopoTools documentation website.

Instructions specific to this package are in the chapter on CRN analysis.

Quick Guide

If you are totally new to LSDTopoTools you can set up your system by following thse instructions: https://lsdtopotools.github.io/LSDTT_documentation/LSDTT_installation.html

If you already know what you are doing, here is a quick guide to walk you through the process. If one of these steps doesn’t make sense see the full documentation.

1. You will want a directory for both the source code and the data. Make these directories.

2. Get the latest version of the source code from https://github.com/LSDtopotools/LSDTopoTools_CRNBasinwide If you don’t have it, use

   $ git clone https://github.com/LSDtopotools/LSDTopoTools_CRNBasinwide.git

   or if you have it use

   $ git pull -u origin master

   in your source code directory.

3. If you have just downloaded the source code, or if it has updates, you need to compile the code. Go into the folder driver_functions_CRNBasinwide and use make:

   $ make -f Spawn_DEMS_for_CRN.make
   $ make -f Shielding_for_CRN.make
   $ make -f Basinwide_CRN.make

   After each call to make there will be a bunch of warnings that you can ignore.

4. In your data folder you will need a _CRNRasters.csv file, a *_CRNData.csv file, and a .CRNParams file. If you don’t know what these are read the relevant parts of the full documentation

5. In your data folder you will also need some python scripts, which you can download individually:

   $ wget https://github.com/LSDtopotools/LSDAutomation/raw/master/JoinSnowShielding.py
   $ wget https://github.com/LSDtopotools/LSDAutomation/raw/master/LSDOSystemTools.py
   $ wget https://github.com/LSDtopotools/LSDAutomation/raw/master/EliminateUnderscoreFromCRNDataSampleNames.py
   $ wget https://github.com/LSDtopotools/LSDAutomation/raw/master/PrepareDirectoriesForBasinSpawn.py

6. In your data folder, run PrepareDirectoriesForBasinSpawn.py. You will need to update the path and the prefix at the bottom of this file.

7. In addition, sample names with the underscore character () are not allowed. The script EliminateUnderscoreFromCRNDataSampleNames.py will replace all characters with - characters. You need to open this file and change the target directory before running. It will modify all *_CRNData.csv files it finds in that directory.

8. Next up, spawn the basins. Go into the source code directory and run:

   $ ./Spawn_DEMs_for_CRN.exe PATHNAME DATAPREFIX

9. Now, you are ready to calculate topographic shielding. You should run:

   $ ./Shielding_for_CRN.exe PATHNAME DATAPREFIX

   Note	If you ran the spawning the data prefix will now have a *_spawned in it.

   Warning

   This is the most computationally expensive component of the process. It could take a while. In the full documentation there is some instructions as to how to do this computation using an embarrassingly parallel approach.

10. If you decide to use previously reported snow shielding values, run the JoinSnowShielding.py function. This will result in data files with the text *_SS in it.

11. Questions? Read the documentation, and if you can’t find the answer email Simon.

Some more information on setting up LSDTopoTools

LSDTopoTools are written in C++ and work best in Linux. We realise, however, not that many people use Linux. We have therefore set up something called a virtual machine that runs a Linux operating system within whichever operating system you normally use (be it Windows, OSX, or Linux). To do this, we use a nifty bit of software called Vagrant that automates the setup process. You can read the instructions on our documentation website, but basically you need to download a few bits of software that are very easy to install, download something called a vagrantfile, and this vagrantfile automates the construction of a working linux system that has several LSDTopoTools packages.

Please have a look at the detailed instructions for setting up LSDTopoTools.