geoschem/geos-chem: GEOS-Chem 14.2.0

Release date: 05 Oct 2023

• Bug fix: restore consideration of sea salt alkalinity to heterogenerous acid-catalyzed reactions of halogens on sea salt aerosols by @yantosca in https://github.com/geoschem/geos-chem/pull/1548
• Consolidate existing integration test scripts (slurm, lsf, interactive); Add LSF capability by @yantosca in https://github.com/geoschem/geos-chem/pull/1565
• Integration/parallelization test scripts now place test scripts & artifacts into subdirectories of the root test folder by @yantosca in https://github.com/geoschem/geos-chem/pull/1636
• Add reminders to compile with CMake options to createRunDir.sh scripts by @yantosca in https://github.com/geoschem/geos-chem/pull/1638
• Convert log file prints to debug prints by @yantosca in https://github.com/geoschem/geos-chem/pull/1549
• Fix bug where writing species metadata yaml file always attempted by @lizziel in https://github.com/geoschem/geos-chem/pull/1644
• Remove NcdfUtil/perl folder by @yantosca in https://github.com/geoschem/geos-chem/pull/1567
• Reset SPC_ time entry from EFYO to CYS for integration tests and fullchem_benchmark runs by @yantosca in https://github.com/geoschem/geos-chem/pull/1647
• Remove LWI from carbon simulation run directories by @lizziel in https://github.com/geoschem/geos-chem/pull/1643
• GEOS-only updates from Christoph Keller by @lizziel in https://github.com/geoschem/geos-chem/pull/1653
• Update rundir configuration files to point to corrected NEI day-of-week scale factors (Closes #1608) by @yantosca in https://github.com/geoschem/geos-chem/pull/1633
• Add entries for GFAS methanol to HEMCO_Config.rc templates by @yantosca in https://github.com/geoschem/geos-chem/pull/1632
• Archive State_Chm%H2SO4_PRDR for production rate of H2SO4 (mol/mol) for CESM-GC by @jimmielin in https://github.com/geoschem/geos-chem/pull/1624
• Apply work-around for GFAS pFe bug in GC-Classic and GCHP by @lizziel in https://github.com/geoschem/geos-chem/pull/1621
• Simplify Github issue and pull request templates by @msulprizio in https://github.com/geoschem/geos-chem/pull/1650
• Avoid compiler warning and compilation restart for KPP/fullchem/gckpp_Jacobian.F90 by @yantosca in https://github.com/geoschem/geos-chem/pull/1657
• Change HEMCO time cycle flag in benchmark rundir & integration tests for 14.1.1 by @yantosca in https://github.com/geoschem/geos-chem/pull/1656
• Removal of module variables from ucx_mod by @jimmielin in https://github.com/geoschem/geos-chem/pull/1583
• Fix incorrect comparison in GET_IJ routine; Fix leftover issues from PR #1656 by @yantosca in https://github.com/geoschem/geos-chem/pull/1663
• Fix bug in RRTMG optic diagnostics (AOD, SSA, Asym) by @lizziel in https://github.com/geoschem/geos-chem/pull/1669
• Ask users for PI at registration; abstract user registration code into a single script by @yantosca in https://github.com/geoschem/geos-chem/pull/1674
• Move GC-Classic run scripts to operational_examples directory by @lizziel in https://github.com/geoschem/geos-chem/pull/1677
• Fix several issues with GitHub issue and PR templates by @yantosca in https://github.com/geoschem/geos-chem/pull/1679
• Remove X-HRS printout from GEOS-Chem log file by @msulprizio in https://github.com/geoschem/geos-chem/pull/1678
• Remove references to Compute Canada from data download scripts by @msulprizio in https://github.com/geoschem/geos-chem/pull/1681
• Add lumped furans to chemistry and biomass burning emissions by @msulprizio in https://github.com/geoschem/geos-chem/pull/1642
• Abstract fullchem mechanism history into CHANGELOG_fullchem.md - closes #1689 by @yantosca in https://github.com/geoschem/geos-chem/pull/1690
• Fix typo in GCClassic/createRunDir.sh preventing benchmark run script from being copied to run directory by @msulprizio in https://github.com/geoschem/geos-chem/pull/1694
• Prevent divide by zero in sulfur chemistry by @lizziel in https://github.com/geoschem/geos-chem/pull/1698
• Turn on sea salt debromination for full-chemistry simulations by @msulprizio in https://github.com/geoschem/geos-chem/pull/1703
• Now use consistent behavior when the first call to "Integrate" fails by @yantosca in https://github.com/geoschem/geos-chem/pull/1609
• Reset "EFY" to "CYS" for nested boundary conditions in GCClassic integration & parallel tests by @yantosca in https://github.com/geoschem/geos-chem/pull/1706
• Restore Iy sink reactions and rebuild fullchem mechanism with KPP 3.0.0 by @yantosca in https://github.com/geoschem/geos-chem/pull/1620
• Restore consideration of sea salt alkalinity to heterogenerous acid-catalyzed reactions of halogens on sea salt aerosols by @msulprizio in https://github.com/geoschem/geos-chem/pull/1702
• Add S(IV) + HOBr and S(IV) + HOCl to the fullchem mechanism (Closes #1627) by @yantosca in https://github.com/geoschem/geos-chem/pull/1630
• Update entrainmment-limited kinetics in clouds by @cdholmes in https://github.com/geoschem/geos-chem/pull/1292
• Include nitrate aerosol photolysis in the troposphere by @viral211 in https://github.com/geoschem/geos-chem/pull/1623
• Update HEMCO_Config.rc and ExtData.rc template files to read GFED4 data thru 2022 by @yantosca in https://github.com/geoschem/geos-chem/pull/1709
• Add lightning climatology option to HEMCO_Config.rc by @msulprizio in https://github.com/geoschem/geos-chem/pull/1628
• Restore vertical emission distributions to CEDS energy and industry emissions by @msulprizio in https://github.com/geoschem/geos-chem/pull/1712
• Add fix for CEDS energy and industry emissions to distribute vertically by @msulprizio in https://github.com/geoschem/geos-chem/pull/1730
• GCHP bug fixes and run directory updates by @lizziel in https://github.com/geoschem/geos-chem/pull/1724
• Add run configuration files for WRF-GC by @jimmielin in https://github.com/geoschem/geos-chem/pull/1692
• Fix bug renaming midrun checkpoint files by @lizziel in https://github.com/geoschem/geos-chem/pull/1737
• Fix computation of planeCount for Harvard Cannon GCHP run scripts and integration test scripts by @yantosca in https://github.com/geoschem/geos-chem/pull/1686
• Restructure photolysis by @lizziel in https://github.com/geoschem/geos-chem/pull/1733
• Update text displayed at user registration during rundir creation by @yantosca in https://github.com/geoschem/geos-chem/pull/1732
• Remove array temporaries in carbon_mod.F90 and seasalt_mod.F90 by @yantosca in https://github.com/geoschem/geos-chem/pull/1729
• Modify HEMCO_Config.rc templates to read HEMCO restart files from the rundir "Restarts/" subdirectory by @yantosca in https://github.com/geoschem/geos-chem/pull/1718
• Prevent repeated printout of concs, rxn rates when KPP fails twice by @yantosca in https://github.com/geoschem/geos-chem/pull/1749
• Fix bug in photolysis off option by @lizziel in https://github.com/geoschem/geos-chem/pull/1750
• Fix bug in HOBr uptake rate calculation (closes #1746) by @yantosca in https://github.com/geoschem/geos-chem/pull/1751
• Set CO2 concentration to 421 ppm in fullchem simulations -- fixes CO2 error norm for KPP by @yantosca in https://github.com/geoschem/geos-chem/pull/1731
• Add GFED4 climatology emissions as an option in HEMCO_Config.rc by @msulprizio in https://github.com/geoschem/geos-chem/pull/1758
• Update global_ch4_mod.F90 to correct bug that incorrectly selects troposphere-stratosphere boundary by @toddmooring in https://github.com/geoschem/geos-chem/pull/1710
• Update global anthropogenic CH4 emissions to EDGARv7.0 by @msulprizio in https://github.com/geoschem/geos-chem/pull/1773
• Remove operator splitting in CH4 simulation that biases diagnostics (closes #1738) by @yantosca in https://github.com/geoschem/geos-chem/pull/1740
• Update CH4 simulation to use loss frequencies from GCClassic 14.0.0 10-year benchmark by @msulprizio in https://github.com/geoschem/geos-chem/pull/1776
• Update README.md and AUTHORS.txt for 14.2.0 by @yantosca in https://github.com/geoschem/geos-chem/pull/1774
• Update GCHP check for python and bc libs to prevent error checking fail by @lizziel in https://github.com/geoschem/geos-chem/pull/1777
• Add modifications to sea salt chemistry in order to avoid KPP integration errors by @yantosca in https://github.com/geoschem/geos-chem/pull/1779
• Add CH4 emissions from hydroelectric reservoirs by @msulprizio in https://github.com/geoschem/geos-chem/pull/1784
• Add RxnConst diagnostic for archiving reaction rate constants by @jimmielin in https://github.com/geoschem/geos-chem/pull/1728
• Fix GCHP time_mod start and elapsed times by @lizziel in https://github.com/geoschem/geos-chem/pull/1781
• Update partitions and env files in Harvard Cannon operational examples by @yantosca in https://github.com/geoschem/geos-chem/pull/1811
• Change relative tolerance back to 0.5e-2 to address model slowdown by @msulprizio in https://github.com/geoschem/geos-chem/pull/1815
• Allow the use of OFFLINE_SEASALT for seasalt alkalinity, Cl, and Br in GEOS-Chem within CESM by @jimmielin in https://github.com/geoschem/geos-chem/pull/1804
• Update transport tracer simulation for consistency with GMAO's tracer gridded component by @msulprizio in https://github.com/geoschem/geos-chem/pull/1816
• Bug fixes for GEOS-only runs by @lizziel in https://github.com/geoschem/geos-chem/pull/1842
• Add correct TransportTracers species names to GCHP HISTORY.rc.TransportTracers template by @yantosca in https://github.com/geoschem/geos-chem/pull/1840
• Prevent run-time crash if using GEOS-IT meteorolology by @lizziel in https://github.com/geoschem/geos-chem/pull/1846
• Fix GC-Classic run directory runScriptSamples symbolic link by @lizziel in https://github.com/geoschem/geos-chem/pull/1852
• Fix bug in state_chm_mod that printed line of equals signs to log from every core by @lizziel in https://github.com/geoschem/geos-chem/pull/1858
• Rename GCHP mid-run restart files in run scripts even if run crashes by @lizziel in https://github.com/geoschem/geos-chem/pull/1868
• Update the LICENSE.txt and AUTHORS.txt in geoschem/geos-chem as of July 2023 by @yantosca in https://github.com/geoschem/geos-chem/pull/1870
• Disable SpeciesConcMND output for benchmark simulations by @msulprizio in https://github.com/geoschem/geos-chem/pull/1887
• Add fixes for transport tracers simulation by @msulprizio in https://github.com/geoschem/geos-chem/pull/1890
• Skip SALAAL+SO2 and SALCAL+SO2 rxns if O3 < 1e10 molec/cm3 by @yantosca in https://github.com/geoschem/geos-chem/pull/1892
• Remove double-counting of IONO2 loss (cf #1880) by @yantosca in https://github.com/geoschem/geos-chem/pull/1893
• Restore IONO2 uptake on tropospheric sulfate aerosols by @msulprizio in https://github.com/geoschem/geos-chem/pull/1899
• Revert PR #1702 for restoring consideration of sea salt alkalinity in heterogeneous chemistry by @msulprizio in https://github.com/geoschem/geos-chem/pull/1905
• Hotfix: Exit routine INIT_PHOTOLYSIS before calling SET_AER when doing dry-run simulations by @yantosca in https://github.com/geoschem/geos-chem/pull/1920
• Seasalt alkalinity bug fix by @viral211 in https://github.com/geoschem/geos-chem/pull/1933
• Restore consideration of sea salt alkalinity to heterogenerous acid-catalyzed reactions of halogens on sea salt aerosols (now fixing typos) by @msulprizio in https://github.com/geoschem/geos-chem/pull/1952

• @viral211 made their first contribution in https://github.com/geoschem/geos-chem/pull/1623
• @toddmooring made their first contribution in https://github.com/geoschem/geos-chem/pull/1710

Full Changelog: https://github.com/geoschem/geos-chem/compare/14.1.0...14.2.0