Add two bioenergy crops (switchgrass and Miscanthus) #884
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It's exciting to see this work moving forward.
I only quickly looked at the code and am not an expert on either the crop model or the land use datasets that could drive the model. Comments here are intended to start a conversation to review the science and code from the pull request.
@danicalombardozzi, do you have suggestions for naming the grainc_to_food flux to avoid confusion with the rest of crop harvest.
@lawrencepj1 My understanding is that this would not change historical simulations, as we don't have biofuels on the surface dataset. Are there future scenarios that call for biofuel expansions in SSP/RCP scenarios?
@yanyanchengHydro your single point simulations look promising. Do you have any plans to consider global-scale simulations to get a first look at the potential climate implications of biofuels (and to test the model can run globally)? Alternatively, what happens in future scenarios at the point scale?
src/biogeochem/CNPhenologyMod.F90
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| ! Y. Cheng, cut 70% AGB for switchgrass and Miscanthus and move to grainc_to_food | ||
| if (ivt(p)==nmiscanthus .or. ivt(p)==nirrig_miscanthus .or. ivt(p)==nswitchgrass .or. ivt(p)==nirrig_switchgrass) then | ||
| leafc_to_litter(p) = t1 * leafc(p)*0.3 + cpool_to_leafc(p) | ||
| grainc_to_food(p) =grainc_to_food(p)+ t1 * leafc(p) * 0.7 |
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Calling this grainc_to_food is potentially confusing if it were summed to provide global 'food' estimates. Instead, should there be a new biofuelc flux that's added to the 1 year products pool? @danicalombardozzi do you have ideas here?
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Would you also want to make a change where currently the grain pool is being added to grainc_to_food (line 2502), instead putting that in the new biofuel flux?
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I agree that putting a product where leaf biomass is added into the grainc_to_food variable is confusing. It's probably best to keep the grainc_to_food variable similar to data available for evaluation, and UNFAO-STAT does not include biofuels in the global grain yield product. As per @wwieder and @billsacks suggestions, is it possible to change this to a new biofuelc flux, where both the grain pool and 70% of the leaf biomass are put into the biofuel flux? It will also then be easier to keep track of the total biofuel production independently of grain products. The biofuelc flux can follow the same pathway as grainc_to_food, where it ends up in the 1-year product pool.
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I also wonder: Would it make sense to introduce another crop-specific parameter for this, specifying the fraction of crop grain that goes to biomass vs. food for each crop? My main thinking is that I'd like to keep logicals on crop type out of the code as much as possible, but I also wonder if this would be a useful flexibility to have. I don't feel strongly about this, but am throwing it out as a suggestion in case others think it could be good to do.
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So @billsacks you are saying that the fraction of biomass that goes to biofuel would be a parameter that is an array of PFT. And likewise the fraction of biomass that goes to food would be a parameter that is an array of PFT. And then this statement wouldn't need to be encapsulated in an if statement but done for every crop type. That is better. If statements tend to be buggy and cause confusion.
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Yes, something like that. We could discuss details of what the parameters should be.
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Yes, this is what I was trying to get across in my earlier comment related to residue harvest. It would be great to have crop-specific parameters for this. I think the challenge will be linking the parameters to the appropriate fluxes (e.g., the grainc_to_food vs litter vs cropprod_1yr), which will also likely vary by crop type.
| @@ -1436,6 +1436,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & | |||
| use pftconMod , only : ntrp_corn, nsugarcane, ntrp_soybean, ncotton, nrice | |||
| use pftconMod , only : nirrig_trp_corn, nirrig_sugarcane, nirrig_trp_soybean | |||
| use pftconMod , only : nirrig_cotton, nirrig_rice | |||
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| ! Y. Cheng | |||
| use pftconMod , only : nmiscanthus, nirrig_miscanthus, nswitchgrass, nirrig_switchgrass | |||
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I'm assuming the new parameters are included in a parameter file that's not provided with this pull request, but are the parameter values sensible (for as much as we know about C4 grasses in CLM)?
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Yes, the parameter file I modified is clm5_params.c190829.nc. Can I also add the parameter file in the pull request?
It's exciting to see this work moving forward.
I only quickly looked at the code and am not an expert on either the crop model or the land use datasets that could drive the model. Comments here are intended to start a conversation to review the science and code from the pull request.
@danicalombardozzi, do you have suggestions for naming the grainc_to_food flux to avoid confusion with the rest of crop harvest.
@lawrencepj1 My understanding is that this would not change historical simulations, as we don't have biofuels on the surface dataset. Are there future scenarios that call for biofuel expansions in SSP/RCP scenarios?
@yanyanchengHydro your single point simulations look promising. Do you have any plans to consider global-scale simulations to get a first look at the potential climate implications of biofuels (and to test the model can run globally)? Alternatively, what happens in future scenarios at the point scale?
@wwieder Thank you Will! We have run two future simulations with biofuel expansions (SSP2-RCP4.5 and SSP5-RCP8.5) at 0.125 degree resolution over the CONUS from 2005 to 2100. I plan to present it at the LMWG meeting on March.
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@yanyanchengHydro. Yes, you can include the paramfile in the Pull Request. It can be pointed to in the bld/namelist_files/namelist_defaults_ctsm.xml file. But, there will likely be permission issues. So do you have access to cheyenne? And could you point us to the file there?
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@wwieder @ekluzek We are working on releasing the files through a public facing server at PNNL so that we don't need to worry about transferring the files. In addition to the clm5_params file, we will release the single point surfacedata, landuse, and forcing files so that the experiments are reproducible. However, if it is easier, @yanyanchengHydro can put a copy on cheyenne.
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Just to clarify what @ekluzek said in case it wasn't clear: you can change the xml file but please do not add the netcdf file to your branch in git.
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I think this is a really good idea. Crops such as sugarcane have multiple
harvested components ie sugar and bargess. Also corn is harvest for grain
but then the stova is used for cattle feed and biofuel production.
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…On Wed, Jan 29, 2020 at 2:09 PM Erik Kluzek ***@***.***> wrote:
***@***.**** commented on this pull request.
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In src/biogeochem/CNPhenologyMod.F90
<#884 (comment)>:
> frootc_to_litter(p) = t1 * frootc(p) + cpool_to_frootc(p)
+
+ ! Y. Cheng, cut 70% AGB for switchgrass and Miscanthus and move to grainc_to_food
+ if (ivt(p)==nmiscanthus .or. ivt(p)==nirrig_miscanthus .or. ivt(p)==nswitchgrass .or. ivt(p)==nirrig_switchgrass) then
+ leafc_to_litter(p) = t1 * leafc(p)*0.3 + cpool_to_leafc(p)
+ grainc_to_food(p) =grainc_to_food(p)+ t1 * leafc(p) * 0.7
So @billsacks <https://github.com/billsacks> you are saying that the
fraction of biomass that goes to biofuel would be a parameter that is an
array of PFT. And likewise the fraction of biomass that goes to food would
be a parameter that is an array of PFT. And then this statement wouldn't
need to be encapsulated in an if statement but done for every crop type.
That is better. If statements tend to be buggy and cause confusion.
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…bon during offset period
…rogen during offset period
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It's very exciting to see all these changes! I include a few additional comments for you to review, including adding the stem carbon to the biofuels pool, adding the biofuels the the one-year product pool, and adding these to the CN balance checks.
In addition, we are now asking that code developers document the new code changes in the CLM Tech Note. We will have a branch on master (hopefully by next week). If you update your branch to master after this change, you should get the Tech Note documentation and can modify it on your branch.
It's possible that we haven't caught everything, so please run a simulation to make sure that there aren't balance check or other issues. You should look at the product pools to make sure that the extra C and N from biofuels are accounted for there.
[Update (2020-03-16)] Yanyan has addressed all of the comments Danica mentioned in this review.
…bon during offset period
…rogen during offset period
…gation.rst Co-authored-by: Danica Lombardozzi <dll@ucar.edu>
…gation.rst Co-authored-by: Danica Lombardozzi <dll@ucar.edu>
…gation.rst Co-authored-by: Danica Lombardozzi <dll@ucar.edu>
…gation.rst Co-authored-by: Danica Lombardozzi <dll@ucar.edu>
…gation.rst Co-authored-by: Danica Lombardozzi <dll@ucar.edu>
…gation.rst Co-authored-by: Danica Lombardozzi <dll@ucar.edu>
….rst Co-authored-by: Danica Lombardozzi <dll@ucar.edu>
…o/CTSM into bioenergy_ctsm1.0.dev080
| Leaf C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. | ||
| Root C and N pools are routed to the litter pools in the same manner as natural vegetation. | ||
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Minor suggestion to reduce confusion:
| Leaf C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. | |
| Root C and N pools are routed to the litter pools in the same manner as natural vegetation. | |
| Biofuel crop leaf C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. | |
| Root C and N pools are routed to the litter pools in the same manner as natural vegetation. | |
| @@ -758,8 +758,8 @@ The values for both of these fields come from the LUMIP time series for each yea | |||
| In addition to the industrial fertilizer, background manure fertilizer is specified | |||
| on the parameter file by the field 'manunitro'. For perennial bioenergy crops, | |||
| little fertilizer (56kg/ha/yr) is applied to switchgrass, no fertilizer is applied to Miscanthus. | |||
| Note this set up is only based on local land management practice at the University of Illinois Energy Farm | |||
| located in Central Midwestern United States :ref:`(Cheng et al., 2019)<Chengetal2019>`. For the current CLM5BGCCROP, | |||
| Note these rates only based on local land management practice at the University of Illinois Energy Farm | |||
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| Note these rates only based on local land management practice at the University of Illinois Energy Farm | |
| Note these rates are only based on local land management practices at the University of Illinois Energy Farm |
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Thanks a lot, @yanyanchengHydro and @danicalombardozzi ! I'll do final testing on this in the next week or so, then bring it to master. @yanyanchengHydro thank you again for all of your work on this!!! |
Add two bioenergy crops (switchgrass and miscanthus) Main change is from Yanyan Cheng: adding parameters and code for two bioenergy crops, switchgrass and miscanthus. Along with this, there is a new potential flux from crop leaves and stems to the crop product pool at harvest, representing biofuel products; a new pft-specific parameter controls this flux (biofuel_harvfrac). Currently, the out-of-the-box surface datasets do not specify any area for these crops, but the new parameter file will allow them to be present if specified on the surface dataset or landuse_timeseries file. Note that this is only an option for CLM5.0, NOT for CLM4.5. (See #884 for details.) Also, some minor fixes from Bill Sacks: - Resolves #203 - Fixes creation of harvest-related variables on surface datasets created with the all_veg option - smallville, PTCLM, etc. (documented in #1019) - Resolves #930 - Makes gindex_ocn intent(inout) rather than intent(out) - Resolves #1021 - Changes SSP test to only do symlink if needed
Add two bioenergy crops (switchgrass and miscanthus) Main change is from Yanyan Cheng: adding parameters and code for two bioenergy crops, switchgrass and miscanthus. Along with this, there is a new potential flux from crop leaves and stems to the crop product pool at harvest, representing biofuel products; a new pft-specific parameter controls this flux (biofuel_harvfrac). Currently, the out-of-the-box surface datasets do not specify any area for these crops, but the new parameter file will allow them to be present if specified on the surface dataset or landuse_timeseries file. Note that this is only an option for CLM5.0, NOT for CLM4.5. (See ESCOMP#884 for details.) Also, some minor fixes from Bill Sacks: - Resolves ESCOMP#203 - Fixes creation of harvest-related variables on surface datasets created with the all_veg option - smallville, PTCLM, etc. (documented in ESCOMP#1019) - Resolves ESCOMP#930 - Makes gindex_ocn intent(inout) rather than intent(out) - Resolves ESCOMP#1021 - Changes SSP test to only do symlink if needed
Add two bioenergy crops (switchgrass and miscanthus) Main change is from Yanyan Cheng: adding parameters and code for two bioenergy crops, switchgrass and miscanthus. Along with this, there is a new potential flux from crop leaves and stems to the crop product pool at harvest, representing biofuel products; a new pft-specific parameter controls this flux (biofuel_harvfrac). Currently, the out-of-the-box surface datasets do not specify any area for these crops, but the new parameter file will allow them to be present if specified on the surface dataset or landuse_timeseries file. Note that this is only an option for CLM5.0, NOT for CLM4.5. (See ESCOMP#884 for details.) Also, some minor fixes from Bill Sacks: - Resolves ESCOMP#203 - Fixes creation of harvest-related variables on surface datasets created with the all_veg option - smallville, PTCLM, etc. (documented in ESCOMP#1019) - Resolves ESCOMP#930 - Makes gindex_ocn intent(inout) rather than intent(out) - Resolves ESCOMP#1021 - Changes SSP test to only do symlink if needed
Add two bioenergy crops (switchgrass and miscanthus) Main change is from Yanyan Cheng: adding parameters and code for two bioenergy crops, switchgrass and miscanthus. Along with this, there is a new potential flux from crop leaves and stems to the crop product pool at harvest, representing biofuel products; a new pft-specific parameter controls this flux (biofuel_harvfrac). Currently, the out-of-the-box surface datasets do not specify any area for these crops, but the new parameter file will allow them to be present if specified on the surface dataset or landuse_timeseries file. Note that this is only an option for CLM5.0, NOT for CLM4.5. (See ESCOMP#884 for details.) Also, some minor fixes from Bill Sacks: - Resolves ESCOMP#203 - Fixes creation of harvest-related variables on surface datasets created with the all_veg option - smallville, PTCLM, etc. (documented in ESCOMP#1019) - Resolves ESCOMP#930 - Makes gindex_ocn intent(inout) rather than intent(out) - Resolves ESCOMP#1021 - Changes SSP test to only do symlink if needed Conflicts: Externals.cfg bld/namelist_files/namelist_defaults_ctsm.xml bld/namelist_files/namelist_definition_ctsm.xml bld/unit_testers/build-namelist_test.pl src/biogeochem/CNBalanceCheckMod.F90 src/biogeochem/CNDriverMod.F90 src/biogeochem/CNVegetationFacade.F90 src/main/clm_driver.F90 src/main/clm_initializeMod.F90 src/main/controlMod.F90
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Hi Thanks in Advance |
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Hello, I can't comment on the external github page you pointed to, but we do have bioenergy crops represented in CTSM. I apologies that our documentation for this is not very up to date, but if start with the latest ctsm5.1 development tag on master you should get the code and parameter files you're looking for? See the quick start on the wiki of this website. Hope that helps, Will |
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Hi |
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I don't think bioenergy crops are on the release (CLM5.0) branch. You need the main CTSM5.1 development branch instead (e.g. I also don't think there is much, or any, miscanthus and switchgrass on the land use time series until you run future scenarios (SSP-RCPs) |
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Ok Thanks. Can you tell me where can I find the surface data or land use time series with miscanthus and switchgrass active for the SSPs? atleast for single point? Thanks in advance |
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If you create a case with an SSP compset you should get a land use time series with mischanthus and switchgrass active If you just want a single point case, we'd recommend using the directions posted here. You can also use following flag in subset data |
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I actually dont want to move to ctsm. I want to stick to CLM5 and icorporate biocrops there by following the suggestions you have given in this page. But I dont see any suitable input files with switchgrass or miscanthus as active, that can be used in CLM5 from here https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/surfdata_map/. |
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This PR was merged to main after we made the CLM5 release tag, and is part of the CTSM series (see above). I'd encourage you to update to CTSM5.1 to get the information you're looking for, as we don't support backwards compatibility of new developments on old code bases. It also may be more appropriate to move this discussion to the discussion forum for user support. |
Description of changes
Two bioenergy crops (switchgrass and Miscanthus) are added into the ctsm1.0.dev080 branch. There are 8 source codes are modified:
Specific notes
Contributors other than yourself, if any: Maoyi Huang @huangmy
Testing performed, if any:
The simulation results are at: /glade/scratch/ycheng/ctsm_bioenergy_inputdata. There is a README file inside the directory for what the data are.
Reference
Cheng, Y., Huang, M., Chen, M., Guan, K., Bernacchi, C., Peng, B. & Tan, Z. (2019). Parameterizing perennial bioenergy crops in Version 5 of the Community Land Model Based on Site‐Level Observations in the Central Midwestern United States. Journal of Advances in Modeling Earth Systems, 2(2013), 1–24. https://doi.org/10.1029/2019MS001719
@billsacks @dlawrenncar @danicalombardozzi @wwieder @ekluzek @lawrencepj1
NOTE: Be sure to check your Coding style against the standard:
https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines