DSMACC-testing

Dan's version of the Dynamically Simple Model For Atmospheric Chemical Complexity --- still in development/testing

##Cite Emmerson, KM; Evans, MJ (2009) Comparison of tropospheric gas-phase chemistry schemes for use within global models, ATMOS CHEM PHYS, 9(5), pp1831-1845 doi: 10.5194/acp-9-1831-2009 .

New user

Run make new to clean everything and update latest TUV.

Updating the submodule (TUV and KPP)

This needs to be done to include contents here. Can be accomplished through git submodule init; git submodule update or typing make update_submodule

Compiling

1. make distclean && make new to clear all, else use make clear or make clean
2. Download mechanism from mcm website and place into mechanisms/organic.kpp
3. Add any emissions into emissions.kpp (these can be disabled in ICs)
4. Adjust deposition constant in ./makedepos.pl if needed (currently being updated)
5. Run kpp and make by typing make kpp
6. make

How to run

1. Create Init cons csv file (methane.csv as a template) .. * different columns are different runs ..* depos and emiss are deposition / emission constants, set 1 to enable 0 do disable ..* run names are useful, see + depos etc for examples.

2. Run python begin.py after setting the number of processes inside ..* this makes Init_cons.dat ..* generates run files. sdout is in run.sdout, individual run.nc ..* concatenates nc files including initial conditions, and run time into one grouped netcdf ..* to see the form of this have a look inside begin, or read_dsmacc

3. to view files: ..* ipython, then type run AnalysisTools/read_dsmacc <ncfilename> for interactive play ..* run the PDF_concentrations.py file for a time series plot of all the runs (diagnostic purposes) - see .pdf files

Updating the rate constants

Rate-constant simplification through the use of a symbolic engine has been applied. This reduces computation and allows the setting of parameters for fixed numeric constants (see KDEC bug). An example of some equations below.

Rate Cefficient	Original-eqn	Simplified-eqn
krd	kd0/kdi	5.79e-23*m*exp(4000/temp)
ncd	0.75-1.27*(log10(fcd))	1.41
kbpan	(kd0*kdi)*fd/(kd0+kdi)	fd*kd0*kdi/(kd0 + kdi)
kr1	k10/k1i	3.32e-18*m*temp**(-1.3)
f1	10**(log10(fc1)/(1+(log10(kr1)/nc1)**2))	10**(-0.07/(1 + log10(kr1)**2/nc1**2))
kmt12	(k120k12if12)/(k120+k12i)	2e-12*f12*k120/(k120 + 2e-12)

To do this place your new rate file in the src folder, run simplfy_rates.py and update the constants.f90 code to inculde the newly generates .def and .var files

Notes:

Dependancies:

• Ifort (Intel)
• Netcdf4 (python)
• Anacondas Python (continuum.io)
• icc & bison for kpp
• perl

Changes:

• Reorganised code / removed unnecessary loops
• CH4 intiation fix
• removed multiline serial read and replaced with initation program
• repaced initial conditions with csv file
• added the output to netcdf (needs netcdf libraries)
• added emission / deposition switches
• improved makefile
• MCM TUV 5 updated
• simplification of rate constants
• start multiple parallel runs
• peters hardwired photolysis rate generator
• depos default + manual override