Closed (replaced with #484) - [DRAFT] Implementing GEOS-Chem chemistry in CESM2.1 (CESM2-GC) #378

fritzt · 2021-05-18T23:54:22Z

Hello!

I have been working on implementing the GEOS-Chem (version 13.0.0) chemistry module in CESM2.1.1. This new option is designated as CESM2-GC. The implementation of GEOS-Chem chemistry inside CESM2 aims to provide an additional chemistry option alongside CAM-Chem.

Since the implementation of GEOS-Chem requires changes to multiple Git repositories, this is the first PR out of three (CAM, CLM, cime).

All GEOS-Chem source code and other dependencies for this project are obtained and handled with the Externals feature. The top-level Externals.cfg is provided as an attachment to this PR (renamed to Externals.txt).

CESM2-GC relies heavily on the implementation of HEMCO in CESM2 (https://github.com/ESCOMP/HEMCO_CESM). HEMCO is an ESMF-compatible interface to perform I/O (e.g. loading emission inventories) in atmospheric models. Note that HEMCO has been implemented in CAM and lives at a higher level than GEOS-Chem. This allows HEMCO to feed data (e.g. emission fluxes) to either GEOS-Chem or CAM-Chem. Compiling CESM2-GC with HEMCO requires the use of ESMF libraries (USE_ESMF_LIB).

Additionally, this implementation comes with a few modifications in cime and CLM. First, we wanted to have the option to let GEOS-Chem compute its own dry deposition velocities. This requires the coupler to pass land types from CLM to CAM. We have modified CLM, cime, and CAM accordingly. Finally, not all files in the GEOS-Chem subdirectories should be compiled. To deal with this, we introduced a feature that can exclude files from the compilation process (ESMCI/cime#3366). This feature, as well as changes to the Henry coefficients (due to added GEOS-Chem species) and the land type changes, will be introduced in another PR.

Because some of GEOS-Chem modules rely on module arrays, CESM2-GC cannot run with NTHRDS_ATM > 1. However, I have noticed that if any NTHRDS_* are greater than 1, then CESM2-GC still crashes, which I haven't been able to understand why.

Some of the input files required for CESM2-GC can be found on Cheyenne.

Let me know if you need anything else.

Regards,
Thibaud Fritz
Laboratory for Aviation and the Environment

Externals.txt

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90484 Committed by Brian Eaton <eaton@ucar.edu> at 2019-01-15 18:16:28 -0700 Original svn commit message: register constituent mixing ratios as dry for WACCM'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90485 Committed by Brian Eaton <eaton@ucar.edu> at 2019-01-15 18:22:06 -0700 Original svn commit message: fix cam tag name'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90496 Committed by Brian Eaton <eaton@ucar.edu> at 2019-01-17 15:54:47 -0700 Original svn commit message: treat tracer mmr as wet in clubb and vertical diffusion code'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90501 Committed by Brian Eaton <eaton@ucar.edu> at 2019-01-18 12:10:08 -0700 Original svn commit message: treat tracer mmr as wet in gravity wave drag code'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90505 Committed by Brian Eaton <eaton@ucar.edu> at 2019-01-18 13:12:58 -0700 Original svn commit message: fix gw_tend'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90578 Committed by Francis Vitt <fvitt@ucar.edu> at 2019-02-07 16:46:06 -0700 Original svn commit message: M components/cam/bld/namelist_files/use_cases/sd_waccm_ma_cam4.xml A + components/cam/bld/namelist_files/use_cases/waccm_tsmlt_ssp126_cam6.xml M components/cam/bld/namelist_files/use_cases/sd_waccm_ma_cam6.xml A + components/cam/bld/namelist_files/use_cases/waccm_tsmlt_ssp534_cam6.xml M components/cam/bld/namelist_files/use_cases/sd_trop_strat_vbs_cam6.xml A + components/cam/bld/namelist_files/use_cases/sd_waccm_mad_cam6.xml M components/cam/bld/namelist_files/use_cases/sd_waccm_tsmlt_cam6.xml M components/cam/bld/namelist_files/use_cases/sd_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_tsmlt_1850_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_sc_1850_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_tsmlt_hist_cam6.xml A + components/cam/bld/namelist_files/use_cases/waccm_tsmlt_ssp585_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_sc_hist_cam6.xml M components/cam/cime_config/config_compsets.xml M components/cam/cime_config/config_component.xml M components/cam/doc/ChangeLog M components/cam/src/physics/cam/physics_types.F90 M components/cam/src/chemistry/utils/apex.F90 M components/cam/src/chemistry/modal_aero/aero_model.F90 '

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90604 Committed by Brian Eaton <eaton@ucar.edu> at 2019-02-13 10:12:20 -0700 Original svn commit message: mods for co2_cycle'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90664 Committed by Brian Eaton <eaton@ucar.edu> at 2019-02-27 16:57:27 -0700 Original svn commit message: mods for co2_cycle'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90669 Committed by Francis Vitt <fvitt@ucar.edu> at 2019-02-28 08:56:16 -0700 Original svn commit message: Updates to WACCM CMIP6 future scenario compsets M bld/namelist_files/use_cases/waccm_tsmlt_ssp126_cam6.xml A + bld/namelist_files/use_cases/waccm_tsmlt_ssp245_cam6.xml A + bld/namelist_files/use_cases/waccm_tsmlt_ssp370_cam6.xml M bld/namelist_files/use_cases/waccm_tsmlt_ssp534_cam6.xml M bld/namelist_files/use_cases/waccm_tsmlt_ssp585_cam6.xml M cime_config/config_component.xml M doc/ChangeLog '

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90679 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-03-05 12:51:17 -0700 Original svn commit message: Add the CAM hooks for SSP585'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90684 Committed by Francis Vitt <fvitt@ucar.edu> at 2019-03-06 10:22:52 -0700 Original svn commit message: Change compset match string for WACCM SSP compsets'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90695 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-03-07 17:04:19 -0700 Original svn commit message: Update files in SSP585 use_case'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90763 Committed by Brian Eaton <eaton@ucar.edu> at 2019-03-15 17:53:13 -0600 Original svn commit message: add mixing_ratio attribute to restart file'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90769 Committed by Brian Eaton <eaton@ucar.edu> at 2019-03-16 14:56:13 -0600 Original svn commit message: new fix for mixing_ratio attribute'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90814 Committed by Chris Fischer <fischer@ucar.edu> at 2019-03-22 12:11:16 -0600 Original svn commit message: Update REFCASES, and fix character length mismatch. '

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90815 Committed by Chris Fischer <fischer@ucar.edu> at 2019-03-22 12:11:37 -0600 Original svn commit message: Update externals '

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90818 Committed by Chris Fischer <fischer@ucar.edu> at 2019-03-22 14:02:55 -0600 Original svn commit message: Update ChangeLog with testing information '

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90854 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-03-29 12:38:11 -0600 Original svn commit message: Create CAM's SSP126 use_case'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90857 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-03-29 14:01:52 -0600 Original svn commit message: Fix typos and replace missing file in CAM's SSP126 use_case'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90860 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-03-29 15:02:54 -0600 Original svn commit message: Another typo and filename update'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90862 Committed by Brian Eaton <eaton@ucar.edu> at 2019-03-29 16:48:31 -0600 Original svn commit message: bug fixes'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90972 Committed by Francis Vitt <fvitt@ucar.edu> at 2019-04-11 08:12:54 -0600 Original svn commit message: M components/cam/bld/namelist_files/use_cases/1850_cam6.xml M components/cam/bld/namelist_files/use_cases/hist_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_ma_hist_cam4.xml M components/cam/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml M components/cam/bld/namelist_files/namelist_defaults_cam.xml M components/cam/doc/ChangeLog '

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@91083 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-04-25 15:54:22 -0600 Original svn commit message: Added SSP245 and SSP360 and modified files in SSP126'

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@91107 Committed by Francis Vitt <fvitt@ucar.edu> at 2019-04-30 17:01:53 -0600 Original svn commit message: M components/cam/bld/namelist_files/namelist_defaults_cam.xml M components/cam/bld/namelist_files/use_cases/waccm_ma_1850_cam6.xml M components/cam/bld/namelist_files/use_cases/waccm_ma_hist_cam6.xml M components/cam/cime_config/config_component.xml M components/cam/cime_config/config_compsets.xml M components/cam/cime_config/testdefs/testlist_cam.xml M components/cam/doc/ChangeLog M components/cam/src/chemistry/modal_aero/aero_model.F90 '

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@91163 Committed by Francis Vitt <fvitt@ucar.edu> at 2019-05-15 08:22:16 -0600 Original svn commit message: Fix WACCMX temperature bug M components/cam/doc/ChangeLog M components/cam/src/utils/physconst.F90 M components/cam/src/physics/cam/physics_types.F90 M components/cam/src/dynamics/fv/dp_coupling.F90 '

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@91243 Committed by Francis Vitt <fvitt@ucar.edu> at 2019-05-29 14:14:18 -0600 Original svn commit message: M bld/namelist_files/use_cases/ssp585_cam6.xml M doc/ChangeLog '

(1) This introduces an option to compile GEOS-Chem src files. (2) Interface is inexistant so far (3) CAM still uses the Terminator chem package to satisfy dependencies Reproducing commit from MSL - Jan 19, 2018

(1) Update config files in cam/bld/ (2) Update config files in cam/cime_config

Reproducing commit from MSL - Mar 6, 2018

(1) The code can now be compiled using a CAM 4.0 + "dummy" GEOS-Chem component set (compset FGC). This is based on the "tropospheric mozart" set. Reproducing commit from SDE - May 17, 2018

(1) Note that most of the mo_drydep routines are unused. We only need to load in landtypes for MAM Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

(1) Emission diameters are taken from: Emmons, Louisa K., et al. "The chemistry mechanism in the Community Earth System Model version 2 (CESM2)." Journal of Advances in Modeling Earth Systems 12.4 (2020). Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

(1) Add mapping (2) Extend number of constituents Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

(1) SO4_gasRatio and binRatio are in mol/mol, not kg/kg Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

This prevents the code from double counting in-cloud sulfur oxidation Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

lizziel · 2022-01-03T20:05:30Z

This PR is superseded by #484. @fritzt and @gold2718, I do not have permissions to close this PR. Could you close it out to avoid confusion?

brian-eaton and others added 30 commits October 3, 2019 14:45

'fix cam tag name

89f2745

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90485 Committed by Brian Eaton <eaton@ucar.edu> at 2019-01-15 18:22:06 -0700 Original svn commit message: fix cam tag name'

'fix gw_tend

b660da2

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90505 Committed by Brian Eaton <eaton@ucar.edu> at 2019-01-18 13:12:58 -0700 Original svn commit message: fix gw_tend'

'mods for co2_cycle

d974159

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90604 Committed by Brian Eaton <eaton@ucar.edu> at 2019-02-13 10:12:20 -0700 Original svn commit message: mods for co2_cycle'

'mods for co2_cycle

bd38265

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90664 Committed by Brian Eaton <eaton@ucar.edu> at 2019-02-27 16:57:27 -0700 Original svn commit message: mods for co2_cycle'

'Add the CAM hooks for SSP585

728b02b

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90679 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-03-05 12:51:17 -0700 Original svn commit message: Add the CAM hooks for SSP585'

'Update files in SSP585 use_case

b4e7145

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90695 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-03-07 17:04:19 -0700 Original svn commit message: Update files in SSP585 use_case'

'add mixing_ratio attribute to restart file

dded6b8

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90763 Committed by Brian Eaton <eaton@ucar.edu> at 2019-03-15 17:53:13 -0600 Original svn commit message: add mixing_ratio attribute to restart file'

'new fix for mixing_ratio attribute

c343b31

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90769 Committed by Brian Eaton <eaton@ucar.edu> at 2019-03-16 14:56:13 -0600 Original svn commit message: new fix for mixing_ratio attribute'

'Update externals

f48ada6

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90815 Committed by Chris Fischer <fischer@ucar.edu> at 2019-03-22 12:11:37 -0600 Original svn commit message: Update externals '

'Update ChangeLog with testing information

f5e01cd

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90818 Committed by Chris Fischer <fischer@ucar.edu> at 2019-03-22 14:02:55 -0600 Original svn commit message: Update ChangeLog with testing information '

'Create CAM's SSP126 use_case

87cf609

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90854 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-03-29 12:38:11 -0600 Original svn commit message: Create CAM's SSP126 use_case'

'Another typo and filename update

d433694

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90860 Committed by Cheryl Craig <cacraig@ucar.edu> at 2019-03-29 15:02:54 -0600 Original svn commit message: Another typo and filename update'

'bug fixes

669ad22

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/branches/cam_cesm2_1_rel@90862 Committed by Brian Eaton <eaton@ucar.edu> at 2019-03-29 16:48:31 -0600 Original svn commit message: bug fixes'

Feat: Changes to include GEOS-Chem as a chemistry option for CESM

7d76398

(1) This introduces an option to compile GEOS-Chem src files. (2) Interface is inexistant so far (3) CAM still uses the Terminator chem package to satisfy dependencies Reproducing commit from MSL - Jan 19, 2018

Feat: Update config files to include GEOS-Chem option for CAM

cbcb9fb

(1) Update config files in cam/bld/ (2) Update config files in cam/cime_config

Feat: Add customized chemistry.F90 for GEOS-Chem

a7336ca

Reproducing commit from MSL - Mar 6, 2018

Feat: Initial implementation of compilable code

d702e46

(1) The code can now be compiled using a CAM 4.0 + "dummy" GEOS-Chem component set (compset FGC). This is based on the "tropospheric mozart" set. Reproducing commit from SDE - May 17, 2018

fritzt added 15 commits March 24, 2021 11:43

Feat: Revert mo_drydep to MOZART's version + Update chemistry.F90

92a1ad9

(1) Note that most of the mo_drydep routines are unused. We only need to load in landtypes for MAM Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Lump GEOS-Chem SO4 with so4_a* and H2SO4

d98860c

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Fix: Remove hard-wired number emissions as this has been moved to HEMCO

d726574

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Update .xml files with GEOS-Chem chemistry (MEGAN)

987966f

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Add MEGAN emissions with GEOS-Chem species

c3dc4ba

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Fix: Update IF condition for SRF diagnostics

0c50dd8

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Add hemco_nl in build-namelist

07d34eb

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Rename geoschem.xml to 2000_geoscheml.xml (FC2000climo_GC)

efd6803

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Add 2010_geoscheml.xml (FC2010climo_GC)

95cf89c

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Update config_component to reflect recent changes to xml files

f6e3da6

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Add SOA mapping between MAM and GEOS-Chem complex SOA option

21575e6

(1) Add mapping (2) Extend number of constituents Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Add AEIC organic species to external forcings list

b5730ff

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Add GEOS-Chem surface boundary conditions

48324be

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Update .gitignore to exclude GEOS-Chem source code

719010c

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

fritzt mentioned this pull request May 19, 2021

Implementing GEOS-Chem chemistry in development (CESM2-GC) ESCOMP/CTSM#1377

Closed

cacraigucar assigned gold2718 May 19, 2021

fritzt mentioned this pull request May 19, 2021

Implementing GEOS-Chem chemistry in CESM2.1 (CESM2-GC) ESMCI/cime#3974

Closed

fritzt added 3 commits May 26, 2021 22:31

Fix: Fix for sulfur mapping between CESM2 and GEOS-Chem

93844ef

(1) SO4_gasRatio and binRatio are in mol/mol, not kg/kg Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Update .exclude for GEOS-Chem 13.1

cede078

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Fix: Update in-cloud opticaldepth with cloud fractions

315f294

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

This was referenced Aug 27, 2021

Changes to incorporate into ESCOMP/CTSM branch master CESM-GC/CTSM#1

Open

Feature: Export land types and LAI ESCOMP/CTSM#1475

Closed

Implementing GEOS-Chem chemistry in CESM (CESM-GC) #424

Open

Feat: Return in sox_cldaero_mod if running with GEOS-Chem

987508d

This prevents the code from double counting in-cloud sulfur oxidation Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

lizziel mentioned this pull request Dec 15, 2021

cam6_3_147: GEOS-Chem chemistry and four new compsets that use it #484

Merged

fritzt closed this Jan 4, 2022

cacraigucar changed the title ~~[DRAFT] Implementing GEOS-Chem chemistry in CESM2.1 (CESM2-GC)~~ Closed (replaced with #484) - [DRAFT] Implementing GEOS-Chem chemistry in CESM2.1 (CESM2-GC) Jan 5, 2022

lizziel deleted the CESM-GC_dev branch March 7, 2022 14:09

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Closed (replaced with #484) - [DRAFT] Implementing GEOS-Chem chemistry in CESM2.1 (CESM2-GC) #378

Closed (replaced with #484) - [DRAFT] Implementing GEOS-Chem chemistry in CESM2.1 (CESM2-GC) #378

fritzt commented May 18, 2021

lizziel commented Jan 3, 2022

Closed (replaced with #484) - [DRAFT] Implementing GEOS-Chem chemistry in CESM2.1 (CESM2-GC) #378

Closed (replaced with #484) - [DRAFT] Implementing GEOS-Chem chemistry in CESM2.1 (CESM2-GC) #378

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fritzt commented May 18, 2021

lizziel commented Jan 3, 2022