From d50ce7b49b08b678eb86da44a438cedb35a7afef Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Fri, 15 Sep 2023 15:53:20 +0200 Subject: [PATCH 01/11] add entry to special cases --- .../Running-with-excess-ground-ice.rst | 40 +++++++++++++++++++ .../running-special-cases/index.rst | 1 + 2 files changed, 41 insertions(+) create mode 100644 doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst new file mode 100644 index 0000000000..23677965a5 --- /dev/null +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -0,0 +1,40 @@ +.. _running-with-excess-ground-ice: + +.. include:: ../substitutions.rst + +=================================== + Running-with-excess-ground-ice +=================================== + + +Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.fasle.``. When +``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option`use_excess_ice_streams` exists to control this process (``.false.`` is default). If ``.true.`` and use_excess_ice is ``.true.``, +initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). +This is useful, since in this way, a run with excess ground ice can be started from a restart or initial dataset, that does not include excess ground ice. +If the run is a continue-run, excess ice variables will **always** be expected on a restart file. + +.. note:: Excess ice ammount provided by the stream file is expressed in excess ice concentration (%) and does not have a vertical distribution. Each soil layer beneath 0.5 m or (maximum active layer depth from the previous year if it is greater) down to bedrock will receive the same concentration but the ice mass will be scaled by the soil layer depth. Both naturally vegetated and crop columns get excess ice. + + +Since presence of excess ice within the soil significantly alters heat diffusion within it, when starting from initial conditions where excess ice was not present, an additional spinup is required. +Usually such spinup takes 100-150 years (depending on your climate) to completely equilibrate soil temperatures. + + + +Example: Crop Simulation +------------------------------------ +:: + + > cd scripts + > ./create_newcase -case I1850Clm50BgcCrop_with_exice -res f19_g17_gl4 -compset I1850Clm50BgcCrop + > cd I1850Clm50BgcCrop_with_exice + + > ./case.setup + + # turn on excess ice and it's "stream" initialization + > echo "use_excess_ice=.true." >> user_nl_clm + > echo "use_excess_ice_streams=.true." >> user_nl_clm + + # Now build and run normally + > ./case.build + > ./case.submit diff --git a/doc/source/users_guide/running-special-cases/index.rst b/doc/source/users_guide/running-special-cases/index.rst index f84b7706fb..d220483dd3 100644 --- a/doc/source/users_guide/running-special-cases/index.rst +++ b/doc/source/users_guide/running-special-cases/index.rst @@ -19,6 +19,7 @@ Running Special Cases running-with-irrigation.rst Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst Spinning-up-the-biogeochemistry-BGC-spinup.rst + Running-with-excess-ground-ice.rst Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst From d160e65b671171c8cc16208720e1a7eb730988fc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:18:50 -0600 Subject: [PATCH 02/11] Minor text fixes. --- .../Running-with-excess-ground-ice.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index 23677965a5..2267d524e5 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -7,13 +7,13 @@ =================================== -Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.fasle.``. When +Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.false.``. When ``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option`use_excess_ice_streams` exists to control this process (``.false.`` is default). If ``.true.`` and use_excess_ice is ``.true.``, initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). This is useful, since in this way, a run with excess ground ice can be started from a restart or initial dataset, that does not include excess ground ice. If the run is a continue-run, excess ice variables will **always** be expected on a restart file. -.. note:: Excess ice ammount provided by the stream file is expressed in excess ice concentration (%) and does not have a vertical distribution. Each soil layer beneath 0.5 m or (maximum active layer depth from the previous year if it is greater) down to bedrock will receive the same concentration but the ice mass will be scaled by the soil layer depth. Both naturally vegetated and crop columns get excess ice. +.. note:: Excess ice amount provided by the stream file is expressed in excess ice concentration (%) and does not have a vertical distribution. Each soil layer beneath 0.5 m (or maximum active layer depth from the previous year if it is greater) down to bedrock will receive the same concentration, but the ice mass will be scaled by the soil layer depth. Both naturally vegetated and crop columns get excess ice. Since presence of excess ice within the soil significantly alters heat diffusion within it, when starting from initial conditions where excess ice was not present, an additional spinup is required. @@ -31,7 +31,7 @@ Example: Crop Simulation > ./case.setup - # turn on excess ice and it's "stream" initialization + # turn on excess ice and its "stream" initialization > echo "use_excess_ice=.true." >> user_nl_clm > echo "use_excess_ice_streams=.true." >> user_nl_clm From bae7793ef7720e9c64367bc67c4c22adbe9810c0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:20:23 -0600 Subject: [PATCH 03/11] Markup fixes. --- .../running-special-cases/Running-with-excess-ground-ice.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index 2267d524e5..f126c00abc 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -8,7 +8,7 @@ Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.false.``. When -``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option`use_excess_ice_streams` exists to control this process (``.false.`` is default). If ``.true.`` and use_excess_ice is ``.true.``, +``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option ``use_excess_ice_streams`` exists to control this process (``.false.`` is default). If ``.true.`` and ``use_excess_ice`` is ``.true.``, initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). This is useful, since in this way, a run with excess ground ice can be started from a restart or initial dataset, that does not include excess ground ice. If the run is a continue-run, excess ice variables will **always** be expected on a restart file. From 5dfd8db7e336db36f81f8afcb7604e68461b04c6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:20:30 -0600 Subject: [PATCH 04/11] Remove hyphens from title. --- .../running-special-cases/Running-with-excess-ground-ice.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index f126c00abc..10b7f3ee98 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -3,7 +3,7 @@ .. include:: ../substitutions.rst =================================== - Running-with-excess-ground-ice + Running with excess ground ice =================================== From 15c4efc5e43ca1debc709689cb69789ae5221cad Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:21:51 -0600 Subject: [PATCH 05/11] Use complete relative path to cime/scripts from top level of checkout. --- .../running-special-cases/Running-with-excess-ground-ice.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index 10b7f3ee98..be818f8f14 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -25,7 +25,7 @@ Example: Crop Simulation ------------------------------------ :: - > cd scripts + > cd cime/scripts > ./create_newcase -case I1850Clm50BgcCrop_with_exice -res f19_g17_gl4 -compset I1850Clm50BgcCrop > cd I1850Clm50BgcCrop_with_exice From 9e633dcdfc00244b2be74f03ef7f45dfc4cdd718 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:23:05 -0600 Subject: [PATCH 06/11] Remove EOL whitespace. --- .../Running-with-excess-ground-ice.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index be818f8f14..d0b29f8682 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -7,11 +7,11 @@ =================================== -Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.false.``. When -``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option ``use_excess_ice_streams`` exists to control this process (``.false.`` is default). If ``.true.`` and ``use_excess_ice`` is ``.true.``, -initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). +Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.false.``. When +``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option ``use_excess_ice_streams`` exists to control this process (``.false.`` is default). If ``.true.`` and ``use_excess_ice`` is ``.true.``, +initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). This is useful, since in this way, a run with excess ground ice can be started from a restart or initial dataset, that does not include excess ground ice. -If the run is a continue-run, excess ice variables will **always** be expected on a restart file. +If the run is a continue-run, excess ice variables will **always** be expected on a restart file. .. note:: Excess ice amount provided by the stream file is expressed in excess ice concentration (%) and does not have a vertical distribution. Each soil layer beneath 0.5 m (or maximum active layer depth from the previous year if it is greater) down to bedrock will receive the same concentration, but the ice mass will be scaled by the soil layer depth. Both naturally vegetated and crop columns get excess ice. From ebffd102e500a15c79f5a42fdda2094511f1821c Mon Sep 17 00:00:00 2001 From: olyson Date: Tue, 24 Oct 2023 19:05:53 +0000 Subject: [PATCH 07/11] Resolve documentation problems in issue #2136 --- doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst | 6 +++--- doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst | 6 +++--- .../tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst | 4 ++-- doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst | 6 +++--- .../Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst | 4 ++-- .../Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst | 6 +++--- .../Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst | 6 +++--- 7 files changed, 19 insertions(+), 19 deletions(-) diff --git a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst index f1dd139cb5..ad593b6060 100644 --- a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst +++ b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst @@ -28,7 +28,7 @@ where :math:`f_{lake}` and :math:`f_{sno}` are the CLM grid cell fractions of la 0\le f_{v} =\frac{L+S}{\left(L+S\right)_{t} } \le 1{\rm \; \; \; \; where\; }\left(L+S\right)_{t} =0.3{\rm \; m}^{2} {\rm m}^{-2} -where equation applies only for dust mobilization and is not related to the plant functional type fractions prescribed from the CLM input data or simulated by the CLM dynamic vegetation model (Chapter 22). :math:`L` and :math:`S` are the CLM leaf and stem area index values (m :sup:`2` m\ :sup:`-2`) averaged at the land unit level so as to include all the pfts and the bare ground present in a vegetated land unit. :math:`L` and :math:`S` may be prescribed from the CLM input data (section :numref:`Phenology and vegetation burial by snow`) or simulated by the CLM biogeochemistry model (Chapter :numref:`rst_Vegetation Phenology and Turnover`). +where equation :eq:`29.3` applies only for dust mobilization and is not related to the plant functional type fractions prescribed from the CLM input data or simulated by the CLM dynamic vegetation model (Chapter 22). :math:`L` and :math:`S` are the CLM leaf and stem area index values (m :sup:`2` m\ :sup:`-2`) averaged at the land unit level so as to include all the pfts and the bare ground present in a vegetated land unit. :math:`L` and :math:`S` may be prescribed from the CLM input data (section :numref:`Phenology and vegetation burial by snow`) or simulated by the CLM biogeochemistry model (Chapter :numref:`rst_Vegetation Phenology and Turnover`). The sandblasting mass efficiency :math:`\alpha` (m :sup:`-1`) is calculated as @@ -78,7 +78,7 @@ and w=\frac{\theta _{1} \rho _{liq} }{\rho _{d,1} } -where :math:`a=M_{clay}^{-1}` for tuning purposes, :math:`\theta _{1}` is the volumetric soil moisture in the top soil layer (m :math:`{}^{3 }`\ m\ :sup:`-3`) (section :numref:`Soil Water`), :math:`\rho _{liq}` is the density of liquid water (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`\rho _{d,\, 1}` is the bulk density of soil in the top soil layer (kg m\ :sup:`-3`) defined as in section :numref:`Soil and Snow Thermal Properties` rather than as in :ref:`Zender et al. (2003)`. :math:`Re_{*t}^{f}` from equation is the threshold friction Reynolds factor +where :math:`a=M_{clay}^{-1}` for tuning purposes, :math:`\theta _{1}` is the volumetric soil moisture in the top soil layer (m :math:`{}^{3 }`\ m\ :sup:`-3`) (section :numref:`Soil Water`), :math:`\rho _{liq}` is the density of liquid water (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`\rho _{d,\, 1}` is the bulk density of soil in the top soil layer (kg m\ :sup:`-3`) defined as in section :numref:`Soil and Snow Thermal Properties` rather than as in :ref:`Zender et al. (2003)`. :math:`Re_{*t}^{f}` from equation :eq:`29.6` is the threshold friction Reynolds factor .. math:: :label: 29.10 @@ -110,7 +110,7 @@ where :math:`u_{*}` is the CLM wind friction speed (m s\ :sup:`-1`), also known U_{10,t} =u_{*t} \frac{U_{10} }{u_{*} } -In equation we sum :math:`M_{i,\, j}` over :math:`I=3` source modes :math:`i` where :math:`M_{i,\, j}` is the mass fraction of each source mode :math:`i` carried in each of *:math:`J=4`* transport bins :math:`j` +In equation :eq:`29.1` we sum :math:`M_{i,\, j}` over :math:`I=3` source modes :math:`i` where :math:`M_{i,\, j}` is the mass fraction of each source mode :math:`i` carried in each of *:math:`J=4`* transport bins :math:`j` .. math:: :label: 29.14 diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index f70ca7c35a..c759d11f92 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -803,7 +803,7 @@ When the expression for :math:`T_{s}` is substituted into equation :eq:`5.88`, t H_{v} = -\rho _{atm} C_{p} \left[c_{a}^{h} \theta _{atm} +c_{g}^{h} T_{g} -\left(c_{a}^{h} +c_{g}^{h} \right)T_{v} \right]\frac{c_{v}^{h} }{c_{a}^{h} +c_{v}^{h} +c_{g}^{h} } . -Similarly, the expression for :math:`T_{s}` can be substituted into equation to obtain the sensible heat flux from ground :math:`H_{g}` +Similarly, the expression for :math:`T_{s}` can be substituted into equations :eq:`5.89`, :eq:`5.90`, :eq:`5.91`, and :eq:`5.92` to obtain the sensible heat flux from ground :math:`H_{g}` .. math:: :label: 5.98 @@ -1199,7 +1199,7 @@ The numerical solution for vegetation temperature and the fluxes of momentum, se #. An initial guess for the wind speed :math:`V_{a}` is obtained from :eq:`5.24` assuming an initial convective velocity :math:`U_{c} =0` m s\ :sup:`-1` for stable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} \ge 0` as evaluated from :eq:`5.50` ) and :math:`U_{c} =0.5` for unstable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} <0`). -#. An initial guess for the Monin-Obukhov length :math:`L` is obtained from the bulk Richardson number using equation and :eq:`5.46` and :eq:`5.48`. +#. An initial guess for the Monin-Obukhov length :math:`L` is obtained from the bulk Richardson number using equations :eq:`5.46` and :eq:`5.48`. #. Iteration proceeds on the following system of equations: @@ -1296,7 +1296,7 @@ The sensible and water vapor heat fluxes derived above for bare soil and soil be E'_{g} =E_{g} +\left(T_{g}^{n+1} -T_{g}^{n} \right)\frac{\partial E_{g} }{\partial T_{g} } -where :math:`H_{g}` and :math:`E_{g}` are the sensible heat and water vapor fluxes derived from equations and for non-vegetated surfaces and equations and for vegetated surfaces using :math:`T_{g}^{n}`. One further adjustment is made to :math:`H'_{g}` and :math:`E'_{g}`. If the soil moisture in the top snow/soil layer is not sufficient to support the updated ground evaporation, i.e., if :math:`E'_{g} > 0` and :math:`f_{evap} < 1` where +where :math:`H_{g}`, :math:`E_{g}`, :math:`\frac{\partial H_{g} }{\partial T_{g} }`, and :math:`\frac{\partial E_{g} }{\partial T_{g} }` are the sensible heat and water vapor fluxes and their partial derivatives derived from equations :eq:`5.62`, :eq:`5.66`, :eq:`5.83`, and :eq:`5.84` for non-vegetated surfaces and equations :eq:`5.89`, :eq:`5.102`, :eq:`5.123`, and :eq:`5.124` for vegetated surfaces using :math:`T_{g}^{n}`. One further adjustment is made to :math:`H'_{g}` and :math:`E'_{g}`. If the soil moisture in the top snow/soil layer is not sufficient to support the updated ground evaporation, i.e., if :math:`E'_{g} > 0` and :math:`f_{evap} < 1` where .. math:: :label: 5.142 diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index 5599eeedd8..02188d5e25 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -358,7 +358,7 @@ For one-dimensional vertical water flow in soils, the conservation of mass is st where :math:`\theta` is the volumetric soil water content (mm\ :sup:`3` of water / mm\ :sup:`-3` of soil), :math:`t` is time (s), :math:`z` is height above some datum in the soil column (mm) (positive upwards), :math:`q` is soil water flux (kg m\ :sup:`-2` s\ :sup:`-1` or mm s\ :sup:`-1`) (positive upwards), and :math:`e` is a soil moisture sink term (mm of water mm\ :sup:`-1` of soil s\ :sup:`-1`) (ET loss). This equation is solved numerically by dividing the soil column into multiple layers in the vertical and integrating downward over each layer with an upper boundary condition of the infiltration flux into the top soil layer :math:`q_{infl}` and a zero-flux lower boundary condition at the bottom of the soil column (sub-surface runoff is removed later in the timestep, section :numref:`Lateral Sub-surface Runoff`). -The soil water flux :math:`q` in equation can be described by Darcy's law :ref:`(Dingman 2002) ` +The soil water flux :math:`q` in equation :eq:`7.79` can be described by Darcy's law :ref:`(Dingman 2002) ` .. math:: :label: 7.80 @@ -641,7 +641,7 @@ where The tridiagonal equation set is solved over :math:`i=1,\ldots,N_{levsoi}`. -The finite-difference forms of the fluxes and partial derivatives in equations :eq:`7.111` - :eq:`7.114` can be obtained from equation as +The finite-difference forms of the fluxes and partial derivatives in equations :eq:`7.111` - :eq:`7.114` can be obtained from equation :eq:`7.82` as .. math:: :label: 7.115 diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index 18f6e1e8f4..88cb77d737 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -316,7 +316,7 @@ The fluxes of momentum, sensible heat, and water vapor are solved for simultaneo E_{g} =-\frac{\rho _{atm} }{r_{aw} } \left[q_{atm} -q_{sat}^{T_{g} } -\frac{\partial q_{sat}^{T_{g} } }{\partial T_{g} } \left(T_{g}^{n+1} -T_{g}^{n} \right)\right] -where the last term on the right side of equation is the change in saturated specific humidity due to the change in :math:`T_{g}` between iterations. +where the last term on the right side of equation :eq:`12.23` is the change in saturated specific humidity due to the change in :math:`T_{g}` between iterations. #. Saturated specific humidity :math:`q_{sat}^{T_{g} }` and its derivative :math:`\frac{dq_{sat}^{T_{g} } }{dT_{g} }` are updated for :math:`T_{g}^{n+1}` (section :numref:`Monin-Obukhov Similarity Theory`). @@ -337,7 +337,7 @@ Once the four iterations for lake surface temperature have been yielded a tentat where :math:`T_{m}` \ is the temperature of maximum liquid water density, 3.85°C (:ref:`Hostetler and Bartlein (1990) `). The first condition requires that, if there is any snow or ice present, the surface temperature is restricted to be less than or equal to freezing. The second and third conditions maintain convective stability in the top lake layer. -If eq. XXX is applied, the turbulent fluxes :math:`H_{g}` and :math:`E_{g}` are re-evaluated. The emitted longwave radiation and the momentum fluxes are re-evaluated in any case. The final ground heat flux :math:`G` is calculated from the residual of the energy balance eq. XXX in order to precisely conserve energy. XXX This ground heat flux is taken as a prescribed flux boundary condition for the lake temperature solution (section :numref:`Boundary Conditions Lake`). An energy balance check is included at each timestep to insure that eq. XXX is obeyed to within 0.1 W m\ :sup:`-2`. +If equation :eq:`12.24` is applied, the turbulent fluxes :math:`H_{g}` and :math:`E_{g}` are re-evaluated. The emitted longwave radiation and the momentum fluxes are re-evaluated in any case. The final ground heat flux :math:`G` is calculated from the residual of the energy balance (equation :eq:`12.7`) in order to precisely conserve energy. This ground heat flux is taken as a prescribed flux boundary condition for the lake temperature solution (section :numref:`Boundary Conditions Lake`). A check is included at each timestep to insure that energy balance is obeyed to within 0.1 W m\ :sup:`-2` (see :numref:`Energy Conservation Lake`). .. _Lake Temperature: @@ -678,7 +678,7 @@ The ice is lumped together at the top. For each lake layer *j* from 1 to *i* + 1 Energy Conservation ^^^^^^^^^^^^^^^^^^^^^^^^^^ -To check energy conservation, the left-hand side of eq. XXX is re-written to yield the total enthalpy of the lake system (J m\ :sup:`-2`) :math:`H_{tot}` : +To check energy conservation, the left-hand side of equation :eq:`12.27` is re-written to yield the total enthalpy of the lake system (J m\ :sup:`-2`) :math:`H_{tot}` : .. math:: :label: 12.57 diff --git a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst index 5ee0087fec..baa05dff59 100644 --- a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst +++ b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst @@ -1,4 +1,4 @@ -.. _rst_Land-only Mode: + _rst_Land-only Mode: Land-Only Mode ================ @@ -21,7 +21,7 @@ The total solar radiation is also provided at three hour intervals. The data is S_{atm} \left(t_{M} \right)=0 & \qquad {\rm for\; }\mu \left(t_{M} \right)\le 0.001 \end{array} -where :math:`\Delta t_{FD}` is the time step of the forcing data (3 hours :math:`\times` 3600 seconds hour\ :sup:`-1` = 10800 seconds), :math:`\Delta t_{M}` is the model time step (seconds), :math:`S_{atm} \left(t_{FD} \right)` is the three-hourly solar radiation from the forcing data (W m\ :sup:`-2`), and :math:`\mu \left(t_{M} \right)` is the cosine of the solar zenith angle at model time step :math:`t_{M}` (section :numref:`Solar Zenith Angle`). The term in the denominator of equation (1) is the sum of the cosine of the solar zenith angle for each model time step falling within the three hour period. For numerical purposes, :math:`\mu \left(t_{M_{i} } \right)\ge 0.001`. +where :math:`\Delta t_{FD}` is the time step of the forcing data (3 hours :math:`\times` 3600 seconds hour\ :sup:`-1` = 10800 seconds), :math:`\Delta t_{M}` is the model time step (seconds), :math:`S_{atm} \left(t_{FD} \right)` is the three-hourly solar radiation from the forcing data (W m\ :sup:`-2`), and :math:`\mu \left(t_{M} \right)` is the cosine of the solar zenith angle at model time step :math:`t_{M}` (section :numref:`Solar Zenith Angle`). The term in the denominator of equation :eq:`31.1` is the sum of the cosine of the solar zenith angle for each model time step falling within the three hour period. For numerical purposes, :math:`\mu \left(t_{M_{i} } \right)\ge 0.001`. The total incident solar radiation :math:`S_{atm}` at the model time step :math:`t_{M}` is then split into near-infrared and visible radiation and partitioned into direct and diffuse according to factors derived from one year's worth of hourly CAM output from CAM version cam3\_5\_55 as diff --git a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst index 5668af1a0b..fdc559e1c2 100644 --- a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst +++ b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst @@ -143,7 +143,7 @@ In the second step, after surface fluxes and snow/soil temperatures have been de w_{ice,\, snl+1}^{n+1} =w_{ice,\, snl+1}^{n} +f_{sno} \left(q_{frost} -q_{subl} \right)\Delta t. -If :math:`w_{ice,\, snl+1}^{n+1} <0` upon solution of equation, the ice content is reset to zero and the liquid water content :math:`w_{liq,\, snl+1}` is reduced by the amount required to bring :math:`w_{ice,\, snl+1}^{n+1}` up to zero. +If :math:`w_{ice,\, snl+1}^{n+1} <0` upon solution of equation :eq:`8.25`, the ice content is reset to zero and the liquid water content :math:`w_{liq,\, snl+1}` is reduced by the amount required to bring :math:`w_{ice,\, snl+1}^{n+1}` up to zero. The snow water equivalent :math:`W_{sno}` is capped to not exceed 10,000 kg m\ :sup:`-2`. If the addition of :math:`q_{frost}` were to result in :math:`W_{sno} > 10,000` kg m\ :sup:`-2`, the frost term :math:`q_{frost}` is instead added to the ice runoff term :math:`q_{snwcp,\, ice}` (section :numref:`Runoff from glaciers and snow-capped surfaces`). @@ -192,7 +192,7 @@ where the volumetric liquid water :math:`\theta _{liq,\, i}` and ice :math:`\the \theta _{liq,\, i} =\frac{w_{liq,\, i} }{f_{sno} \Delta z_{i} \rho _{liq} } \le 1-\theta _{ice,\, i} , -and :math:`S_{r} =0.033` is the irreducible water saturation (snow holds a certain amount of liquid water due to capillary retention after drainage has ceased (:ref:`Anderson (1976) `)). The water holding capacity of the underlying layer limits the flow of water :math:`q_{liq,\, i}` calculated in equation, unless the underlying layer is the surface soil layer, as +and :math:`S_{r} =0.033` is the irreducible water saturation (snow holds a certain amount of liquid water due to capillary retention after drainage has ceased (:ref:`Anderson (1976) `)). The water holding capacity of the underlying layer limits the flow of water :math:`q_{liq,\, i}` calculated in equation :eq:`8.29`, unless the underlying layer is the surface soil layer, as .. math:: :label: 8.32 @@ -206,7 +206,7 @@ The liquid water content :math:`w_{liq,\, i}` is updated as w_{liq,\, i}^{n+1} =w_{liq,\, i}^{n} +\left(q_{i-1} -q_{i} \right)\Delta t. -Equations - are solved sequentially from top (:math:`i=snl+1`) to bottom (:math:`i=0`) snow layer in each time step. The total flow of liquid water reaching the soil surface is then :math:`q_{liq,\, 0}` which is used in the calculation of surface runoff and infiltration (sections :numref:`Surface Runoff` and :numref:`Infiltration`). +Equations :eq:`8.29` - :eq:`8.33` are solved sequentially from top (:math:`i=snl+1`) to bottom (:math:`i=0`) snow layer in each time step. The total flow of liquid water reaching the soil surface is then :math:`q_{liq,\, 0}` which is used in the calculation of surface runoff and infiltration (sections :numref:`Surface Runoff` and :numref:`Infiltration`). .. _Black and organic carbon and mineral dust within snow: diff --git a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst index 54c50486f1..405a0bd014 100644 --- a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst +++ b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst @@ -105,7 +105,7 @@ where :math:`\bar{\theta }` is the mean leaf inclination angle relative to the h \cos \bar{\theta }=\frac{1+\chi _{L} }{2} -Using this approximation, for vertical leaves (:math:`\chi _{L} =-1`, :math:`\bar{\theta }=90^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =0.5\left(\alpha _{\Lambda } +\tau _{\Lambda } \right)`, and for horizontal leaves (:math:`\chi _{L} =1`, :math:`\bar{\theta }=0^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =\alpha _{\Lambda }`, which agree with both :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) `. For random (spherically distributed) leaves (:math:`\chi _{L} =0`, :math:`\bar{\theta }=60^{{\rm o}}` ), the approximation yields :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right.} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right.} 8} \tau _{\Lambda }` whereas the approximate solution of :ref:`Dickinson (1983) ` is :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={2\mathord{\left/ {\vphantom {2 3}} \right.} 3} \alpha _{\Lambda } +{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} \tau _{\Lambda }`. This discrepancy arises from the fact that a spherical leaf angle distribution has a true mean leaf inclination :math:`\bar{\theta }\approx 57` :ref:`(Campbell and Norman 1998) ` in equation, while :math:`\bar{\theta }=60` in equation. The upscatter for direct beam radiation is +Using this approximation, for vertical leaves (:math:`\chi _{L} =-1`, :math:`\bar{\theta }=90^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =0.5\left(\alpha _{\Lambda } +\tau _{\Lambda } \right)`, and for horizontal leaves (:math:`\chi _{L} =1`, :math:`\bar{\theta }=0^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =\alpha _{\Lambda }`, which agree with both :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) `. For random (spherically distributed) leaves (:math:`\chi _{L} =0`, :math:`\bar{\theta }=60^{{\rm o}}` ), the approximation yields :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right.} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right.} 8} \tau _{\Lambda }` whereas the approximate solution of :ref:`Dickinson (1983) ` is :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={2\mathord{\left/ {\vphantom {2 3}} \right.} 3} \alpha _{\Lambda } +{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} \tau _{\Lambda }`. This discrepancy arises from the fact that a spherical leaf angle distribution has a true mean leaf inclination :math:`\bar{\theta }\approx 57` :ref:`(Campbell and Norman 1998) ` in equation :eq:`3.13`, while :math:`\bar{\theta }=60` in equation :eq:`3.14`. The upscatter for direct beam radiation is .. math:: :label: 3.15 @@ -572,7 +572,7 @@ Soil albedo (or underlying substrate albedo), which is defined for visible and N The radiative transfer calculation is performed twice for each column containing a mass of snow greater than :math:`1 \times 10^{-30}` kg\ m\ :sup:`-2` (excluding lake and urban columns); once each for direct-beam and diffuse incident flux. Absorption in each layer :math:`i` of pure snow is initially recorded as absorbed flux per unit incident flux on the ground (:math:`S_{sno,\, i}` ), as albedos must be calculated for the next timestep with unknown incident flux. The snow absorption fluxes that are used for column temperature calculations are .. math:: - :label: ZEqnNum275338 + :label: 3.69 S_{g,\, i} =S_{sno,\, i} \left(1-\alpha _{sno} \right) @@ -599,7 +599,7 @@ Broadband single-scatter albedo (:math:`\bar{\omega }`) is additionally weighted Inclusion of this additional albedo weight was found to improve accuracy of the five-band albedo solutions (relative to 470-band solutions) because of the strong dependence of optically-thick snowpack albedo on ice grain single-scatter albedo (:ref:`Flanner et al. (2007) `). The lookup tables contain optical properties for lognormal distributions of ice particles over the range of effective radii: 30\ :math:`\mu`\ m :math:`< r _{e} < \text{1500} \mu \text{m}`, at 1 :math:`\mu` m resolution. Single-scatter albedos for the end-members of this size range are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`. -Optical properties for black carbon are described in :ref:`Flanner et al. (2007) `. Single-scatter albedo, mass extinction cross-section, and asymmetry parameter values for all snowpack species, in the five spectral bands used, are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`, :numref:`Table Mass extinction values`, and :numref:`Table Asymmetry scattering parameters used for snowpack impurities and ice`. These properties were also derived with Mie Theory, using various published sources of indices of refraction and assumptions about particle size distribution. Weighting into the five CLM spectral bands was determined only with incident solar flux, as in equation. +Optical properties for black carbon are described in :ref:`Flanner et al. (2007) `. Single-scatter albedo, mass extinction cross-section, and asymmetry parameter values for all snowpack species, in the five spectral bands used, are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`, :numref:`Table Mass extinction values`, and :numref:`Table Asymmetry scattering parameters used for snowpack impurities and ice`. These properties were also derived with Mie Theory, using various published sources of indices of refraction and assumptions about particle size distribution. Weighting into the five CLM spectral bands was determined only with incident solar flux, as in equation :eq:`3.69`. .. _Table Single-scatter albedo values used for snowpack impurities and ice: From 88d8fa16cfa47d4e7c823bf6046de99ce97c18da Mon Sep 17 00:00:00 2001 From: olyson Date: Tue, 24 Oct 2023 20:02:37 +0000 Subject: [PATCH 08/11] Resolve documentation issues identified in issue #872 --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index ecffe65660..0b87314361 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -533,25 +533,25 @@ The soil moisture deficit :math:`D_{irrig}` is D_{irrig} = \left\{ \begin{array}{lr} - w_{thresh} - w_{avail} &\qquad w_{thresh} > w_{avail} \\ + w_{target} - w_{avail} &\qquad w_{thresh} > w_{avail} \\ 0 &\qquad w_{thresh} \le w_{avail} \end{array} \right\} -where :math:`w_{thresh}` is the irrigation moisture threshold (mm) and :math:`w_{avail}` is the available moisture (mm). The moisture threshold is +where :math:`w_{target}` is the irrigation target soil moisture (mm) .. math:: :label: 25.62 - w_{thresh} = f_{thresh} \left(w_{target} - w_{wilt}\right) + w_{wilt} + w_{target} = \sum_{j=1}^{N_{irr}} \theta_{target} \Delta z_{j} \ . -where :math:`w_{target}` is the irrigation target soil moisture (mm) +The irrigation moisture threshold (mm) is .. math:: :label: 25.63 - w_{target} = \sum_{j=1}^{N_{irr}} \theta_{target} \Delta z_{j} \ , + w_{thresh} = f_{thresh} \left(w_{target} - w_{wilt}\right) + w_{wilt} -:math:`w_{wilt}` is the wilting point soil moisture (mm) +where :math:`w_{wilt}` is the wilting point soil moisture (mm) .. math:: :label: 25.64 @@ -559,13 +559,15 @@ where :math:`w_{target}` is the irrigation target soil moisture (mm) w_{wilt} = \sum_{j=1}^{N_{irr}} \theta_{wilt} \Delta z_{j} \ , and :math:`f_{thresh}` is a tuning parameter. The available moisture in -the soil is +the soil (mm) is .. math:: :label: 25.65 w_{avail} = \sum_{j=1}^{N_{irr}} \theta_{j} \Delta z_{j} \ , +Note that :math:`w_{target}` is truly supposed to give the target soil moisture value that we're shooting for whenever irrigation happens; then the soil moisture deficit :math:`D_{irrig}` gives the difference between this target value and the current soil moisture. The irrigation moisture threshold :math:`w_{thresh}`, on the other hand, gives a threshold at which we decide to do any irrigation at all. The way this is written allows for the possibility that one may not want to irrigate every time there becomes even a tiny soil moisture deficit. Instead, one may want to wait until the deficit is larger before initiating irrigation; at that point, one doesn't want to just irrigate up to the "threshold" but instead up to the higher "target". The target should always be greater than or equal to the threshold. + :math:`N_{irr}` is the index of the soil layer corresponding to a specified depth :math:`z_{irrig}` (:numref:`Table Irrigation parameters`) and :math:`\Delta z_{j}` is the thickness of the soil layer in layer :math:`j` (section :numref:`Vertical Discretization`). :math:`\theta_{j}` is the volumetric soil moisture in layer :math:`j` (section :numref:`Soil Water`). :math:`\theta_{target}` and :math:`\theta_{wilt}` are the target and wilting point volumetric soil moisture values, respectively, and are determined by inverting :eq:`7.94` using soil matric potential parameters :math:`\Psi_{target}` and :math:`\Psi_{wilt}` (:numref:`Table Irrigation parameters`). After the soil moisture deficit :math:`D_{irrig}` is calculated, irrigation in an amount equal to :math:`\frac{D_{irrig}}{T_{irrig}}` (mm/s) is applied uniformly over the irrigation period :math:`T_{irrig}` (s). Irrigation water is applied directly to the ground surface, bypassing canopy interception (i.e., added to :math:`{q}_{grnd,liq}`: section :numref:`Canopy Water`). To conserve mass, irrigation is removed from river water storage (Chapter :numref:`rst_River Transport Model (RTM)`). When river water storage is inadequate to meet irrigation demand, there are two options: 1) the additional water can be removed from the ocean model, or 2) the irrigation demand can be reduced such that river water storage is maintained above a specified threshold. From f54d15cf7453597fb0ac8857fa81352c9b043898 Mon Sep 17 00:00:00 2001 From: olyson Date: Tue, 24 Oct 2023 22:00:50 +0000 Subject: [PATCH 09/11] Resolve documentation problems identified in issue #993 --- ...LM50_Tech_Note_Photosynthetic_Capacity.rst | 110 +++++++++--------- 1 file changed, 55 insertions(+), 55 deletions(-) diff --git a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst index 68b2853bda..2250139c01 100755 --- a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst +++ b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst @@ -22,7 +22,7 @@ The LUNA model includes the following four unitless parameters: - :math:`t_{c,j0}` , which defines the baseline ratio of Rubisco-limited rate to light-limited rate; - :math:`H` , which determines the response of electron transport rate to relative humidity. -The above four parameters are estimated by fitting the LUNA model to a global compilation of >800 obervations located at different biomes, canopy locations, and time of the year from 1993-2013 (Ali et al. 2015). The model inputs are area-based leaf nitrogen content, leaf mass per unit leaf area and the driving environmental conditions (average of past 10 days) including temperature, CO :sub:`2` concentrations, daily mean and maximum radiation, relative humidity and day length. The estimated values in CLM5 for the listed parameters are 0.0311, 0.1745, 0.8054, and 6.0999, repectively. In LUNA V1.0, the estimated parameter values are for C3 natural vegetations. In view that potentially large differences in photosythetic capacity could exist between crops and natural vegetations due to human selection and genetic modifications, in CLM5, the LUNA model are used only for C3 natural vegetations. The photosynthetic capacity for crops and C4 plants are thus still kept the same as CLM4.5. Namely, it is estimated based on the leaf nitrogen content, fixed RUBISCO allocations for :math:`V_{c\max 25}` and an adjusting factor to account for the impact of day length. In CLM5, the model simulates both sun-lit and shaded leaves; however, because the sun-lit and shaded leaves can changes through the day based on the sun angles, we do not differentiate the photosynthetic capacity difference for sun-lit or shaded leaves. +The above four parameters are estimated by fitting the LUNA model to a global compilation of >800 obervations located at different biomes, canopy locations, and time of the year from 1993-2013 (Ali et al. 2015). The model inputs are area-based leaf nitrogen content, leaf mass per unit leaf area and the driving environmental conditions (average of past 10 days) including temperature, CO :sub:`2` concentrations, daily mean and maximum radiation, relative humidity and day length. The estimated values in CLM5 for the listed parameters are 0.0311, 0.17, 0.8054, and 6.0999, repectively. In LUNA V1.0, the estimated parameter values are for C3 natural vegetations. In view that potentially large differences in photosythetic capacity could exist between crops and natural vegetations due to human selection and genetic modifications, in CLM5, the LUNA model are used only for C3 natural vegetations. The photosynthetic capacity for crops and C4 plants are thus still kept the same as CLM4.5. Namely, it is estimated based on the leaf nitrogen content, fixed RUBISCO allocations for :math:`V_{c\max 25}` and an adjusting factor to account for the impact of day length. In CLM5, the model simulates both sun-lit and shaded leaves; however, because the sun-lit and shaded leaves can changes through the day based on the sun angles, we do not differentiate the photosynthetic capacity difference for sun-lit or shaded leaves. .. _Model structure: @@ -53,65 +53,65 @@ The structural nitrogen, :math:`N_{\text{str}}`, is calculated as the multiplica N_{\text{str}} = \text{SNC} \cdot \text{LMA} -where :math:`\text{SNC}` is set to be fixed at 0.002 (gN/g biomass), based on data on C:N ratio from dead wood (White etal.,2000), and :math:`\text{LMA}` is the inverse of specific leaf area at the canopy top (:math:`SLA_{\text{0}}`), a PFT-level parameter (:numref:`Table Plant functional type (PFT) leaf N parameters`). +where :math:`\text{SNC}` is set to be fixed at 0.004 (gN/g biomass), based on data on C:N ratio from dead wood (White etal.,2000), and :math:`\text{LMA}` is the inverse of specific leaf area at the canopy top (:math:`SLA_{\text{0}}`), a PFT-level parameter (:numref:`Table Plant functional type (PFT) leaf N parameters`). .. _Table Plant functional type (PFT) leaf N parameters: .. table:: Plant functional type (PFT) leaf N parameters. - +----------------------------------+--------------------------+--------------------------+ - | PFT | :math:`SLA_{\text{0}}` | :math:`N_{\text{cb}}` | - +==================================+==========================+==========================+ - | NET Temperate | 0.0100 | 0.0509 | - +----------------------------------+--------------------------+--------------------------+ - | NET Boreal | 0.0100 | 0.0466 | - +----------------------------------+--------------------------+--------------------------+ - | NDT Boreal | 0.0202 | 0.0546 | - +----------------------------------+--------------------------+--------------------------+ - | BET Tropical | 0.0190 | 0.0461 | - +----------------------------------+--------------------------+--------------------------+ - | BET temperate | 0.0190 | 0.0515 | - +----------------------------------+--------------------------+--------------------------+ - | BDT tropical | 0.0308 | 0.0716 | - +----------------------------------+--------------------------+--------------------------+ - | BDT temperate | 0.0308 | 0.1007 | - +----------------------------------+--------------------------+--------------------------+ - | BDT boreal | 0.0308 | 0.1007 | - +----------------------------------+--------------------------+--------------------------+ - | BES temperate | 0.0180 | 0.0517 | - +----------------------------------+--------------------------+--------------------------+ - | BDS temperate | 0.0307 | 0.0943 | - +----------------------------------+--------------------------+--------------------------+ - | BDS boreal | 0.0307 | 0.0943 | - +----------------------------------+--------------------------+--------------------------+ - | C\ :sub:`3` arctic grass | 0.0402 | 0.1365 | - +----------------------------------+--------------------------+--------------------------+ - | C\ :sub:`3` grass | 0.0402 | 0.1365 | - +----------------------------------+--------------------------+--------------------------+ - | C\ :sub:`4` grass | 0.0385 | 0.0900 | - +----------------------------------+--------------------------+--------------------------+ - | Temperate Corn | 0.0500 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - | Spring Wheat | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Temperate Soybean | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Cotton | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Rice | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Sugarcane | 0.0500 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - | Tropical Corn | 0.0500 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - | Tropical Soybean | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Miscanthus | 0.0570 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - | Switchgrass | 0.0490 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - -Notes: :math:`SLA_{\text{0}}` is the specific leaf area at the canopy top (m :sup:`2` leaf/g biomass), and :math:`N_{\text{cb}}` is the fraction of leaf nitrogen in Rubisco (g N in Rubisco g :sup:`-1` N) + +----------------------------------+--------------------------+ + | PFT | :math:`SLA_{\text{0}}` | + +==================================+==========================+ + | NET Temperate | 0.01000 | + +----------------------------------+--------------------------+ + | NET Boreal | 0.01000 | + +----------------------------------+--------------------------+ + | NDT Boreal | 0.02018 | + +----------------------------------+--------------------------+ + | BET Tropical | 0.01900 | + +----------------------------------+--------------------------+ + | BET temperate | 0.01900 | + +----------------------------------+--------------------------+ + | BDT tropical | 0.03080 | + +----------------------------------+--------------------------+ + | BDT temperate | 0.03080 | + +----------------------------------+--------------------------+ + | BDT boreal | 0.03080 | + +----------------------------------+--------------------------+ + | BES temperate | 0.01798 | + +----------------------------------+--------------------------+ + | BDS temperate | 0.03072 | + +----------------------------------+--------------------------+ + | BDS boreal | 0.02800 | + +----------------------------------+--------------------------+ + | C\ :sub:`3` arctic grass | 0.02100 | + +----------------------------------+--------------------------+ + | C\ :sub:`3` grass | 0.04024 | + +----------------------------------+--------------------------+ + | C\ :sub:`4` grass | 0.03846 | + +----------------------------------+--------------------------+ + | Temperate Corn | 0.05000 | + +----------------------------------+--------------------------+ + | Spring Wheat | 0.03500 | + +----------------------------------+--------------------------+ + | Temperate Soybean | 0.03500 | + +----------------------------------+--------------------------+ + | Cotton | 0.03500 | + +----------------------------------+--------------------------+ + | Rice | 0.03500 | + +----------------------------------+--------------------------+ + | Sugarcane | 0.05000 | + +----------------------------------+--------------------------+ + | Tropical Corn | 0.05000 | + +----------------------------------+--------------------------+ + | Tropical Soybean | 0.03500 | + +----------------------------------+--------------------------+ + | Miscanthus | 0.03500 | + +----------------------------------+--------------------------+ + | Switchgrass | 0.03500 | + +----------------------------------+--------------------------+ + +Notes: :math:`SLA_{\text{0}}` is the specific leaf area at the canopy top (m :sup:`2` leaf/g biomass) We assume that plants optimize their nitrogen allocations (i.e., :math:`N_{\text{store}}`, :math:`N_{\text{resp}}`, :math:`N_{\text{lc}}`, :math:`N_{\text{et}}`, :math:`N_{\text{cb}}`) to maximize the photosynthetic carbon gain, defined as the gross photosynthesis ( :math:`A` ) minus the maintenance respiration for photosynthetic enzymes ( :math:`R_{\text{psn}}` ), under specific environmental conditions and given plant's strategy of leaf nitrogen use. Namely, the solutions of nitrogen allocations \{ :math:`N_{\text{store}}`, :math:`N_{\text{resp}}`, :math:`N_{\text{lc}}`, :math:`N_{\text{et}}`, :math:`N_{\text{cb}}` \} can be estimated as follows, From f8c2c71c46c7259e55c018a333e6843361d1033f Mon Sep 17 00:00:00 2001 From: olyson Date: Tue, 24 Oct 2023 22:23:44 +0000 Subject: [PATCH 10/11] Resolve documentation problems identified in issue #2194 --- doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index 02188d5e25..130629f0eb 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -895,7 +895,7 @@ The specific yield, :math:`S_{y}`, which depends on the soil properties and the where B is the Clapp-Hornberger exponent. Because :math:`S_{y}` is a function of the soil properties, it results in water table dynamics that are consistent with the soil water fluxes described in section :numref:`Soil Water`. -After the above calculations, two numerical adjustments are implemented to keep the liquid water content of each soil layer (:math:`w_{liq,\, i}` ) within physical constraints of :math:`w_{liq}^{\min } \le w_{liq,\, i} \le \left(\theta_{sat,\, i} -\theta_{ice,\, i} \right)\Delta z_{i}` where :math:`w_{liq}^{\min } =0.01` (mm). First, beginning with the bottom soil layer :math:`i=N_{levsoi}`, any excess liquid water in each soil layer (:math:`w_{liq,\, i}^{excess} =w_{liq,\, i} -\left(\theta_{sat,\, i} -\theta_{ice,\, i} \right)\Delta z_{i} \ge 0`) is successively added to the layer above. Any excess liquid water that remains after saturating the entire soil column (plus a maximum surface ponding depth :math:`w_{liq}^{pond} =10` kg m\ :sup:`-2`), is added to drainage :math:`q_{drai}`. Second, to prevent negative :math:`w_{liq,\, i}`, each layer is successively brought up to :math:`w_{liq,\, i} =w_{liq}^{\min }` by taking the required amount of water from the layer below. If this results in :math:`w_{liq,\, N_{levsoi} } Date: Thu, 26 Oct 2023 15:48:22 +0000 Subject: [PATCH 11/11] Changes in response to review. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 3 +-- .../Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 0b87314361..013efdca08 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -558,8 +558,7 @@ where :math:`w_{wilt}` is the wilting point soil moisture (mm) w_{wilt} = \sum_{j=1}^{N_{irr}} \theta_{wilt} \Delta z_{j} \ , -and :math:`f_{thresh}` is a tuning parameter. The available moisture in -the soil (mm) is +and :math:`f_{thresh}` is a tuning parameter. The available moisture in the soil (mm) is .. math:: :label: 25.65 diff --git a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst index baa05dff59..c233a0cb4b 100644 --- a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst +++ b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst @@ -1,4 +1,4 @@ - _rst_Land-only Mode: +.. _rst_Land-only Mode: Land-Only Mode ================