I just want to note this here to hopefully benefit the next person googling this error:
*** ERROR ABORT in subroutine VDIFFPROC on PE 044 ; Failure initializing index mapping module
Opening the specific cpu’s log with the error:
DEP V_INIT: completed INIT_GAS_DV block
ERROR: No deposition velocity for DDEP species CLNO2
>>--->> WARNING in subroutine VDIFF_MAP on PE 044
*** Species mapping error(s) in VDIFF_MAP
*** ERROR ABORT in subroutine VDIFFPROC on PE 044
Failure initializing index mapping module
I found this resource helpful, as it points me to the right namelist files: CMAQ/DOCS/Users_Guide/CMAQ_UG_ch07_model_outputs.md at main · USEPA/CMAQ · GitHub
The culprit is (BLD)/GC_saprc07tc_ae6_aq.nml, where (as I understand it) per-species depositions are defined. There is a line for ClNO2 that is marked as ‘yes’ in the DDEP column, but has no DRYDEP_SURR defined and otherwise looks like the other species that have nothing in the ‘DDEP’ column.
For the headers and comparison:
The line for CLNO2 looks extremely similar to HNO4, just to pick one, but has a ‘Yes’ under the DDEP column.
This is in the saprc07-m3dry namelist from the 5.5 repo. I simply turned the ‘Yes’ in the DDEP column to ‘’ (two apostrophes) and it stopped throwing the error. Whether it should have other dry deposition parameters defined for this scheme is beyond me for now.
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Hello Calvin,
thank you very much for reporting this issue and sharing how you tracked down and implemented the solution that works for your case.
This is indeed an error in the GC_saprc07tc_ae6_aq.nml released with CMAQv55 that was introduced when we updated the definition of the post-processed DD_OXN_OTHR variable in the SpecDef_Dep_saprc07tc_ae6_aq.txt file used by the combine utility. Inconsistent with the WD_OXN_OTHR and WDEP_TCL definitions, DD_OXN_OTHR did not include (dry) deposition of CLNO2.
To enable output of that species by the CCTM, we added a ‘Yes’ to the DDEP column of the GC_saprc07tc_ae6_aq.nml file, but we overlooked that the file did not actually define an entry in the “DRYDEP_SURR” column for CLNO2, so the model could not compute its dry deposition. This is the error you encountered, and it was isolated to the SAPRC family of chemical mechanisms.
While the solution you implemented (changing the ‘Yes’ entry in the DDEP column back to ‘’) will avoid the CCTM crash since CLNO2 dry deposition output is no longer requested, it would cause a problem if you then were to use the combine utility with the SpecDef_Dep_saprc07tc_ae6_aq.txt file provided in the repository to post-process your CCTM deposition output files.
After our group recently also discovered this problem with the CMAQv55 saprc07tc_ae6_aq.nml file (as well as the corresponding files for saprc07tic_ae7i_aq and saprc07tic_ae7i_aqkmt2), we implemented a different fix that actually enables the output of CLNO2 dry deposition fields which can then be used by combine. To do this, you need to update the entry in the DRYDEP_SURR column from ‘’ to ‘VD_CLNO2’, change the factor of ‘-1’ in the FAC column following the DRYDEP_SURR column to ‘1’, and keep ‘Yes’ in the DDEP column. We plan to make this fix available via our github repository in the near future.
Thanks again for sharing your findings,
Christian
