geoschem/geos-chem: GEOS-Chem 14.2.0

<p>Release date: 05 Oct 2023</p> What's Changed <ul> <li>Bug fix: restore consideration of sea salt alkalinity to heterogenerous acid-catalyzed reactions of halogens on sea salt aerosols by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1548">https://github.com/geoschem/geos-chem/pull/1548</a></li> <li>Consolidate existing integration test scripts (slurm, lsf, interactive); Add LSF capability by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1565">https://github.com/geoschem/geos-chem/pull/1565</a></li> <li>Integration/parallelization test scripts now place test scripts & artifacts into subdirectories of the root test folder by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1636">https://github.com/geoschem/geos-chem/pull/1636</a></li> <li>Add reminders to compile with CMake options to createRunDir.sh scripts by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1638">https://github.com/geoschem/geos-chem/pull/1638</a></li> <li>Convert log file prints to debug prints by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1549">https://github.com/geoschem/geos-chem/pull/1549</a></li> <li>Fix bug where writing species metadata yaml file always attempted by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1644">https://github.com/geoschem/geos-chem/pull/1644</a></li> <li>Remove NcdfUtil/perl folder by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1567">https://github.com/geoschem/geos-chem/pull/1567</a></li> <li>Reset SPC_ time entry from EFYO to CYS for integration tests and fullchem_benchmark runs by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1647">https://github.com/geoschem/geos-chem/pull/1647</a></li> <li>Remove LWI from carbon simulation run directories by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1643">https://github.com/geoschem/geos-chem/pull/1643</a></li> <li>GEOS-only updates from Christoph Keller by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1653">https://github.com/geoschem/geos-chem/pull/1653</a></li> <li>Update rundir configuration files to point to corrected NEI day-of-week scale factors (Closes #1608) by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1633">https://github.com/geoschem/geos-chem/pull/1633</a></li> <li>Add entries for GFAS methanol to HEMCO_Config.rc templates by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1632">https://github.com/geoschem/geos-chem/pull/1632</a></li> <li>Archive State_Chm%H2SO4_PRDR for production rate of H2SO4 (mol/mol) for CESM-GC by @jimmielin in <a href="https://github.com/geoschem/geos-chem/pull/1624">https://github.com/geoschem/geos-chem/pull/1624</a></li> <li>Apply work-around for GFAS pFe bug in GC-Classic and GCHP by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1621">https://github.com/geoschem/geos-chem/pull/1621</a></li> <li>Simplify Github issue and pull request templates by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1650">https://github.com/geoschem/geos-chem/pull/1650</a></li> <li>Avoid compiler warning and compilation restart for KPP/fullchem/gckpp_Jacobian.F90 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1657">https://github.com/geoschem/geos-chem/pull/1657</a></li> <li>Change HEMCO time cycle flag in benchmark rundir & integration tests for 14.1.1 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1656">https://github.com/geoschem/geos-chem/pull/1656</a></li> <li>Removal of module variables from ucx_mod by @jimmielin in <a href="https://github.com/geoschem/geos-chem/pull/1583">https://github.com/geoschem/geos-chem/pull/1583</a></li> <li>Fix incorrect comparison in GET_IJ routine; Fix leftover issues from PR #1656 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1663">https://github.com/geoschem/geos-chem/pull/1663</a></li> <li>Fix bug in RRTMG optic diagnostics (AOD, SSA, Asym) by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1669">https://github.com/geoschem/geos-chem/pull/1669</a></li> <li>Ask users for PI at registration; abstract user registration code into a single script by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1674">https://github.com/geoschem/geos-chem/pull/1674</a></li> <li>Move GC-Classic run scripts to operational_examples directory by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1677">https://github.com/geoschem/geos-chem/pull/1677</a></li> <li>Fix several issues with GitHub issue and PR templates by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1679">https://github.com/geoschem/geos-chem/pull/1679</a></li> <li>Remove X-HRS printout from GEOS-Chem log file by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1678">https://github.com/geoschem/geos-chem/pull/1678</a></li> <li>Remove references to Compute Canada from data download scripts by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1681">https://github.com/geoschem/geos-chem/pull/1681</a></li> <li>Add lumped furans to chemistry and biomass burning emissions by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1642">https://github.com/geoschem/geos-chem/pull/1642</a></li> <li>Abstract fullchem mechanism history into CHANGELOG_fullchem.md - closes #1689 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1690">https://github.com/geoschem/geos-chem/pull/1690</a></li> <li>Fix typo in GCClassic/createRunDir.sh preventing benchmark run script from being copied to run directory by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1694">https://github.com/geoschem/geos-chem/pull/1694</a></li> <li>Prevent divide by zero in sulfur chemistry by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1698">https://github.com/geoschem/geos-chem/pull/1698</a></li> <li>Turn on sea salt debromination for full-chemistry simulations by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1703">https://github.com/geoschem/geos-chem/pull/1703</a></li> <li>Now use consistent behavior when the first call to "Integrate" fails by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1609">https://github.com/geoschem/geos-chem/pull/1609</a></li> <li>Reset "EFY" to "CYS" for nested boundary conditions in GCClassic integration & parallel tests by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1706">https://github.com/geoschem/geos-chem/pull/1706</a></li> <li>Restore Iy sink reactions and rebuild fullchem mechanism with KPP 3.0.0 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1620">https://github.com/geoschem/geos-chem/pull/1620</a></li> <li>Restore consideration of sea salt alkalinity to heterogenerous acid-catalyzed reactions of halogens on sea salt aerosols by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1702">https://github.com/geoschem/geos-chem/pull/1702</a></li> <li>Add S(IV) + HOBr and S(IV) + HOCl to the fullchem mechanism (Closes #1627) by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1630">https://github.com/geoschem/geos-chem/pull/1630</a></li> <li>Update entrainmment-limited kinetics in clouds by @cdholmes in <a href="https://github.com/geoschem/geos-chem/pull/1292">https://github.com/geoschem/geos-chem/pull/1292</a></li> <li>Include nitrate aerosol photolysis in the troposphere by @viral211 in <a href="https://github.com/geoschem/geos-chem/pull/1623">https://github.com/geoschem/geos-chem/pull/1623</a></li> <li>Update HEMCO_Config.rc and ExtData.rc template files to read GFED4 data thru 2022 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1709">https://github.com/geoschem/geos-chem/pull/1709</a></li> <li>Add lightning climatology option to HEMCO_Config.rc by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1628">https://github.com/geoschem/geos-chem/pull/1628</a></li> <li>Restore vertical emission distributions to CEDS energy and industry emissions by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1712">https://github.com/geoschem/geos-chem/pull/1712</a></li> <li>Add fix for CEDS energy and industry emissions to distribute vertically by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1730">https://github.com/geoschem/geos-chem/pull/1730</a></li> <li>GCHP bug fixes and run directory updates by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1724">https://github.com/geoschem/geos-chem/pull/1724</a></li> <li>Add run configuration files for WRF-GC by @jimmielin in <a href="https://github.com/geoschem/geos-chem/pull/1692">https://github.com/geoschem/geos-chem/pull/1692</a></li> <li>Fix bug renaming midrun checkpoint files by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1737">https://github.com/geoschem/geos-chem/pull/1737</a></li> <li>Fix computation of planeCount for Harvard Cannon GCHP run scripts and integration test scripts by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1686">https://github.com/geoschem/geos-chem/pull/1686</a></li> <li>Restructure photolysis by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1733">https://github.com/geoschem/geos-chem/pull/1733</a></li> <li>Update text displayed at user registration during rundir creation by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1732">https://github.com/geoschem/geos-chem/pull/1732</a></li> <li>Remove array temporaries in carbon_mod.F90 and seasalt_mod.F90 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1729">https://github.com/geoschem/geos-chem/pull/1729</a></li> <li>Modify HEMCO_Config.rc templates to read HEMCO restart files from the rundir "Restarts/" subdirectory by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1718">https://github.com/geoschem/geos-chem/pull/1718</a></li> <li>Prevent repeated printout of concs, rxn rates when KPP fails twice by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1749">https://github.com/geoschem/geos-chem/pull/1749</a></li> <li>Fix bug in photolysis off option by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1750">https://github.com/geoschem/geos-chem/pull/1750</a></li> <li>Fix bug in HOBr uptake rate calculation (closes #1746) by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1751">https://github.com/geoschem/geos-chem/pull/1751</a></li> <li>Set CO2 concentration to 421 ppm in fullchem simulations -- fixes CO2 error norm for KPP by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1731">https://github.com/geoschem/geos-chem/pull/1731</a></li> <li>Add GFED4 climatology emissions as an option in HEMCO_Config.rc by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1758">https://github.com/geoschem/geos-chem/pull/1758</a></li> <li>Update global_ch4_mod.F90 to correct bug that incorrectly selects troposphere-stratosphere boundary by @toddmooring in <a href="https://github.com/geoschem/geos-chem/pull/1710">https://github.com/geoschem/geos-chem/pull/1710</a></li> <li>Update global anthropogenic CH4 emissions to EDGARv7.0 by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1773">https://github.com/geoschem/geos-chem/pull/1773</a></li> <li>Remove operator splitting in CH4 simulation that biases diagnostics (closes #1738) by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1740">https://github.com/geoschem/geos-chem/pull/1740</a></li> <li>Update CH4 simulation to use loss frequencies from GCClassic 14.0.0 10-year benchmark by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1776">https://github.com/geoschem/geos-chem/pull/1776</a></li> <li>Update README.md and AUTHORS.txt for 14.2.0 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1774">https://github.com/geoschem/geos-chem/pull/1774</a></li> <li>Update GCHP check for python and bc libs to prevent error checking fail by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1777">https://github.com/geoschem/geos-chem/pull/1777</a></li> <li>Add modifications to sea salt chemistry in order to avoid KPP integration errors by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1779">https://github.com/geoschem/geos-chem/pull/1779</a></li> <li>Add CH4 emissions from hydroelectric reservoirs by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1784">https://github.com/geoschem/geos-chem/pull/1784</a></li> <li>Add RxnConst diagnostic for archiving reaction rate constants by @jimmielin in <a href="https://github.com/geoschem/geos-chem/pull/1728">https://github.com/geoschem/geos-chem/pull/1728</a></li> <li>Fix GCHP time_mod start and elapsed times by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1781">https://github.com/geoschem/geos-chem/pull/1781</a></li> <li>Update partitions and env files in Harvard Cannon operational examples by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1811">https://github.com/geoschem/geos-chem/pull/1811</a></li> <li>Change relative tolerance back to 0.5e-2 to address model slowdown by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1815">https://github.com/geoschem/geos-chem/pull/1815</a></li> <li>Allow the use of OFFLINE_SEASALT for seasalt alkalinity, Cl, and Br in GEOS-Chem within CESM by @jimmielin in <a href="https://github.com/geoschem/geos-chem/pull/1804">https://github.com/geoschem/geos-chem/pull/1804</a></li> <li>Update transport tracer simulation for consistency with GMAO's tracer gridded component by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1816">https://github.com/geoschem/geos-chem/pull/1816</a></li> <li>Bug fixes for GEOS-only runs by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1842">https://github.com/geoschem/geos-chem/pull/1842</a></li> <li>Add correct TransportTracers species names to GCHP HISTORY.rc.TransportTracers template by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1840">https://github.com/geoschem/geos-chem/pull/1840</a></li> <li>Prevent run-time crash if using GEOS-IT meteorolology by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1846">https://github.com/geoschem/geos-chem/pull/1846</a></li> <li>Fix GC-Classic run directory runScriptSamples symbolic link by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1852">https://github.com/geoschem/geos-chem/pull/1852</a></li> <li>Fix bug in state_chm_mod that printed line of equals signs to log from every core by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1858">https://github.com/geoschem/geos-chem/pull/1858</a></li> <li>Rename GCHP mid-run restart files in run scripts even if run crashes by @lizziel in <a href="https://github.com/geoschem/geos-chem/pull/1868">https://github.com/geoschem/geos-chem/pull/1868</a></li> <li>Update the LICENSE.txt and AUTHORS.txt in geoschem/geos-chem as of July 2023 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1870">https://github.com/geoschem/geos-chem/pull/1870</a></li> <li>Disable SpeciesConcMND output for benchmark simulations by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1887">https://github.com/geoschem/geos-chem/pull/1887</a></li> <li>Add fixes for transport tracers simulation by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1890">https://github.com/geoschem/geos-chem/pull/1890</a></li> <li>Skip SALAAL+SO2 and SALCAL+SO2 rxns if O3 < 1e10 molec/cm3 by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1892">https://github.com/geoschem/geos-chem/pull/1892</a></li> <li>Remove double-counting of IONO2 loss (cf #1880) by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1893">https://github.com/geoschem/geos-chem/pull/1893</a></li> <li>Restore IONO2 uptake on tropospheric sulfate aerosols by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1899">https://github.com/geoschem/geos-chem/pull/1899</a></li> <li>Revert PR #1702 for restoring consideration of sea salt alkalinity in heterogeneous chemistry by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1905">https://github.com/geoschem/geos-chem/pull/1905</a></li> <li>Hotfix: Exit routine INIT_PHOTOLYSIS before calling SET_AER when doing dry-run simulations by @yantosca in <a href="https://github.com/geoschem/geos-chem/pull/1920">https://github.com/geoschem/geos-chem/pull/1920</a></li> <li>Seasalt alkalinity bug fix by @viral211 in <a href="https://github.com/geoschem/geos-chem/pull/1933">https://github.com/geoschem/geos-chem/pull/1933</a></li> <li>Restore consideration of sea salt alkalinity to heterogenerous acid-catalyzed reactions of halogens on sea salt aerosols (now fixing typos) by @msulprizio in <a href="https://github.com/geoschem/geos-chem/pull/1952">https://github.com/geoschem/geos-chem/pull/1952</a></li> </ul> New Contributors <ul> <li>@viral211 made their first contribution in <a href="https://github.com/geoschem/geos-chem/pull/1623">https://github.com/geoschem/geos-chem/pull/1623</a></li> <li>@toddmooring made their first contribution in <a href="https://github.com/geoschem/geos-chem/pull/1710">https://github.com/geoschem/geos-chem/pull/1710</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/geoschem/geos-chem/compare/14.1.0...14.2.0">https://github.com/geoschem/geos-chem/compare/14.1.0...14.2.0</a></p&gt