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Tools for calculating erosion rates from 10Be and 26Al collected in stream sediments
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TNT First commit Oct 14, 2015
driver_functions_CRNBasinwide Adding a few objects for the 21Ne tool Oct 3, 2018
.travis.yml Getting the correct makefile for the soil_CRN Aug 26, 2017
LICENSE Adding the travis and license files Aug 26, 2017
LSDBasin.cpp
LSDBasin.hpp Updated objects to latest version Aug 10, 2016
LSDCRNParameters.cpp Updated to latest version Dec 7, 2016
LSDCRNParameters.hpp
LSDChannel.cpp
LSDChannel.hpp Fixed the bug in the UTM zone so cosmo points may be from other zones Apr 12, 2016
LSDChiNetwork.cpp Updated objects to latest version Aug 10, 2016
LSDChiNetwork.hpp
LSDCosmoData.cpp
LSDCosmoData.hpp
LSDFlowInfo.cpp
LSDFlowInfo.hpp
LSDIndexChannel.cpp Updated to latest version Dec 7, 2016
LSDIndexChannel.hpp
LSDIndexChannelTree.cpp
LSDIndexChannelTree.hpp Fixed the bug in the UTM zone so cosmo points may be from other zones Apr 12, 2016
LSDIndexRaster.cpp Updated to latest version Dec 7, 2016
LSDIndexRaster.hpp
LSDJunctionNetwork.cpp Updated to latest version Dec 7, 2016
LSDJunctionNetwork.hpp
LSDMostLikelyPartitionsFinder.cpp Updated objects to latest version Aug 10, 2016
LSDMostLikelyPartitionsFinder.hpp
LSDParameterParser.cpp Adding a few objects for the 21Ne tool Oct 3, 2018
LSDParameterParser.hpp
LSDParticle.cpp Updated objects to latest version Aug 10, 2016
LSDParticle.hpp Updated objects to latest version Aug 10, 2016
LSDRaster.cpp Updated to latest version Dec 7, 2016
LSDRaster.hpp
LSDRasterInfo.cpp
LSDRasterInfo.hpp
LSDShapeTools.cpp Updated objects to latest version Aug 10, 2016
LSDShapeTools.hpp
LSDSoilHydroRaster.cpp Updated objects to latest version Aug 10, 2016
LSDSoilHydroRaster.hpp
LSDSpatialCSVReader.cpp Adding a few objects for the 21Ne tool Oct 3, 2018
LSDSpatialCSVReader.hpp Adding a few objects for the 21Ne tool Oct 3, 2018
LSDStatsTools.cpp
LSDStatsTools.hpp
LSDStrahlerLinks.cpp
LSDStrahlerLinks.hpp
README.asc Updated readme for the latest documentation Jan 9, 2018
SnowShieldFit.py Updated snow script to deal with cases where maximum SWE data is at m… Sep 14, 2016

README.asc

LSDTopoTools CRNBasinwide License GPL%20v3 blue

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.

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