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EcoExtreML / STEMMUS_SCOPE

Integrated code of SCOPE and STEMMUS
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STEMMUS_SCOPE BMI: which variables to expose #209

Open BSchilperoort opened 7 months ago

BSchilperoort commented 7 months ago

In #208 and https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/pull/89 I have implemented a BMI for STEMMUS_SCOPE.

For testing purposes I have exposed two variables: the output variable fluxes.Resp and input+output variable TT (soil temperature).

For the implementation of the full BMI we will need to know which variables we want to expose. For these variables we will also need a long or standard name, as well as their unit.

Variables can be an "input variable" an "output variable" or both.

Variable standard name Variable name in code Input/output? Unit Grid
vegetation_respiration fluxes.Resp out ? none
soil_temperature TT in+out degC ModelSettings.mN

@yijianzeng @bobzsu @Yunfei-Wang1993 could you fill in this table for all variables that need to be exposed?

SarahAlidoost commented 7 months ago

@MostafaGomaa93 please see the comment above. Which variables do you need to couple STEMMUS_SCOPE to the groundwater model (MODFLOW 6), please add them to the table above, thanks. relates #205

MostafaGomaa93 commented 7 months ago

@SarahAlidoost. thanks. I am still not yet familiar with the variable names in the code, but I tried my best above. @yijianzeng can confirm the variables I add.

Variable standard name Variable name in code Input/output? Unit Grid
Sum of liquid and vapor water fluxes sum of (QL, Qv, Qa) out kg/m2/s none
Specified matric head at the deepest sublayer (Groundwater head) hN (used when BoundaryCondition.NBChB == 1) in m none
BSchilperoort commented 7 months ago

Hi @MostafaGomaa93, I've moved the variables you added to your own comment.

By grid I mean if they are on a certain model grid (for example the soil layers, or fluorescent wavelengths). I think the variables you specify are not on a specific model grid (if they are just one value, not an array).

MostafaGomaa93 commented 7 months ago

Hi @BSchilperoort, thanks for your update. Sorry for my misunderstanding of what it means by "Grid". I think indeed the variables I add are one value, not an array.

yijianzeng commented 7 months ago
Variable standard name (refers to ALMA) Variable name in code variable name in equation (add also a link to paper) Input/output? Unit Grid
vegetation_respiration fluxes.Resp out ? none
soil_temperature TT in+out degC ModelSettings.mN
SoilVariables.hh 'hh' in+out mH2O ModelSettings.mN+KT
not_availalbe (leaf water potential) 'PSI' in+out mH2O(need to check) ModelSettings.mN+KT

Before i continue further, these two important soil-plant state varables (soil matric water potential and leaf water potential) are not output with time dimensions?

@Yunfei-Wang1993

MostafaGomaa93 commented 2 weeks ago

Here are the variables needed for groundwater coupling (implemented in the SSM_v.0.3.2 branch)

Variable standard name Variable name in code Input/output? Unit in STEMMUS Grid Unit in MODFLOW
Groundwater level GroundwaterSettings.headBotmLayer in cm none m
Groundwater temperature GroundwaterSettings.tempBotm in degC none degC
Elevation of top surface level and all bottom levels of aquifer layers GroundwaterSettings.aqLayers in cm none m
Groundwater recharge gwfluxes.recharge out cm/s none m/day
Evaporation EVAP out cm/s none m/day
Soil water root uptake RWUs out cm/s none m/day
Groundwater root uptake RWUg out cm/s none m/day
Dunnian runoff ForcingData.R_Dunn out cm/s none m/day
Hortonian runoff ForcingData.R_Hort out cm/s none m/day
Total runoff RS out cm/s none m/day

For the variables (gwfluxes.recharge, EVAP, RWUs, RWUg, R_Dunn, R_Hort, RS), aggregation from STEMMUS time step (30 mins) to MODFLOW time step (1 day) is needed in the BMI.

For the gwfluxes.recharge, change sign (positive to negative and vice versa) is needed in the BMI.

For the variables (GroundwaterSettings.headBotmLayer, GroundwaterSettings.tempBotm), interpolation is needed in the BMI

Yunfei-Wang1993 commented 1 week ago

In #208 and EcoExtreML/STEMMUS_SCOPE_Processing#89 I have implemented a BMI for STEMMUS_SCOPE.

For testing purposes I have exposed two variables: the output variable fluxes.Resp and input+output variable TT (soil temperature).

For the implementation of the full BMI we will need to know which variables we want to expose. For these variables we will also need a long or standard name, as well as their unit.

Variables can be an "input variable" an "output variable" or both.

Variable standard name Variable name in code Input/output? Unit Grid vegetation_respiration fluxes.Resp out ? none soil_temperature TT in+out degC ModelSettings.mN @yijianzeng @bobzsu @Yunfei-Wang1993 could you fill in this table for all variables that need to be exposed? Hi, Bart, please find the variable table for BMI. Variable Table_STEMMUS-SCOPE.xlsx

SarahAlidoost commented 1 week ago

@Yunfei-Wang1993 , @DanyangYu , @EntingTang , @Crystal-szj and @yijianzeng Thanks for preparing the variable names. I moved the content of the excel file to a table in this issue, see below. Is this the final version? if so, see the questions:

  1. Variables Rli and Rin don't exist in the source code butmeteo.Rli, ScopeParameters.Rli, meteo.Rin, ScopeParameters.Rin. Which one should be in the table?
  2. Variables Rntot, lEstot, LEctot, Hctot, Hstot, and Gtot should be fluxes.Rntot, fluxes.lEstot, fluxes.LEctot, fluxes.Hctot, fluxes.Hstot, and fluxes.Gtot, right?
  3. Variables Tsave and Tcave should be thermal.Tsave and thermal.Tcave, right?
  4. What is the standard name of SoilVariables.hh? see the section The carbon budget, in the table.
Variable standard name (refers to ALMA) Variable name in code variable name in equation (add also a link to paper) Input/output? Unit Grid
General energy balance components
surface_net_downward_shortwave_flux
Incoming longwave radiation ScopeParameters.Rli in W m-2 none
Incoming shortwave radiation ScopeParameters.Rin in W m-2 none
Net radiation Rntot out W m-2 none
latent heat flux of sunlit leaves lEch out W m-2 none
latent heat flux of shaded leaves lEcu out W m-2 none
latent heat flux of soil lEstot out W m-2 none
latent heat flux of canopy LEctot out W m-2 none
sensible heat flux of sunlit leaves Hch out W m-2 none
sensible heat flux of shaded leaves Hcu out W m-2 none
sensible heat of canopy Hctot out W m-2 none
sensible heat flux of soil Hstot out W m-2 none
gound heat flux Gtot out W m-2 none
General water balance components
Precipitation Precip_msr in mm none
Root water uptake RWU out m2 s-1 none
Surface state variable
soil surface_temperature thermal.Tsave out degC none
canopy temperature thermal.Tcave out degC none
Subsurface state variables
mositure_content_of_soil_layer Theta_UUU out m3 m-3 none
Evaporation components
Evaporation Evap out cm s-1 none
Transpiration Tp_t out cm s-1 none
The carbon budget
gross primary production biochem_out.A out umol m-2 s-1 none
gross assimilation rate Ag out umol m-2 s-1 none
soil_respiration Resp out umol m-2 s-1 none
soil_temperature TT out degC ModelSettings.mN
soil water potential SoilVariables.hh out cm ModelSettings.mN
leaf water potential PSI in+out m ModelSettings.mN
Yunfei-Wang1993 commented 1 week ago

@Yunfei-Wang1993 , @DanyangYu , @EntingTang , @Crystal-szj and @yijianzeng Thanks for preparing the variable names. I moved the content of the excel file to a table in this issue, see below. Is this the final version? if so, see the questions:

  1. Variables Rli and Rin don't exist in the source code butmeteo.Rli, ScopeParameters.Rli, meteo.Rin, ScopeParameters.Rin. Which one should be in the table?
  2. Variables Rntot, lEstot, LEctot, Hctot, Hstot, and Gtot should be fluxes.Rntot, fluxes.lEstot, fluxes.LEctot, fluxes.Hctot, fluxes.Hstot, and fluxes.Gtot, right?
  3. Variables Tsave and Tcave should be thermal.Tsave and thermal.Tcave, right?
  4. What is the standard name of SoilVariables.hh? see the section The carbon budget, in the table.

Variable standard name (refers to ALMA) Variable name in code variable name in equation (add also a link to paper) Input/output? Unit Grid General energy balance components
surface_net_downward_shortwave_flux
Incoming longwave radiation Rli in W m-2 none Incoming shortwave radiation Rin in W m-2 none Net radiation Rntot out W m-2 none latent heat flux of sunlit leaves lEch out W m-2 none latent heat flux of shaded leaves lEcu out W m-2 none latent heat flux of soil lEstot out W m-2 none latent heat flux of canopy LEctot out W m-2 none sensible heat flux of sunlit leaves Hch out W m-2 none sensible heat flux of shaded leaves Hcu out W m-2 none sensible heat of canopy Hctot out W m-2 none sensible heat flux of soil Hstot out W m-2 none gound heat flux Gtot out W m-2 none General water balance components
Precipitation Precip_msr in mm none Root water uptake RWU out m2 s-1 none Surface state variable
soil surface_temperature Tsave out degC none canopy temperature Tcave out degC none Subsurface state variables
mositure_content_of_soil_layer Theta_UUU out m3 m-3 none Evaporation components
Evaporation Evap out cm s-1 none Transpiration Tp_t out cm s-1 none The carbon budget
gross primary production biochem_out.A out umol m-2 s-1 none gross assimilation rate Ag out umol m-2 s-1 none soil_respiration Resp out umol m-2 s-1 none soil_temperature TT out degC ModelSettings.mN SoilVariables.hh hh out cm ModelSettings.mN leaf water potential PSI in+out m ModelSettings.mN

Hi, Sarah, 1: ScopeParameters.Rli and ScopeParameters.Rin should be used here. 2 and 3: You are right. 4: The last three variables we can name them the 'soil and leaf state variables'. SoilVariables.hh means the soil water potential.

MostafaGomaa93 commented 1 week ago

Just for the record, the whole SoilVariables structure is exposed to BMI (see here), so we may not need to specify soil_temperature and SoilVariables.hh separately (I leave this decision to @SarahAlidoost).

Evap and RWU are already included in the BMI variables list (here). I already add them.

SarahAlidoost commented 1 week ago

Just for the record, the whole SoilVariables structure is exposed to BMI (see here), so we may not need to specify soil_temperature and SoilVariables.hh separately (I leave this decision to @SarahAlidoost).

@MostafaGomaa93 you are right, the structure SoilVariables is already in STEMMUS_SCOPE_exe.m. However, in BMI get_variable function (python implementation), the variable name in a structure is needed, see examples here. This function does not return the whole structure. Since the standard names are not fully documented in the source code, we use the information in this table.

MostafaGomaa93 commented 5 days ago

Three additional values are needed in BMI (according to discussion of issue 237)

Variable standard name Variable name in code Input/output? Unit Grid
Total soil depth ModelSettings.Tot_Depth in cm none
Number of soil layers ModelSettings.NL in - none
Maximum rooting depth ModelSettings.R_depth in cm none
SarahAlidoost commented 5 days ago

Three additional values are needed in BMI (according to discussion of issue 237)

Variable standard name Variable name in code Input/output? Unit Grid ModelSettings.Tot_Depth Total soil depth in cm none ModelSettings.NL Number of soil layers in - none ModelSettings.R_depth Maximum rooting depth in cm none

thanks for adding these variables. The content of the first two columns should be switched. can you please fix it? also, see my comment.