As well as a human-readable summary of the reactions modified by the tagging system,
this directory contains all input files and code necessary to modify CESM1.2.2-CAM4
to perform simulations with tagged ozone attributed to NOx or VOC precursors.
Machine-readable minimally-tagged chemical mechanisms are also included for
both NOx and VOC tagging, and modified CESM source code is also included for
NOx tagging (consistent with the nox-tagged mechanism). See below for details.
It is assumed that the user already knows how to compile, configure, and run
CESM simulations.

==============
Supplement.pdf
==============
A human-readable list of the reactions from the base chemical mechanism which are
modified by the tagging software. Also contains a larger set of figures than the
manuscript itself.

==========
cam_chempp
==========
The modified chemical mechanism preprocessor source files which must replace the
original preprocessor files in CESM-1.2.2 in order to process tagged chemical mechanisms.
All files should be added to the directory ./models/atm/cam/chem_proc/src/cam_chempp/
from the top level of the untarred model code distribution before compiling the
model for the first time.

============
chem_mech.in
============
The original "base" chemical mechainsm.

====================
chem_mech_ox_tags.in
====================
Modified mechanism file containing reactions of odd oxygen species (Ox)
species common to both NOx and VOC tagging.

===========================
chem_mech_nox_extra_tags.in
chem_mech_nox_tags.in
chem_mech_ox_tags_nox.in
===========================
Modified mechanism files containing reactions specific to NOx tagging.

===========================
chem_mech_voc_extra_tags.in
chem_mech_ho2_tags.in
chem_mech_ox_tags_voc.in
===========================
Modified mechanism files containing reactions specific to VOC tagging.

===============
tag_nox.pl
===============
Program to add tagged tracers and reactions to the base mechanism for NOx tagging.
The list of tag identities to be applied to emitted NOx (and subsequently produced NOy)
is specified as a list within the code. Similarly, tag identities specific to Ox species
are also specified as a list.
./tag_nox.pl
The tagged mechanism will appear in the file "chem_mech_nox_tagged.in".

===============
tag_voc.pl
===============
Program to add tagged tracers and reactions to the base mechanism for VOC tagging.
The list of tag identities to be applied to each emitted VOC (and subsequently produced intermediates)
is specified as a list of lists within the code. Similarly, tag identities specific to HO2 and Ox species
are also specified as lists.
./tag_voc.pl
The tagged mechanism will appear in the file "chem_mech_voc_tagged.in",

===========
add_tags.pl
===========
Program to produce modified CESM source code which includes the tagged
tracers and reactions added to the chemical mechanism.
Tagging of NOx or VOC is controlled by a switch within the source code of this program.
The list of precursor tags and special Ox tags (which includes special HO2 tags in the
case of VOC tagging) must be consistent with the tagged chemical mechanism.
./add_tags.pl
The tagged source code files will appear in the directory "SourceMods".

============
Mechanism.pm
============
Support routines used by the tagging software.

=========
templates
=========
This directory contains hand-modified versions of the CESM1.2.2 source code which are used
by add_tags.pl.
