the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 29 Sep 2025
TChem-atm (v2.0.0): Scalable Performance-Portable Multiphase Atmospheric Chemistry
Abstract. We present TChem-atm, a performance-portable approach that enables efficient simulation of chemically detailed and multiphase atmospheric chemistry on modern heterogeneous computing architectures. Unlike previous efforts that rely on architecture-specific code or focus exclusively on gas-phase chemistry, TChem-atm supports fully coupled gas–aerosol systems with execution across CPUs, NVIDIA GPUs, and AMD GPUs through the Kokkos programming model. It integrates the flexible multiphase capabilities of the Community Atmospheric Model Chemistry Package (CAMP) with the high performance kinetic routines of TChem, and includes automatic Jacobian construction with support for a range of stiff ODE solvers. We demonstrate TChem-atm's integration into the particle-resolved aerosol model PartMC and validate its accuracy against the existing PartMC–CAMP implementation, showing agreement within solver tolerances. Performance benchmarks reveal substantial speedups on GPU platforms, particularly for large particle populations, with consistent results across hardware backends. By enabling chemically detailed, multiphase simulations with true performance portability and host-model flexibility, TChem-atm provides a new foundation for next-generation atmospheric models.
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Status: open (until 24 Nov 2025)
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CEC1: 'No compliance with the policy of the journal', Juan Antonio Añel, 07 Oct 2025
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AC1: 'Reply on CEC1', Nicole Riemer, 11 Oct 2025
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Dear Dr. Añel,
Thank you for your message regarding our manuscript and for highlighting the requirements of GMD’s Code and Data Policy. We want to ensure our work is fully compliant and reproducible.
Code repository: We prepared an archival release of the full software stack required for our study (TChem-atm, PartMC, Kokkos, SUNDIALS, and Tines). This has been deposited in Zenodo at DOI: https://doi.org/10.5281/zenodo.17309370, and we will explicitly list version numbers for each component in the revised manuscript.
Data repository: Regarding the data, our intent in using the Illinois Data Bank was precisely to comply with the requirements outlined in the GMD policy (https://www.geoscientific-model-development.net/policies/code_and_data_policy.html#item3). The Illinois Data Bank provides:
- Institutional support at the University of Illinois, ensuring long-term availability.
- Preservation guarantees that prevent depositors from unilaterally removing materials.
- Persistent identifiers (DOIs) and versioning mechanisms that enable citation of the exact dataset used in our study.
These features appear to meet the criteria listed in the GMD Code and Data Policy for acceptable repositories. The Data Bank’s policies are publicly documented here: https://databank.illinois.edu/policies.
We therefore respectfully request clarification on why the Illinois Data Bank would not be considered a suitable repository under GMD’s standards. If there are specific aspects that do not align with the policy, we would be grateful to know so we can address them directly.
We look forward to your guidance.
Best regards,
Nicole Riemer on behalf of all co-authors
Citation: https://doi.org/10.5194/egusphere-2025-4376-AC1 -
CEC2: 'Reply on AC1', Juan Antonio Añel, 12 Oct 2025
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Dear authors,
The Illinois Data Bank does not comply with our policy because its data preservation policy does assure long-term preservation, but at maximum five-years, and even in such cases with potential data removal happening. We usually request a period of 15-20 yeas minimum with proved funding for it.
Regards,
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-4376-CEC2 -
AC2: 'Reply on CEC2', Nicole Riemer, 14 Oct 2025
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Dear Dr. Añel,
Thank you for the response.
As I understand GMD’s policy, repositories should have institutional support that provides “reasonable confidence that the material will remain available for many years/decades.” The Illinois Data Bank (IDB) is operated by the University of Illinois Library with a long-term preservation mandate and funding.
To clarify, IDB’s stated five-year retention is a minimum commitment, after which a formal preservation review is conducted. In practice, datasets are retained unless there is a specific reason for deaccession, and descriptive metadata are planned to be kept persistently. The Library maintains documented preservation and sustainability procedures that ensure continuity of service beyond the minimum term. In our view, this aligns with the policy’s standard of “reasonable confidence.”
Could you please confirm whether GMD’s enforcement standard is:
1. the published policy text (“reasonable confidence… many years/decades”), under which documented institutional preservation frameworks like IDB’s qualify; or
2. a fixed multi-decade requirement (e.g., an explicit unconditional guarantee)?
If it is the latter, could you please point me to where this requirement is posted in the journal’s policies or guidance so we can follow the documented standard?
Best regards,
Nicole Riemer
Citation: https://doi.org/10.5194/egusphere-2025-4376-AC2 -
CEC3: 'Reply on AC2', Juan Antonio Añel, 14 Oct 2025
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Dear authors,
The text in our policy is a guide. Our policy clearly links you to a list of acceptable repositories, and when a new one appears we are happy to work with the managers of such repository to assess if it is acceptable or to guide them in the process to make the repository acceptable to store assets of the papers submitted to the journal.
The Illinois Data Bank is not in our list of acceptable repositories, and given the information that makes available, it is clear that it does not comply with our requirements and does not meet the standards of other repositories that we accept. I have mentioned the five years preservation period as the most clear feature that makes the Illinois Data Bank unable to comply with our policy. Moreover, the Preservation Review Guidelines of the Illinois Data Bank clearly establish that after the five-years period a dataset could be removed considering factors such as cost. This cast serious doubts about if a dataset will be available after such initial period, as it could be decided by the managers of the Data Bank not to preserve it. I insist, we can not accept this.
Please, store you datasets in one of the many repositories that we have listed in our policy and can accept, to be able to continue with the review process of your manuscript.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-4376-CEC3 -
AC3: 'Reply on CEC3', Nicole Riemer, 16 Oct 2025
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Dear Dr. Añel,
Thank you for the clarification. To keep the review moving, we have deposited the dataset in Zenodo and updated our records accordingly. The archived dataset is available at:
https://doi.org/10.5281/zenodo.17362352
If I may offer brief feedback on the policy text for archive standards: The current wording is criteria-based (institutional support providing “reasonable confidence” for many years/decades; persistent identifiers; depositor cannot unilaterally remove material) and then provides examples (Zenodo, arXiv, and repository lists from Springer Nature, PLOS, ESSD). It does not explicitly state that only repositories on a maintained, approved list are accepted. If the journal intends to enforce using specific repositories, it would be helpful to state this explicitly. We also noticed several links to external repository lists on the policy page appear to be broken.
We appreciate your guidance and have proceeded with Zenodo as requested. Please let us know if anything further is needed on our side.
Best regards,
Nicole Riemer
Citation: https://doi.org/10.5194/egusphere-2025-4376-AC3 -
CEC4: 'Reply on AC3', Juan Antonio Añel, 16 Oct 2025
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Dear authors,
Many thanks for your reply. We can consider now the current version of your manuscript in compliance with the code and data policy of the journal.
I appreciate your comment regarding the wording of our policy. We think that it is clear enough, and serves the purpose of listing acceptable options to store assets for manuscripts submitted to the journal.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-4376-CEC4
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CEC4: 'Reply on AC3', Juan Antonio Añel, 16 Oct 2025
reply
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AC3: 'Reply on CEC3', Nicole Riemer, 16 Oct 2025
reply
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CEC3: 'Reply on AC2', Juan Antonio Añel, 14 Oct 2025
reply
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AC2: 'Reply on CEC2', Nicole Riemer, 14 Oct 2025
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AC1: 'Reply on CEC1', Nicole Riemer, 11 Oct 2025
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Data sets
Data for TChem-atm (v2.0.0): Scalable Performance-Portable Multiphase Atmospheric Chemistry O. H. Díaz-Ibarra et al. https://doi.org/10.13012/B2IDB-3697767_V1
Model code and software
TChem-atm version 2.0.0, O. H. Díaz-Ibarra et al. https://doi.org/10.5281/zenodo.17058144
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Dear authors,
Unfortunately, after checking your manuscript, it has come to our attention that it does not comply with our "Code and Data Policy".
https://www.geoscientific-model-development.net/policies/code_and_data_policy.html
The causes are both lack of compliance with code sharing and with data sharing. Regarding the code, you state in your manuscript that to replicate it is necessary to use Kokkos, SUNDIALS, Tines, and PartMC. However, first you do not provide a link to a repository where to find the three first, and for PartMC you link a Git site. However, GitHub is not a suitable repository for scientific publication. GitHub itself instructs authors to use other long-term archival and publishing alternatives, such as Zenodo. You must store the mentioned software packages in a repository that complies with our policy, and reply to this comment with the permanent handler (e.g. DOI) and link for it. Also you must identify the version numbers for such software packages.
Regarding the data, you have stored it at the Illinois Data Bank. However, this is not a suitable repository for scientific publication. You must store your data in one of the repositories listed in our policy.
Please, address this comment and solve the situation as soon as possible, as the current situation with your manuscript is irregular. It should have never been accepted for Discussions given such violations of our policy.
Please, remind that you must include a modified 'Code and Data Availability' section in a potentially reviewed manuscript, containing the information of the new repositories.
I must note that if you do not fix this problem, we cannot continue with the peer-review process or accept your manuscript for publication in our journal.
Juan A. Añel
Geosci. Model Dev. Executive Editor