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Trim trailing whitespace in "What's new in CTSM 5.3."
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samsrabin committed Jan 27, 2025
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### New features

* `manage_externals` replaced by [`git-fleximod`](https://github.com/ESMCI/git-fleximod/blob/main/README.md). ([PR \#2559](https://github.com/ESCOMP/CTSM/pull/2559))
* No longer runs the 0th time step in first segment of startup and hybrid runs; branch and continue runs never had this 0th time step. ([PR \#2084](https://github.com/ESCOMP/CTSM/pull/2084))
* New CN Matrix method speeds up spinup for the BGC model. ([PR \#640](https://github.com/ESCOMP/CTSM/pull/640); [Liao et al. 2023](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023MS003625)).
* New `Leung_2023` dust emissions. ([PR \#1897](https://github.com/ESCOMP/CTSM/pull/1897); [Leung et al 2023](https://doi.org/10.5194/acp-23-6487-2023), [Leung et al. 2024](https://doi.org/10.5194/acp-24-2287-2024))
* Explicit air conditioning for the urban model. ([PR \#2275](https://github.com/ESCOMP/CTSM/pull/2275); [Li et al. 2024](https://agupubs.onlinelibrary.wiley.com/share/NY4AYPREB8Y8BUDP7DXD?target=10.1029/2023MS004107))
* FATES compsets can now be run with transient land use; off by default. ([PR \#2507](https://github.com/ESCOMP/CTSM/pull/2507))
* `manage_externals` replaced by [`git-fleximod`](https://github.com/ESMCI/git-fleximod/blob/main/README.md). ([PR \#2559](https://github.com/ESCOMP/CTSM/pull/2559))
* No longer runs the 0th time step in first segment of startup and hybrid runs; branch and continue runs never had this 0th time step. ([PR \#2084](https://github.com/ESCOMP/CTSM/pull/2084))
* New CN Matrix method speeds up spinup for the BGC model. ([PR \#640](https://github.com/ESCOMP/CTSM/pull/640); [Liao et al. 2023](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023MS003625)).
* New `Leung_2023` dust emissions. ([PR \#1897](https://github.com/ESCOMP/CTSM/pull/1897); [Leung et al 2023](https://doi.org/10.5194/acp-23-6487-2023), [Leung et al. 2024](https://doi.org/10.5194/acp-24-2287-2024))
* Explicit air conditioning for the urban model. ([PR \#2275](https://github.com/ESCOMP/CTSM/pull/2275); [Li et al. 2024](https://agupubs.onlinelibrary.wiley.com/share/NY4AYPREB8Y8BUDP7DXD?target=10.1029/2023MS004107))
* FATES compsets can now be run with transient land use; off by default. ([PR \#2507](https://github.com/ESCOMP/CTSM/pull/2507))
* Ability to handle CAM7 in `LND_TUNING_MODE`. ([PR \#2632](https://github.com/ESCOMP/CTSM/pull/2632))

### Answer changes

Changes to defaults for `clm6_0` physics:

* Urban explicit A/C turned on (links above).
* Snow thermal conductivity method is now `Sturm1997`. ([PR \#2348](https://github.com/ESCOMP/CTSM/pull/2348); see also [discussion \#1960](https://github.com/ESCOMP/CTSM/discussions/1960))
* New initial conditions files for f09 ("1-degree" 1850, 2000), f19 (“2-degree” 1850), and ne30 (1850, 1979, 2000) resolutions.
* New crop calendars. ([PR \#2664](https://github.com/ESCOMP/CTSM/pull/2664); informed by [Rabin et al., 2023](https://gmd.copernicus.org/articles/16/7253/2023/gmd-16-7253-2023.html))
* Dust emissions method is now `Leung_2023` (links above).
* Excess ice is turned on. ([PR \#1787](https://github.com/ESCOMP/CTSM/pull/1787))
* Updates to MEGAN for BVOCs. ([PR \#2588](https://github.com/ESCOMP/CTSM/pull/2588))
* Urban explicit A/C turned on (links above).
* Snow thermal conductivity method is now `Sturm1997`. ([PR \#2348](https://github.com/ESCOMP/CTSM/pull/2348); see also [discussion \#1960](https://github.com/ESCOMP/CTSM/discussions/1960))
* New initial conditions files for f09 ("1-degree" 1850, 2000), f19 (“2-degree” 1850), and ne30 (1850, 1979, 2000) resolutions.
* New crop calendars. ([PR \#2664](https://github.com/ESCOMP/CTSM/pull/2664); informed by [Rabin et al., 2023](https://gmd.copernicus.org/articles/16/7253/2023/gmd-16-7253-2023.html))
* Dust emissions method is now `Leung_2023` (links above).
* Excess ice is turned on. ([PR \#1787](https://github.com/ESCOMP/CTSM/pull/1787))
* Updates to MEGAN for BVOCs. ([PR \#2588](https://github.com/ESCOMP/CTSM/pull/2588))
* New BGC fire method `li2024crujra`: Avoid crop fires during growing season; allow lightning ignitions in tropical closed forests; add effect of landscape fragmentation on ignitions and duration; recalibrate against GFED5 burned area and with CRU-JRA climate. ([PR \#2684](https://github.com/ESCOMP/CTSM/pull/2684), [PR \#2711](https://github.com/ESCOMP/CTSM/pull/2711), [PR \#2715](https://github.com/ESCOMP/CTSM/issues/2715))

Changes for all physics versions:

* Parameters updated for CRU-JRA forcing: PPE-based modifications were made to the parameters `leafcn`, `slatop`, `froot_leaf`, `medlynslope`, and `kmax`. Lowers LAI and biomass in boreal and tropical forests, without reducing latent heat in the tropics. Affected PFTs: NET temperate, NET boreal, BET tropical, BDS boreal, C3 arctic grass. ([PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
* FATES parameter file updated (see section below).
* Pass active glacier (CISM) runoff directly to river model (MOSART) ([MOSART PR \#94](https://github.com/ESCOMP/MOSART/pull/94))
* New surface datasets and landuse timeseries files (see section below).
* Parameters updated for CRU-JRA forcing: PPE-based modifications were made to the parameters `leafcn`, `slatop`, `froot_leaf`, `medlynslope`, and `kmax`. Lowers LAI and biomass in boreal and tropical forests, without reducing latent heat in the tropics. Affected PFTs: NET temperate, NET boreal, BET tropical, BDS boreal, C3 arctic grass. ([PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
* FATES parameter file updated (see section below).
* Pass active glacier (CISM) runoff directly to river model (MOSART) ([MOSART PR \#94](https://github.com/ESCOMP/MOSART/pull/94))
* New surface datasets and landuse timeseries files (see section below).
* CNMatrix is new default spinup method (links above).

### Heads up

* Small glacier changes mean that you can’t use a 5.3 surface dataset with pre-5.3 code and vice versa anymore. (Merged with [PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
* Updates the definition of history variable “time” from *end* of `time_bounds` to *middle* of `time_bounds`. ([PR \#2838](https://github.com/ESCOMP/CTSM/pull/2838); see section below)
* Small glacier changes mean that you can’t use a 5.3 surface dataset with pre-5.3 code and vice versa anymore. (Merged with [PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))
* Updates the definition of history variable “time” from *end* of `time_bounds` to *middle* of `time_bounds`. ([PR \#2838](https://github.com/ESCOMP/CTSM/pull/2838); see section below)
* Standardizes history variable attributes and a history dimension name. ([PR \#2052](https://github.com/ESCOMP/CTSM/pull/2052); see section below)

##
##

## Additional detail

Expand All @@ -55,24 +55,24 @@ The history dimension name `hist_interval` (of output variable `time_bounds`) is

### New surface datasets and landuse timeseries files ([PR \#2500](https://github.com/ESCOMP/CTSM/pull/2500))

* Transient landuse timeseries files going back to 1700 now possible (and made for f09).
* Fix an important bug on soil fields that was there since `ctsm5.2.0`. This has the side effect of `mksurfdata_esmf` now giving identical answers with a change in number of processors, as it should. ([Issue \#2744](https://github.com/ESCOMP/CTSM/issues/2744))
* Surface datasets now provided for the `ne0np4.POLARCAP.ne30x4` grid. ([PR \#2716](https://github.com/ESCOMP/CTSM/pull/2716), [issue \#2720](https://github.com/ESCOMP/CTSM/issues/2720))
* Surface datasets now have their version number embedded to prevent mismatch of surface dataset and CTSM version. ([Issue \#2723](https://github.com/ESCOMP/CTSM/issues/2723))
* Remove outdated hydrology `VIC` (Variable Infiltration Capacity Hydrology model) fields from surface datasets.
* Updates to input datasets:
* PFT/LAI/soil-color raw datasets; now from the TRENDY2024 timeseries that ends in 2023. (Issues [\#2570](https://github.com/ESCOMP/CTSM/issues/2570) and [\#2452](https://github.com/ESCOMP/CTSM/issues/2452))
* Two fire datasets: crop fire peak month and peatland fraction. (Issue [\#2618](https://github.com/ESCOMP/CTSM/issues/2618))
* Transient landuse timeseries files going back to 1700 now possible (and made for f09).
* Fix an important bug on soil fields that was there since `ctsm5.2.0`. This has the side effect of `mksurfdata_esmf` now giving identical answers with a change in number of processors, as it should. ([Issue \#2744](https://github.com/ESCOMP/CTSM/issues/2744))
* Surface datasets now provided for the `ne0np4.POLARCAP.ne30x4` grid. ([PR \#2716](https://github.com/ESCOMP/CTSM/pull/2716), [issue \#2720](https://github.com/ESCOMP/CTSM/issues/2720))
* Surface datasets now have their version number embedded to prevent mismatch of surface dataset and CTSM version. ([Issue \#2723](https://github.com/ESCOMP/CTSM/issues/2723))
* Remove outdated hydrology `VIC` (Variable Infiltration Capacity Hydrology model) fields from surface datasets.
* Updates to input datasets:
* PFT/LAI/soil-color raw datasets; now from the TRENDY2024 timeseries that ends in 2023. (Issues [\#2570](https://github.com/ESCOMP/CTSM/issues/2570) and [\#2452](https://github.com/ESCOMP/CTSM/issues/2452))
* Two fire datasets: crop fire peak month and peatland fraction. (Issue [\#2618](https://github.com/ESCOMP/CTSM/issues/2618))
* Glacier behavior dataset (related to how non-Greenland glaciers are handled). (Issue [\#423](https://github.com/ESCOMP/CTSM/issues/423))

### Changes to FATES parameter file

* [PR \#2507](https://github.com/ESCOMP/CTSM/pull/2507) ([ctsm5.2.013](https://github.com/ESCOMP/CTSM/releases/tag/ctsm5.2.013)) / [FATES PR \#1116](https://github.com/NGEET/fates/pull/1116) ([sci.1.77.1\_api.36.0.0](https://github.com/NGEET/fates/releases/tag/sci.1.77.0_api.36.0.0))
* Adds new parameters for new land use harvest mode and land use by PFT capabilities
* [PR \#2700](https://github.com/ESCOMP/CTSM/pull/2700) ([ctsm5.3.003](https://github.com/ESCOMP/CTSM/releases/tag/ctsm5.3.003)) / [FATES PR \#1255](https://github.com/NGEET/fates/pull/1255) ([sci.1.78.3\_api.36.1.0](https://github.com/NGEET/fates/releases/tag/sci.1.78.3_api.36.1.0))
* Adds two arctic shrub PFTs, increasing the number of default PFTs to 14 and update arctic grass parameters ([FATES PR\#1236](https://github.com/NGEET/fates/pull/1236))
* Splits `fates_turnover_leaf` parameter into canopy and understory specific turnover rates and provides new values for both ([FATES PR\#1136](https://github.com/NGEET/fates/pull/1136))
* Updates grass allometry parameters ([FATES PR\#1206](https://github.com/NGEET/fates/pull/1206))
* [PR \#2507](https://github.com/ESCOMP/CTSM/pull/2507) ([ctsm5.2.013](https://github.com/ESCOMP/CTSM/releases/tag/ctsm5.2.013)) / [FATES PR \#1116](https://github.com/NGEET/fates/pull/1116) ([sci.1.77.1\_api.36.0.0](https://github.com/NGEET/fates/releases/tag/sci.1.77.0_api.36.0.0))
* Adds new parameters for new land use harvest mode and land use by PFT capabilities
* [PR \#2700](https://github.com/ESCOMP/CTSM/pull/2700) ([ctsm5.3.003](https://github.com/ESCOMP/CTSM/releases/tag/ctsm5.3.003)) / [FATES PR \#1255](https://github.com/NGEET/fates/pull/1255) ([sci.1.78.3\_api.36.1.0](https://github.com/NGEET/fates/releases/tag/sci.1.78.3_api.36.1.0))
* Adds two arctic shrub PFTs, increasing the number of default PFTs to 14 and update arctic grass parameters ([FATES PR\#1236](https://github.com/NGEET/fates/pull/1236))
* Splits `fates_turnover_leaf` parameter into canopy and understory specific turnover rates and provides new values for both ([FATES PR\#1136](https://github.com/NGEET/fates/pull/1136))
* Updates grass allometry parameters ([FATES PR\#1206](https://github.com/NGEET/fates/pull/1206))
* Changes the prescribe nutrient uptake defaults from 1 to 0 for all PFTs (only relevant to ELM-FATES)

### Changes to rpointer files
Expand All @@ -85,14 +85,14 @@ Now, with this update, the `lnd`, `cpl`, and `atm` rpointer files have the simul

Old rpointer filenames:

* `rpointer.atm`
* `rpointer.cpl`
* `rpointer.atm`
* `rpointer.cpl`
* `rpointer.lnd`

New names:

* `rpointer.atm.YYYY-MM-DD-SSSSS`
* `rpointer.cpl.YYYY-MM-DD-SSSSS`
* `rpointer.atm.YYYY-MM-DD-SSSSS`
* `rpointer.cpl.YYYY-MM-DD-SSSSS`
* `rpointer.lnd.YYYY-MM-DD-SSSSS`

Where `YYYY-MM-DD-SSSSS` is the year, month, day, and seconds into the day for the simulation timestamp. For example, `rpointer.lnd.2000-01-01-00000` for a rpointer file for starting at midnight (beginning of the day) on January 1st, 2000\.
Expand All @@ -101,8 +101,8 @@ Note that this is backwards-compatible, so for all the components you can use ei

## Simulations supporting this release

- f19 `Clm60Bgc` 16pft: [https://github.com/NCAR/LMWG\_dev/issues/70](https://github.com/NCAR/LMWG_dev/issues/70)
- f09 with `Clm60BgcCrop`: [https://github.com/NCAR/LMWG\_dev/issues/69](https://github.com/NCAR/LMWG_dev/issues/69)
- f19 `Clm60Bgc` 16pft: [https://github.com/NCAR/LMWG\_dev/issues/70](https://github.com/NCAR/LMWG_dev/issues/70)
- f09 with `Clm60BgcCrop`: [https://github.com/NCAR/LMWG\_dev/issues/69](https://github.com/NCAR/LMWG_dev/issues/69)
- ne30 with `Clm60BgcCrop`: [https://github.com/NCAR/LMWG\_dev/issues/68](https://github.com/NCAR/LMWG_dev/issues/68)

Note: Dust emissions in CTSM 5.3 will be different from the above simulations because of a tuning update that came in after those.

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