This is EMC flake model (NOAA-EMC#164)

* This is EMC flake model
* Updated .gitmodules file under ufs-weather-model and tests/rt.conf
* Updated .gitmodules file under usf-weather-model
* Point to fv3 flake branch
* Updated ccpp_gfs_v16_flake_run.IN to use the new oro data for flake test
* Updated the following files and directories
* update to  the latest ccpp/physics branch
* Updated compile and regression test log files
* Updated ccpp-physics
* point to NOAA-EMC fv3 repo

parm/ccpp_v16beta_flake_c96.nml.IN

@@ -0,0 +1,338 @@
+&amip_interp_nml
+  interp_oi_sst = .true.
+  use_ncep_sst = .true.
+  use_ncep_ice = .false.
+  no_anom_sst = .false.
+  data_set = 'reynolds_oi'
+  date_out_of_range = 'climo'
+/
+
+&atmos_model_nml
+  blocksize = 32
+  chksum_debug = .false.
+  dycore_only = .false.
+  fdiag = 1
+  fhmax = 384
+  fhout = 3
+  fhmaxhf = 120
+  fhouthf = 1
+  ccpp_suite = 'FV3_GFS_v16beta_flake'
+/
+
+&diag_manager_nml
+  prepend_date = .false.
+/
+
+&fms_io_nml
+  checksum_required = .false.
+  max_files_r = 100
+  max_files_w = 100
+/
+
+&mpp_io_nml
+shuffle=1
+deflate_level=1
+/
+
+&fms_nml
+  clock_grain = 'ROUTINE'
+  domains_stack_size = 3000000
+  print_memory_usage = .false.
+/
+
+&fv_core_nml
+  layout = 3,8
+  io_layout = 1,1
+  npx = 97
+  npy = 97
+  ntiles = 6
+  npz = 64
+  grid_type = -1
+  make_nh = .false.
+  fv_debug = .false.
+  range_warn = .false.
+  reset_eta = .false.
+  n_sponge = 10
+  nudge_qv = .true.
+  nudge_dz = .false.
+  tau = 10.
+  rf_cutoff = 7.5e2
+  d2_bg_k1 = 0.20
+  d2_bg_k2 = 0.0
+  kord_tm = -9
+  kord_mt = 9
+  kord_wz = 9
+  kord_tr = 9
+  hydrostatic = .false.
+  phys_hydrostatic = .false.
+  use_hydro_pressure = .false.
+  beta = 0.
+  a_imp = 1.
+  p_fac = 0.1
+  k_split = 2
+  n_split = 6
+  nwat = 6
+  na_init = 0
+  d_ext = 0.
+  dnats = 1
+  fv_sg_adj = 450
+  d2_bg = 0.
+  nord = 2
+  dddmp = 0.1
+  d4_bg = 0.12
+  vtdm4 = 0.02
+  delt_max = 0.002
+  ke_bg = 0.
+  do_vort_damp = .true.
+  external_ic = .true.
+  external_eta = .true.
+  gfs_phil = .false.
+  nggps_ic = .true.
+  mountain = .false.
+  ncep_ic = .false.
+  d_con = 1.
+  hord_mt = 5
+  hord_vt = 5
+  hord_tm = 5
+  hord_dp = -5
+  hord_tr = 8
+  adjust_dry_mass = .false.
+  consv_te = 1.
+  do_sat_adj = .true.
+  consv_am = .false.
+  fill = .true.
+  dwind_2d = .false.
+  print_freq = 6
+  warm_start = .false.
+  no_dycore = .false.
+  z_tracer = .true.
+  agrid_vel_rst = .true.
+  read_increment = .false.
+  res_latlon_dynamics = ""
+/
+
+&external_ic_nml
+  filtered_terrain = .true.
+  levp = 65
+  gfs_dwinds = .true.
+  checker_tr = .false.
+  nt_checker = 0
+/
+
+&gfs_physics_nml
+  fhzero       = 6
+  h2o_phys     = .true.
+  ldiag3d      = .false.
+  fhcyc        = 24
+  use_ufo      = .true.
+  pre_rad      = .false.
+  ncld         = 5
+  imp_physics  = 11
+  pdfcld       = .false.
+  fhswr        = 3600.
+  fhlwr        = 3600.
+  ialb         = 1
+  iems         = 1
+  iaer         = 5111
+  icliq_sw     = 2
+  iovr_lw      = 3
+  iovr_sw      = 3
+  ico2         = 2
+  isubc_sw     = 2
+  isubc_lw     = 2
+  isol         = 2
+  lwhtr        = .true.
+  swhtr        = .true.
+  cnvgwd       = .true.
+  shal_cnv     = .true.
+  cal_pre      = .false.
+  redrag       = .true.
+  dspheat      = .true.
+  hybedmf      = .false.
+  satmedmf     = .true.
+  isatmedmf    = 1
+  lheatstrg    = .true.
+  random_clds  = .false.
+  trans_trac   = .true.
+  cnvcld       = .true.
+  imfshalcnv   = 2
+  imfdeepcnv   = 2
+  cdmbgwd      = 4.0,0.15,1.0,1.0
+  prslrd0      = 0.
+  ivegsrc      = 1
+  isot         = 1
+  lsoil        = 4
+  lsm          = 1
+  iopt_dveg    = 1
+  iopt_crs     = 1
+  iopt_btr     = 1
+  iopt_run     = 1
+  iopt_sfc     = 1
+  iopt_frz     = 1
+  iopt_inf     = 1
+  iopt_rad     = 1
+  iopt_alb     = 2
+  iopt_snf     = 4
+  iopt_tbot    = 2
+  iopt_stc     = 1
+  debug        = .false.
+  oz_phys      = .F.
+  oz_phys_2015 = .T.
+  nstf_name    = 2,1,0,0,0
+  nst_anl      = .true.
+  psautco      = 0.0008,0.0005
+  prautco      = 0.00015,0.00015
+  lgfdlmprad   = .true.
+  effr_in      = .true.
+  ldiag_ugwp   = .false.
+  do_ugwp      = .false.
+  do_tofd      = .true.
+  do_sppt      = .true.
+  do_shum      = .true.
+  do_skeb      = .true.
+  do_sfcperts  = .false.
+/
+
+&gfdl_cloud_microphysics_nml
+  sedi_transport = .true.
+  do_sedi_heat = .false.
+  rad_snow = .true.
+  rad_graupel = .true.
+  rad_rain = .true.
+  const_vi = .F.
+  const_vs = .F.
+  const_vg = .F.
+  const_vr = .F.
+  vi_max = 1.
+  vs_max = 2.
+  vg_max = 12.
+  vr_max = 12.
+  qi_lim = 1.
+  prog_ccn = .false.
+  do_qa = .true.
+  fast_sat_adj = .true.
+  tau_l2v = 225.
+  tau_v2l = 150.
+  tau_g2v = 900.
+  rthresh = 10.e-6  ! This is a key parameter for cloud water
+  dw_land  = 0.16
+  dw_ocean = 0.10
+  ql_gen = 1.0e-3
+  ql_mlt = 1.0e-3
+  qi0_crt = 8.0E-5
+  qs0_crt = 1.0e-3
+  tau_i2s = 1000.
+  c_psaci = 0.05
+  c_pgacs = 0.01
+  rh_inc = 0.30
+  rh_inr = 0.30
+  rh_ins = 0.30
+  ccn_l = 300.
+  ccn_o = 100.
+  c_paut = 0.5
+  c_cracw = 0.8
+  use_ppm = .false.
+  use_ccn = .true.
+  mono_prof = .true.
+  z_slope_liq  = .true.
+  z_slope_ice  = .true.
+  de_ice = .false.
+  fix_negative = .true.
+  icloud_f = 1
+  mp_time = 150.
+  reiflag = 2
+/
+
+&interpolator_nml
+  interp_method = 'conserve_great_circle'
+/
+
+&namsfc
+  FNGLAC   = 'global_glacier.2x2.grb'
+  FNMXIC   = 'global_maxice.2x2.grb'
+  FNTSFC   = 'RTGSST.1982.2012.monthly.clim.grb'
+  FNSNOC   = 'global_snoclim.1.875.grb'
+  FNZORC   = 'igbp'
+  FNALBC   = 'global_snowfree_albedo.bosu.t126.384.190.rg.grb'
+  FNALBC2  = 'global_albedo4.1x1.grb'
+  FNAISC   = 'CFSR.SEAICE.1982.2012.monthly.clim.grb'
+  FNTG3C   = 'global_tg3clim.2.6x1.5.grb'
+  FNVEGC   = 'global_vegfrac.0.144.decpercent.grb'
+  FNVETC   = 'global_vegtype.igbp.t126.384.190.rg.grb'
+  FNSOTC   = 'global_soiltype.statsgo.t126.384.190.rg.grb'
+  FNSMCC   = 'global_soilmgldas.t126.384.190.grb'
+  FNMSKH   = 'seaice_newland.grb'
+  FNTSFA   = ''
+  FNACNA   = ''
+  FNSNOA   = ''
+  FNVMNC   = 'global_shdmin.0.144x0.144.grb'
+  FNVMXC   = 'global_shdmax.0.144x0.144.grb'
+  FNSLPC   = 'global_slope.1x1.grb'
+  FNABSC   = 'global_mxsnoalb.uariz.t126.384.190.rg.grb'
+  LDEBUG   = .false.
+  FSMCL(2) = 99999
+  FSMCL(3) = 99999
+  FSMCL(4) = 99999
+  LANDICE  = .true.
+  FTSFS    = 90
+  FAISL    = 99999
+  FAISS    = 99999
+  FSNOL    = 99999
+  FSNOS    = 99999
+  FSICL    = 99999
+  FSICS    = 99999
+  FTSFL    = 99999
+  FVETL    = 99999
+  FSOTL    = 99999
+  FvmnL    = 99999
+  FvmxL    = 99999
+  FSLPL    = 99999
+  FABSL    = 99999
+/
+
+&fv_grid_nml
+  grid_file = 'INPUT/grid_spec.nc'
+/
+
+&nam_stochy
+  ntrunc = 766
+  lon_s = 1536
+  lat_s = 768
+  skeb = 0.3
+  iseed_skeb = 2019102712451
+  iseed_shum = 2019102712452
+  iseed_sppt = 2019102712453
+  skeb_tau = 21600.
+  skeb_lscale = 500000.
+  skebnorm = 0
+  skeb_npass = 30
+  skeb_vdof = 5
+  shum = 0.005
+  shum_tau = 21600.
+  shum_lscale = 500000.
+  sppt = 0.5
+  sppt_tau = 21600.
+  sppt_lscale = 500000.
+  sppt_logit = .true.
+  sppt_sfclimit = .true.
+  use_zmtnblck = .true.
+/
+
+&nam_sfcperts
+/
+
+&cires_ugwp_nml
+  knob_ugwp_solver  = 2
+  knob_ugwp_source  = 1,1,0,0
+  knob_ugwp_wvspec  = 1,25,25,25
+  knob_ugwp_azdir   = 2,4,4,4
+  knob_ugwp_stoch   = 0,0,0,0
+  knob_ugwp_effac   = 1,1,1,1
+  knob_ugwp_doaxyz  = 1
+  knob_ugwp_doheat  = 1
+  knob_ugwp_dokdis  = 1
+  knob_ugwp_ndx4lh  = 1
+  knob_ugwp_version = 0
+  launch_level      = 27
+/
+