Is there a tutorial about modified AEROSOL_CHEMISTRY.F ？

bandaoshutiao · May 18, 2023, 7:01am

Hi. I want to add a heterogeneous reactions in CMAQ. But I have some difficulties modifying this file. I am not particularly familiar with the F language, but I have a need to change this file. I want to add a few reactions where aerosols consume (absorb) free radicals, but this seems to require modifying many parts of this source code. Is there a tutorial available? Or any explanation of this source code?
Thanks!!

lizadams · May 19, 2023, 6:17pm

Hello,
I would recommend looking into the CHEMMECH utility routine described in the following links.

github.com

USEPA/CMAQ/blob/main/CCTM/src/MECHS/README.md


### CMAQ Chemical Mechanisms

The CMAQ modeling system accounts for chemistry in three phases: gas, aerosol, and cloud droplets. Available mechanisms include variations of three photochemistry schemes such as different representations of secondary organic aerosols, additional model species representing Hazardous Air Pollutants, inclusion of dimethyl sulfide chemistry or detailed isoprene chemistry. Please consult the release notes for changes to mechanisms available in a specific version of CMAQ. 

Fortran modules and namelists define a chemical mechanisms for the CMAQ model. Subdirectories of the $CMAQ_MODEL/CCTM/src/MECHS directory contain the files for available mechanisms. The species and emission control namelists enable setting runtime options for a mechanism. Species namelists define names, molecular weights and atmospheric processes (e.g., transport, cloud chemistry, and deposition). The files also determine whether the species concentrations and deposition results are written to output files. Emission control namelists define the emission inputs for model species. Two Fortran modules, RXNS_DATA_MODULE.F90 and RXNS_FUNC_MODULE.F90, define photochemistry for a mechanism. The data module specifies reactions and parameters. The functions module initializes photochemistry and calculates reaction rates constants. Because model source code define photochemistry for a mechanism, an executable version of the CMAQ model has a fixed photochemistry. 
To modify or change photochemistry, requires modifying or replacing the modules then recompiling. The approach may not work because data hardcoded within the photochemistry solver is not correct, _if using an Euler Backward Interative (EBI) solver_, or because data used to calculate photolysis rates is not complete.

### Using predefined chemical mechanisms

To select a predefined mechanism configuration in CMAQ, set the *Mechanism* variable in the build scripts to a one of the mechanism subdirectories located under $CMAQ_MODEL/CCTM/src/MECHS. The below table lists mechanisms available in this version of the CMAQ model.

Table 1.  CMAQv5.4 Chemical Mechanisms

|**Mechanism Name** | **Photochemistry**                                   | **Model Species<sup>1,2</sup>**    | **Cloud Chemistry Module<sup>3</sup>** |
| ----------------- | ---------------------------------------------------- | -------------------- | ---------------------- |
| cb6r3_ae7_aq      | [Carbon Bond 6 version r3 with aero7 treatment of SOA](mechanism_information/cb6r3_ae7_aq/mech_cb6r3_ae7_aq.md) |  [species table](mechanism_information/cb6r3_ae7_aq/cb6r3_ae7_aq_species_table.md)                 | acm_ae7          |
| cb6r5_ae7_aq      | [Carbon Bond 6 version r5 with aero7 treatment of SOA](mechanism_information/cb6r5_ae7_aq/mech_cb6r5_ae7_aq.md) |  [species table](mechanism_information/cb6r5_ae7_aq/cb6r5_ae7_aq_species_table.md)                 | acm_ae7          |
| cb6r5hap_ae7_aq   | [Carbon Bond 6 version r5 with air toxics and aero7 treatment of SOA](mechanism_information/cb6r5_ae7_aq/mech_cb6r5_ae7_aq.md) | [species table](mechanism_information/cb6r5hap_ae7_aq/cb6r5hap_ae7_aq_species_table.md)               | acm_ae7          |
| cb6r5_ae7_aqkmt2  | [Carbon Bond 6 version r5 with aero7 treatment of SOA](mechanism_information/cb6r5_ae7_aq/mech_cb6r5_ae7_aq.md) | [species table](mechanism_information/cb6r5_ae7_aq/cb6r5_ae7_aq_species_table.md)                   | acm_ae7_kmt2          |

This file has been truncated. show original

bandaoshutiao · May 22, 2023, 7:10am

Hi

What confused me is all routine seems like only deal with photo chemical reactions but not heterogeneous reactions. This is the most detailed tutorial about hetergeneous reaction?

Thanks!

Havala.Pye · May 23, 2023, 6:15pm

Hello. You may be able to use an existing heterogeneous reaction as a template. For a very simple reaction, see uptake of glyoxal (GLY) to aerosol (AGLYJ) in the HET_GLY reaction on line 445 of the cb6r5 with ae7 mechanism. The rate of the reaction is specified by the <HETERO_GLY> label. HETERO_GLY is calculated in AEROSOL_CHEMISTRY.F as a function of aerosol surface area, gas-phase diffusion, and an uptake coefficient. Since the mechanism file mech_cb6r5_ae7_aq.def isn’t actually used in the CMAQ executable, you will need to propagate the mechanism to the RXNS* files using CHEMMECH as Liz mentions. If you want to use the ebi solver, you will also need to run create_ebi. You can run CHEMMECH and create_ebi manually, or you can turn on the build_mech flag on line 49 of the bldit_cctm.csh file. build_mech will run the CHEMMECH and create_ebi functionality for you (just double check you use the output files). In short:

add your reaction to the mech.def file with a string label for the rate
update AEROSOL_CHEMISTRY.F to calculate the rate
update the gas phase or other relevant species name lists (GC*.nml; AE*.nml, etc) if you have a new species
run CHEMMECH and create_ebi OR turn on bldit_mech when you build CMAQ so the chemistry in mech.def is propagated to RXNS*.F90 files and the ebi solver files

bandaoshutiao · May 24, 2023, 1:36am

Wonderful!

Very thanks for your help!!

Topic		Replies	Views
How to add new chemical mechanism CMAQ	6	1435	March 9, 2021
CMAQ STM calculation method and reference CMAQ	2	660	December 9, 2020
Add a new heterogeneous reaction that only happens with sunlight CMAQ cmaq	6	7286	February 17, 2023
Add new aerosol particles and turn off their chemical reaction CMAQ	3	4028	January 11, 2023
Add new gaseous reaction considering small water cluster concentration at each simulation time step Chemistry and Aerosols	2	23	October 17, 2024

Is there a tutorial about modified AEROSOL_CHEMISTRY.F ？

Related topics