Difference between revisions of "HEMCO data directories"

Revision as of 15:16, 18 February 2015

On this page we describe the directory tree from which the HEMCO emissions component can read emissions inventories and other atmospheric data sets.

Overview

The HEMCO emissions component can read several types of emission inventories, as well as other types atmospheric data sets, such as production and loss rates, or concentration data. We have collated all of this data into a comprehensive directory tree structure. Each folder of the HEMCO data directory tree represents a particular emissions inventory or other data set.

At present, the HEMCO data directory tree resides on the disk servers at Harvard University (and soon at Dalhousie University). We have created a package that will let you download this directory tree to your local disk storage space. For more information, please see the Downloading the HEMCO data directories section below.

--Bob Y. 10:22, 13 February 2015 (EST)

HEMCO data directory structure

The sections below describe each of the data sets contained in the HEMCO directory tree, grouped by type. Each data set is contained in a subdirectory of the HEMCO root directory, which is specified by the $ROOT token. (For example, on the Harvard disk server, $ROOT points to the directory /mnt/gcgrid/data/ExtData/HEMCO/.)

--Bob Y. 10:49, 13 February 2015 (EST)

Aerosols

The following subdirectories of the HEMCO directory tree contain aerosol emission inventories.

--Bob Y. 15:35, 12 February 2015 (EST)

Anthropogenic and biofuel emissions

The following subdirectories of the HEMCO directory tree contain inventories of anthropogenic and biofuel emissions.

--Bob Y. 16:23, 13 February 2015 (EST)

Anthropogenic aircraft and ship emissions

The following subdirectories of the HEMCO directory tree contain inventories of anthropogenic aircraft and ship emissions.

--Bob Y. 11:03, 13 February 2015 (EST)

Biomass burning emissions

The following subdirectories of the HEMCO directory tree contain inventories of biomass burning emissions.

--Bob Y. 15:48, 13 February 2015 (EST)

Emissions implemented as HEMCO extensions

The following subdirectories of the HEMCO directory tree contain input data used by various HEMCO extensions. These HEMCO extensions compute emissions for quantities that depend on meteorological variables (e.g. emissions from lighting, biogenic processes, etc.).

NOTE: GFED3 and FINN are implemented as HEMCO extensions, but we have listed them with the other biomass burning inventories, for clarity.

--Bob Y. 10:49, 13 February 2015 (EST)

Future and historical emissions

The following subdirectories of the HEMCO directory tree contain historical and future emissions inventories.

--Bob Y. 11:07, 13 February 2015 (EST)

GEOS-Chem specialty simulation data

The following subdirectories of the HEMCO directory tree input data (emissions, oxidants, etc.) for use with the GEOS-Chem specialty simulations. If you do not regularly use these simulations, you may choose not to download these data directories.

--Bob Y. 11:17, 13 February 2015 (EST)

Seawater concentrations

The following subdirectories of the HEMCO directory tree input data contains seawater concentrations used by the acetone ocean loss and sulfate chemistry modules.

--Bob Y. 11:22, 13 February 2015 (EST)

Stratospheric data and bromine data

The following subdirectories of the HEMCO directory tree input data contains data for use with the GEOS-Chem's stratospheric chemistry mechanism.

--Bob Y. 15:53, 17 February 2015 (EST)

Other inputs for HEMCO

The following subdirectories of the HEMCO directory tree input data for various HEMCO functions. These include regional masks, timezones, and emission scale factors.

--Bob Y. 11:23, 13 February 2015 (EST)

Downloading the HEMCO data directories

The GEOS-Chem Support Team has created a package called hemco_data_download. With this package, you can download the various emissions inventories and related data files for HEMCO to your own disk server. Furthermore, you can specify which data directories that you would like to download (as well as those you would like to ignore) via a configuration file.

Obtaining the hemco_data_download package

To obtain the hemco_data_download package, use Git to clone this repository

git clone https://github.com/GCST/hemco_data_download.git

This will create a directory named hemco_data_download, in which you should see the following files:

README 

File with an overall description of the directory contents

hemcoDataDownload.pl 

Perl script to download HEMCO data directories

hemcoDataDownload.rc 

Configuration file for the hemcoDataDownload.pl script. In this file you can specify which HEMCO data directories you would like to download and which you would like to omit.

forTesting.rc 

A configuration file that you can use for testing or debugging. This will tell hemcoDataDownload.pl only to download a couple of emissions inventories with files that do not take up much disk space.

--Bob Y. 13:58, 12 February 2015 (EST)

Setting up the configuration file

The configuration files (i.e. hemcoDataDownload.rc and forTesting.rc) are pretty much self-explanatory.

At the top of the configuration file you will see this section:

###############################################################################
#                                                                             #
#  Specify the remote and local HEMCO data paths, plus other options.         #
#                                                                             #
###############################################################################

Remote HEMCO data path | ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO
Your HEMCO data path   | /as/scratch/bmy/HEMCO
Verbose output         | yes
Dryrun only?           | no

1. Remote HEMCO data path is the location on the FTP server from which you are going to download the data. This can be from either Harvard or from Dalhousie. (For now we will use the Harvard server). You can edit this accordingly.
2. Your HEMCO data path specifies the root-level directory for HEMCO data on your own disk space. If you are not sure where to place this, then ask your sysadmin.
3. Verbose output lets you specify if you want to print out extra output during the download process. This can be set to either "yes" or "no".
4. Dryrun only flag allows you to print out the data download commands without actually downloading the data. This is useful for debugging.

In the next section you specify all of the HEMCO inventories that you want to download. You will see this header:

###############################################################################
#                                                                             #
#  THE FOLLOWING DATA DIRECTORIES WILL BE DOWNLOADED.                         #
#                                                                             #
#  These data directories comprise the recommended emissions configuration    #
#  for typical GEOS-Chem full-chemistry and specialty simulations.            #
#                                                                             #
###############################################################################

#=============================+================================================
# AEROSOLS                    | Directory paths
#=============================+================================================
AEROCOM volcano emissions     | $ROOT/VOLCANO/v2014-10
Bond et al BC/OC              | $ROOT/BCOC_BOND/v2014-07
Cooke et al BC/OC             | $ROOT/BCOC_COOKE/v2014-07
Secondary organic aerosols    | $ROOT/SOA/v2014-07
... etc ...

Each line specifies the name of a HEMCO emissions inventory and the data path where it can be found on disk, relative to the root data path. NOTE: The script will replace the $ROOT token with the value you gave to the "HEMCO remote data path" above. (Lines starting with the comment character # will be ignored.)

Any inventory found in this section will be downloaded. To prevent an inventory from being downloaded you can either comment it out (i.e. place a # in the first column) or move the inventory to the next section.

The final section specifies HEMCO emission inventories that you do not wish to download. The section looks like this:

###############################################################################
#                                                                             #
#  THE FOLLOWING DATA DIRECTORIES WILL NOT BE DOWNLOADED.                     #
#                                                                             #
#  These data directories contain are optional emissions inventories that     #
#  are not used in typical GEOS-Chem simulations.  If you wish to download    #
#  any of these inventories, simply move the corresponding entry for each     #
#  inventory to the previous section.                                         #
#                                                                             #
###############################################################################

CH3I simulation (obsolete)    | $ROOT/CH3I/v2014-07
Chlorophyll A                 | $ROOT/CHLA/v2014-07
... etc ...

--Bob Y. 13:55, 12 February 2015 (EST)

Downloading the data

Once you have set up your configuration file, you can run the hemcoDataDownload.pl script to start downloading the HEMCO data to your local server. To run the script you can type:

hemcoDataDownload.pl

If you do not specify a configuration file name, then the hemcoDataDownload.pl scriptwill read the default configuration file hemcoDataDownload.rc configuration file. If you wish to specify a different configuration file name, simply pass that as an argument to the script, e.g.

hemcoDataDownload.pl myNewConfigFile.rc

Before you start downloading GB's of data, we recommend that you run a short test to make sure that the data directories are being copied to the proper locations on your disk server. For this purpose, we have provided a configuration file named forTesting.rc. Typing

hemcoDataDownload.pl forTesting.pl

will only download a couple of data inventories that do not take up much disk space. This allows you to ensure that the data transfer is sucessful without making you wait a long time.

--Bob Y. 13:57, 12 February 2015 (EST)