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input-data-catalogs's Introduction

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GEOS-Chem Input Data

This repository has input data catalogs for GEOS-Chem. The catalog files are intended for downloading GEOS-Chem input data with the bashdatacatalog. You can to obtain input data according to

  • the GEOS-Chem versions you use (e.g., 13.2 + 13.4)
  • the meteorology you use (e.g., MERRA2 2x2.5 + GEOS-FP 0.25x0.3125 NA nested)
  • time spans of your simulation (e.g., 2019-01-01 to 2020-01-01)

Instructions for users

NOTE: You do not need to clone this repository. You can download data catalogs from here.

Create a directory called MyCatalogs/ in the top-level of your GEOS-Chem input data directory (the directory that has HEMCO/, CHEM_INPUTS/, etc. ). This directory is where you will put the catalog files you are actively using.

liam:~$ cd /ExtData  
liam:/ExtData$ mkdir MyCatalogs

Next, download the data catalogs for the GEOS-Chem versions you use from here: http://geoschemdata.wustl.edu/ExtData/DataCatalogs/. For example, I am going to use 13.2 and 13.4 so I am going to download the catalog files to MyCatalogs/13.2 and MyCatalogs/13.4. Meteorological inputs do not change between GEOS-Chem versions so you can put MeteorologicalInputs.csv at MyCatalogs/MeteorologicalInputs.csv. Here is what MyCatalogs/` looks like after downloading the catalog files.

liam:/ExtData$ tree MyCatalogs 
MyCatalogs
├── 13.2
│   ├── ChemistryInputs.csv
│   ├── EmissionsInputs.csv
│   └── InitialConditions.csv
├── 13.4
│   ├── ChemistryInputs.csv
│   ├── EmissionsInputs.csv
│   └── InitialConditions.csv
└── MeteorologicalInputs.csv

Next, edit MeteorologicalInputs.csv so that the meteorological data collections you use are enabled (i.e., set column 3 to 1 for every collection you need, and set it to 0 for collections you do not use).

Now you can run bashdatacatalog commands like

liam:/ExtData$ bashdatacatalog MyCatalogs/**/*.csv list-missing url 2019-01-01 2020-01-01

NOTE: You should always run bashdatacatalog from the top-level of input data repository (i.e., /ExtData in my case).

Instructions for the GCST

When a collection is added/removed - Make the appropriate changes to the catalog files on the dev branch.

When a new version of GEOS-Chem is released - Tag dev with the new GEOS-Chem version number.

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input-data-catalogs's Issues

probelm with bashdatacatalog-list

I am trying to download the chem input files for GCHP 13.4. The command
bashdatacatalog-fetch InputDataCatalogs/13.4/ChemistryInputs.csv
from my ExtData directory seems to work fine. Output is attached below.

But when I give the command
bashdatacatalog-list -am -r 2019-06-30,2019-08-02 -f xargs-curl InputDataCatalogs/13.4/ChemistryInputs.csv | xargs curl
I get a bunch of numbers on the screen. Here are the first few lines of what I see:

(gchp-openmpi-env) psk9@dcc-login-01  /work/psk9/Data/ExtData $ bashdatacatalog-list -am -r 2019-06-30,2019-08-02 -f xargs-curl InputDataCatalogs/13.4/ChemistryInputs.csv | xargs curl
curl: option --write-out: requires parameter
curl: try 'curl --help' for more information
curl: option --write-out: requires parameter
curl: try 'curl --help' for more information
curl: option --url: requires parameter
curl: try 'curl --help' for more information
curl: option --url: requires parameter
curl: try 'curl --help' for more information
curl: option --url: requires parameter
curl: try 'curl --help' for more information
curl: option -o: requires parameter
curl: try 'curl --help' for more information
curl: option --write-out: requires parameter
curl: try 'curl --help' for more information
8.621e-28 8.621e-28 8.621e-28 1.526e-26 1.526e-26 2.224e-25 2.224e-25 2.224e-25 2.700e-24 2.700e-24 1.037e-25 1.037e-25 3.833e-28 3.833e-28 3.833e-28 1.275e-30 1.275e-30 4.538e-33 4.538e-33 9.746e-35 9.746e-35 9.746e-35 1.645e-35 1.645e-35 0.000e+00 0.000e+00 0.000e+00 1.168e-36 1.168e-36 5.806e-35 5.806e-35 1.690e-34 1.690e-34 1.690e-34 3.137e-34 3.137e-34 2.057e-34 2.057e-34 4.358e-35 4.358e-35 4.358e-35 2.697e-37 2.697e-37 0.000e+00 0.000e+00 0.000e+00 
1.507e-28 1.507e-28 1.507e-28 7.446e-27 7.446e-27 4.232e-25 4.232e-25 4.232e-25 2.522e-23 2.522e-23 7.689e-25 7.689e-25 2.125e-27 2.125e-27 2.125e-27 5.511e-30 5.511e-30 1.354e-32 1.354e-32 1.325e-34 1.325e-34 1.325e-34 2.230e-36 2.230e-36 0.000e+00 0.000e+00 0.000e+00 8.795e-36 8.795e-36 1.102e-34 1.102e-34 3.159e-34 3.159e-34 3.159e-34 7.244e-34 7.244e-34 4.216e-34 4.216e-34 1.184e-35 1.184e-35 1.184e-35 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 
5.333e-28 5.333e-28 5.333e-28 5.029e-26 5.029e-26 4.204e-24 4.204e-24 4.204e-24 2.432e-22 2.432e-22 5.353e-24 5.353e-24 9.517e-27 9.517e-27 9.517e-27 1.452e-29 1.452e-29 2.247e-32 2.247e-32 4.036e-35 4.036e-35 4.036e-35 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.412e-35 3.412e-35 1.615e-34 1.615e-34 3.813e-34 3.813e-34 3.813e-34 8.920e-34 8.920e-34 4.539e-34 4.539e-34 5.912e-37 5.912e-37 5.912e-37 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00

The bashdatacatalog-list seems to work fine for fetching the met data and the hemco files.
chem_meta.txt

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