The Community Model of Aerosol Nucleation (CMAN)
Creators: name: Mao, Lizhuo
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 370103
subject: Atmospheric aerosols
classificationCode: 370104
subject: Atmospheric composition, chemistry and processes

description: The Community Model of Aerosol Nucleation (CMAN) is a comprehensive 3-D numerical model for new particle formation (NPF), developed by Tsinghua University in collaboration with the Pacific Northwest National Laboratory, Carnegie Mellon University, Beijing Institute of Technology, and Ocean University of China. The CMAN model integrates molecular-level results from CLOUD chamber experiments, quantum chemistry calculations, and molecular cluster dynamics simulations to establish NPF parameterizations under various environmental conditions. The model also simulates the complex sources, sinks, and chemical transformation processes of nucleation precursors, including the ultralow and extremely low volatility organics (ULVOC and ELVOC), iodic acid, and amines. Specifically, it calculates the concentrations of ULVOC and ELVOC that drive organic nucleation, by developing a 3-D model representation of the formation chemistry of these compounds based on a Radical Two-Dimensional Volatility Basis Set (R2D-VBS). It also explicitly represents the emissions, deposition, aerosol uptake, and multiphase chemical transformation cycles of iodine-containing species and amines, thus effectively reproducing concentrations of key nucleation precursors like iodic acid and dimethylamine (DMA). Based on the above, CMAN can comprehensively simulate various NPF mechanisms driven by multiple precursors such as sulfuric acid, ammonia, nitric acid, amines, other organics, and iodine oxoacids, including:Neutral sulfuric acid-water nucleationIon-induced sulfuric acid-water nucleationNeutral sulfuric acid-ammonia-water nucleationIon-induced sulfuric acid-ammonia-water nucleationNeutral pure organic nucleationIon-induced pure organic nucleationNeutral iodine oxoacids nucleationIon-induced iodine oxoacids nucleationSulfuric acid-organic nucleationSulfuric acid-amine nucleationSulfuric acid-nitric acid-ammonia nucleationNote: 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 TeamDevelopers:Tsinghua University: Bin Zhao (bzhao@mail.tsinghua.edu.cn), Shuxiao Wang, Jiewen Shen, Jingkun Jiang, Yuyang Li, Lizhuo Mao, Kebin He, Jiming HaoPacific Northwest National Laboratory: Jerome Fast, Manish Shrivastava, Kai Zhang, Jian Sun, Po-Lun MaCarnegie Mellon University: Neil Donahue, Hamish Gordon, Meredith SchervishBeijing Institute of Technology: Xiuhui Zhang, An NingOcean University of China: Yang GaoOther Collaborators and Supporters:Nanjing University: Aijun Ding, Wei Nie, Chao Yan, Sijia Lou, Yuliang LiuPeking University: Qi Chen, Xi ChengFudan University: Lin Wang, Jianmin Chen, Defeng Zhao, Lei Yao, Runlong CaiUniversity of Helsinki: Markku KulmalaBeijing University of Chemical Technology: Yongchun LiuUniversity of Chicago: Mingyi WangRegional Version (CMAN-R)File DirectoryCompressed package containing the codes of the CMAN-R model: WRF_CMAN-Rv1.tar.gz(789 MB)Example of an ion production rate file: CRII_cn27_interp_01.nc(7.24 MB)Example of the namelist.input configuration file for initiating the CMAN-R model: namelist.input_example(7.08 KB)Code OverviewThe 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.FWRF_CMAN-Rv1/chem/KPP/mechanisms/saprc99_mosaic_20bin_vbs2_aq/saprc99_mosaic_20bin_vbs2_aq.eqnWRF_CMAN-Rv1/chem/module_mosaic_therm.FWRF_CMAN-Rv1/chem/module_mosaic_cloudchem.FWRF_CMAN-Rv1/chem/module_cmu_bulkaqchem.FSimulation of nucleation processes:WRF_CMAN-Rv1/chem/module_mosaic_newnuc.FNoteThe 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 DirectoryCompressed package containing the codes of the CMAN-G model: E3SM-Private.zip (1.66 GB)Compressed package containing some input data for the CMAN-G model: sample_data.zip(13.1 GB)Code OverviewThe 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.F90components/cam/src/chemistry/mozart/mo_srf_emissions.F90components/cam/src/chemistry/modal_aero/modal_aero_coag.F90components/cam/src/chemistry/modal_aero/modal_aero_gasaerexch.F90components/cam/src/chemistry/modal_aero/modal_aero_convproc.F90Simulation of nucleation processes:components/cam/src/chemistry/modal_aero/modal_aero_newnuc.F90NoteThe 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).Important NotesThe 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: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.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.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.ReferencesRegion 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 &amp; 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.1c00303Rasool, 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 InformationName: Bin Zhao, Associate ProfessorAffiliation: School of Environment, Tsinghua UniversityEmail: bzhao@mail.tsinghua.edu.cnWeChat: zhaob06