{{ ABaCAS_CMAN.title }}
{{ ABaCAS_CMAN.description }}
Neutral sulfuric acid-water nucleation
Ion-induced sulfuric acid-water nucleation
Neutral sulfuric acid-ammonia-water nucleation
Ion-induced sulfuric acid-ammonia-water nucleation
Neutral pure organic nucleation
Ion-induced pure organic nucleation
Neutral iodine oxoacids nucleation
Ion-induced iodine oxoacids nucleation
Sulfuric acid-organic nucleation
Sulfuric acid-amine nucleation
Sulfuric acid-nitric acid-ammonia nucleation.
Note: The last three nucleation mechanisms do not distinguish between neutral and ion-induced nucleation pathways, representing the combined effect of both.
The CMAN model is still under continuous development, with future updates planned. The model includes a regional version (CMAN-R) and a global version (CMAN-G). The specific details are provided below.
Development Team
Developers:
Tsinghua University: Bin Zhao (bzhao@mail.tsinghua.edu.cn), Shuxiao Wang, Jiewen Shen, Jingkun Jiang, Yuyang Li, Lizhuo Mao, Kebin He, Jiming Hao
Pacific Northwest National Laboratory: Jerome Fast, Manish Shrivastava, Kai Zhang, Jian Sun, Po-Lun Ma
Carnegie Mellon University: Neil Donahue, Hamish Gordon, Meredith Schervish
Beijing Institute of Technology: Xiuhui Zhang, An Ning
Ocean University of China: Yang Gao
Other Collaborators and Supporters:
Nanjing University: Aijun Ding, Wei Nie, Chao Yan, Sijia Lou, Yuliang Liu
Peking University: Qi Chen, Xi Cheng
Fudan University: Lin Wang, Jianmin Chen, Defeng Zhao, Lei Yao, Runlong Cai
University of Helsinki: Markku Kulmala
Beijing University of Chemical Technology: Yongchun Liu
University of Chicago: Mingyi Wang
Regional Version (CMAN-R)
File Directory:
Compressed package containing the codes of the CMAN-R model:
{{ file.FileName }}{{ file.FileSize }}
Example of an ion production rate file:
{{ file.Example_one_name }}{{ file.Example_one_size }}
Example of the namelist.input configuration file for initiating the CMAN-R model:
{{ file.Example_two_name }}{{ file.Example_two_size }}
Code Overview:
The CMAN-R model is currently integrated into the WRF-Chem model that is widely used in atmospheric chemistry research. Available from this site are the codes for the fully integrated WRF-Chem/CMAN-R model, with the following key code files related to CMAN-R:
Simulation of precursor sources, sinks, and chemical transformation processes:
WRF_CMAN-Rv1/chem/emissions_driver.F
WRF_CMAN-Rv1/chem/KPP/mechanisms/saprc99_mosaic_20bin_vbs2_aq/saprc99_mosaic_20bin_vbs2_aq.eqn
WRF_CMAN-Rv1/chem/module_mosaic_therm.F
WRF_CMAN-Rv1/chem/module_mosaic_cloudchem.F
WRF_CMAN-Rv1/chem/module_cmu_bulkaqchem.F
Simulation of nucleation processes:
WRF_CMAN-Rv1/chem/module_mosaic_newnuc.F
User Instructions:
The steps to run the CMAN-R model are similar to those for running the conventional WRF-Chem model. For detailed instructions, refer to WRF-Chem User's Guide (https://ruc.noaa.gov/wrf/wrf-chem/). In addition to the emissions inputs, meteorological inputs, and model configurations required for the conventional WRF-Chem model, the following are needed:
1) Additional Emissions Variables for NPF Precursors:
E_AMINE_C2 (Dimethylamine emissions)
E_HI/E_I2 (HI and I2 emissions as precursors for iodic acid; natural emissions of HOI and I2 from ocean sources are calculated online during simulation, so only anthropogenic emissions need to be included in the emissions file)
E_TERP (Monoterpene emissions as precursors for ultralow and extremely low volatility organic compounds; natural emissions of monoterpenes are calculated online by MEGAN during simulation, so only anthropogenic emissions need to be included in the emissions file)
2) Preparation of Ion Production Rate File:
For each simulation run, ion production rate data must be pre-written into the wrfinput.nc file to calculate ion concentrations and ion-induced nucleation rates in real-time. An example of ion production rate file is provided as an attachment.
3) Model Configuration:
The following options need to be added to the namelist to activate CMAN-R:
emiss_opt = 13
chem_opt = 205
newnuc_method = 3
Note:
The publicly available codes of WRF-Chem/CMAN-R also include modules developed by Manish Shrivastava’s team (Email: ManishKumar.Shrivastava@pnnl.gov) at Pacific Northwest National Laboratory, such as the multiphase isoprene epoxydiol (IEPOX) secondary organic aerosol (SOA) module that incorporates updated acid- and SOA-viscosity dependent reactive uptake kinetics of IEPOX forming 2-methyltetrols and organosulfates, and the module to calculate viscosity and diffusivity of organic aerosols. Additional SOA modules due to gas-phase chemistry followed by partitioning of the oxidation products into organic aerosol phase are represented by NOx-dependent 4-product VBS yields for isoprene and sesquiterpenes (due to their reactions with OH, ozone, and NO3 radicals), a 4-product VBS that represents multigenerational aging of anthropogenic and biomass burning volatile, semi-volatile and intermediate volatility organic gases. Note that the SOA formation from monoterpenes is represented by the R2D-VBS module from Bin Zhao’s group.
Global Version (CMAN-G)
File Directory:
Compressed package containing the codes of the CMAN-G model:
{{ file.FileName }}{{ file.FileSize }}
Compressed package containing some input data for the CMAN-G model:
{{ file.Example_one_name }}{{ file.Example_one_size }}
These files can also be downloaded from https://figshare.com/s/71bf2a48657a2f5deb76.
Code Overview:
The CMAN-G model is currently integrated into the E3SM model that is widely used in atmospheric research. Available from this site are the codes for the fully integrated E3SM/CMAN-G model, with the following key code files related to CMAN-G:
Simulation of precursor sources, sinks, and chemical transformation processes:
components/cam/src/chemistry/pp_linoz_mam5_resus_soa_mom_soag_r2dvbs/*
components/cam/src/chemistry/modal_aero/modal_aero_amicphys.F90
components/cam/src/chemistry/mozart/mo_srf_emissions.F90
components/cam/src/chemistry/modal_aero/modal_aero_coag.F90
components/cam/src/chemistry/modal_aero/modal_aero_gasaerexch.F90
components/cam/src/chemistry/modal_aero/modal_aero_convproc.F90
Simulation of nucleation processes:
components/cam/src/chemistry/modal_aero/modal_aero_newnuc.F90
User Instructions:
This model can be run on most Linux systems, requiring sufficient CPU cores and memory. The specific steps to run are as follows:
1) unzip E3SM-Private.zip && unzip sample_data.zip
Unzip the code and data packages.
2) cd E3SM-Private_completeIodineChem/scripts
(or cd E3SM-Private_simplifiedIodineChem/scripts)
Navigate to the directory containing the model run scripts. Here “completeIodineChem” represents a version where all 14 iodine-containing species and the associated chemical reactions are included; “simplifiedIodineChem” represents a simplified version where minor species, i.e., I2O3, I2O4, INO, INO2, and IONO2, as well as the associated chemical reactions were removed from the complete version.
3) vi ./run_eagles_maint1.0_F20TRC5-CMIP6.csh
Edit run_eagles_maint1.0_F20TRC5-CMIP6.csh to modify directories to the input data, the desired output variables and output frequency, as well as parameters related to the job management system (core number, queue name, run time, etc.). Other machine-specific parameters may need to be modified as well, depending on the machine you use (see details in the E3SM users guide on https://e3sm.org/).
4) ./run_eagles_maint1.0_F20TRC5-CMIP6.csh
Compile and run the CMAN-G model to generate model output files.
Compared to the standard E3SM model, the CMAN-G model requires the following additional configurations on top of the original emissions input, meteorological input, and model configuration:
1) Include additional emission files of nucleation precursors, including:
SFDMA (DMA surface flux, i.e. dimethylamine emissions)
SFC10H16 (C10H16 surface flux, i.e. emissions of monoterpenes as precursors of ULVOC and ELVOC)
2) Prepare ion production rate and key nucleation precursor concentration files: Before running the simulation, prepare the oxid_1.9x2.5_L26_xxx.nc file, which contains ion production rates (used for real-time calculation of ion concentration and ion-induced nucleation rates) and concentrations of species such as NO, NH3, and HNO3 (the concentrations of these species are prescribed based on external data sources rather than being calculated from emissions within the model).
Note:
The publicly available codes of E3SM/CMAN-G also include the biogenic, anthropogenic and biomass burning SOA modules (except for the R2D-VBS SOA module), including the dynamic gas-particle partitioning of oxidation products (generated by the multigenerational gas-phase chemistry of organic gases), particle-phase oligomerization, and the photolytic sinks of organic aerosols developed by Manish Shrivastava’s team at Pacific Northwest National Laboratory (Email: ManishKumar.Shrivastava@pnnl.gov).
Model Outputs:
In the CMAN-R and CMAN-G models, in addition to the conventional WRF-Chem or E3SM output variables, the following variables are CMAN-specific outputs:
Precursor Concentrations:
HIO3 (Iodic acid concentration)
DMA (Dimethylamine concentration)
H2SO4 (Sulfuric acid concentration)
HNO3 (Nitric acid concentration)
NH3 (Ammonia concentration)
qopcg1_f_c_g, qopcg2_f_c_g, qopcg3_f_c_g, qopcg4_f_c_g, qopcg5_f_c_g, qopcg6_f_c_g, qopcg7_f_c_g, qopcg8_f_c_g, qopcg1_b_c_g, qopcg2_b_c_g, qopcg3_b_c_g, qopcg4_b_c_g, qopcg5_b_c_g, qopcg6_b_c_g, qopcg7_b_c_g, qopcg8_b_c_g, qopcg8_b_o_g (Concentrations of monoterpene oxidation products (O:C > 0.4) output by R2D-VBS in CMAN-R, with saturation vapor concentrations ranging from 10-10 to 106 μg/m3, separated by one order of magnitude.)
BSOAG1, BSOAG2, BSOAG3, BSOAG4, BSOAG5, BSOAG6, BSOAG7, BSOAG8, BSOAG9, BSOAG10, BSOAG11, BSOAG12, BSOAG13, BSOAG14, BSOAG15, BSOAG16, BSOAG17 (Concentrations of monoterpene oxidation products (O:C > 0.4) output by R2D-VBS in CMAN-G, with saturation vapor concentrations ranging from 10-10 to 106 μg/m3, separated by one order of magnitude.)
Nucleation Rates:
JBNRATE (Neutral sulfuric acid-water nucleation rate)
JBCHRATE (Ion-induced sulfuric acid-water nucleation rate)
JTNRATE (Neutral sulfuric acid-ammonia-water nucleation rate)
JTCHRATE (Ion-induced sulfuric acid-ammonia-water nucleation rate)
JBNORGRATE (Neutral pure organic nucleation rate)
JBCHORGRATE (Ion-induced pure organic nucleation rate)
JTNRICRATE (Sulfuric acid-organic nucleation rate)
JDMASARATE (Sulfuric acid-dimethylamine nucleation rate)
JIANRATE (Neutral iodine oxoacids nucleation rate)
JIACHRATE (Ion-induced iodine oxoacids nucleation rate)
JSANANH3RATE (Sulfuric acid-nitric acid-ammonia nucleation rate)
JRATE (Total nucleation rate)
Important Notes:
The CMAN-R and CMAN-G models are released under the BSD 3-Clause License. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain, and redistributions in binary form must reproduce CMAN’s name, copyright notice, list of conditions, and disclaimer, which are included in the code package.
2. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
3. This software is provided by the copyright holders and contributors "as is", and any express or implied warranties, including but not limited to the implied warranties of merchantability and fitness for a particular purpose, are disclaimed.
We welcome researchers to use the CMAN-R and CMAN-G models and ask that the sources be stated and appropriate references be cited. We also encourage researchers to collaborate with us for further development of the CMAN-R and CMAN-G models.
References:
Region Version (CMAN-R):
Primary References for CMAN-R:
Ning, A.#; Shen, J.#; Zhao, B.*; Wang, S.; Cai, R.; Jiang, J.; Yan, C.; Fu, X.; Zhang, Y.; Li, J.; Ouyang, D.; Sun, Y.; Saiz-Lopez, A.; Francisco, J. S.*; Zhang, X.*, Overlooked significance of iodic acid in new particle formation in the continental atmosphere. Proc Natl Acad Sci U S A, 121 (31), e2404595121, 2024.
Li, Y. Y.#, Shen, J. W.#, Zhao, B.*, Cai, R. L., Wang, S. X., Gao, Y., Shrivastava, M., Gao, D., Zheng, J., Kulmala, M. and Jiang, J. K.*: A dynamic parameterization of sulfuric acid–dimethylamine nucleation and its application in three-dimensional modeling, Atmospheric Chemistry and Physics, 23(15), 8789-8804, DOI 10.5194/acp-23-8789-2023, 2023.
Zhao, B.*, Shrivastava, M., Donahue, N. M., Gordon, H., Schervish, M., Shilling, J. E., Zaveri, R. A., Wang, J., Andreae, M. O., Zhao, C., Gaudet, B., Liu, Y., Fan, J. W., and Fast, J. D.*: High concentration of ultrafine particles in the Amazon free troposphere produced by organic new particle formation, Proceedings of the National Academy of Sciences of the United States of America, 117(41), 25344-25351, DOI 10.1073/pnas.2006716117, 2020.
Other CMAN-R Related Papers:
Shen, J. W., Zhao, B., Wang, S. X.*, Ning, A., Li, Y. Y., Cai, R. L., Gao, D., Chu, B. W., Gao, Y., Shrivastava, M., Jiang, J. K., Zhang, X. H. and He, H.: Cluster Dynamics-based Parameterization for Sulfuric Acid-Dimethylamine Nucleation: Comparison and Selection through Box-and Three-Dimensional-Modeling, Atmospheric Chemistry and Physics, 24, 10261-10278, 10.5194/acp-24-10261-2024, 2024.
Zhao, B.*, Fast, J., Shrivastava, M., Donahue, N. M., Gao, Y., Shilling, J. E., Liu, Y., Zaveri, R. A., Gaudet, B., Wang, S. X., Wang, J., Li, Z. Q. and Fan, J. W.: Formation process of particles and cloud condensation nuclei over the Amazon rainforest: The role of local and remote new-particle formation, Geophysical Research Letters, 49(22), e2022GL100940, DOI 10.1029/2022GL100940, 2022.
Zhao, B.*, Fast, J. D., Donahue, N. M., Shrivastava, M., Schervish, M., Shilling, J. E., Gordon, H., Wang, J., Gao, Y., Zaveri, R. A., Liu, Y., Gaudet, B.: Impact of urban pollution on organic-mediated new particle formation and particle number concentration in the Amazon rainforest, Environmental Science & Technology, 55, 8, 4357-4367, DOI 10.1021/acs.est.0c07465, 2021.
References for IEPOX SOA, treatments of phase state/viscosity of organic aerosols, and anthropogenic/biomass burning SOA modules:
Shrivastava, M.*, M. O. Andreae, P. Artaxo, H. M. J. Barbosa, L. K. Berg, J. Brito, J. Ching, R. C. Easter, J. Fan, J. D. Fast, Z. Feng, J. D. Fuentes, M. Glasius, A. H. Goldstein, E. G. Alves, H. Gomes, D. Gu, A. Guenther, S. H. Jathar, S. Kim, Y. Liu, S. Lou, S. T. Martin, V. F. McNeill, A. Medeiros, S. S. de Sá, J. E. Shilling, S. R. Springston, R. A. F. Souza, J. A. Thornton, G. Isaacman-VanWertz, L. D. Yee, R. Ynoue, R. A. Zaveri, A. Zelenyuk, and C. Zhao. 2019. Urban Pollution Greatly Enhances Formation of Natural Aerosols over the Amazon Rainforest. Nature Communications, 10 (1). https://doi.org/10.1038/s41467-019-08909-4.
Shrivastava, M.*, Fan, J. W.*, Zhang, Y. W., Rasool, Q. Z., Zhao, B., Shen, J. W., Pierce, J. R., Jathar, S. H., Akherati, A., Zhang, J., Zaveri, R. A., Gaudet, B., Liu, Y., Andreae, M. O., Pöhlker, M. L., Donahue, N. M., Wang, Y. and Seinfeld, J. H.: Intense formation of secondary ultrafine particles from Amazonian vegetation fires and their invigoration of deep clouds and precipitation, One Earth, 7(6), 1029-1043, DOI 10.1016/j.oneear.2024.05.015, 2024.
Shrivastava, M.*, Rasool, Q. Z., Zhao, B., Octaviani, M., Zaveri, R. A., Zelenyuk, A., Gaudet, B., Liu, Y., Shilling, J. E., Schneider, J., Schulz, C., Zöger, M., Martin, S. T., Ye, J., Guenther, A., Souza, R. F., Wendisch, M., Pöschl, U.: Tight Coupling of Surface and In-Plant Biochemistry and Convection Governs Key Fine Particulate Components over the Amazon Rainforest, ACS Earth and Space Chemistry, 6(2) 380–390, DOI 10.1021/acsearthspacechem.1c00356, 2022.
Zhang J., Shrivastava M.*, Zelenyuk A., Zaveri R.A., Surratt J.D., Riva M., Bell D., Glasius M. Observationally Constrained Modeling of the Reactive Uptake of Isoprene-Derived Epoxydiols under Elevated Relative Humidity and Varying Acidity of Seed Aerosol Conditions, ACS Earth and Space Chemistry, 7 (4), 788-799, 2023.
Octaviani, M.; Shrivastava, M.*; Zaveri, R. A.; Zelenyuk, A.; Zhang, Y.; Rasool, Q. Z.; Bell, D. M.; Riva, M.; Glasius, M.; Surratt, J. D. Modeling the Size Distribution and Chemical Composition of Secondary Organic Aerosols during the Reactive Uptake of Isoprene-Derived Epoxydiols under Low-Humidity Condition. ACS Earth and Space Chemistry 2021, 5, 3247– 3257, DOI:10.1021/acsearthspacechem.1c00303
Rasool, Q. Z., Shrivastava*, M., Octaviani, M., Zhao, B., Gaudet, B., and Liu, Y.: Modeling Volatility-Based Aerosol Phase State Predictions in the Amazon Rainforest, ACS Earth and Space Chemistry, 5(10), 2910–2924, DOI 10.1021/acsearthspacechem.1c00255, 2021.
Global Version (CMAN-G):
References for CMAN-G:
Zhao, B.*, Donahue, N. M., Zhang, K., Mao, L. Z., Shrivastava, M., Ma, P. L., Shen, J. W., Wang, S. X., Sun, J., Gordon, H., Tang, S. Q., Fast, J., Wang, M. Y., Gao, Y., Yan, C., Singh, B., Li, Z. Q., Huang, L. Y., Lou, S. J., Lin, G. X., Wang, H. L., Jiang, J. K., Ding, A. J., Nie, W., Qi, X. M., Chi, X. G. and Wang, L.: Global variability in atmospheric new particle formation mechanisms, Nature, 631, 98-105, DOI 10.1038/s41586-024-07547-1, 2024.
References for biogenic, anthropogenic and biomass burning SOA modules (except for the R2D-VBS SOA module), including multigenerational gas-phase chemistry, particle-phase oligomerization and photolytic sinks of organic aerosols:
Lou, S.; Shrivastava, M.*; Easter, R. C.; Yang, Y.; Ma, P.-L.; Wang, H.; Cubison, M. J.; Campuzano-Jost, P.; Jimenez, J. L.; Zhang, Q.; Rasch, P. J.; Shilling, J. E.; Zelenyuk, A.; Dubey, M.; Cameron-Smith, P.; Martin, S. T.; Schneider, J.; Schulz, C., New SOA Treatments Within the Energy Exascale Earth System Model (E3SM): Strong Production and Sinks Govern Atmospheric SOA Distributions and Radiative Forcing. J Adv Model Earth Syst 2020, 12, (12), e2020MS002266.
Contact Information
Name: Bin Zhao, Associate Professor
Affiliation: School of Environment, Tsinghua University
Email: bzhao@mail.tsinghua.edu.cn
WeChat: zhaob06