================= VermeuelJGRA2024_Readme Updated 11/19/2024 ================= This .zip folder contains model code, input, and output data to constrain the 1D Multi-Layer Canopy CHemistry and Exchange Model (MLC-CHEM) for simulations used in the following manuscript: M.P. Vermeuel, D.B. Millet, D.K. Farmer, L.N. Ganzeveld, A.J. Visser, H.D. Alwe, T.H. Bertram, P.A. Cleary, A.R. Desai, D. Helmig, S.C. Kavassalis, M.F. Link, M.A. Pothier, M. Riches, W. Wang, S. Williams (2024), A vertically-resolved canopy improves chemical transport model predictions of ozone deposition to north temperate forests, J. Geophys. Res., Accepted The DOI for the preprint can be found at:10.22541/essoar.172313458.86659538/v1 Suggested citation for dataset: Vermeuel, Michael; Millet, Dylan; Farmer, Delphine; Ganzeveld, Laurens; Visser, Auke; Alwe, Hariprasad; Bertram, Timothy; Cleary, Patricia; Desai, Ankur; Helmig, Detlev; Kavassalis, Sarah; Link, Michael; Pothier, Matson; Riches, Mj; Wang, Wei; Williams, Sara. (2024). MLC-CHEM code and data for A vertically-resolved canopy improves chemical transport model predictions of ozone deposition to north temperate forests. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/h966-ms14 ================= File descriptions ================= In the main directory you can find the manual for running MLC-CHEM. This folder contains subdirectories for individual MLC-CHEM runs simulations over a. Manitou Experimental Forest Observatory during the FluCS 2021 study, Woodland Park, CO Aug-Sep 2021 (FluCS) b. Chequamegon-Nicolet National Forest at the Us-PFA/WLEF-TV tower during the CHEESHEAD19 field study, Park Falls, WI Jul 2019 (C19) c. University of Michigan Biological Station during the PROPHET AMOS field study, MI, Jul 2016 (PROPHET) d. Chequamegon-Nicolet National Forest at the Us-PFA/WLEF-TV tower during the PEcoRINO field study, Park Falls, WI Sep 2020 (LEF) Subdirectories for study-specific runs are divided into INF and REF folders: a. MLC folders constrained by observations, and use the INFERRED (INF) method for eddy diffusivity calculations b. MLC/GC folders constrained lowest layer GEOS-Chemchemical abundances and meteorology using the REFERENCE (REF) method for eddy diffusivity calculations. Within each MLC or MLC/GC folder contains a. an input folder containing relevant constraints b. an output folder for model simulation results c. MLC-CHEM source code as explained in the manual All MLC-CHEM runs use the initial code optimized for simulations of the Bosco Fontana forest in northern Italy: A.J. Visser, L.N. Ganzeveld, A. Finco, M.C. Krol, R. Marzuoli, K.F. Boersma (2022), The Combined Impact of Canopy Stability and Soil NOx Exchange on Ozone Removal in a Temperate Deciduous Forest, J. Geophys. Biogeosci., https://doi.org/10.1029/2022JG006997 Specific updates to the code for this study can be found in the manuscript or by searching source code edits marked "MPV". ================= Contact ================= Dylan Millet (dbm@umn.edu); Michael Vermeuel (mvermeue@purdue.edu) ================= Data Tree ================= | Manual_MLC_CHEM.docx | README.txt | +---C19 | +---MLCGC_REF | | | depend.mk | | | depend.mk.old | | | emdep.nml | | | emdep_xtsurf.exe | | | main.mk | | | make.bat | | | Makefile | | | Makefile.e | | | makeoutput.txt | | | Manual_MLC_CHEM.docx | | | Manual_MLC_CHEM.pdf | | | messy_emdep.f90 | | | messy_emdep.mod | | | messy_emdep.o | | | messy_emdep_emis.f90 | | | messy_emdep_emis.mod | | | messy_emdep_emis.o | | | messy_emdep_emis_mem.f90 | | | messy_emdep_emis_mem.mod | | | messy_emdep_emis_mem.o | | | messy_emdep_mem.f90 | | | messy_emdep_mem.mod | | | messy_emdep_mem.o | | | messy_emdep_xtsurf.f90 | | | messy_emdep_xtsurf.mod | | | messy_emdep_xtsurf.o | | | messy_emdep_xtsurf_box.f90 | | | messy_emdep_xtsurf_box.mod | | | messy_emdep_xtsurf_box.o | | | messy_main_constants_mem.f90 | | | messy_main_constants_mem.mod | | | messy_main_constants_mem.o | | | messy_main_tools.f90 | | | messy_main_tools.mod | | | messy_main_tools.o | | | README.txt | | | sfmakedepend | | | solve_tridiag.f90 | | | solve_tridiag.o | | | surf_out | | | thirtyfour | | | | | +---input | | | | BFt_20120624_20120711.inp | | | | | | | +---.svn | | | | | entries.gz | | | | | | | | | \---text-base | | | | example_obs.inp.svn-base.gz | | | | | | | \---BoscoFontana | | | C19_2019070100.inp | | | | | \---output | | AGS.out | | avg_obs.out | | Radiation_canopy.out | | soilNOxemis.out | | VdO3_bigleaf.out | | veg_mlay.out | | VOCemis.out | | xttend.out | | | \---MLC_INF | | depend.mk | | depend.mk.old | | emdep.nml | | emdep_xtsurf.exe | | main.mk | | make.bat | | Makefile | | Makefile.e | | makeoutput.txt | | Manual_MLC_CHEM.docx | | Manual_MLC_CHEM.pdf | | messy_emdep.f90 | | messy_emdep.mod | | messy_emdep.o | | messy_emdep_emis.f90 | | messy_emdep_emis.mod | | messy_emdep_emis.o | | messy_emdep_emis_mem.f90 | | messy_emdep_emis_mem.mod | | messy_emdep_emis_mem.o | | messy_emdep_mem.f90 | | messy_emdep_mem.mod | | messy_emdep_mem.o | | messy_emdep_xtsurf.f90 | | messy_emdep_xtsurf.mod | | messy_emdep_xtsurf.o | | messy_emdep_xtsurf_box.f90 | | messy_emdep_xtsurf_box.mod | | messy_emdep_xtsurf_box.o | | messy_main_constants_mem.f90 | | messy_main_constants_mem.mod | | messy_main_constants_mem.o | | messy_main_tools.f90 | | messy_main_tools.mod | | messy_main_tools.o | | README.txt | | sfmakedepend | | solve_tridiag.f90 | | solve_tridiag.o | | surf_out | | thirtyfour | | xtend | | | +---input | | | BFt_20120624_20120711.inp | | | | | +---.svn | | | | entries.gz | | | | | | | \---text-base | | | example_obs.inp.svn-base.gz | | | | | +---BoscoFontana | | | C19_2019070100.inp | | | | | \---MEGAN | | EFisop2000m302a.txt | | PFT2000m302a.txt | | | \---output | AGS.out | avg_obs.out | Radiation_canopy.out | soilNOxemis.out | VdO3_bigleaf.out | veg_mlay.out | VOCemis.out | xttend.out | +---FluCS | +---MLCGC_REF | | | depend.mk | | | depend.mk.old | | | emdep.nml | | | emdep_xtsurf.exe | | | KH_out | | | KH_test | | | main.mk | | | make.bat | | | Makefile | | | Makefile.e | | | makeoutput.txt | | | Manual_MLC_CHEM.docx | | | Manual_MLC_CHEM.pdf | | | messy_emdep.f90 | | | messy_emdep.mod | | | messy_emdep.o | | | messy_emdep_emis.f90 | | | messy_emdep_emis.mod | | | messy_emdep_emis.o | | | messy_emdep_emis_mem.f90 | | | messy_emdep_emis_mem.mod | | | messy_emdep_emis_mem.o | | | messy_emdep_mem.f90 | | | messy_emdep_mem.mod | | | messy_emdep_mem.o | | | messy_emdep_xtsurf.f90 | | | messy_emdep_xtsurf.mod | | | messy_emdep_xtsurf.o | | | messy_emdep_xtsurf_box.f90 | | | messy_emdep_xtsurf_box.mod | | | messy_emdep_xtsurf_box.o | | | messy_main_constants_mem.f90 | | | messy_main_constants_mem.mod | | | messy_main_constants_mem.o | | | messy_main_tools.f90 | | | messy_main_tools.mod | | | messy_main_tools.o | | | rahveg_out | | | README.txt | | | sfmakedepend | | | solve_tridiag.f90 | | | solve_tridiag.o | | | surf_out | | | thirtyfour | | | ustar_out | | | | | +---input | | | | BFt_20120624_20120711.inp | | | | | | | +---.svn | | | | | entries.gz | | | | | | | | | \---text-base | | | | example_obs.inp.svn-base.gz | | | | | | | \---BoscoFontana | | | FluCS_2021081300.inp | | | | | \---output | | AGS.out | | avg_obs.out | | Radiation_canopy.out | | soilNOxemis.out | | VdO3_bigleaf.out | | veg_mlay.out | | VOCemis.out | | xttend.out | | | \---MLC_INF | | depend.mk | | depend.mk.old | | emdep.nml | | emdep_xtsurf.exe | | main.mk | | make.bat | | Makefile | | Makefile.e | | makeoutput.txt | | Manual_MLC_CHEM.docx | | Manual_MLC_CHEM.pdf | | messy_emdep.f90 | | messy_emdep.mod | | messy_emdep.o | | messy_emdep_emis.f90 | | messy_emdep_emis.mod | | messy_emdep_emis.o | | messy_emdep_emis_mem.f90 | | messy_emdep_emis_mem.mod | | messy_emdep_emis_mem.o | | messy_emdep_mem.f90 | | messy_emdep_mem.mod | | messy_emdep_mem.o | | messy_emdep_xtsurf.f90 | | messy_emdep_xtsurf.mod | | messy_emdep_xtsurf.o | | messy_emdep_xtsurf_box.f90 | | messy_emdep_xtsurf_box.mod | | messy_emdep_xtsurf_box.o | | messy_main_constants_mem.f90 | | messy_main_constants_mem.mod | | messy_main_constants_mem.o | | messy_main_tools.f90 | | messy_main_tools.mod | | messy_main_tools.o | | README.txt | | sfmakedepend | | solve_tridiag.f90 | | solve_tridiag.o | | surf_out | | thirtyfour | | xtend | | | +---input | | | BFt_20120624_20120711.inp | | | | | +---.svn | | | | entries.gz | | | | | | | \---text-base | | | example_obs.inp.svn-base.gz | | | | | +---BoscoFontana | | | FluCS_2021081300.inp | | | | | \---MEGAN | | EFisop2000m302a.txt | | PFT2000m302a.txt | | | \---output | AGS.out | avg_obs.out | Radiation_canopy.out | soilNOxemis.out | VdO3_bigleaf.out | veg_mlay.out | VOCemis.out | xttend.out | +---LEF | +---MLCGC_REF | | | depend.mk | | | depend.mk.old | | | emdep.nml | | | emdep_xtsurf.exe | | | main.mk | | | make.bat | | | Makefile | | | Makefile.e | | | makeoutput.txt | | | Manual_MLC_CHEM.docx | | | Manual_MLC_CHEM.pdf | | | messy_emdep.f90 | | | messy_emdep.mod | | | messy_emdep.o | | | messy_emdep_emis.f90 | | | messy_emdep_emis.mod | | | messy_emdep_emis.o | | | messy_emdep_emis_mem.f90 | | | messy_emdep_emis_mem.mod | | | messy_emdep_emis_mem.o | | | messy_emdep_mem.f90 | | | messy_emdep_mem.mod | | | messy_emdep_mem.o | | | messy_emdep_xtsurf.f90 | | | messy_emdep_xtsurf.mod | | | messy_emdep_xtsurf.o | | | messy_emdep_xtsurf_box.f90 | | | messy_emdep_xtsurf_box.mod | | | messy_emdep_xtsurf_box.o | | | messy_main_constants_mem.f90 | | | messy_main_constants_mem.mod | | | messy_main_constants_mem.o | | | messy_main_tools.f90 | | | messy_main_tools.mod | | | messy_main_tools.o | | | README.txt | | | sfmakedepend | | | solve_tridiag.f90 | | | solve_tridiag.o | | | surf_out | | | thirtyfour | | | tsurfcheck | | | | | +---input | | | | BFt_20120624_20120711.inp | | | | | | | +---.svn | | | | | entries.gz | | | | | | | | | \---text-base | | | | example_obs.inp.svn-base.gz | | | | | | | \---BoscoFontana | | | LEF_2020090700.inp | | | | | \---output | | AGS.out | | avg_obs.out | | Radiation_canopy.out | | soilNOxemis.out | | VdO3_bigleaf.out | | veg_mlay.out | | VOCemis.out | | xttend.out | | | \---MLC_INF | | depend.mk | | depend.mk.old | | emdep.nml | | emdep_xtsurf.exe | | main.mk | | make.bat | | Makefile | | Makefile.e | | makeoutput.txt | | Manual_MLC_CHEM.docx | | Manual_MLC_CHEM.pdf | | messy_emdep.f90 | | messy_emdep.mod | | messy_emdep.o | | messy_emdep_emis.f90 | | messy_emdep_emis.mod | | messy_emdep_emis.o | | messy_emdep_emis_mem.f90 | | messy_emdep_emis_mem.mod | | messy_emdep_emis_mem.o | | messy_emdep_mem.f90 | | messy_emdep_mem.mod | | messy_emdep_mem.o | | messy_emdep_xtsurf.f90 | | messy_emdep_xtsurf.mod | | messy_emdep_xtsurf.o | | messy_emdep_xtsurf_box.f90 | | messy_emdep_xtsurf_box.mod | | messy_emdep_xtsurf_box.o | | messy_main_constants_mem.f90 | | messy_main_constants_mem.mod | | messy_main_constants_mem.o | | messy_main_tools.f90 | | messy_main_tools.mod | | messy_main_tools.o | | README.txt | | sfmakedepend | | solve_tridiag.f90 | | solve_tridiag.o | | surf_out | | thirtyfour | | xtend | | | +---input | | | BFt_20120624_20120711.inp | | | | | +---.svn | | | | entries.gz | | | | | | | \---text-base | | | example_obs.inp.svn-base.gz | | | | | +---BoscoFontana | | | LEF_2020090700.inp | | | | | \---MEGAN | | EFisop2000m302a.txt | | PFT2000m302a.txt | | | \---output | AGS.out | avg_obs.out | Radiation_canopy.out | soilNOxemis.out | VdO3_bigleaf.out | veg_mlay.out | VOCemis.out | xttend.out | \---PROPHET +---MLCGC_REF | | checkout | | depend.mk | | depend.mk.old | | emdep.nml | | emdep_xtsurf.exe | | main.mk | | make.bat | | Makefile | | Makefile.e | | makeoutput.txt | | Manual_MLC_CHEM.docx | | Manual_MLC_CHEM.pdf | | messy_emdep.f90 | | messy_emdep.mod | | messy_emdep.o | | messy_emdep_emis.f90 | | messy_emdep_emis.mod | | messy_emdep_emis.o | | messy_emdep_emis_mem.f90 | | messy_emdep_emis_mem.mod | | messy_emdep_emis_mem.o | | messy_emdep_mem.f90 | | messy_emdep_mem.mod | | messy_emdep_mem.o | | messy_emdep_xtsurf.f90 | | messy_emdep_xtsurf.mod | | messy_emdep_xtsurf.o | | messy_emdep_xtsurf_box.f90 | | messy_emdep_xtsurf_box.mod | | messy_emdep_xtsurf_box.o | | messy_main_constants_mem.f90 | | messy_main_constants_mem.mod | | messy_main_constants_mem.o | | messy_main_tools.f90 | | messy_main_tools.mod | | messy_main_tools.o | | outcheck | | README.txt | | sfmakedepend | | solve_tridiag.f90 | | solve_tridiag.o | | surf_out | | thirtyfour | | | +---input | | | BFt_20120624_20120711.inp | | | | | +---.svn | | | | entries.gz | | | | | | | \---text-base | | | example_obs.inp.svn-base.gz | | | | | \---BoscoFontana | | PROPHET_2016070100.inp | | | \---output | AGS.out | avg_obs.out | Radiation_canopy.out | soilNOxemis.out | VdO3_bigleaf.out | veg_mlay.out | VOCemis.out | xttend.out | \---MLC_INF | AGS_search | depend.mk | depend.mk.old | emdep.nml | emdep_xtsurf.exe | main.mk | make.bat | Makefile | Makefile.e | makeoutput.txt | Manual_MLC_CHEM.docx | Manual_MLC_CHEM.pdf | messy_emdep.f90 | messy_emdep.mod | messy_emdep.o | messy_emdep_emis.f90 | messy_emdep_emis.mod | messy_emdep_emis.o | messy_emdep_emis_mem.f90 | messy_emdep_emis_mem.mod | messy_emdep_emis_mem.o | messy_emdep_mem.f90 | messy_emdep_mem.mod | messy_emdep_mem.o | messy_emdep_xtsurf.f90 | messy_emdep_xtsurf.mod | messy_emdep_xtsurf.o | messy_emdep_xtsurf_box.f90 | messy_emdep_xtsurf_box.mod | messy_emdep_xtsurf_box.o | messy_main_constants_mem.f90 | messy_main_constants_mem.mod | messy_main_constants_mem.o | messy_main_tools.f90 | messy_main_tools.mod | messy_main_tools.o | README.txt | sfmakedepend | solve_tridiag.f90 | solve_tridiag.o | surf_out | thirtyfour | xtend | +---input | | BFt_20120624_20120711.inp | | | +---.svn | | | entries.gz | | | | | \---text-base | | example_obs.inp.svn-base.gz | | | +---BoscoFontana | | PROPHET_2016070100.inp | | | \---MEGAN | EFisop2000m302a.txt | PFT2000m302a.txt | \---output AGS.out avg_obs.out Radiation_canopy.out soilNOxemis.out VdO3_bigleaf.out veg_mlay.out VOCemis.out xttend.out