DOI: 10.5061/dryad.pvmcvdntz
title: Community Earth System Model (CESM) simulations disentangling CO2 effects - PHYS (2 of 4)

description: It is widely recognized that water availability influences plant growth,
 but plants also exert a strong control on the water cycle. Plant
 transpiration constitutes about 60% of the total flux of water from the
 land to the atmosphere, and changes in vegetation coverage and ecosystem
 functioning can substantially alter land surface water and energy
 fluxes. A growing body of research has found that plant responses
 to increasing atmospheric CO2 can modify the water cycle. Rising CO2
 concentrations at the land surface directly alter plant water use and land
 evapotranspiration, which previous studies have found can drive
 global-scale changes in precipitation, runoff, and streamflow.
 Concomitantly, the radiative effects of increasing CO2  modify
 atmospheric variables that affect plant functioning, such as temperature,
 vapor pressure deficit, and precipitation. Plant responses to these
 radiatively driven climate changes can further influence the hydrologic
 cycle. While multiple studies have found that plant responses to the
 physiological and radiative effects of CO2 can drive hydrologic impacts,
 there is limited consensus on the magnitude of plant responses’ overall
 influence. Significant uncertainty surrounds how plants respond to
 increasing CO2 and changing climate, as well as how a given plant change
 can impact the hydrologic cycle. This overall uncertainty is often
 discussed (e.g. IPCC 2021), but we still lack a systematic quantification
 of which processes are contributing the most to uncertainty in the
 hydrologic impact of plant responses to CO2. Ultimately,
 disentangling this uncertainty requires analysis of plants’ influence on
 the coupled biosphere-atmosphere system, because plant responses to
 increasing CO2 generate atmospheric feedbacks which can further modify
 land surface hydrology. In order to improve understanding of how
 plant responses to increasing atmospheric CO2 feed back on the global
 hydrologic cycle, we ran model experiments in the Community Earth System
 Model to systematically quantify the separate impacts of leaf-level and
 plant-level changes to different atmospheric drivers.
description: We ran simulations in a partially coupled configuration of the
 Community Earth System Model version 2 (CESM2; git tag: cesm2_3_beta03)
 using an active atmosphere (CAM6; git tag cam6_3_017), an active land
 model (CLM5; git tag branch_tags/PPE.n08_ctsm5.1.dev030), and a slab ocean
 which is based on q-fluxes from preindustrial simulations of the full
 dynamic ocean model. The land was initialized with the spun-up land state
 from the default model parameterization which includes the carbon content
 of soil and vegetation pools. We ran a suite of model
 experiments to disentangle the physiological and radiative effects of
 CO<sub>2</sub>, and to identify how leaf area responses
 modulate those effects. The model output from this suite of simulations is
 divided among four repositories which isolate the physiological (PHYS),
 radiative (RAD), and full physiological+radiative (FULL) effects of
 CO<sub>2 </sub>compared to the preindustrial control (PI). All
 simulations branched from a preindustrial control simulation at year 41.
 Simulations in the PHYS, RAD, and FULL repositories were run for 160
 additional years (i.e., ending at year 200), including spin up. This
 repository contains model output from simulations to quantify how leaf
 area responses influence the physiological effects of
 CO<sub>2.</sub> We ran two simulations: one where the leaf
 area was held fixed at preindustrial levels, and one where the leaf area
 was dynamically calculated by the model. Both simulations were equilibrium
 concentration-driven experiments where both the atmosphere experienced
 preindustrial CO<sub>2</sub> (284.7 ppm) and the land
 experienced a doubling of CO<sub>2</sub> (569.4 ppm). The spin
 up period is included in this model output.
description: # CESM simulations disentangling CO2 effects - PHYS
 [https://doi.org/10.5061/dryad.pvmcvdntz](https://doi.org/10.5061/dryad.pvmcvdntz) ## Related datasets We ran a suite of model experiments to disentangle the physiological and radiative effects of CO2, and to identify how leaf area responses modulate those effects. The model output from this suite of simulations is divided among four repositories which isolate the physiological (PHYS), radiative (RAD), and full physiological+radiative (FULL) effects of CO2 compared to the preindustrial control (PI). This repository contains model output from the physiological (PHYS) simulations. ## Description of the data and file structure This dataset is organized into two zipped files, each of which contains model output from a different simulation: `coupled_DEFmedslope_2xCO2_BGConly_03.tar.gz` and `coupled_SP_DEFmedslope_2xCO2_FULL_03.tar.gz`. Each of these files contain model output from simulations where the land experiences a doubling of CO2 and the atmosphere experiences preindustrial CO2 concentrations. `coupled_DEFmedslope_2xCO2_BGConly_03` was run with dynamic leaf area (i.e., BGC mode) and `coupled_SP_DEFmedslope_2xCO2_BGConly_05` was run with fixed leaf area (i.e., SP mode, where the fixed leaf area was determined from the preindustrial modeled leaf area climatology). Within each of these zipped files, there are four folders: `lnd`, `atm`, `rest`, and `run_info`. `lnd` and `atm` contain model output in the form of postprocessed netcdf files from the land model and atmosphere model, respectively, where each file is a timeseries for a single variable. Each variable is described in the netcdf metadata. `rest` contains the restart file from the end of the simulation, which can be used to continue the simulation for additional years, also in the form of netcdf files. Netcdf files can be opened and viewed using the [xarray python package](https://docs.xarray.dev/en/stable/index.html), HDFview, or Panoply. `run_info` documents how simulations were configured in more detail, and is likely only relevant to people already familiar with running the Community Earth System Model (CESM). The [CESM user guide](https://escomp.github.io/CESM/versions/cesm2.2/html/introduction.html) describes how to run CESM and how different inputs (e.g., namelist settings) are used when running the model. `run_info` contains the shell script used to generate the simulation (e.g., `coupled_BGC_DEFmedslope_2xCO2_BGConly.sh`), the `namelists` directory which contains files that document how each simulation was configured, and the `SourceMods` directory which contains Fortran source files which document changes to the CESM code. All the files in `run_info` can be opened in a text editor.  ``` ├── coupled_DEFmedslope_2xCO2_BGConly_03.tar.gz │ ├── atm │ │ └── proc │ │ └── tseries │ │ ├── day_1 │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h1.PRECT.00410101-00510101.nc │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h1.PRECT.00510102-00610101.nc │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h1.PRECT.00610102-00710101.nc │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h1.PRECT.00710102-00810101.nc │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h1.PRECT.00810102-00910101.nc │ │ │ └── ...(48 files total) │ │ └── month_1 │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h0.CLDHGH.004101-009012.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h0.CLDHGH.009101-014012.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h0.CLDHGH.014101-019012.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h0.CLDHGH.019101-020012.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h0.CLDLOW.004101-009012.nc │ │ └── ... (244 files total) │ ├── lnd │ │ └── proc │ │ └── tseries │ │ ├── day_1 │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h2.BTRAN2.00410101-00910101.nc │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h2.BTRAN2.00910102-01410101.nc │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h2.BTRAN2.01410102-01910101.nc │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h2.BTRAN2.01910102-02001231.nc │ │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h2.EFLX_LH_TOT.00410101-00910101.nc │ │ │ └── ... (144 files total) │ │ └── month_1 │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h0.ACTUAL_IMMOB.004101-009012.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h0.ACTUAL_IMMOB.009101-014012.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h0.ACTUAL_IMMOB.014101-019012.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h0.ACTUAL_IMMOB.019101-020012.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.clm2.h0.AGNPP.004101-009012.nc │ │ └── ... (1896 files total) │ ├── rest │ │ └── 0201-01-01-00000 │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h0.0200-12.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.h1.0200-01-02-00000.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.i.0201-01-01-00000.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.r.0201-01-01-00000.nc │ │ ├── coupled_DEFmedslope_2xCO2_BGConly_03.cam.rs.0201-01-01-00000.nc │ │ └── ... (17 files total) │ └── run_info │ ├── coupled_BGC_DEFmedslope_2xCO2_BGConly.sh │ ├── namelists │ │ ├── user_nl_cam │ │ ├── user_nl_clm │ │ └── user_nl_cpl │ └── SourceMods │ └── src.clm │ ├── BareGroundFluxesMod.F90 │ ├── CanopyFluxesMod.F90 │ ├── PhotosynthesisMod.F90 │ ├── README │ ├── UrbanFluxesMod.F90 │ └── WaterFluxType.F90 └── coupled_SP_DEFmedslope_2xCO2_BGConly_05.tar.gz ├── atm │ └── proc │ ├── day_1 │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h1.PRECT.00410101-00510101.nc │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h1.PRECT.00510102-00610101.nc │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h1.PRECT.00610102-00710101.nc │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h1.PRECT.00710102-00810101.nc │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h1.PRECT.00810102-00910101.nc │ │ └── ... (48 files total) │ └── month_1 │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h0.CLDHGH.004101-009012.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h0.CLDHGH.009101-014012.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h0.CLDHGH.014101-019012.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h0.CLDHGH.019101-020012.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h0.CLDLOW.004101-009012.nc │ └── ... (244 files total) ├── lnd │ └── proc │ └── tseries │ ├── day_1 │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h2.ANSHA_LN.00410101-00910101.nc │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h2.ANSHA_LN.00910102-01410101.nc │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h2.ANSHA_LN.01410102-01910101.nc │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h2.ANSHA_LN.01910102-02001231.nc │ │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h2.ANSUN_LN.00410101-00910101.nc │ │ └── ... (136 files total) │ └── month_1 │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h0.ANSHA_LN.004101-009012.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h0.ANSHA_LN.009101-014012.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h0.ANSHA_LN.014101-019012.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h0.ANSHA_LN.019101-020012.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.clm2.h0.ANSUN_LN.004101-009012.nc │ └── ... (920 files total) ├── rest │ └── 0201-01-01-00000 │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h0.0200-12.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.h1.0200-01-02-00000.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.i.0201-01-01-00000.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.r.0201-01-01-00000.nc │ ├── coupled_SP_DEFmedslope_2xCO2_BGConly_05.cam.rs.0201-01-01-00000.nc │ └── ... (17 files total) └── run_info ├── coupled_SP_DEFmedslope_2xCO2_BGConly.sh ├── namelists │ ├── user_nl_cam │ ├── user_nl_clm │ └── user_nl_cpl └── SourceMods └── src.clm ├── BareGroundFluxesMod.F90 ├── CanopyFluxesMod.F90 ├── PhotosynthesisMod.F90 ├── README ├── UrbanFluxesMod.F90 └── WaterFluxType.F90 ```