CCPP V4.0 scidoc update (#402)

* scientific documentation update for UFS public release, add two additional xml files for GFSv15p2 and GFSv16beta

* add two new suites: GFSv15p2_no_nsst and GFSv16beta_no_nsst and GFS ocean scientific documentation

physics/cires_ugwp.F90

@@ -187,7 +187,8 @@ end subroutine cires_ugwp_finalize
 !! \section arg_table_cires_ugwp_run Argument Table
 !! \htmlinclude cires_ugwp_run.html
 !!
-!>\section gen_cires_ugwp_run General Algorithm
+!> \section gen_cires_ugwp CIRES UGWP Scheme General Algorithm
+!! @{
      subroutine cires_ugwp_run(do_ugwp, me,  master, im,  levs, ntrac, dtp, kdt, lonr, &
          oro, oro_uf, hprime, nmtvr, oc, theta, sigma, gamma, elvmax, clx, oa4,        &
          do_tofd, ldiag_ugwp, cdmbgwd, xlat, xlat_d, sinlat, coslat, area,             &
@@ -410,5 +411,6 @@ subroutine cires_ugwp_run(do_ugwp, me,  master, im,  levs, ntrac, dtp, kdt, lonr
     gw_dudt = gw_dudt*(1.-pked) +  ed_dudt*pked
 
     end subroutine cires_ugwp_run
+!! @}
 !>@}
 end module cires_ugwp

physics/docs/ufs_doxyfile → physics/docs/ccppv4_doxyfile

@@ -103,12 +103,19 @@ WARN_LOGFILE           =
 INPUT                  =  pdftxt/mainpage.txt     \
                           pdftxt/all_shemes_list.txt     \
                           pdftxt/GFSv15p2_suite.txt \
+                          pdftxt/GFSv15p2_no_nsst_suite.txt    \              
+                          pdftxt/suite_FV3_GFS_v15p2.xml.txt \
+                          pdftxt/suite_FV3_GFS_v15p2_no_nsst.xml.txt \
                           pdftxt/GFSv16beta_suite.txt \
+                          pdftxt/GFSv16beta_no_nsst_suite.txt \
+                          pdftxt/suite_FV3_GFS_v16beta.xml.txt   \
+                          pdftxt/suite_FV3_GFS_v16beta_no_nsst.xml.txt   \
                           pdftxt/GSD_adv_suite.txt \
                           pdftxt/CPT_adv_suite.txt   \
                           pdftxt/GFS_RRTMG.txt    \
                           pdftxt/GFS_SFCLYR.txt   \
                           pdftxt/GFS_NSST.txt     \
+                          pdftxt/GFS_OCEAN.txt    \
                           pdftxt/GFS_NOAH.txt     \
                           pdftxt/GFS_SFCSICE.txt  \
                           pdftxt/GFS_HEDMF.txt    \
@@ -171,6 +178,7 @@ INPUT                  =  pdftxt/mainpage.txt     \
 ### Land Surface
                         ../sfc_diff.f \
                         ../sfc_nst.f \
+                        ../sfc_ocean.F  \
                         ../module_nst_model.f90 \
                         ../module_nst_parameters.f90 \
                         ../module_nst_water_prop.f90  \

physics/docs/pdftxt/GFS_OCEAN.txt

@@ -0,0 +1,16 @@
+/**
+\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.
+
+\section intra_sfcocean Intraphysics Communication
+\ref arg_table_sfc_ocean_run
+
+
+
+
+
+*/

physics/docs/pdftxt/GFS_UGWPv0.txt

@@ -112,6 +112,6 @@ and dynamical instability of waves described by the linear
 \ref arg_table_cires_ugwp_run
 
 \section gen_al_ugwpv0 General Algorithm
-\ref gen_cires_ugwp_run
+\ref gen_cires_ugwp
 
 */

physics/docs/pdftxt/GFSv15p2_no_nsst_suite.txt

@@ -0,0 +1,127 @@
+/**
+\page GFS_v15p2_no_nsst_page GFS_v15p2_no_nsst Suite 
+
+\section gfsv15_no_nsst_suite_overview Overview
+
+Suite GFS_v15p2_no_nsst is a companion suite of GFS_v15p2 with GRIB2 data initialization.
+
+The GFS_v15p2_no_nsst physics suite uses the parameterizations in the following order:
+ - \ref GFS_RRTMG
+ - \ref GFS_SFCLYR
+ - \ref GFS_OCEAN
+ - \ref GFS_NOAH
+ - \ref GFS_SFCSICE
+ - \ref GFS_HEDMF
+ - \ref GFS_UGWP_v0
+ - \ref GFS_RAYLEIGH
+ - \ref GFS_OZPHYS
+ - \ref GFS_H2OPHYS
+ - \ref GFS_SAMFdeep
+ - \ref GFS_SAMFshal
+ - \ref GFDL_cloud
+ - \ref GFS_CALPRECIPTYPE
+
+\section sdf_gfsv15p2_no_nsst Suite Definition File 
+- For GRIB2  initialization data: \subpage suite_FV3_GFS_v15p2_no_nsst_xml
+
+\section gfs15p2nonsst_nml_opt_des Namelist 
+
+- \b &gfs_physics_nml
+\n \c fhzero         = 6
+\n \c h2o_phys       = .true.
+\n \c ldiag3d        = .false.
+\n \c fhcyc          = 24
+\n \c use_ufo        = .true.
+\n \c pre_rad        = .false.
+\n \c ncld           = 5
+\n \c imp_physics    = 11
+\n \c pdfcld         = .false.
+\n \c fhswr          = 3600.
+\n \c fhlwr          = 3600.
+\n \c ialb           = 1
+\n \c iems           = 1
+\n \c iaer           = 111
+\n \c ico2           = 2
+\n \c isubc_sw       = 2
+\n \c isubc_lw       = 2
+\n \c isol           = 2
+\n \c lwhtr          = .true.
+\n \c swhtr          = .true.
+\n \c cnvgwd         = .true.
+\n \c shal_cnv       = .true.
+\n \c cal_pre        = .false.
+\n \c redrag         = .true.
+\n \c dspheat        = .true.
+\n \c hybedmf        = .true.
+\n \c random_clds    = .false.
+\n \c trans_trac     = .true.
+\n \c cnvcld         = .true.
+\n \c imfshalcnv     = 2
+\n \c imfdeepcnv     = 2
+\n \c cdmbgwd        = 3.5,0.25 <span style="color:red">[1.0,1.2]</span> <span style="color:purple">[0.2,2.5]</span> <span style="color:orange">[0.125,3.0]</span>       ! <span style="color:black">[C768]</span> <span style="color:red">[C384]</span> <span style="color:purple">[C192]</span> <span style="color:orange">[C96]</span>L64
+\n \c prslrd0        = 0.
+\n \c ivegsrc        = 1
+\n \c isot           = 1
+\n \c debug          = .false.
+\n \c oz_phys        = .F.
+\n \c oz_phys_2015   = .T.
+\n \c nstf_name      = 0,0,0,0,0
+\n \c nst_anl        = .true.
+\n \c psautco        = 0.0008,0.0005
+\n \c prautco        = 0.00015,0.00015
+\n \c lgfdlmprad     = .true.
+\n \c effr_in        = .true.
+\n \c do_sppt        = .false.
+\n \c do_shum        = .false.
+\n \c do_skeb        = .false.
+\n \c do_sfcperts    = .false.
+
+- \b &gfdl_cloud_microphysics_nml
+\n \c sedi_transport = .true.
+\n \c do_sedi_heat   = .false.
+\n \c rad_snow       = .true.
+\n \c rad_graupel    = .true.
+\n \c rad_rain       = .true.
+\n \c const_vi       = .F.
+\n \c const_vs       = .F.
+\n \c const_vg       = .F.
+\n \c const_vr       = .F.
+\n \c vi_max         = 1.
+\n \c vs_max         = 2.
+\n \c vg_max         = 12.
+\n \c vr_max         = 12.
+\n \c qi_lim         = 1.
+\n \c prog_ccn       = .false.
+\n \c do_qa          = .true.
+\n \c fast_sat_adj   = .true.
+\n \c tau_l2v        = 225.
+\n \c tau_v2l        = 150.
+\n \c tau_g2v        = 900.
+\n \c rthresh        = 10.e-6  
+\n \c dw_land        = 0.16
+\n \c dw_ocean       = 0.10
+\n \c ql_gen         = 1.0e-3
+\n \c ql_mlt         = 1.0e-3
+\n \c qi0_crt        = 8.0E-5
+\n \c qs0_crt        = 1.0e-3
+\n \c tau_i2s        = 1000.
+\n \c c_psaci        = 0.05
+\n \c c_pgacs        = 0.01
+\n \c rh_inc         = 0.30
+\n \c rh_inr         = 0.30
+\n \c rh_ins         = 0.30
+\n \c ccn_l          = 300.
+\n \c ccn_o          = 100.
+\n \c c_paut         = 0.5
+\n \c c_cracw        = 0.8
+\n \c use_ppm        = .false.
+\n \c use_ccn        = .true.
+\n \c mono_prof      = .true.
+\n \c z_slope_liq    = .true.
+\n \c z_slope_ice    = .true.
+\n \c de_ice         = .false.
+\n \c fix_negative   = .true.
+\n \c icloud_f       = 1
+\n \c mp_time        = 150.
+
+*/