Difference between revisions of "HEMCO data directories"

Revision as of 21:46, 3 November 2016

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.

In each of the tables below:

The Inventory column contains a link that describes each data set in more detail. Most of these links point to existing pages on the GEOS-Chem wiki.

The Data file info column points to the README files that are stored with each data set. Each README provides a list of the files contained within a given folder, information about the data contained in each file, and (often) a description of how the files were created.

The Path column shows the location of each data set, with respect to $ROOT, the top-level HEMCO directory. For example, on the Harvard disk server, $ROOT points to the directory /mnt/gcgrid/data/ExtData/HEMCO/.

The Status column describes the current status of each data set:

CURRENTLY USED	Denotes that the data set is part of the standard emissions configuration for GEOS-Chem, that is: It is used in the GEOS-Chem 1-month and 1-year full-chemistry benchmark simulations, or It is used in one or more of the GEOS-Chem specialty simulations.
OPTIONAL	Denotes that the data set is not part of the the standard GEOS-Chem emissions configuration. But you can still use the data set in your research applications if you wish.
TO BE ADDED SOON	Denotes that the data set is not yet ready for use with HEMCO, but will be added soon.
OBSOLETE	Denotes that the data set has been removed from the standard GEOS-Chem emissions configuration. In most cases, OBSOLETE means that a newer version of the data is available and should be used instead.
NOT USED	Denotes that the data set is not used in the standard GEOS-Chem emissions configuration, even if it is current. For example, another data source is being used in place of this data set for a particular reason.

If use GEOS-Chem, then we recommend that you download the data sets that are listed as CURRENTLY USED, as these form the standard GEOS-Chem emissions configuration. You are free, however, to use any of the data sets listed below. Your choice of data sets will depend on your particular research needs.

--Bob Y. 10:53, 18 March 2015 (EDT)

Aerosol emissions

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

--Bob Y. 10:15, 18 March 2015 (EDT)

Anthropogenic and biofuel emissions

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

Please also see list of species included in each of these global inventories and regional inventories.

--Bob Yantosca (talk) 20:27, 1 November 2016 (UTC)

Anthropogenic aircraft and ship emissions

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

--Bob Y. 10:07, 18 March 2015 (EDT)

Biomass burning emissions

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

--Bob Yantosca (talk) 20:47, 1 November 2016 (UTC)

Bromine emissions

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

NOTE: See our Non-emissions data section for information about stratospheric bromine concentration data.

--Bob Y. 15:03, 17 March 2015 (EDT)

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, GFED4 and FINN are implemented as HEMCO extensions, but we have listed them with the other biomass burning inventories, for clarity.

--Bob Y. 10:09, 18 March 2015 (EDT)

Future and historical emissions

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

--Bob Y. 15:04, 17 March 2015 (EDT)

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 Yantosca (talk) 20:53, 1 November 2016 (UTC)

Non-emissions data

The following subdirectories of the HEMCO directory tree input data contains non-emissions data sets. Most of these are used as inputs to GEOS-Chem's chemistry modules (i.e. photolysis, stratospheric chemistry, etc.).

--Bob Yantosca (talk) 21:45, 3 November 2016 (UTC)

Other inputs for HEMCO

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

--Bob Y. 15:08, 17 March 2015 (EDT)

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.            #
#                                                                             #
#  NOTE: In most cases, you only have to specify the top-level folder.        #
#  All subfolders will be downloaded automatically.                           #
#                                                                             #
###############################################################################

#=============================+================================================
# 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)

New features for the GEOS-Chem v10-01 public release

For the GEOS-Chem v10-01 public release, we modified the default download options in the hemcoDataDownload.pl script. We changed the default wget options from:

wget r -nH -q ... 

to

wget -r -nH -c -N -q ...

This will tell wget to only download new or modified files, instead of trying to download the entire data archive from scratch. This should hopefully subsequent data download processes faster.

--Bob Y. (talk) 18:35, 16 June 2015 (UTC)

Submitting new data for use with HEMCO

If you have a new emissions inventory or other atmospheric data set that you would like to add to the HEMCO data directories, then please contact the GEOS-Chem Support Team. Data files must be in COARDS-compliant or CF-compliant netCDF format. Please see our Preparing data files for use with HEMCO wiki page for more information.

--Bob Y. 11:49, 5 March 2015 (EST)