7 Nov 2011
Script notes for the 2005v4_3 platform (2005ct, 2017ct_ref, 2017ct_ref_mats)

--directory structure--

To use these scripts, unzip these script .zips, the ancillary file .zips located in 
  ../ancillary_smoke, and the inventory file .zips located in ../2005emis, 
  and ../2017emis, to the following directories:
  
Choose a directory into which unzip the script .zips. Call this directory
${INSTALL_DIR}; you will need to edit the INSTALL_DIR definition within each of the
run scripts accordingly.
Ancillary and inventory file .zips should be unzipped in the same directory,
${INSTALL_DIR}.

To run SMOKE, execute the scripts that are unzipped to
${INSTALL_DIR}/tier3_prop/.../scripts/. Separate scripts are provided
for each sector and grid.

--SMOKE, I/O API--

The proper SMOKE version to use with these scripts is SMOKE v2.7.
The SMOKE source code and executables that we used have NOT been provided
at this time.

The scripts assume the SMOKE executables are located in
$INSTALL_DIR/smoke/smoke2.7/$SMOKE_EXE
where SMOKE_EXE is set by the subsys/scripts/platform script described below.
(example: SMOKE_EXE = Linux_ia64ifort)

Required I/O API programs must be here:
$INSTALL_DIR/smoke/ioapi/$SMOKE_EXE

Additional files may need to be downloaded from the EPA website if you wish to
process biogenic emissions (see --land use-- below).

--meteorology--

Meteorological inputs, needed for biogenics and the onroad MOVES PM temperature
adjustment, are not provided.

Change the definition of MET_ROOT at the top of the beis and
on_moves scripts to point to your copy of the meteorological inputs (MCIP).

--script order--

Each point sector has two scripts, a "Onetime" script and an "Annual" script.
The "Onetime" script comes first.

For the onroad sectors, the RPP/RPD/RPV scripts come first, followed by the 
onroad merge script. Onroad is processed using SMOKE-MOVES integration, and
is first processed at a large 12km grid (12MERGEUS1); the onroad merge script
then creates the 36US1, 12EUS1, and 12WUS1 emissions from that.

For all sectors besides onroad, separate scripts are provided for each grid
(36US1, 12EUS1, and 12WUS1). Run the 36km jobs before running the 12km jobs.
You could skip the 36km runs and start with the 12km jobs if you only want 
to process emissions at 12km resolution, but you would have to edit the run 
settings file (RUNSET) so that the scripts do not skip the non-grid-dependent 
SMOKE programs (e.g. Smkinven, Spcmat, Temporal).

--domain totals--

Included in the script package is an optional QA program called "domain totals".
After Mrggrid is run for each day, this program outputs a file containing
domain-wide daily totals for each species from the merged model-ready emissions.

By default, this program is turned off. To use the domain totals program, follow
these instructions:
- Compile the following Fortran program
  ${INSTALL_DIR}/smoke/smoke2.7/scripts/run/domain_totals/domaintotal_all_species.F
A Makefile is provided in the same directory.
- Move the resulting executable (domaintotal_new.x) to the parent directory:
  ${INSTALL_DIR}/smoke/smoke2.7/scripts/run/
- In the runsettings file (.../${CASE}/scripts/run_settings_*.txt), 
  comment out the lines that say "mrggrid, [grid name], domain, ..."

--python--

These scripts require the following python prerequesites:

1) Python__ 2.4.x or newer

2) Numerical python 24.2 
This is an older version of the more robust numPy package.  It is available at:
http://sourceforge.net/projects/numpy/files/Old%20Numeric/

3) Scientific python
This package allows interfacing with netCDF files.  It is available at:
http://sourcesup.cru.fr/projects/scientific-py/

4) UNIX-type system with the csh installed

5) netCDF C libraries in your LD_LIBRARY_PATH environment variable
These libraries are required by scientific python and available at:
http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_3/index.jsp

--land use--

Make sure your copies of the biogenic land use files (BELD3_A, BELD3_B, and
BELD3_TOT) are in the ${INSTALL_DIR}/tier3_prop/2005ck_05b/inputs/beis/ directory and that
the filenames match the run script. See [**Note B3**] in the beis run scripts.

The beld3 inputs required to create the land use files are here:
ftp://ftp.epa.gov/EmisInventory/beld_3/b3_files/

--ptipm NAMEBREAK_DAILY--

For the automatic creation of PTDAY .lst files to work, the variable
NAMEBREAK_DAILY may need to be adjusted. See [**Note 1P**] in the 
ptipm run script.

--chlorine--

For the final merge, be sure to install the contents of the following .tar and 
.zip files according to the these instructions:
- Install .../2005v4/mercury_cl2_seasalt/ocean_cl2*.zip to
  ${INSTALL_DIR}/tier3_prop/2005ct_05b/intermed/.

--future year and control case dependencies--

The 2017ct_ref_05b future year emissions case reuses 2005ct_05b
emissions for the following sectors: avefire, beis, othar, othon, othpt.

The 2017ct_ref_mats_05b future year control case uses 2017ct_ref_05b emissions
for all sectors except ptipm.

--CAMX conversion scripts--

These emissions were not converted to CAMx format, so scripts have not been
provided for this purpose.