AMET Data Analysis

Atmospheric Model Evaluation Tool (AMET)

Using AMET on Valkyr

Loading New Simulations

Load script location: /home/AMET/AMET_v13/scripts_db

The first step in using the AMET installation is to load PGM simulation data into the database. The load step automatically pairs the model output with observations and then loads the paired data into the AMET MySQL database. Output from the program combine is the format of model output to use with AMET.

Use the script aqProject.csh to pair/load the combine output data into AMET. You need to configure the variables in the script for the simulation ID, time period, and networks to load. See the script WAQS_Base11b/WAQS_Base11b_CAMx12k.csh for an example operational script that loads the WAQS Base11b CAMx 12km results into AMET.

Creating Plots

Analysis script location: /home/AMET/AMET_v13/scripts_analysis

See the scripts under WAQS_Base11b_CAMx12k for an example of operational scripts used to plot results from the WAQS Base11b CAMx 12km simulation.

The script run_AMET_batch_scripts.csh is a batch script to create multiple AMET plots with a single execution.

The rest of the scripts in this directory are used to create specific plots/figures.

As with the load scripts, the analysis scripts need to be configured for a simulation, time periods, and species/networks. Note that when a species is selected to plot, you must also select the appropriate network. For example, if you select O3 as the species and IMPROVE as the network, the AMET scripts will fail with a nebulous error message. It is up to the user to select the right species/network combinations.

Model -> AMET Workflow

After installation the CAMx AVRG or CMAQ ACONC files on the IWDW data server, use the following steps to load these data into AMET.

1. CAMx files, convert to I/O API netCDF 2. netCDF formatted CAMx and CMAQ files are run through Combine to create monthly combined data (see /valkyr/data1/IWDW/WAQS/combine_test/combine_3SAQS_CAMx_conc_batch.csh) 3. Load monthly Combine outputs into AMET database with scripts_db 4. Create AMET plots with scripts_analysis

Installing new AQ Obs Data by Year

Data are available here: https://drive.google.com/drive/u/1/folders/0B2kjxCwKICxUZ3ZyNEVld2F6bHc
Install to /home/AMET/AMET_v13/obs/AQ
Find the file that you want to download and copy the alphanumeric part of the HTTP address into the following command. Also change the name of the filename to download (e.g. 2014_Obs.tar.gz)

 perl /usr/local/etc/gdown/gdown.pl "https://drive.google.com/uc?export=download&id=0B2kjxCwKICxUZFdlT2ExZWlpT1U" 2014_Obs.tar.gz

Note that when you untar the new obs data you'll need to move it to the appropriate AMET directory. For example, for the 2014 archive it will unpack into obs/2014. Move the 2014 directory to /home/AMET/AMET_v13/obs/AQ

Installation Notes

Location: /home/AMET/AMET_v13
Installation Command for AMET:

  git clone -b 1.3 https://github.com/USEPA/AMET.git AMET_v13

Upgrade R to the latest version:

sudo yum install R

Install required R packages for AMET

sudo R
> install.packages(c("RMySQL", "date", "maps", "mapdata","stats","plotrix", "fields"))

Manual install of ncdf4 for R

wget http://cirrus.ucsd.edu/~pierce/ncdf/ncdf4_1.13.tar.gz
sudo R CMD INSTALL ncdf4_1.13.tar.gz

Set AMETBASE and username/pass in /home/AMET/AMET_v13/configure/amet-config.R
Create the AMET user ametiwdw (only needs to be done once)

cd /home/AMET/AMET_v13/scripts_db/dbSetup
./create_amet_user.csh
user: ametiwdw
pass: winter********

Run the AMET test case

cd /home/AMET/AMET_v13/scripts_analysis/aqExample
./run_AMET_batch_scripts.csh