Teaching


Analytical Instrumental Laboratory

CHEM F314 (CRN:33323)
Spring of 2019
Meeting Time: M 9:15-10:15am (lecture), MW 2:15-5:15pm (lab)
Office Hours: T&TH 3-4PM (other times by appointment)

Papers to be reviewed (click the following links for each paper):

  1. Barsanti_2007_NMR
  2. Bates_2015_EST_ROS
  3. Charrier_2015_EST
  4. Clifton_1988_EST
  5. Faust_1993_EST
  6. Fraser_2000_EST_levoglucosan
  7. Gouin_2010_PAHs_AtmosPolRes_Fairbanks
  8. Hopmans_2013_OrganicGeochem_Levoglucosan
  9. Oakes_2010
  10. Chanlon_2005
  11. Graham_2002_JGR_NMR

Atmospheric Chemistry

CHEM F406 (CRN:36497)
CHEM F606 (CRN:36498)
ATM F606 (CRN:35142)
Fall of 2018
Tu/Th 9:45—11:15
REIC 204

Term project (photochemical box modeling)

Introduction

Photochemical box model has been an extremely useful tool to understand the evolution of atmospheric composition in the presence of sunlight, natural and anthropogenic emissions. This project is designed to explore the evolution of certain atmospheric species (ozone, carbon monoxide, formaldehyde, bromine monoxide etc.) under different nitrogen oxides (NOx) conditions . So you can see how human activities may impact chemical transformation of  atmospheric composition, and the implication for air quality and climate change.

In this box model, the sunlight intensity is calculated based on location and the local time of model simulation, and updated every time step. This information will be used to drive diurnal cycle in model runs.

By setting up some initial values, you will be able to see the diurnal cycle of those species you are interested. After you familiar with running the model, we will design some numerical experiments that can help to understand the chemical transformation of atmospheric composition in the real world.

Login

By now, I assume that you already have an account on chinook.

To login into Chinook, the instructions can be found here:

http://www.gi.alaska.edu/research-computing-systems/hpc/chinook/logging-in

You should just install the terminal and have X window ready. You do NOT need VNC.

Notes: if you find that your terminal is slow, you can try to log in with another node.

ssh -Y uausername@chinook01.alaska.edu

or

ssh -Y uausername@chinook03.alaska.edu

Here Y is for graphic display from your terminal.

Model setup

1.  First, download the code and configure

curl -kLO https://github.com/barronh/DSMACC/archive/master.zip
unzip master.zip
cd DSMACC-master/
module load lang/flex/2.6.0-foss-2016b for free open source system
module load lang/flex/2.6.0-pic-intel-2016b for intel compiler
./configure (to generate Makefile.defs)

2.  The second step is to add these two lines to your .cshrc or .bashrc
.cshrc:

setenv KPP_HOME $HOME/DSMACC-master/kpp
setenv PATH $HOME/DSMACC-master/kpp/bin:${PATH}

AFter you finish editing, exit and type:

source $HOME/.cshrc

.bashrc:

KPP_HOME=$HOME/DSMACC-master/kpp
export KPP_HOME
export PATH=$KPP_HOME/bin:$PATH

AFter you finish editing, exit and type:

source $HOME/.bashrc

3.  The next step is to modify Makefile.defs change this line

FLEX_LIB=

to

FLEX_LIB=/usr/local/pkg/lang/flex/2.6.0/lib/libfl.a

4. Fourth step is to generate the executable for kpp

 make kpp/bin/kpp

This will generate the executable file kpp.

Generate mechanism

cd $HOME/DSMACC-master/kpp/models

cp /import/u/u1/uaf/jmao2/DSMACC-master/kpp/models/mcm33.kpp .

cp -rf /import/u/u1/uaf/jmao2/DSMACC-master/kpp/models/MCM .

cd $HOME/DSMACC-master/
cp /import/u/u1/uaf/jmao2/DSMACC-master/src/constants.f90 ./src/
cp /import/u/u1/uaf/jmao2/DSMACC-master/rate.inc .
cd $HOME/DSMACC-master/src

../kpp/bin/kpp ../kpp/models/mcm33.kpp dsmacc

make

This will generate a series of .f90 files under this directory and compile them to an executable file ($HOME/bin/dsmacc).

You could create your own mechanism by going to this MCM website. Here is some brief instruction:

https://github.com/barronh/DSMACC/blob/master/README.md#mcm-input

Run the model

First, you need to get a file for initial conditions.

cd $HOME/DSMACC-master/test
cp /import/u/u1/uaf/jmao2/DSMACC-master/test/Init_cons.dat .

The explanation for the initial condition file can be found here:

https://github.com/barronh/DSMACC/blob/master/README.md#mcm-input

Then run the model:

../bin/dsmacc > test.log

Plot results

You can choose to either use IDL or Python. You need to make sure you have X windows set up correctly.

IDL (recommended for checking all species in this model)

To use IDL, type:

cp /import/u/u1/uaf/jmao2/DSMACC-master/test/output_reader_mat.pro .

module load idl

idl

In IDL environment, type:

>.r  output_reader_mat.pro

>output_reader

>exit

Plot the results with gv:

gv Plot1.ps

Python (check targeted species)

To use Python, type:

cp /import/u/u1/uaf/jmao2/DSMACC-master/test/plotMCM.py .

module load vis/matplotlib/1.5.1-pic-intel-2016b-Python-2.7.12

python plotMCM.py

display NO.png

Basic Unix Commands/Tools

Command Example Description
1.     ls ls
ls -alF
Lists files in current directory
List in long format
2.     cd cd tempdir
cd ..
cd ~dhyatt/web-docs
Change directory to tempdir
Move back one directory
Move into dhyatt’s web-docs directory
3.     mkdir mkdir graphics Make a directory called graphics
4.     rmdir rmdir emptydir Remove directory (must be empty)
5.     cp cp file1 web-docs
cp file1 file1.bak
Copy file into directory
Make backup of file1
6.     rm rm file1.bak
rm *.tmp
Remove or delete file
Remove all file
7.     mv mv old.html new.html Move or rename files
8.     more more index.html Look at file, one page at a time
9.     pwd pwd Show current directory
10.   man man ls Online manual (help) about command

Text editing tools

There are a few tools for text editing in Unix environment, including vi/emacs/nano. If you have not done any text editing, gvim might be a good choice as it offers graphic interface (just type “gvim” when you log into Chinook).

Copy files between Chinook and your own computer

For Mac, you can use SCP.

Using SCP

SCP is ideal for quick transfer of single files, such as email attachments. Syntax is similar to the Unix copy command. For demonstration purposes, we’ll use two computers (nearand far) with the usernames this and that, respectively.

scp path/to/file that@remote.computer:path/to/destination

For example, if you want to transfer the file example.txt from your home directory on near to your home directory on far, the command might look like this:

scp /home/this/example.txt that@far.uiuc.edu:/home/that/

Note that you can also use SCP in reverse. If you want to transfer a file from far to near, you can type something like this:

scp that@far.uiuc.edu:/home/that/example.txt /home/this/

If you need to copy an entire directory, you’ll need to use the recursive flag, like this:

scp -r thisdirectory that@far.uiuc.edu:/home/that/

Obviously, this system is a bit cumbersome for multiple file transfers.

For Windows, you can use winscp, which can be downloaded here.

How to change input file?

Follow this link to modify Init_cons.dat you copied to your folder.

https://github.com/barronh/DSMACC/wiki/Inputs%20and%20Initial%20Conditions

 

Project 1: Numerical solvers

In order to change the numerical solvers, you should modify this file:

$HOME/DSMACC-master/kpp/models/mcm33.kpp

Where you can find:

#INTEGRATOR rosenbrock
//#INTEGRATOR kpp_lsode
// #INTEGRATOR ros2_manual
// #INTEGRATOR radau5

The detailed documentation for solvers can be found here:

http://people.cs.vt.edu/~asandu/Software/Kpp/Download/kpp-2.1_UsersManual.pdf

Project 2: HCHO yield from biogenic VOCs

This project is designed to understand the relationship between isoprene/monoterpene emissions and HCHO using MCM chemical mechanism. This will help to derive isoprene/monoterpene emissions with satellite observed HCHO column.

The idea is to set isoprene  (or monterpene) to initial concentration, and let it evolve in your photochemical box model. If you turn off HCHO loss in your model, you will cumulative production of HCHO in your model after In order to do that, you need to download the chemical mechanism for isoprene or monoterpene from MCM website. The default mechanism is for isoprene. You can swap the mechanism to monoterpene by downloading the file from MCM website.

Calculate HCHO yield from isoprene

  1. Find mcm_setup.kpp located at $HOME/DSMACC-master/kpp/models/. This is the file for your chemical mechanism.
  2. Turn off the HCHO loss in your mechanism. Find the reactions where HCHO is the reactant, you can either deactivate this reaction, or add HCHO to the product side, so HCHO will not be consumed.
  3. Recompile the model. This is because you have changed the model mechanism in step 2.
    cd $HOME/DSMACC-master/src
    
    ../kpp/bin/kpp ../kpp/models/mcm33.kpp dsmacc
    
    make
    
  4. Run the model once, make sure you go through the initial condition file Init_cons.dat, see descriptions above (https://github.com/barronh/DSMACC/wiki/Inputs%20and%20Initial%20Conditions).
  5. Run the model by varying NOx concentrations.

Calculate HCHO yield from monoterpenes

  1. Download the chemical mechanism for monoterpenes (ALPHA-PINENE, or BETA-PINENE). Instructions can be found here: https://github.com/barronh/DSMACC/blob/master/README.md#mcm-input
  2. Make sure you put the downloaded mcm_setup.kpp in this folder $HOME/DSMACC-master/kpp/models/.
  3. Turn off the HCHO loss in your mechanism. Find the reactions where HCHO is the reactant, you can either deactivate this reaction, or add HCHO to the product side, so HCHO will not be consumed.
  4. Recompile the model. This is because you have changed the model mechanism in step 2.
    cd $HOME/DSMACC-master/src
    
    ../kpp/bin/kpp ../kpp/models/mcm33.kpp dsmacc
    
    make
    
  5. Run the model once, make sure you go through the initial condition file Init_cons.dat, see descriptions above (https://github.com/barronh/DSMACC/wiki/Inputs%20and%20Initial%20Conditions).
  6. Run the model by varying NOx concentrations.

 

Project 3: Bromine chemistry

This project can be done by using a different chemical mechanism (GEOS-Chem).

A full set of GEOS-Chem mechanism can be found here:

$HOME/DSMACC-master/kpp/models/geoschem-09-02.eqn

To run this mechanism, you need to do a few things:

  1. Type:
    cd $HOME/DSMACC-master/src
    rm -f depend.mk
  2. Type (to make your executable file):
    ../kpp/bin/kpp ../test/geoschem-09-02.kpp dsmacc
    make
  3. Type (you need to check your initial input file):
    mv ../bin/dsmacc ../test/geoschem-09-02
    cd $HOME/DSMACC-master/test
    ./geoschem-09-02