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Merge pull request #420 from mzhangw/scidoc_update
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SCI doc v4.0 updates
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@climbfuji
climbfuji authored Mar 31, 2020
2 parents e0a32c4 + fd0698c commit c385ad4
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7 changes: 4 additions & 3 deletions physics/docs/pdftxt/GFS_OCEAN.txt
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Expand Up @@ -2,9 +2,10 @@
\page GFS_OCEAN GFS Simple Ocean Scheme
\section des_sfcocean Description

The Sea Surface Temperature (SST) is a required filed in Numerical Weather Prediciton (NWP) systems because it
functions as the lower foundary condition for the calculation of air-sea heat fluxes. When the GFS Simple Ocean
Scheme is evoked, the SST is kept constant throughout the forecast.
The Sea Surface Temperature (SST) is a required field in Numerical Weather Prediciton (NWP) systems because it
functions as the lower boundary condition for the calculation of air-sea heat fluxes. The GFS Simple Ocean Scheme
does not change the SST. Therefore, the SST stays constant throughout the forecast unless it is updated by other processes.
In some models, such as the UFS atmosphere, the SST can change if forcing towards the climatology is turned on.

\section intra_sfcocean Intraphysics Communication
\ref arg_table_sfc_ocean_run
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25 changes: 16 additions & 9 deletions physics/docs/pdftxt/all_shemes_list.txt
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Expand Up @@ -85,18 +85,25 @@ at multiple research centers and universities, including Colorado State, Utah, N
uses the convection, microphysics, and boundary layer schemes employed in the Rapid Refresh (RAP) and High-Resolution Rapid Refresh (HRRR \cite Benjamin_2016 )
operational models and was assembled by NOAA/GSD. An assessment of an earlier version of these suites can be found in
<a href="https://ufscommunity.org/#/science/physics"> the UFS portal </a>
and in <a href="https://dtcenter.org/eval/gmtb/phytest2019/"> the DTC website </a> .
and in <a href="https://dtcenter.org/eval/gmtb/phytest2019/"> the DTC website </a> . Two variant suites labelled as \a no_nsst are simplification of GFS_v15p2 and GFS_v16beta.
This simplification is needed when the UFS is initialized with files in GRIdded Binary Edition 2 (GRIB2) format instead of files in NOAA Environmental Modeling
System (NEMS) Input/Output (NEMSIO) format because the fields necesary to predict (SST) are not available in the GRIB2 files.

Table 1. Physics suites option included in this documentation.
\tableofcontents
| Phys suites | GFS_v15p2 | GFS_v16beta | csawmg | GSD_v1 |
|------------------|-----------------------------------|----------------------|---------------------|----------------------|
| Deep Cu | \ref GFS_SAMFdeep | \ref GFS_SAMFdeep | \ref CSAW_scheme | \ref GSD_CU_GF |
| Shallow Cu | \ref GFS_SAMFshal | \ref GFS_SAMFshal | \ref GFS_SAMFshal | \ref GSD_MYNNEDMF and \ref cu_gf_sh_group |
| Microphysics | \ref GFDL_cloud | \ref GFDL_cloud | \ref CPT_MG3 | \ref GSD_THOMPSON |
| PBL/TURB | \ref GFS_HEDMF | \ref GFS_SATMEDMFVDIFQ | \ref GFS_HEDMF | \ref GSD_MYNNEDMF |
| Land | \ref GFS_NOAH | \ref GFS_NOAH | \ref GFS_NOAH | \ref GSD_RUCLSM |
| Gravity Wave Drag| \ref GFS_UGWP_v0 | \ref GFS_UGWP_v0 | \ref GFS_UGWP_v0 | \ref GFS_UGWP_v0 |
| Physics suites | GFS_v15p2 | GFS_v16beta | csawmg | GSD_v1 | GFS_v15p2_no_nsst | GFS_v16beta_no_nsst |
|------------------|----------------------|--------------------------|---------------------|---------------------------------------------|-------------------------|---------------------------|
| Deep Cu | \ref GFS_SAMFdeep | \ref GFS_SAMFdeep | \ref CSAW_scheme | \ref GSD_CU_GF | \ref GFS_SAMFdeep | \ref GFS_SAMFdeep |
| Shallow Cu | \ref GFS_SAMFshal | \ref GFS_SAMFshal | \ref GFS_SAMFshal | \ref GSD_MYNNEDMF and \ref cu_gf_sh_group | \ref GFS_SAMFshal | \ref GFS_SAMFshal |
| Microphysics | \ref GFDL_cloud | \ref GFDL_cloud | \ref CPT_MG3 | \ref GSD_THOMPSON | \ref GFDL_cloud | \ref GFDL_cloud |
| PBL/TURB | \ref GFS_HEDMF | \ref GFS_SATMEDMFVDIFQ | \ref GFS_HEDMF | \ref GSD_MYNNEDMF | \ref GFS_HEDMF | \ref GFS_SATMEDMFVDIFQ |
| Radiation | \ref GFS_RRTMG | \ref GFS_RRTMG | \ref GFS_RRTMG | \ref GFS_RRTMG | \ref GFS_RRTMG | \ref GFS_RRTMG |
| Surface Layer | \ref GFS_SFCLYR | \ref GFS_SFCLYR | \ref GFS_SFCLYR | \ref GFS_SFCLYR | \ref GFS_SFCLYR | \ref GFS_SFCLYR |
| Land | \ref GFS_NOAH | \ref GFS_NOAH | \ref GFS_NOAH | \ref GSD_RUCLSM | \ref GFS_NOAH | \ref GFS_NOAH |
| Gravity Wave Drag| \ref GFS_UGWP_v0 | \ref GFS_UGWP_v0 | \ref GFS_UGWP_v0 | \ref GFS_UGWP_v0 | \ref GFS_UGWP_v0 | \ref GFS_UGWP_v0 |
| Ocean | \ref GFS_NSST | \ref GFS_NSST | \ref GFS_NSST | \ref GFS_NSST | \ref GFS_OCEAN | \ref GFS_OCEAN |
| Ozone | \ref GFS_OZPHYS | \ref GFS_OZPHYS | \ref GFS_OZPHYS | \ref GFS_OZPHYS | \ref GFS_OZPHYS | \ref GFS_OZPHYS |
| Water Vapor | \ref GFS_H2OPHYS | \ref GFS_H2OPHYS | \ref GFS_H2OPHYS | \ref GFS_H2OPHYS | \ref GFS_H2OPHYS | \ref GFS_H2OPHYS |
\tableofcontents


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4 changes: 2 additions & 2 deletions physics/docs/pdftxt/mainpage.txt
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Expand Up @@ -11,8 +11,8 @@ operational implementations. This version contains all parameterizations of the
plus additional developmental schemes. There are four suites supported for use with the Single Column Model (SCM)
developed by the Development Testbed Center (GFS_v15p2, GFS_v16beta, GSD_v1, and csawmg), and four suites
supported for use with the atmospheric component of the UFS (i.e., GFS_v15p2, GFS_v15p2_no_nsst, GFS_v16beta and
GFS_v16beta_no_nsst). The variants labelled as \a no_nsst are a simplification that uses constant sea surface
temperature (SST). This simplification is needed when the UFS is initialized with files in GRIdded Binary Edition 2 (GRIB2)
GFS_v16beta_no_nsst). The variants labelled as \a no_nsst are a simplification of GFS_v15p2 and GFS_v16beta suites
. This simplification is needed when the UFS is initialized with files in GRIdded Binary Edition 2 (GRIB2)
format instead of files in NOAA Environmental Modeling System (NEMS) Input/Output (NEMSIO) format because the
fields necessary to predict (SST) are not available in the GRIB2 files.

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2 changes: 1 addition & 1 deletion physics/docs/pdftxt/suite_input.nml.txt
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Expand Up @@ -484,7 +484,7 @@ and how stochastic perturbations are used in the Noah Land Surface Model.
<tr><td>icloud_f <td>gfdl_cloud_microphys_mod <td>flag (0,1,or 2) for cloud fraction diagnostic scheme <td>0
<tr><td>irain_f <td>gfdl_cloud_microphys_mod <td>flag (0 or 1) for cloud water autoconversion to rain scheme. 0: with subgrid variability; 1: no subgrid variability <td>0
<tr><td>mp_time <td>gfdl_cloud_microphys_mod <td>time step of GFDL cloud microphysics (MP). If \p mp_time isn't divisible by physics time step or is larger than physics time step, the actual MP time step becomes \p dt/NINT[dt/MIN(dt,mp_time)] <td>150.
<tr><td>alin <td>gfdl_cloud_microphys_mod <td>parameter \a a in Lin et al.(1983). Constant in empirical formula for \f$U_R\f$. Increasing(decreasing) \p alin can boost(decrease) accretion of cloud water by rain and rain evaporation <tb>842.
<tr><td>alin <td>gfdl_cloud_microphys_mod <td>parameter \a a in Lin et al.(1983). Constant in empirical formula for \f$U_R\f$. Increasing(decreasing) \p alin can boost(decrease) accretion of cloud water by rain and rain evaporation <td>842.
<tr><td>clin <td>gfdl_cloud_microphys_mod <td>parameter \a c in Lin et al.(1983). Constant in empirical formula for \f$U_S\f$. Increasing(decreasing) \p clin can boost(decrease) accretion of cloud water by snow, accretion of cloud ice by snow, snow sublimation and deposition, and snow melting <td>4.8
<tr><td>t_min <td>gfdl_cloud_microphys_mod <td>temperature threshold for instant deposition. Deposit all water vapor to cloud ice when temperature is lower than \p t_min <td>178.
<tr><td>t_sub <td>gfdl_cloud_microphys_mod <td>temperature threshold for sublimation. Cloud ice, snow or graupel stops(starts) sublimation when temperature is lower(higher) then \p t_sub <td>184.
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21 changes: 6 additions & 15 deletions physics/m_micro.F90
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Expand Up @@ -14,8 +14,7 @@ module m_micro

contains

!>\ingroup mg_driver
!! This subroutine is the MG initialization.
!> This subroutine is the MG initialization.
!> \section arg_table_m_micro_init Argument Table
!! \htmlinclude m_micro_init.html
!!
Expand Down Expand Up @@ -103,20 +102,13 @@ end subroutine m_micro_init
subroutine m_micro_finalize
end subroutine m_micro_finalize

!> \defgroup mg2mg3 Morrison-Gettelman MP scheme Module
!! This module contains the the entity of MG2 and MG3 schemes.
!> @{
!> \defgroup mg_driver Morrison-Gettelman MP Driver Module
!> \defgroup mg2mg3 Morrison-Gettelman MP Driver Module
!! \brief This subroutine is the Morrison-Gettelman MP driver, which computes
!! grid-scale condensation and evaporation of cloud condensate.

#if 0

!!
!> \section arg_table_m_micro_run Argument Table
!! \htmlinclude m_micro_run.html
!> \htmlinclude m_micro_run.html
!!
#endif
!>\ingroup mg_driver
!>\section detail_m_micro_run MG m_micro_run Detailed Algorithm
!> @{
subroutine m_micro_run( im, ix, lm, flipv, dt_i &
Expand Down Expand Up @@ -1869,7 +1861,7 @@ end subroutine m_micro_run
!DONIF Calculate the Brunt_Vaisala frequency

!===============================================================================
!>\ingroup mg_driver
!>\ingroup mg2mg3
!> This subroutine computes profiles of background state quantities for
!! the multiple gravity wave drag parameterization.
!!\section gw_prof_gen MG gw_prof General Algorithm
Expand Down Expand Up @@ -1956,7 +1948,7 @@ subroutine gw_prof (pcols, pver, ncol, t, pm, pi, rhoi, ni, ti, &
end subroutine gw_prof
!> @}

!>\ingroup mg_driver
!>\ingroup mg2mg3
!! This subroutine is to find cloud top based on cloud fraction.
subroutine find_cldtop(ncol, pver, cf, kcldtop)
implicit none
Expand Down Expand Up @@ -1990,6 +1982,5 @@ subroutine find_cldtop(ncol, pver, cf, kcldtop)


end subroutine find_cldtop
!> @}

end module m_micro
4 changes: 0 additions & 4 deletions physics/mp_thompson.F90
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Expand Up @@ -21,11 +21,9 @@ module mp_thompson
contains

!> This subroutine is a wrapper around the actual mp_gt_driver().
#if 0
!! \section arg_table_mp_thompson_init Argument Table
!! \htmlinclude mp_thompson_init.html
!!
#endif
subroutine mp_thompson_init(ncol, nlev, is_aerosol_aware, &
nwfa2d, nifa2d, nwfa, nifa, &
mpicomm, mpirank, mpiroot, &
Expand Down Expand Up @@ -130,11 +128,9 @@ subroutine mp_thompson_init(ncol, nlev, is_aerosol_aware, &
end subroutine mp_thompson_init


#if 0
!> \section arg_table_mp_thompson_run Argument Table
!! \htmlinclude mp_thompson_run.html
!!
#endif
!>\ingroup aathompson
!>\section gen_thompson_hrrr Thompson MP General Algorithm
!>@{
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2 changes: 0 additions & 2 deletions physics/sfc_drv_ruc.F90
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Expand Up @@ -130,11 +130,9 @@ end subroutine lsm_ruc_finalize
!> \defgroup lsm_ruc_group GSD RUC LSM Model
!! This module contains the RUC Land Surface Model developed by NOAA/GSD
!! (Smirnova et al. 2016 \cite Smirnova_2016).
#if 0
!> \section arg_table_lsm_ruc_run Argument Table
!! \htmlinclude lsm_ruc_run.html
!!
#endif
!>\section gen_lsmruc GSD RUC LSM General Algorithm
! DH* TODO - make order of arguments the same as in the metadata table
subroutine lsm_ruc_run & ! inputs
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