From 55b85b1d452bb38ef335762911e0b0cac5ae11f2 Mon Sep 17 00:00:00 2001 From: sit23 Date: Tue, 14 May 2019 16:15:15 +0100 Subject: [PATCH 01/24] Added code necessary to run shallow water and barotropic vorticity codes to Isca. Downloaded necessary files from ftp://ftp.gfdl.noaa.gov/perm/GFDL_pubrelease/Spectral_Idealized_Atmospheric_Models/spectral_idealized_public_release.tar.gz on 14/05/19. --- src/atmos_spectral_barotropic/atmosphere.F90 | 246 +++++++ src/atmos_spectral_barotropic/atmosphere.html | 174 +++++ src/atmos_spectral_barotropic/barotropic.pdf | Bin 0 -> 80013 bytes .../barotropic_diagnostics.F90 | 152 +++++ .../barotropic_diagnostics.html | 152 +++++ .../barotropic_dynamics.F90 | 573 +++++++++++++++++ .../barotropic_dynamics.html | 371 +++++++++++ .../barotropic_physics.F90 | 173 +++++ .../barotropic_physics.html | 165 +++++ src/atmos_spectral_barotropic/stirring.F90 | 252 ++++++++ src/atmos_spectral_shallow/atmosphere.F90 | 279 ++++++++ src/atmos_spectral_shallow/atmosphere.html | 164 +++++ src/atmos_spectral_shallow/shallow.pdf | Bin 0 -> 62941 bytes .../shallow_diagnostics.F90 | 139 ++++ .../shallow_diagnostics.html | 150 +++++ .../shallow_dynamics.F90 | 607 ++++++++++++++++++ .../shallow_dynamics.html | 370 +++++++++++ .../shallow_physics.F90 | 232 +++++++ .../shallow_physics.html | 210 ++++++ 19 files changed, 4409 insertions(+) create mode 100644 src/atmos_spectral_barotropic/atmosphere.F90 create mode 100644 src/atmos_spectral_barotropic/atmosphere.html create mode 100644 src/atmos_spectral_barotropic/barotropic.pdf create mode 100644 src/atmos_spectral_barotropic/barotropic_diagnostics.F90 create mode 100644 src/atmos_spectral_barotropic/barotropic_diagnostics.html create mode 100644 src/atmos_spectral_barotropic/barotropic_dynamics.F90 create mode 100644 src/atmos_spectral_barotropic/barotropic_dynamics.html create mode 100644 src/atmos_spectral_barotropic/barotropic_physics.F90 create mode 100644 src/atmos_spectral_barotropic/barotropic_physics.html create mode 100644 src/atmos_spectral_barotropic/stirring.F90 create mode 100644 src/atmos_spectral_shallow/atmosphere.F90 create mode 100644 src/atmos_spectral_shallow/atmosphere.html create mode 100644 src/atmos_spectral_shallow/shallow.pdf create mode 100644 src/atmos_spectral_shallow/shallow_diagnostics.F90 create mode 100644 src/atmos_spectral_shallow/shallow_diagnostics.html create mode 100644 src/atmos_spectral_shallow/shallow_dynamics.F90 create mode 100644 src/atmos_spectral_shallow/shallow_dynamics.html create mode 100644 src/atmos_spectral_shallow/shallow_physics.F90 create mode 100644 src/atmos_spectral_shallow/shallow_physics.html diff --git a/src/atmos_spectral_barotropic/atmosphere.F90 b/src/atmos_spectral_barotropic/atmosphere.F90 new file mode 100644 index 000000000..40a01ebb1 --- /dev/null +++ b/src/atmos_spectral_barotropic/atmosphere.F90 @@ -0,0 +1,246 @@ +module atmosphere_mod + +!----------------------------------------------------------------------- +! GNU General Public License +! +! This program is free software; you can redistribute it and/or modify it and +! are expected to follow the terms of the GNU General Public License +! as published by the Free Software Foundation; either version 2 of +! the License, or (at your option) any later version. +! +! This program is distributed in the hope that it will be useful, but WITHOUT +! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY +! or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public +! License for more details. +! +! For the full text of the GNU General Public License, +! write to: Free Software Foundation, Inc., +! 675 Mass Ave, Cambridge, MA 02139, USA. +! or see: http://www.gnu.org/licenses/gpl.html +!----------------------------------------------------------------------- + +use fms_mod, only: open_namelist_file, & + open_restart_file, & + file_exist, & + check_nml_error, & + error_mesg, & + FATAL, WARNING, & + write_version_number, & + mpp_pe, & + mpp_root_pe, & + close_file, & + stdlog, stdout + +use transforms_mod, only: get_deg_lon, & + get_deg_lat, & + get_grid_boundaries, & + get_grid_domain, & + get_spec_domain, & + area_weighted_global_mean, & + atmosphere_domain + +use time_manager_mod, only: time_type, & + set_time, & + get_time, & + interval_alarm, & + operator(+), & + operator(<), & + operator(==) + +use barotropic_dynamics_mod, only: barotropic_dynamics_init, & + barotropic_dynamics, & + barotropic_dynamics_end, & + dynamics_type + +use barotropic_physics_mod, only: barotropic_physics_init, & + barotropic_physics, & + barotropic_physics_end, & + phys_type + +use diag_manager_mod, only: diag_manager_init, & + diag_manager_end + +use barotropic_diagnostics_mod, only: barotropic_diagnostics_init, & + barotropic_diagnostics + +!======================================================================== +implicit none +private +!======================================================================== + +! version information +!======================================================================== +character(len=128) :: version = '$Id: atmosphere.F90,v 17.0 2009/07/21 03:00:15 fms Exp $' +character(len=128) :: tagname = '$Name: siena_201207 $' +!======================================================================== + +public :: atmosphere_init, & + atmosphere, & + atmosphere_end, & + atmosphere_domain + +!======================================================================== + +integer :: unit, seconds, days +integer :: pe, npes, itmp, m, n +integer :: previous, current, future +logical :: root + +integer :: dt_integer +real :: dt_real +type(time_type) :: dt_time_type, Time_init, Time_step + +real :: delta_t ! = 2*dt_real for leapfrog step + +type(phys_type), save :: Phys +type(dynamics_type), save :: Dyn + +integer :: is, ie, js, je, ms, me, ns, ne +integer :: num_lon, num_lat + +logical :: module_is_initialized =.false. + +integer :: print_interval=86400 + +! namelist +!======================================================================== +namelist /atmosphere_nml/ print_interval +!======================================================================== + +contains +!======================================================================= + +subroutine atmosphere_init(Time_init_in, Time, Time_step_in) + +type (time_type), intent(in) :: Time_init_in, Time, Time_step_in + +integer :: i, j, n, nn, ierr, io, unit +integer :: nlon, nlat +integer :: id_lon, id_lat, id_lonb, id_latb + +pe = mpp_pe() +root = (pe == mpp_root_pe()) + +Time_step = Time_step_in +call get_time( Time_step, seconds, days) +dt_integer = 86400*days + seconds +dt_real = float(dt_integer) +dt_time_type = Time_step +Time_init = Time_init_in + +! read the namelist + +if (file_exist('input.nml')) then + unit = open_namelist_file () + ierr=1 + do while (ierr /= 0) + read (unit, nml=atmosphere_nml, iostat=io, end=10) + ierr = check_nml_error (io, 'atmosphere_nml') + enddo + 10 call close_file (unit) +endif +call write_version_number(version, tagname) +if (root) write (stdlog(), nml=atmosphere_nml) + +call barotropic_dynamics_init (Dyn, Time, Time_init, dt_real, id_lon, id_lat, id_lonb, id_latb) + +call get_grid_domain(is,ie,js,je) +call get_spec_domain(ms,me,ns,ne) + +num_lon = Dyn%num_lon +num_lat = Dyn%num_lat + +nlon = ie+1-is ! size of grid on each processor +nlat = je+1-js + +call barotropic_physics_init(Phys) +call barotropic_diagnostics_init(Time, num_lon, num_lat, id_lon, id_lat, id_lonb, id_latb) + +if(Time == Time_init) then + previous = 1 + current = 1 ! starting with a forward step before settling into leapfrog +else + previous = 1 + current = 2 +endif + +module_is_initialized = .true. + +return +end subroutine atmosphere_init + +!===================================================================== + +subroutine atmosphere(Time) + +type (time_type), intent(in) :: Time +integer :: day, second, dt +real :: energy, enstrophy + +if(.not.module_is_initialized) then + call error_mesg('atmosphere', & + 'atmosphere_init has not been called', FATAL) +end if + +call get_time(Time_step, second, day) +dt = second + 86400*day + +Dyn%Tend%u = 0.0 +Dyn%Tend%v = 0.0 +if(Dyn%grid_tracer) Dyn%Tend%tr = 0.0 +if(Dyn%spec_tracer) Dyn%Tend%trs = 0.0 + +if(Time == Time_init) then + delta_t = dt_real + future = 2 +else + delta_t = 2.0*dt_real + future = previous +endif + +call barotropic_physics(Time, & + Dyn%Tend%u, Dyn%Tend%v, & + Dyn%Grid%u, Dyn%Grid%v, & + delta_t, previous, current, & + Phys) + +call barotropic_dynamics(Time, Time_init, & + Dyn, previous, current, future, delta_t) + +previous = current +current = future + +call barotropic_diagnostics (Time+Time_step, Dyn, Phys, current) + +enstrophy = area_weighted_global_mean(Dyn%grid%vor(:,:,current)*Dyn%grid%vor(:,:,previous)) +energy = -area_weighted_global_mean(Dyn%grid%stream*Dyn%grid%vor(:,:,previous)) + +if(root) then + call get_time(Time+Time_step, second, day) + if(mod(second+86400*day, print_interval) < dt) then + write(stdout(),1000) day, second, energy, enstrophy + end if +end if +1000 format(1x, 'day =',i6,2x,'second =', i6,2x,'energy = ',e13.6,3x,'enstrophy = ',e13.6) + +return +end subroutine atmosphere + +!======================================================================================= + +subroutine atmosphere_end + +if(.not.module_is_initialized) then + call error_mesg('atmosphere_end', & + 'atmosphere_init has not been called.', FATAL) +end if + +call barotropic_physics_end (Phys) +call barotropic_dynamics_end (Dyn, previous, current) +module_is_initialized = .false. + +return +end subroutine atmosphere_end + +!======================================================================================= +end module atmosphere_mod diff --git a/src/atmos_spectral_barotropic/atmosphere.html b/src/atmos_spectral_barotropic/atmosphere.html new file mode 100644 index 000000000..7b937f1f1 --- /dev/null +++ b/src/atmos_spectral_barotropic/atmosphere.html @@ -0,0 +1,174 @@ + +module atmosphere_mod + + +
+PUBLIC INTERFACE / +DATA / +ROUTINES / +NAMELIST / +ERRORS + +

+ +

module atmosphere_mod

+ + +
+     Contact: Isaac Held
+     Reviewers: Peter Phillipps
+
+ + + +
+

OVERVIEW

+ +
+   A spectral transform model for two-dimensional, non-divergent flow on the
+   surface of the sphere.  
+
+ + + +
+

DESCRIPTION

+ +
+   Integrates the barotropic vorticity equation for nondivergent flow on the
+   sphere using the spectral transform technique.  Also allows for the
+   inclusion of a passive tracer advected by the same spectral advection
+   algorithm as  the vorticity, and a gridpoint tracer advected with a finite
+   volume  algorithm on the transform grid.  The default initial condition 
+   provided as an example is a zonal flow resembling that in the Northern
+   winter,  plus a sinusoidal disurbance localized in midlatitudes.
+
+   For a full description of the model and algorithms used, see barotropic.ps
+
+   The interfaces in this module are the generic intefaces required by the
+   main program that can be used to drive various idealized atmospheric
+   models within FMS. Model resolution and related paramters are set in
+   namelists within the modules barotropic_xxx.
+
+ + + +
+

OTHER MODULES USED

+ +
+     fms_mod
+     constants_mod
+     transforms_mod
+     time_manager_mod
+     diag_manager_mod
+     barotropic_dynamics_mod
+     barotropic_physics_mod
+     barotopic_diagnostics_mod
+
+ + + +
+

PUBLIC INTERFACE

+ +
+
+  use atmosphere_mod [,only: atmosphere_init,       
+                             atmosphere,
+			     atmosphere_end]
+                                
+
+ + + +
+

PUBLIC DATA

+ +
+     
+  There are no pubic data types
+ 
+
+ + + +
+

PUBLIC ROUTINES

+ +
+
+subroutine atmosphere_init. Initializes the model.
+subroutine atmosphere.      Integrates forward one time step
+subroutine atmosphere_end.  Terminates model, cleaning up memory and finalizing diagnostics.
+
+
+
+
+ subroutine atmosphere_init(Time_init, Time, Time_step)
+
+    input:
+ 
+    type(time_type) :: Time_init -- Initial model time
+
+    type(time_type) :: Time      -- Model time
+
+    type(time_type) :: Time_step -- Time step
+       
+    When Time=Time_init, the first time step is a forward
+    step rather than leap frog because a cold start is assumed.
+
+    The FMS main program that runs the solo atmospheric models
+    obtains Time_init from the diag_table and Time from its namelist.
+
+
+

+
+
+  subroutine atmosphere(Time)
+
+    input:
+ 
+    type(time_type) :: Time -- Model time
+      
+    Integrates forward one time step
+
+
+

+ 
+   subroutine atmosphere_end(Atmos)
+   
+    No calling arguments.
+      
+    Terminates model, cleaning up memory and finalizing diagnostics
+    
+
+

+

+
+
+
NAMELIST

+
+
+&atmosphere_nml
+
+   print_interval, integer : time interval in seconds 
+   between prints of global mean energy and enstrophy to standard output
+

+
+
+
+

+
ERROR MESSAGES

+
+
+
+  Fatal error message if any public routine is called prior to atmosphere_init
+
+

+
+
+
+

+
+
diff --git a/src/atmos_spectral_barotropic/barotropic.pdf b/src/atmos_spectral_barotropic/barotropic.pdf
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diff --git a/src/atmos_spectral_barotropic/barotropic_diagnostics.F90 b/src/atmos_spectral_barotropic/barotropic_diagnostics.F90
new file mode 100644
index 000000000..69cfc096e
--- /dev/null
+++ b/src/atmos_spectral_barotropic/barotropic_diagnostics.F90
@@ -0,0 +1,152 @@
+
+module barotropic_diagnostics_mod
+
+!-----------------------------------------------------------------------
+!                   GNU General Public License                        
+!                                                                      
+! This program is free software; you can redistribute it and/or modify it and  
+! are expected to follow the terms of the GNU General Public License  
+! as published by the Free Software Foundation; either version 2 of   
+! the License, or (at your option) any later version.                 
+!                                                                      
+! This program is distributed in the hope that it will be useful, but WITHOUT    
+! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  
+! or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public    
+! License for more details.                                           
+!                                                                      
+! For the full text of the GNU General Public License,                
+! write to: Free Software Foundation, Inc.,                           
+!           675 Mass Ave, Cambridge, MA 02139, USA.                   
+! or see:   http://www.gnu.org/licenses/gpl.html                      
+!-----------------------------------------------------------------------
+
+use              fms_mod, only: write_version_number, &
+                                mpp_pe,      &
+                                mpp_root_pe, &
+                                error_mesg, FATAL
+
+use       transforms_mod, only: get_grid_domain,     &
+                                get_spec_domain,     & 
+                                grid_domain,         &
+                                trans_spherical_to_grid
+
+use     diag_manager_mod, only: register_diag_field, &
+                                register_static_field, &
+                                send_data
+
+use     time_manager_mod, only: time_type, &
+                                get_time
+
+use barotropic_physics_mod,  only:  phys_type
+use barotropic_dynamics_mod, only:  grid_type, dynamics_type
+
+implicit none
+private
+
+public :: barotropic_diagnostics_init, &
+          barotropic_diagnostics
+
+character(len=84), parameter :: version = '$Id: barotropic_diagnostics.F90,v 17.0 2009/07/21 03:00:18 fms Exp $'
+character(len=84), parameter :: tagname = '$Name: siena_201207 $'
+
+logical :: module_is_initialized = .false.
+
+character(len=8)  :: axiset   = 'barotropic'
+character(len=84) :: mod_name = 'barotropic_diagnostics'
+
+integer :: id_vor, id_stream, id_pv, id_u, id_v, id_trs, id_tr, id_eddy_vor, id_delta_u
+integer :: is, ie, js, je, ms, me, ns, ne
+
+contains
+
+!-----------------------------------------------------------------------------------------------------------------
+subroutine barotropic_diagnostics_init(Time, lon_max, lat_max, id_lon, id_lat, id_lonb, id_latb)
+
+type(time_type), intent(in) :: Time
+integer, intent(in) :: lon_max, lat_max, id_lon, id_lat, id_lonb, id_latb
+
+integer, dimension(2) :: axis_2d
+
+integer :: log_unit
+integer :: namelist_unit, ierr, io
+logical :: used
+
+call write_version_number(version, tagname)
+
+call get_grid_domain(is, ie, js, je)
+call get_spec_domain(ms, me, ns, ne)
+
+axis_2d(1) = id_lon
+axis_2d(2) = id_lat 
+
+id_u       = register_diag_field(mod_name, 'ucomp'   , axis_2d, Time, 'u_wind'            , 'm/s'  ) 
+id_v       = register_diag_field(mod_name, 'vcomp'   , axis_2d, Time, 'v_wind'            , 'm/s'  ) 
+id_vor     = register_diag_field(mod_name, 'vor'     , axis_2d, Time, 'relative vorticity', '1/s'  )
+id_pv      = register_diag_field(mod_name, 'pv'      , axis_2d, Time, 'absolute vorticity', '1/s'  )
+id_stream  = register_diag_field(mod_name, 'stream'  , axis_2d, Time, 'streamfunction'    , 'm^2/s')
+id_trs     = register_diag_field(mod_name, 'trs'     , axis_2d, Time, 'spectral tracer'   , 'none' )
+id_tr      = register_diag_field(mod_name, 'tr'      , axis_2d, Time, 'grid tracer'       , 'none' )
+id_eddy_vor= register_diag_field(mod_name, 'eddy_vor', axis_2d, Time, 'eddy vorticity'    , '1/s'  )
+id_delta_u = register_diag_field(mod_name, 'delta_u' , axis_2d, Time, 'change in zonal wind','m/s' )
+
+module_is_initialized = .true.
+
+return
+end subroutine barotropic_diagnostics_init
+
+!--------------------------------------------------------------------------------------------
+
+subroutine barotropic_diagnostics(Time, Dyn, Phys, time_index)
+
+type(time_type), intent(in) :: Time
+type(phys_type), intent(in) :: Phys
+type(dynamics_type), intent(in) :: Dyn
+integer,         intent(in) :: time_index
+
+real,    dimension(is:ie,js:je) :: grid_tmp
+real,    dimension(is:ie,js:je) :: delta_zonal_u
+complex, dimension(ms:me,ns:ne) :: spec_tmp
+logical :: used
+integer :: j
+
+if(.not.module_is_initialized) call error_mesg('barotropic_diagnostics', &
+                              'barotropic_diagnostics_init has not been called', FATAL)
+   
+if(id_u        > 0) used = send_data(id_u       , Dyn%Grid%u       (:,:,time_index) , time)
+if(id_v        > 0) used = send_data(id_v       , Dyn%Grid%v       (:,:,time_index) , time)
+if(id_vor      > 0) used = send_data(id_vor     , Dyn%Grid%vor     (:,:,time_index) , time)
+if(id_pv       > 0) used = send_data(id_pv      , Dyn%Grid%pv      (:,:)            , time)
+if(id_stream   > 0) used = send_data(id_stream  , Dyn%Grid%stream  (:,:)            , time)
+if(id_tr       > 0) used = send_data(id_tr      , Dyn%Grid%tr      (:,:,time_index) , time)
+if(id_trs      > 0) used = send_data(id_trs     , Dyn%Grid%trs     (:,:,time_index) , time)
+if(id_eddy_vor > 0) then
+  spec_tmp = Dyn%Spec%vor(:,:,time_index)
+  if(ms == 0) spec_tmp(0,:) = cmplx(0.0,0.0)
+  call trans_spherical_to_grid(spec_tmp, grid_tmp)
+  used = send_data(id_eddy_vor, grid_tmp, time)
+endif
+if(id_delta_u > 0) then
+  do j=js,je
+    delta_zonal_u(:,j) = sum(Dyn%Grid%u(:,j,time_index))/Dyn%num_lon - Dyn%Grid%zonal_u_init(j)
+  enddo
+  used = send_data(id_delta_u, delta_zonal_u, time)
+endif
+
+return
+end subroutine barotropic_diagnostics
+!--------------------------------------------------------------------------------------------
+
+subroutine barotropic_diagnostics_end(Time)
+
+type(time_type), intent(in) :: Time
+
+if(.not.module_is_initialized) call error_mesg('barotropic_diagnostics_end', &
+                              'barotropic_diagnostics_init has not been called', FATAL)
+
+module_is_initialized = .false.
+
+return
+end subroutine barotropic_diagnostics_end
+!--------------------------------------------------------------------------------------------
+
+end module barotropic_diagnostics_mod
diff --git a/src/atmos_spectral_barotropic/barotropic_diagnostics.html b/src/atmos_spectral_barotropic/barotropic_diagnostics.html
new file mode 100644
index 000000000..d852a921d
--- /dev/null
+++ b/src/atmos_spectral_barotropic/barotropic_diagnostics.html
@@ -0,0 +1,152 @@
+
+module barotropic_diagnostics_mod
+
+
+

+
+
+
module barotropic_diagnostics_mod

+
+
+
+     Contact: Isaac Held
+     Reviewers: Peter Phillipps
+
+

+
+
+
+

+
OVERVIEW

+
+
+
+   The diagnostics module for the model that solves the barotropic vorticity
+   equation on the sphere  
+   
+

+
+
+
+

+
DESCRIPTION

+
+
+
+   Using the diagnostics manager, creates output files for the barotropic model.
+   Variables currently available for output are
+       zonal wind 
+       meridional wind 
+       relative vorticity
+       absolute vorticity
+       streamfunction
+       spectral tracer in grid domain
+       grid tracer
+       
+   Whether or not these fields are actually output, the location of the 
+   output, the frequency of output, whether or not the output is averaged
+   in time or an instantaneous snapshot, is controlled by a 
+   diag_table file utilized by the diagnostics manager module
+       
+   One can add other diagnostics by following the (somewhat convoluted)
+       pattern within the program
+
+
+

+
+
+
+

+
OTHER MODULES USED

+
+
+
+     diag_manaager_mod
+     transforms_mod
+     time_manager_mod
+     barotropic_dynamics_mod
+     barotropic_physics_mod
+
+

+
+
+
+

+
PUBLIC INTERFACE

+
+
+
+  use barotropic_diagnostics_mod [,only: barotropic_diagnostics_init,       
+                                         barotropic_diagnostics]
+                                
+

+
+
+
+
+

+
PUBLIC ROUTINES

+
+
+
+subroutine  barotropic_diagnostics_init
+subroutine  barotropic_diagnostics
+
+
+
+
+ subroutine barotropic_diagnostics_init(Time, num_lon, num_lat)
+ 
+   type(time_type)    , intent(in)     :: Time
+         current time 
+   integer, intent(in) :: num_lon, num_lat
+      num_lon = number of longitudes in global domain
+      num_lat = number of latitudes in global domain
+         
+
+   Initializes module
+
+
+
+

+
+
+
+  subroutine barotropic_diagnostics (Time, Grid, Phys, time_index)
+  
+    type(time_type), intent(in) :: Time
+    type(phys_type), intent(in) :: Phys
+    type(grid_type), intent(in) :: Grid
+    integer,         intent(in) :: time_index
+    
+    phys_type is defined in barotropic_physics_mod; 
+       Phys is currently empty as there is no information generated in 
+       barotropic_physics_mod to be output;
+       
+    grid_type is defined in barotropic_dynamics_mod: 
+      Grid contains all of the fields to be output
+      
+    many of the grid fields in grid_type are dimensioned (lon, lat, time_index)
+     where time_index = 1 or 2 -- the two time levels needed to update the
+     state of the model using a leapfrog step are toggled between (:,:,1)
+     and (:,:,2).  The input time_index (which must equal either 1 or 2) 
+     determines which of these two fields is output)
+     
+     (this is confusing -- the calling program needs to know what has
+      been placed in which slot -- it would be better to store this 
+      information within the data type)
+ 
+
+
+
+

+
+
+
diff --git a/src/atmos_spectral_barotropic/barotropic_dynamics.F90 b/src/atmos_spectral_barotropic/barotropic_dynamics.F90
new file mode 100644
index 000000000..07922fdbc
--- /dev/null
+++ b/src/atmos_spectral_barotropic/barotropic_dynamics.F90
@@ -0,0 +1,573 @@
+module barotropic_dynamics_mod
+
+!-----------------------------------------------------------------------
+!                   GNU General Public License                        
+!                                                                      
+! This program is free software; you can redistribute it and/or modify it and  
+! are expected to follow the terms of the GNU General Public License  
+! as published by the Free Software Foundation; either version 2 of   
+! the License, or (at your option) any later version.                 
+!                                                                      
+! This program is distributed in the hope that it will be useful, but WITHOUT    
+! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  
+! or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public    
+! License for more details.                                           
+!                                                                      
+! For the full text of the GNU General Public License,                
+! write to: Free Software Foundation, Inc.,                           
+!           675 Mass Ave, Cambridge, MA 02139, USA.                   
+! or see:   http://www.gnu.org/licenses/gpl.html                      
+!-----------------------------------------------------------------------
+
+use               fms_mod, only: open_namelist_file,   &
+                                 open_restart_file,    &
+                                 file_exist,           &
+                                 check_nml_error,      &
+                                 error_mesg,           &
+                                 mpp_error,            &
+                                 FATAL, WARNING,       &
+                                 write_version_number, &
+                                 mpp_pe,               &
+                                 mpp_root_pe,          &
+                                 read_data,            &
+                                 write_data,           &
+                                 set_domain,           &
+                                 close_file,           &
+                                 stdlog
+
+use    time_manager_mod,  only : time_type,      &
+                                 get_time,       &
+                                 operator(==),   &
+                                 operator(-)
+
+use         constants_mod,  only: radius, omega
+
+use         transforms_mod, only: transforms_init,         transforms_end,          &
+                                  get_grid_boundaries,                              &
+                                  trans_spherical_to_grid, trans_grid_to_spherical, &  
+                                  compute_laplacian,                                &
+                                  get_sin_lat,             get_cos_lat,             &
+                                  get_deg_lon,             get_deg_lat,             &
+                                  get_grid_domain,         get_spec_domain,         &
+                                  spectral_domain,         grid_domain,             &
+                                  vor_div_from_uv_grid,    uv_grid_from_vor_div,    &
+                                  horizontal_advection
+
+use   spectral_damping_mod, only: spectral_damping_init,  &
+                                  compute_spectral_damping
+
+use           leapfrog_mod, only: leapfrog
+
+use       fv_advection_mod, only: fv_advection_init, &
+                                  a_grid_horiz_advection
+
+use           stirring_mod, only: stirring_init, stirring, stirring_end
+
+!===============================================================================================
+implicit none
+private
+!===============================================================================================
+
+public :: barotropic_dynamics_init, &
+          barotropic_dynamics,      &
+          barotropic_dynamics_end,  &
+          dynamics_type,            &
+          grid_type,                &
+          spectral_type,            &
+          tendency_type
+
+
+! version information 
+!===================================================================
+character(len=128) :: version = '$Id: barotropic_dynamics.F90,v 17.0 2009/07/21 03:00:21 fms Exp $'
+character(len=128) :: tagname = '$Name: siena_201207 $'
+!===================================================================
+
+type grid_type
+   real, pointer, dimension(:,:,:) :: u=>NULL(), v=>NULL(), vor=>NULL(), trs=>NULL(), tr=>NULL()
+   real, pointer, dimension(:,:)   :: pv=>NULL(), stream=>NULL()
+   real, pointer, dimension(:)     :: zonal_u_init=>NULL()
+end type
+type spectral_type
+   complex, pointer, dimension(:,:,:) :: vor=>NULL(), trs=>NULL()
+end type
+type tendency_type
+   real, pointer, dimension(:,:) :: u=>NULL(), v=>NULL(), trs=>NULL(), tr=>NULL()
+end type
+type dynamics_type
+   type(grid_type)     :: grid
+   type(spectral_type) :: spec
+   type(tendency_type) :: tend
+   integer             :: num_lon, num_lat
+   logical             :: grid_tracer, spec_tracer
+end type
+
+integer, parameter :: num_time_levels = 2
+
+integer :: is, ie, js, je, ms, me, ns, ne
+
+logical :: module_is_initialized = .false.
+
+real,  allocatable, dimension(:)   :: sin_lat, cos_lat, rad_lat, rad_lon, &
+                                      deg_lat, deg_lon, &
+                                      coriolis, glon_bnd, glat_bnd
+
+integer :: pe, npes
+
+! namelist parameters with default values
+
+logical :: check_fourier_imag = .false.
+logical :: south_to_north     = .true.
+logical :: triang_trunc       = .true.
+
+real    :: robert_coeff       = 0.04
+real    :: longitude_origin   = 0.0
+
+character(len=64) :: damping_option = 'resolution_dependent'
+integer :: damping_order      = 4
+real    :: damping_coeff      = 1.e-04
+real    :: damping_coeff_r    = 0.0
+
+real     :: zeta_0     = 8.e-05
+integer  :: m_0        = 4
+real     :: eddy_width = 15.0
+real     :: eddy_lat   = 45.0
+
+logical :: spec_tracer      = .true.
+logical :: grid_tracer      = .true.
+
+integer :: num_lat            = 128
+integer :: num_lon            = 256
+integer :: num_fourier        = 85
+integer :: num_spherical      = 86
+integer :: fourier_inc        = 1
+
+real, dimension(2) :: valid_range_v = (/-1.e3,1.e3/)
+character(len=64) :: initial_zonal_wind = 'two_jets'
+
+namelist /barotropic_dynamics_nml/ check_fourier_imag, south_to_north, &
+                                 triang_trunc,                         &
+                                 num_lon, num_lat, num_fourier,        &
+                                 num_spherical, fourier_inc,           &
+                                 longitude_origin, damping_option,     &
+                                 damping_order,     damping_coeff,     &
+                                 damping_coeff_r,   robert_coeff,      &
+                                 spec_tracer, grid_tracer,             &
+                                 eddy_lat, eddy_width, zeta_0, m_0,    &
+                                 valid_range_v, initial_zonal_wind
+
+contains
+
+!===============================================================================================
+
+subroutine barotropic_dynamics_init (Dyn, Time, Time_init, dt_real, id_lon, id_lat, id_lonb, id_latb)
+
+type(dynamics_type), intent(inout)  :: Dyn
+type(time_type)    , intent(in)     :: Time, Time_init
+real, intent(in) :: dt_real
+integer, intent(out) :: id_lon, id_lat, id_lonb, id_latb
+
+integer :: i, j
+
+real,    allocatable, dimension(:)   :: glon_bnd, glat_bnd
+complex, allocatable, dimension(:,:) :: div
+real :: xx, yy, dd
+
+integer  :: ierr, io, unit, pe
+logical  :: root
+
+! < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < >
+
+call write_version_number (version, tagname)
+
+pe   =  mpp_pe()
+root = (pe == mpp_root_pe())
+
+if (file_exist('input.nml')) then
+  unit = open_namelist_file ()
+  ierr=1
+  do while (ierr /= 0)
+    read  (unit, nml=barotropic_dynamics_nml, iostat=io, end=10)
+    ierr = check_nml_error (io, 'barotropic_dynamics_nml')
+  enddo
+  10 call close_file (unit)
+endif
+
+
+if (root) write (stdlog(), nml=barotropic_dynamics_nml)
+
+call transforms_init(radius, num_lat, num_lon, num_fourier, fourier_inc, num_spherical, &
+         south_to_north=south_to_north,   &
+         triang_trunc=triang_trunc,       &
+         longitude_origin=longitude_origin       )
+
+call get_grid_domain(is,ie,js,je)
+call get_spec_domain(ms,me,ns,ne)
+
+Dyn%num_lon      = num_lon
+Dyn%num_lat      = num_lat
+Dyn%spec_tracer  = spec_tracer
+Dyn%grid_tracer  = grid_tracer
+
+allocate (sin_lat   (js:je))
+allocate (cos_lat   (js:je))
+allocate (deg_lat   (js:je))
+allocate (deg_lon   (is:ie))
+allocate (rad_lat   (js:je))
+allocate (rad_lon   (is:ie))
+allocate (coriolis  (js:je))
+
+allocate (glon_bnd  (num_lon + 1))
+allocate (glat_bnd  (num_lat + 1))
+
+call get_deg_lon (deg_lon)
+call get_deg_lat (deg_lat)
+call get_sin_lat (sin_lat)
+call get_cos_lat (cos_lat)
+call get_grid_boundaries (glon_bnd, glat_bnd, global=.true.)
+
+coriolis = 2*omega*sin_lat
+
+rad_lat = deg_lat*atan(1.0)/45.0
+rad_lon = deg_lon*atan(1.0)/45.0
+
+call spectral_damping_init(damping_coeff, damping_order, damping_option, num_fourier, num_spherical, 1, 0., 0., 0., &
+                           damping_coeff_r=damping_coeff_r)
+call stirring_init(dt_real, Time, id_lon, id_lat, id_lonb, id_latb)
+
+allocate (Dyn%spec%vor (ms:me, ns:ne, num_time_levels))
+allocate (Dyn%grid%u   (is:ie, js:je, num_time_levels))
+allocate (Dyn%grid%v   (is:ie, js:je, num_time_levels))
+allocate (Dyn%grid%vor (is:ie, js:je, num_time_levels))
+
+allocate (Dyn%tend%u        (is:ie, js:je))
+allocate (Dyn%tend%v        (is:ie, js:je))
+allocate (Dyn%grid%stream   (is:ie, js:je))
+allocate (Dyn%grid%pv       (is:ie, js:je))
+allocate (Dyn%grid%zonal_u_init(js:je))
+
+allocate (div (ms:me, ns:ne))
+
+call fv_advection_init(num_lon, num_lat, glat_bnd, 360./float(fourier_inc))
+if(Dyn%grid_tracer) then
+  allocate(Dyn%Grid%tr (is:ie, js:je, num_time_levels))
+  allocate(Dyn%Tend%tr (is:ie, js:je))
+endif
+
+if(Dyn%spec_tracer) then
+  allocate(Dyn%Grid%trs (is:ie, js:je, num_time_levels))
+  allocate(Dyn%Tend%trs (is:ie, js:je))
+  allocate(Dyn%Spec%trs (ms:me, ns:ne, num_time_levels))
+endif
+
+if(trim(initial_zonal_wind) == 'zero') then
+  Dyn%grid%zonal_u_init = 0.0
+else if(trim(initial_zonal_wind) == 'two_jets') then
+  do j = js, je
+    Dyn%grid%zonal_u_init(j) = 25.0*cos_lat(j)                     &
+                           - 30.0*(cos_lat(j)**3)                &
+                           + 300.0*(sin_lat(j)**2)*(cos_lat(j)**6)
+  enddo
+else
+  call error_mesg('barotropic_dynamics_init',trim(initial_zonal_wind)// &
+                  ' is not a valid value of initial_zonal_wind ', FATAL)
+endif
+
+if(Time == Time_init) then
+
+  do j = js, je
+    Dyn%Grid%u(:,j,1) = Dyn%grid%zonal_u_init(j)
+    Dyn%Grid%v(:,j,1) = 0.0
+  end do
+
+  call vor_div_from_uv_grid(Dyn%Grid%u  (:,:,1), Dyn%Grid%v  (:,:,1),   &
+                            Dyn%Spec%vor(:,:,1), div) 
+
+  call trans_spherical_to_grid(Dyn%Spec%vor(:,:,1), Dyn%Grid%vor(:,:,1))
+
+  do j = js, je
+    do i = is, ie
+      yy = (deg_lat(j)- eddy_lat)/eddy_width
+      Dyn%Grid%vor(i,j,1) = Dyn%Grid%vor(i,j,1) + &
+              0.5*zeta_0*cos_lat(j)*exp(-yy*yy)*cos(m_0*rad_lon(i))
+    end do
+  end do
+  
+  call trans_grid_to_spherical(Dyn%Grid%vor(:,:,1), Dyn%Spec%vor(:,:,1))
+  
+  div = (0.,0.)
+  call uv_grid_from_vor_div   (Dyn%Spec%vor(:,:,1), div,        &
+                               Dyn%Grid%u  (:,:,1), Dyn%Grid%v  (:,:,1))
+
+  if(Dyn%grid_tracer) then
+    Dyn%Grid%tr = 0.0
+    do j = js, je
+      if(deg_lat(j) > 10.0 .and. deg_lat(j) < 20.0) Dyn%Grid%tr(:,j,1) =  1.0
+      if(deg_lat(j) > 70.0 )                        Dyn%Grid%tr(:,j,1) = -1.0
+    end do
+  endif
+  
+  if(Dyn%spec_tracer) then
+    Dyn%Grid%trs = 0.0
+    do j = js, je
+      if(deg_lat(j) > 10.0 .and. deg_lat(j) < 20.0) Dyn%Grid%trs(:,j,1) =  1.0
+      if(deg_lat(j) > 70.0 )                        Dyn%Grid%trs(:,j,1) = -1.0
+    end do
+    call trans_grid_to_spherical(Dyn%Grid%trs(:,:,1), Dyn%Spec%trs(:,:,1))
+  endif
+  
+else
+
+  call read_restart(Dyn)
+  
+endif
+
+module_is_initialized = .true.
+
+return
+end subroutine barotropic_dynamics_init
+
+!===============================================================================================
+
+subroutine barotropic_dynamics(Time, Time_init, Dyn, previous, current, future, delta_t)
+
+type(time_type)    , intent(in)     :: Time, Time_init
+type(dynamics_type), intent(inout)  :: Dyn
+integer, intent(in   )  :: previous, current, future
+real,    intent(in   )  :: delta_t
+
+! < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < >
+
+complex, dimension(ms:me, ns:ne)  :: dt_vors, dt_divs, stream, zeros, spec_diss
+real,    dimension(is:ie, js:je)  :: dt_vorg
+integer :: j, seconds, days
+
+! < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < >
+
+if(.not.module_is_initialized) then
+  call error_mesg('barotropic_dynamics','dynamics has not been initialized ', FATAL)
+endif
+
+zeros = (0.,0.)
+
+do j = js, je
+  Dyn%grid%pv(:,j)  = Dyn%grid%vor(:,j,current)  + coriolis(j) 
+end do
+
+Dyn%Tend%u = Dyn%Tend%u + Dyn%grid%pv*Dyn%Grid%v(:,:,current)
+Dyn%Tend%v = Dyn%Tend%v - Dyn%grid%pv*Dyn%Grid%u(:,:,current)
+
+call vor_div_from_uv_grid (Dyn%Tend%u, Dyn%Tend%v, dt_vors, dt_divs)
+
+call compute_spectral_damping(Dyn%Spec%vor(:,:,previous), dt_vors, delta_t)
+
+call stirring(Time, dt_vors)
+
+call leapfrog(Dyn%Spec%vor , dt_vors  , previous, current, future, delta_t, robert_coeff)
+
+call trans_spherical_to_grid(Dyn%Spec%vor(:,:,future), Dyn%Grid%vor(:,:,future))
+  
+call uv_grid_from_vor_div  (Dyn%Spec%vor (:,:,future),  zeros, &
+                            Dyn%Grid%u   (:,:,future),  Dyn%Grid%v  (:,:,future))
+
+if(minval(Dyn%Grid%v) < valid_range_v(1) .or. maxval(Dyn%Grid%v) > valid_range_v(2)) then
+  call get_time (Time, seconds, days)
+  call mpp_error(FATAL,'barotropic_dynamics:  Meridional wind out of valid range. Model time=',days,' days  ',seconds,' seconds')
+endif
+
+if(Dyn%spec_tracer) call update_spec_tracer(Dyn%Spec%trs, Dyn%Grid%trs, Dyn%Tend%trs, &
+                         Dyn%Grid%u, Dyn%Grid%v, previous, current, future, delta_t)
+
+if(Dyn%grid_tracer) call update_grid_tracer(Dyn%Grid%tr, Dyn%Tend%tr, &
+                         Dyn%Grid%u, Dyn%Grid%v, previous, current, future, delta_t)
+
+stream = compute_laplacian(Dyn%Spec%vor(:,:,current), -1) 
+call trans_spherical_to_grid(stream, Dyn%grid%stream)
+
+return
+end subroutine barotropic_dynamics
+
+!===================================================================================
+
+subroutine update_spec_tracer(tr_spec, tr_grid, dt_tr, ug, vg, &
+                              previous, current, future, delta_t)
+
+complex, intent(inout), dimension(ms:me, ns:ne, num_time_levels) :: tr_spec
+real   , intent(inout), dimension(is:ie, js:je, num_time_levels) :: tr_grid
+real   , intent(inout), dimension(is:ie, js:je                 ) :: dt_tr
+real   , intent(in   ), dimension(is:ie, js:je, num_time_levels) :: ug, vg  
+real   , intent(in   )  :: delta_t
+integer, intent(in   )  :: previous, current, future
+
+complex, dimension(ms:me, ns:ne) :: dt_trs
+
+call horizontal_advection     (tr_spec(:,:,current), ug(:,:,current), vg(:,:,current), dt_tr)
+call trans_grid_to_spherical  (dt_tr, dt_trs)
+call compute_spectral_damping (tr_spec(:,:,previous), dt_trs, delta_t)
+call leapfrog                 (tr_spec, dt_trs, previous, current, future, delta_t, robert_coeff)
+call trans_spherical_to_grid  (tr_spec(:,:,future), tr_grid(:,:,future))
+
+return
+end subroutine update_spec_tracer
+!==========================================================================
+
+subroutine update_grid_tracer(tr_grid, dt_tr_grid, ug, vg, &
+                              previous, current, future, delta_t)
+
+real   , intent(inout), dimension(is:ie, js:je, num_time_levels) :: tr_grid
+real   , intent(inout), dimension(is:ie, js:je                 ) :: dt_tr_grid
+real   , intent(in   ), dimension(is:ie, js:je, num_time_levels) :: ug, vg
+
+real   , intent(in   )  :: delta_t
+integer, intent(in   )  :: previous, current, future
+
+real, dimension(size(tr_grid,1),size(tr_grid,2)) :: tr_current, tr_future
+
+tr_future = tr_grid(:,:,previous) + delta_t*dt_tr_grid
+dt_tr_grid = 0.0
+call a_grid_horiz_advection (ug(:,:,current), vg(:,:,current), tr_future, delta_t, dt_tr_grid)
+tr_future = tr_future + delta_t*dt_tr_grid
+tr_current = tr_grid(:,:,current) + &
+    robert_coeff*(tr_grid(:,:,previous) + tr_future - 2.0*tr_grid(:,:,current))
+tr_grid(:,:,current) = tr_current
+tr_grid(:,:,future)  = tr_future
+
+return
+end subroutine update_grid_tracer
+
+!==========================================================================
+
+subroutine read_restart(Dyn)
+
+type(dynamics_type), intent(inout)  :: Dyn
+
+integer :: unit, m, n, nt
+real, dimension(ms:me, ns:ne) :: real_part, imag_part
+
+if(file_exist('INPUT/barotropic_dynamics.res.nc')) then
+  do nt = 1, 2
+    call read_data('INPUT/barotropic_dynamics.res.nc', 'vors_real', real_part, spectral_domain, timelevel=nt)
+    call read_data('INPUT/barotropic_dynamics.res.nc', 'vors_imag', imag_part, spectral_domain, timelevel=nt)
+    do n=ns,ne
+      do m=ms,me
+        Dyn%Spec%vor(m,n,nt) = cmplx(real_part(m,n),imag_part(m,n))
+      end do
+    end do
+    if(Dyn%spec_tracer) then
+      call read_data('INPUT/barotropic_dynamics.res.nc', 'trs_real', real_part, spectral_domain, timelevel=nt)
+      call read_data('INPUT/barotropic_dynamics.res.nc', 'trs_imag', imag_part, spectral_domain, timelevel=nt)
+      do n=ns,ne
+        do m=ms,me
+           Dyn%Spec%trs(m,n,nt) = cmplx(real_part(m,n),imag_part(m,n))
+        end do
+      end do
+    endif
+    call read_data('INPUT/barotropic_dynamics.res.nc', 'u',   Dyn%Grid%u  (:,:,nt), grid_domain, timelevel=nt)
+    call read_data('INPUT/barotropic_dynamics.res.nc', 'v',   Dyn%Grid%v  (:,:,nt), grid_domain, timelevel=nt)
+    call read_data('INPUT/barotropic_dynamics.res.nc', 'vor', Dyn%Grid%vor(:,:,nt), grid_domain, timelevel=nt)
+    if(Dyn%spec_tracer) then
+      call read_data('INPUT/barotropic_dynamics.res.nc', 'trs', Dyn%Grid%trs(:,:,nt), grid_domain, timelevel=nt)
+    endif
+    if(Dyn%grid_tracer) then
+      call read_data('INPUT/barotropic_dynamics.res.nc', 'tr', Dyn%Grid%tr(:,:,nt), grid_domain, timelevel=nt)
+    endif
+  end do
+else if(file_exist('INPUT/barotropic_dynamics.res')) then
+  unit = open_restart_file(file='INPUT/barotropic_dynamics.res',action='read')
+
+  do nt = 1, 2
+    call set_domain(spectral_domain)
+    call read_data(unit,Dyn%Spec%vor(:,:, nt))
+    if(Dyn%spec_tracer) call read_data(unit,Dyn%Spec%trs(:,:, nt))
+
+    call set_domain(grid_domain)
+    call read_data(unit,Dyn%Grid%u   (:,:, nt))
+    call read_data(unit,Dyn%Grid%v   (:,:, nt))
+    call read_data(unit,Dyn%Grid%vor (:,:, nt))
+    if(Dyn%spec_tracer) call read_data(unit,Dyn%Grid%trs(:,:, nt))
+    if(Dyn%grid_tracer) call read_data(unit,Dyn%Grid%tr (:,:, nt))
+    
+  end do
+  call close_file(unit)
+  
+else
+  call error_mesg('read_restart', 'restart does not exist', FATAL)
+endif
+  
+return
+end subroutine read_restart
+
+!====================================================================
+
+subroutine write_restart(Dyn, previous, current)
+
+type(dynamics_type), intent(in)  :: Dyn
+integer, intent(in) :: previous, current
+
+integer :: unit, nt, nn
+
+do nt = 1, 2
+  if(nt == 1) nn = previous
+  if(nt == 2) nn = current
+  call write_data('RESTART/barotropic_dynamics.res.nc', 'vors_real',  real(Dyn%Spec%vor(:,:,nn)), spectral_domain)
+  call write_data('RESTART/barotropic_dynamics.res.nc', 'vors_imag', aimag(Dyn%Spec%vor(:,:,nn)), spectral_domain)
+  if(Dyn%spec_tracer) then
+    call write_data('RESTART/barotropic_dynamics.res.nc', 'trs_real',  real(Dyn%Spec%trs(:,:,nn)), spectral_domain)
+    call write_data('RESTART/barotropic_dynamics.res.nc', 'trs_imag', aimag(Dyn%Spec%trs(:,:,nn)), spectral_domain)
+  endif
+  call write_data('RESTART/barotropic_dynamics.res.nc', 'u',   Dyn%Grid%u  (:,:,nn), grid_domain)
+  call write_data('RESTART/barotropic_dynamics.res.nc', 'v',   Dyn%Grid%v  (:,:,nn), grid_domain)
+  call write_data('RESTART/barotropic_dynamics.res.nc', 'vor', Dyn%Grid%vor(:,:,nn), grid_domain)
+  if(Dyn%spec_tracer) then
+    call write_data('RESTART/barotropic_dynamics.res.nc', 'trs', Dyn%Grid%trs(:,:,nn), grid_domain)
+  endif
+  if(Dyn%grid_tracer) then
+    call write_data('RESTART/barotropic_dynamics.res.nc', 'tr', Dyn%Grid%tr(:,:,nn), grid_domain)
+  endif
+enddo
+
+!unit = open_restart_file(file='RESTART/barotropic_dynamics.res', action='write')
+
+!do nt = 1, 2
+!  if(nt == 1) nn = previous
+!  if(nt == 2) nn = current
+  
+!  call set_domain(spectral_domain)
+!  call write_data(unit,Dyn%Spec%vor(:,:, nn))
+!  if(Dyn%spec_tracer) call write_data(unit,Dyn%Spec%trs(:,:, nn))
+
+!  call set_domain(grid_domain)
+!  call write_data(unit,Dyn%Grid%u   (:,:, nn))
+!  call write_data(unit,Dyn%Grid%v   (:,:, nn))
+!  call write_data(unit,Dyn%Grid%vor (:,:, nn))
+!  if(Dyn%spec_tracer) call write_data(unit,Dyn%Grid%trs(:,:, nn))
+!  if(Dyn%grid_tracer) call write_data(unit,Dyn%Grid%tr (:,:, nn))
+!end do
+
+!call close_file(unit)
+
+end subroutine write_restart
+
+!====================================================================
+
+subroutine barotropic_dynamics_end (Dyn, previous, current)
+
+type(dynamics_type), intent(inout)  :: Dyn
+integer, intent(in) :: previous, current
+
+if(.not.module_is_initialized) then
+  call error_mesg('barotropic_dynamics','dynamics has not been initialized ', FATAL)
+endif
+
+call transforms_end()
+call stirring_end()
+
+call write_restart (Dyn, previous, current)
+
+module_is_initialized = .false.
+
+return
+end subroutine barotropic_dynamics_end
+!===================================================================================
+
+end module barotropic_dynamics_mod
diff --git a/src/atmos_spectral_barotropic/barotropic_dynamics.html b/src/atmos_spectral_barotropic/barotropic_dynamics.html
new file mode 100644
index 000000000..62c97898a
--- /dev/null
+++ b/src/atmos_spectral_barotropic/barotropic_dynamics.html
@@ -0,0 +1,371 @@
+
+module barotropic_dynamics_mod
+
+
+

+
+
+
module barotropic_dynamics_mod

+
+
+
+     Contact: Isaac Held
+     Reviewers: Peter Phillipps
+
+

+
+
+
+

+
OVERVIEW

+
+
+
+   The dynamical core of the spectral transform model for 
+   two-dimensional, non-divergent flow on the surface of the sphere.  
+   
+

+
+
+
+

+
DESCRIPTION

+
+
+
+   Integrates the barotropic vorticity equation for nondivergent flow on the
+   sphere using the spectral transform technique.  Also allows for the
+   inclusion of a passive tracer advected by the same spectral advection
+   algorithm as  the vorticity, and a gridpoint tracer advected with a finite
+   volume  algorithm on the transform grid.  The default initial condition 
+   provided as an example is a zonal flow resembling that in the Northern
+   winter,  plus a sinusoidal disurbance localized in midlatitudes.
+
+   For a full description of the model and algorithms used, see 
+     barotropic.ps 
+   
+   For higher level routines for running this barotropic spectral model,
+   see  atmosphere_mod 
+
+
+

+
+
+
+

+
OTHER MODULES USED

+
+
+
+     fms_mod
+     constants_mod
+     time_manager_mod
+     transforms_mod
+     spectral_damping_mod
+     leapfrog_mod
+     fv_advection_mod
+
+

+
+
+
+

+
PUBLIC INTERFACE

+
+
+
+  use barotropic_dynamics_mod [,only: barotropic_dynamics_init,       
+                                      barotropic_dynamics,
+			              barotropic_dynamics_end,
+                                      dynamics_type,
+				      grid_type,
+				      spectral_type,
+				      tendency_type]
+                                
+

+
+
+
+

+
PUBLIC DATA

+
+
+     
+

+ 
+
+type grid_type
+   real, pointer, dimension(:,:,:) :: u, v, vor, trs, tr, pv
+   real, pointer, dimension(:,:)   :: stream
+end type
+
+   allocated space for grid fields
+
+   (:,:,:) => (lon, lat, time_level)
+   (:,:)   => (lon, lat)
+      (lon, lat) on local computational domain
+      time_level stores the two time levels needed for the
+          leapfrog step
+   
+   u      -- eastward velocity (m/s)
+   v      -- northward velocity (m/s)
+   vor    -- vorticity (1/s)
+   trs    -- tracer advected spectrally
+   tr     -- tracer advected on grid
+   pv     -- absolute vorticity, f + vor, where f = 2*omega*sin(lat) (1/s)
+   stream -- streamfunction (m^2/s) at current time
+   
+ 
+ 
+ 

+ 
+ 
+type spectral_type
+   complex, pointer, dimension(:,:,:) :: vor, trs
+end type
+
+   allocated space for spectral fields
+   
+      (:,:,:) => (zonal, meridional, time_level)
+
+   vor -- spectral vorticity
+   trs -- spectral tracer
+
+ 

+ 
+ 
+type tendency_type
+    real, pointer, dimension(:,:) :: u, v, trs, tr
+end type
+
+   allocated space for accumulating tendencies, d/dt, in grid space, 
+           for prognostic variables
+   
+      (:,:,:) => (lon, lat)
+
+ 

+ 
+ 
+type dynamics_type
+   type(grid_type)     :: grid
+   type(spectral_type) :: spec
+   type(tendency_type) :: tend
+   integer             :: num_lon, num_lat  ! size of global domain
+   logical             :: grid_tracer, spec_tracer 
+end type
+
+   grid_tracer = .true. => tracer with gridpoint advection is beign integrated
+   similarly for spec_tracer
+ 
+ 

+ 
+

+
+
+
+

+
PUBLIC ROUTINES

+
+
+
+subroutine  barotropic_dynamics_init
+subroutine  barotropic _dynamics
+subroutine  barotropic_dynamics_end
+type (grid_type)
+type (spectral_type)
+type (tendency_type)
+type (dynamics_type)
+
+
+
+
+
+ subroutine barotropic_dynamics_init(Dyn,  Time, Time_init)
+ 
+   type(dynamics_type), intent(inout)  :: Dyn
+         type containing all dynamical fields and related information
+	 (see type (dynamics_type))
+	 
+   type(time_type)    , intent(in)     :: Time, Time_init
+         current time and time at which integeration began
+	 time_type defined by time_manager_mod
+         
+
+   Initializes the module;
+   Reads restart from 'INPUT/barotropic_dynamics.res' if Time = Time_init;
+     otherwise uses default initial conditions
+
+
+
+

+
+
+
+  subroutine barotropic_dynamics &
+     (Time, Time_init, Dyn, previous, current, future, delta_t)
+ 
+     type(time_type)    , intent(inout)  :: Time, Time_init
+     type(dynamics_type), intent(inout)  :: Dyn
+     integer            , intent(in   )  :: previous, current, future
+     real               , intent(in   )  :: delta_t
+      
+     previous, current and future = 1 or 2
+       these integers refer to the third dimension of the 
+         three-dimensional fields in Dyn
+       the fields at time t - delta_t are assumed to be in (:,:,previous)
+       the fields at time t           are assumed to be in (:,:,current)
+       the fields at time t + delta_t are placed        in (:,:,future)
+          overwriting whatever is already there
+
+     delta_t = time step in seconds
+     
+     updates dynamical fields by one time step
+
+
+
+

+
+ 
+   subroutine barotropic_dynamics_end(Dyn, previous, current)
+   
+     type(dynamics_type), intent(inout)  :: Dyn
+     integer, intent(in) :: previous, current
+   
+      
+    Terminates module; 
+     writes restart file to 'RESTART/barotropic_dynamics.res'
+    
+    
+
+
+

+

+
+
+
+

+
NAMELIST

+
+
+
+&barotropic_dynamics_nml
+
+  integer :: num_lat            = 128  
+        number of latitudes in global grid
+       
+  integer :: num_lon            = 256
+        number of longitudes in global grid
+        should equal 2*num_lat for Triangular truncation
+  
+  integer :: num_fourier        = 85
+        the retained fourier wavenumber are n*fourier_inc, where
+        n ranges from 0 to num_fourier
+	 
+  integer :: num_spherical      = 86
+        the maximum number of meridional modes for any zonal wavenumber
+        for triangular truncation, set num_spherical = num_fourier +1
+         
+  integer :: fourier_inc        = 1
+        creates a "sector" model if fourier_inc > 1; integration domain is
+	(360 degrees longitude)/fourier_inc
+	
+  (the default values listed above define a standard T85 model)
+
+  logical :: check_fourier_imag = .false.
+        if true, checks to see if fields to be transformed to grid 
+	domain have zero imaginary part to their zonally symmetric
+	modes; useful for debugging
+	
+  logical :: south_to_north     = .true.
+        true => grid runs from south to north
+	false => grid runs from north to south
+	
+  logical :: triangular_trunc   = .true.
+        true  => shape of truncation is triangular
+	false => shape of truncation is rhomboidal
+
+  real    :: robert_coeff       = 0.04
+        x(current) => (1-2r)*x(current) + r*(x(future)+x(previous))
+	where r = robert_coeff (non-dimensional)
+	
+  real    :: longitude_origin   = 0.0
+        longitude of first longitude, in degrees
+	(if you want the westgern boundary of first grid boc to be at 
+         0.0, set longitude_origin = 0.5*360./float(num_lon))
+	 
+  integer :: damping_option     = 'resolution_dependent'
+  integer :: damping_order      = 4
+  real    :: damping_coeff      = 1.e-04
+  
+        damping = nu*(del^2)^n where n = damping order
+	damping_option = 'resolution_dependent' or 'resolution_independent'
+	  = 'resolution_dependent' => nu is set so that the damping rate for the 
+	        mode (m=0,n=num_spherical-1) equals damping_coeff (in 1/s)
+	        For triangular truncation, damping_coeff is then the 
+	        rate of damping of the highest retained mode
+	     
+	  = 'resolution_independent' => nu = damping_coef
+	
+	
+  real     :: zeta_0     = 8.e-05
+  integer  :: m_0        = 4
+  real     :: eddy_width = 15.0
+  real     :: eddy_lat   = 45.0
+  
+         eddy component of the initial condition is sinusoidal with
+	 wavenumber m_0 and with a gaussian distribution of 
+	 vorticity in latitude, centered at eddy_lat with half-width
+	 eddy_width
+	 
+	 zeta_0 ( 1/s)
+	 eddy_width and eddy_lat (degrees)
+
+  logical :: spec_tracer      = .true.
+  logical :: grid_tracer      = .true.
+       spec_tracer = true => a passive tracer is carried that is advected
+          spectrally, with the same algorithm as the vorticity
+       grid_tracer = ture => a passive tracer is carried that is advected
+          on the spectral transform grid by a finite-volume algorithm
+	  (see  barotropic.ps )
+       Both tracers can be carried simultaeneously
+	  
+The vorticity and the tracers are initialized within subroutine
+     barotropic_dynamics_init
+
+  real, dimension(2) :: valid_range_v = -1000., 1000.
+        A valid range for meridional wind. Model terminates if meridional wind
+        goes outside the valid range. Allows model to terminate gracefully when,
+        for example, the model becomes numerically unstable.
+
+

+
+
+
+

+
ERROR MESSAGES

+
+
+
+   "Dynamics has not been initialized"
+      -- barotropic_dynamics_init must be called before any other
+         routines in the module are called
+	 
+   "restart does not exist" 
+      -- Time is not equal to Time_init at initalization, but the file
+          'INPUT/barotropic_dynamics.res' does not exit 
+	 
+
+

+
+
+
+

+
+
diff --git a/src/atmos_spectral_barotropic/barotropic_physics.F90 b/src/atmos_spectral_barotropic/barotropic_physics.F90
new file mode 100644
index 000000000..8590bacce
--- /dev/null
+++ b/src/atmos_spectral_barotropic/barotropic_physics.F90
@@ -0,0 +1,173 @@
+module barotropic_physics_mod
+
+!-----------------------------------------------------------------------
+!                   GNU General Public License                        
+!                                                                      
+! This program is free software; you can redistribute it and/or modify it and  
+! are expected to follow the terms of the GNU General Public License  
+! as published by the Free Software Foundation; either version 2 of   
+! the License, or (at your option) any later version.                 
+!                                                                      
+! This program is distributed in the hope that it will be useful, but WITHOUT    
+! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  
+! or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public    
+! License for more details.                                           
+!                                                                      
+! For the full text of the GNU General Public License,                
+! write to: Free Software Foundation, Inc.,                           
+!           675 Mass Ave, Cambridge, MA 02139, USA.                   
+! or see:   http://www.gnu.org/licenses/gpl.html                      
+!-----------------------------------------------------------------------
+
+use               fms_mod, only: open_namelist_file,   &
+                                 open_restart_file,    &
+                                 file_exist,           &
+                                 check_nml_error,      &
+                                 error_mesg,           &
+                                 FATAL, WARNING,       &
+                                 write_version_number, &
+                                 mpp_pe,               &
+                                 mpp_root_pe,          &
+                                 fms_init, fms_end,    &
+                                 read_data,            &
+                                 write_data,           &
+                                 set_domain,           &
+                                 close_file,           &
+                                 stdlog
+
+use         transforms_mod, only: get_sin_lat, get_cos_lat,         &
+                                  get_deg_lon, get_deg_lat,         &
+                                  get_wts_lat,                      &
+                                  get_grid_domain, get_spec_domain, &
+                                  grid_domain
+
+use       time_manager_mod, only: time_type
+
+!========================================================================
+implicit none
+private
+!========================================================================
+
+public :: barotropic_physics_init,    &
+          barotropic_physics,         &
+          barotropic_physics_end,     &
+          phys_type
+
+! version information 
+!========================================================================
+character(len=128) :: version = '$Id: barotropic_physics.F90,v 10.0 2003/10/24 22:00:58 fms Exp $'
+character(len=128) :: tagname = '$Name: siena_201207 $'
+!========================================================================
+
+type phys_type
+   real, pointer, dimension(:,:)   :: empty=>NULL()
+end type
+
+logical :: module_is_initialized = .false.
+
+integer :: is, ie, js, je
+
+
+integer :: pe
+logical :: root
+
+real, allocatable, dimension(:) :: rad_lat, &
+                                   deg_lat, &
+                                   sin_lat, &
+                                   cos_lat, &
+                                   wts_lat
+
+! namelist 
+!========================================================================
+
+logical :: empty
+
+namelist /barotropic_physics_nml/ empty
+!========================================================================
+
+contains
+
+!========================================================================
+
+subroutine barotropic_physics_init(Phys) 
+
+type(phys_type), intent(inout) :: Phys
+
+integer :: j, unit, ierr, io
+
+call write_version_number (version, tagname)
+
+pe = mpp_pe()
+root = (pe == mpp_root_pe())
+
+! read the namelist
+
+if (file_exist('input.nml')) then
+  unit = open_namelist_file ()
+  ierr=1
+  do while (ierr /= 0)
+    read  (unit, nml=barotropic_physics_nml, iostat=io, end=10)
+    ierr = check_nml_error (io, 'barotropic_physics_nml')
+  enddo
+  10 call close_file (unit)
+endif
+
+call get_grid_domain(is,ie,js,je)
+
+allocate ( rad_lat      (js:je) )
+allocate ( deg_lat      (js:je) )
+allocate ( sin_lat      (js:je) )
+allocate ( cos_lat      (js:je) )
+allocate ( wts_lat      (js:je) )
+
+call get_wts_lat(wts_lat)
+call get_deg_lat(deg_lat)
+rad_lat = deg_lat*atan(1.)/45. 
+sin_lat = sin(rad_lat)
+cos_lat = cos(rad_lat)
+
+module_is_initialized = .true.
+
+return
+end subroutine barotropic_physics_init
+
+!=======================================================================
+
+subroutine barotropic_physics(Time, dt_ug, dt_vg, ug, vg,    &
+                             delta_t, previous, current, Phys)
+
+real, intent(inout),  dimension(is:ie, js:je)    :: dt_ug, dt_vg
+real, intent(in)   ,  dimension(is:ie, js:je, 2) :: ug, vg
+
+real   , intent(in)  :: delta_t
+integer, intent(in)  :: previous, current
+
+type(time_type), intent(in)    :: Time
+type(phys_type), intent(inout) :: Phys
+
+if(.not.module_is_initialized) call error_mesg('barotropic_physics', &
+                       'barotropic_physics is not initialized', FATAL)
+
+! dt_ug = dt_ug +f(ug,vg)
+! dt_vg = dt_vg +f(ug,vg)
+! Phys%empty = 
+  
+return
+end subroutine barotropic_physics
+
+!======================================================================
+
+subroutine barotropic_physics_end(Phys)
+
+type(phys_type), intent(in) :: Phys
+
+if(.not.module_is_initialized) call error_mesg('barotropic_physics_end', &
+                       'barotropic_physics is not initialized', FATAL)
+
+module_is_initialized = .false.
+return
+end subroutine barotropic_physics_end
+
+!======================================================================
+
+end module barotropic_physics_mod
diff --git a/src/atmos_spectral_barotropic/barotropic_physics.html b/src/atmos_spectral_barotropic/barotropic_physics.html
new file mode 100644
index 000000000..e391ca50f
--- /dev/null
+++ b/src/atmos_spectral_barotropic/barotropic_physics.html
@@ -0,0 +1,165 @@
+
+module barotropic_physics_mod
+
+
+

+
+
+
module barotropic_physics_mod

+
+
+
+     Contact: Isaac Held
+     Reviewers: Peter Phillipps
+
+

+
+
+
+

+
OVERVIEW

+
+
+
+   A module that allows one to add processes that act in the grid domain
+   to the dynamics of the barotropic model on the sphere
+   
+

+
+
+
+

+
DESCRIPTION

+
+
+
+   A module that allows one to add processes that act in the grid domain
+   to the dynamics of the barotropic model on the sphere.  Currently,
+   does nothing!
+
+

+
+
+
+

+
OTHER MODULES USED

+
+
+
+     fms_mod
+     transforms_mod
+     time_manager_mod
+
+

+
+
+
+

+
PUBLIC INTERFACE

+
+
+
+  use barotropic_physics_mod [,only: barotropic_physics_init,       
+                                         barotropic_physics,
+					 barotropic_physics_end,
+					 phys_type]
+                                
+

+
+
+
+

+
PUBLIC DATA

+
+
+     
+

+ 
+
+type phys_type
+   real, pointer, dimension(:,:)   :: empty
+end type
+
+  fields from physics module made available for diagnostics
+  
+ 

+ 
+
+

+
+
+

+
PUBLIC ROUTINES

+
+
+
+subroutine  barotropic_physics_init
+subroutine  barotropic_physics
+subroutine  barotropic_physics_end
+type(phys_type)
+
+
+
+
+
+ subroutine barotropic_physics_init(Phys)
+ 
+   type(phys_type)    , intent(inout)     :: Phys
+  
+ 
+   Initializes module
+
+
+
+

+
+
+
+  subroutine barotropic_physics (Time, dt_ug, dt_vg, ug, vg,    &
+                             delta_t, previous, current, Phys)
+
+      real, intent(inout),  dimension(:,:)    :: dt_ug, dt_vg
+      
+         the u and v tendencies onto which tendencies due to 
+	    the grid-point physics are added (m/(s^2))
+	 
+      real, intent(in)   ,  dimension(:,:, 2) :: ug, vg
+         the grid zonal and meridional velocities (m/s)
+	 the third index is the time-index used in the leapfrog step
+
+      real   , intent(in)  :: delta_t  
+         time step (s)
+	 
+      integer, intent(in)  :: previous, current
+         = 1 or 2
+	 ug(:,:,previous) is the velocity at t-delta_t
+	 ug(:,:,current ) is the velocity at t
+
+      type(time_type), intent(in)    :: Time
+      type(phys_type), intent(inout) :: Phys
+ 
+
+
+
+

+
+
+
+  subroutine barotropic_physics_end (Phys)
+
+      type(phys_type), intent(inout) :: Phys
+ 
+
+
+
+

+
+
+
diff --git a/src/atmos_spectral_barotropic/stirring.F90 b/src/atmos_spectral_barotropic/stirring.F90
new file mode 100644
index 000000000..04bdfc280
--- /dev/null
+++ b/src/atmos_spectral_barotropic/stirring.F90
@@ -0,0 +1,252 @@
+module stirring_mod
+
+!-----------------------------------------------------------------------
+!                   GNU General Public License                        
+!                                                                      
+! This program is free software; you can redistribute it and/or modify it and  
+! are expected to follow the terms of the GNU General Public License  
+! as published by the Free Software Foundation; either version 2 of   
+! the License, or (at your option) any later version.                 
+!                                                                      
+! This program is distributed in the hope that it will be useful, but WITHOUT    
+! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  
+! or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public    
+! License for more details.                                           
+!                                                                      
+! For the full text of the GNU General Public License,                
+! write to: Free Software Foundation, Inc.,                           
+!           675 Mass Ave, Cambridge, MA 02139, USA.                   
+! or see:   http://www.gnu.org/licenses/gpl.html                      
+!-----------------------------------------------------------------------
+
+! Stirring is computed as described in the following paper:
+
+! Vallis, Gerber, Kushner, Cash, 2003: A Mechanism and Simple Dynamical Model of the North Atlantic Oscillation and Annular Modes.
+! J. Atmos. Sci., 61, 264-280.
+
+! Stirring is not part of barotropic_physics because barotropic_physics appears to be intended for
+! operations that are done completely in grid space. Stirring is computed partly in spectral space.
+
+use    constants_mod, only: pi
+
+use time_manager_mod, only: time_type
+
+use          fms_mod, only: open_namelist_file, check_nml_error, close_file, write_version_number, &
+                            stdlog, mpp_pe, mpp_root_pe, file_exist, read_data, write_data, error_mesg, FATAL
+
+use   transforms_mod, only: get_spec_domain, get_grid_domain, trans_spherical_to_grid, trans_grid_to_spherical, &
+                            grid_domain, get_lon_max, get_lat_max, get_deg_lon, get_deg_lat, get_grid_boundaries, &
+                            get_num_fourier, get_num_spherical, spectral_domain
+
+use diag_manager_mod, only: diag_axis_init, register_static_field, register_diag_field, send_data
+
+implicit none
+private
+
+integer :: ms,me,ns,ne,is,ie,js,je
+integer :: id_str_amp, id_g_stir_sqr, id_stir
+logical :: used
+logical, allocatable, dimension(:,:) :: wave_mask   ! wave_mask(m,n) = .true. if spherical wave (m,n) is to be excited
+complex, allocatable, dimension(:,:) :: s_stir      ! stirring. Saved from one time step to the next
+real,    allocatable, dimension(:,:) :: localize    ! localizes the stirring
+real,    allocatable, dimension(:,:) :: g_stir_sqr  ! time mean of g_stir**2 over entire integration
+integer, allocatable, dimension(:)   :: seed        ! random number seed
+real ::  astir, bstir
+integer :: num_steps, num_fourier, num_spherical, nseed
+character(len=8)  :: axiset   = 'barotropic'
+character(len=84) :: mod_name = 'barotropic_diagnostics'
+
+logical :: module_is_initialized = .false.
+
+character(len=128) :: version = '$Id: stirring.F90,v 17.0 2009/07/21 03:00:25 fms Exp $'
+character(len=128) :: tagname = '$Name: siena_201207 $'
+
+public :: stirring_init, stirring, stirring_end
+
+real :: decay_time=2*86400, amplitude=0.0, lat0=45., widthy=12.
+
+! Set B to a non-zero value for stirring that has zonal structure.
+! The strength of the stirring at latitude=lat0 is: amplitude*(1.0 + B*exp(-.5*((lon-lon0)/widthx)**2))
+real :: lon0=180., B=0.0, widthx=45. ! widthx
+
+namelist / stirring_nml / decay_time, amplitude, lat0, lon0, widthy, widthx, B
+
+contains
+
+!================================================================================================================================
+subroutine stirring_init(dt, Time, id_lon, id_lat, id_lonb, id_latb)
+real, intent(in) :: dt
+type(time_type), intent(in) :: Time
+integer, intent(out) :: id_lon, id_lat, id_lonb, id_latb
+real :: xx, kk, rad_to_deg
+integer :: i,j,m,n,ierr,io,unit,lon_max,lat_max
+real, allocatable, dimension(:) :: ampx, ampy, lon, lat, lonb, latb
+real, allocatable, dimension(:,:) :: real_part, imag_part
+
+if(module_is_initialized) return
+
+call write_version_number (version, tagname)
+
+if (file_exist('input.nml')) then
+  unit = open_namelist_file ()   
+  ierr=1                         
+  do while (ierr /= 0)           
+    read  (unit, nml=stirring_nml, iostat=io, end=10)
+    ierr = check_nml_error (io, 'stirring_nml')
+  enddo                          
+  10 call close_file (unit)      
+endif
+if(mpp_pe() == mpp_root_pe()) write(stdlog(), nml=stirring_nml)
+
+call get_lon_max(lon_max)
+call get_lat_max(lat_max)
+
+allocate(lon (lon_max  )) ; lon  = 0.0
+allocate(lat (lat_max  )) ; lat  = 0.0
+allocate(lonb(lon_max+1)) ; lonb = 0.0
+allocate(latb(lat_max+1)) ; latb = 0.0
+
+call get_deg_lon(lon)          
+call get_deg_lat(lat)
+call get_grid_boundaries(lonb,latb,global=.true.)
+
+rad_to_deg = 180./pi
+id_lonb=diag_axis_init('lonb', rad_to_deg*lonb, 'degrees_E', 'x', 'longitude edges', set_name='barotropic', Domain2=grid_domain)
+id_latb=diag_axis_init('latb', rad_to_deg*latb, 'degrees_N', 'y', 'latitude edges',  set_name='barotropic', Domain2=grid_domain)
+id_lon =diag_axis_init('lon', lon, 'degrees_E', 'x', 'longitude', set_name='barotropic', Domain2=grid_domain, edges=id_lonb)
+id_lat =diag_axis_init('lat', lat, 'degrees_N', 'y', 'latitude',  set_name='barotropic', Domain2=grid_domain, edges=id_latb)
+
+module_is_initialized = .true.
+if(amplitude == 0.0) return ! stirring does nothing more unless amplitude is non-zero
+
+call get_spec_domain(ms,me,ns,ne)
+call get_grid_domain(is,ie,js,je)
+call get_num_fourier(num_fourier)
+call get_num_spherical(num_spherical)
+
+allocate(wave_mask(ms:me,ns:ne)); wave_mask = .false.
+allocate(s_stir(ms:me,ns:ne)); s_stir = cmplx(0.0,0.0)
+allocate(ampx(is:ie)); ampx = 0.0
+allocate(ampy(js:je)); ampy = 0.0
+allocate(localize(is:ie,js:je)); localize = 0.0
+allocate(g_stir_sqr(is:ie,js:je)); g_stir_sqr = 0.0
+
+! wave_mask is .true. when  (m+n > 9) .and. (m+n < 15) .and. (m > 3)
+do m=4,14
+  if(m >= ms .and. m <= me) then
+    do n=10-m,14-m
+      if(n >= ns .and. n <= ne) then
+        wave_mask(m,n) = .true.
+      endif
+    enddo
+  endif
+enddo
+
+astir = sqrt(1.0 - exp(-2*dt/decay_time))
+bstir = exp(-dt/decay_time)
+
+do i=is,ie
+  xx = lon(i)-lon0
+  ! Make sure xx falls in the range -180. to +180.
+  kk = nint(xx/360.)
+  xx = xx - 360.*kk
+  ampx(i) = (1 + B*exp(-.5*(xx/widthx)**2))
+enddo
+do j=js,je
+  ampy(j) = exp(-.5*((lat(j)-lat0)/widthy)**2)
+enddo
+do j=js,je
+do i=is,ie
+  localize(i,j) = ampx(i)*ampy(j)
+enddo
+enddo
+deallocate(ampx, ampy)
+
+num_steps = 0
+id_g_stir_sqr = register_static_field('stirring_mod', 'stirring_sqr', (/id_lon,id_lat/), 'stirring sqrared', '1/sec^4')
+id_str_amp    = register_static_field('stirring_mod', 'stirring_amp', (/id_lon,id_lat/), 'amplitude of stirring', 'none')
+id_stir       = register_diag_field  ('stirring_mod', 'stirring',     (/id_lon,id_lat/), Time, 'stirring', '1/sec^2')
+used = send_data(id_str_amp, amplitude*localize)
+
+call random_seed(size=nseed)
+allocate(seed(nseed))
+
+if(file_exist('INPUT/stirring.res.nc')) then
+  allocate(real_part(ms:me,ns:ne), imag_part(ms:me,ns:ne))
+  call read_data('INPUT/stirring.res.nc', 'stir_real', real_part, spectral_domain)
+  call read_data('INPUT/stirring.res.nc', 'stir_imag', imag_part, spectral_domain)
+  do n=ns,ne
+    do m=ms,me
+      s_stir(m,n) = cmplx(real_part(m,n),imag_part(m,n))
+    end do
+  end do
+  deallocate(real_part, imag_part)
+  call read_data('INPUT/stirring.res.nc', 'ran_nmbr_seed', seed, no_domain=.true.)
+  call random_seed(put=seed)
+endif
+
+end subroutine stirring_init
+!================================================================================================================================
+subroutine stirring(Time, dt_vors)
+type(time_type), intent(in) :: Time
+complex, dimension(ms:me,ns:ne), intent(inout) :: dt_vors
+real,    dimension(is:ie,js:je) :: g_stir
+complex, dimension(ms:me,ns:ne) :: new_stirring
+real,    dimension(0:num_fourier,0:num_spherical,2) :: ran_nmbrs
+integer :: i,j,m,n
+real :: x,y
+
+if(.not.module_is_initialized) then
+  call error_mesg('stirring', 'stirring_init has not been called', FATAL)
+end if
+
+if(amplitude == 0.0) return ! stirring does nothing unless amplitude is non-zero
+
+call random_number(ran_nmbrs)
+
+do n=ns,ne
+do m=ms,me
+  if(wave_mask(m,n)) then
+    new_stirring(m,n) = amplitude*astir*cmplx(2*ran_nmbrs(m,n,1)-1, 2*ran_nmbrs(m,n,2)-1)
+  else
+    new_stirring(m,n) = cmplx(0.0,0.0)
+  endif
+enddo
+enddo
+call trans_spherical_to_grid(new_stirring,g_stir)
+g_stir = localize*g_stir
+call trans_grid_to_spherical(g_stir,new_stirring)
+if(ms == 0 .and. ns == 0) then
+  new_stirring(0,0)=cmplx(0.0,0.0) ! A non-zero global mean is introduced by the grid space computation, but we don't want it.
+endif
+s_stir = bstir*s_stir + new_stirring
+
+dt_vors = dt_vors + s_stir
+call trans_spherical_to_grid(s_stir,g_stir)
+g_stir_sqr = g_stir_sqr + g_stir*g_stir
+num_steps = num_steps + 1
+used = send_data(id_stir, g_stir, Time)
+
+end subroutine stirring
+!================================================================================================================================
+subroutine stirring_end
+
+if(.not.module_is_initialized) return
+
+if(amplitude == 0.0) return ! stirring does nothing unless amplitude is non-zero
+
+g_stir_sqr = g_stir_sqr/num_steps
+used = send_data(id_g_stir_sqr, g_stir_sqr)
+
+call write_data('RESTART/stirring.res.nc', 'stir_real',  real(s_stir), spectral_domain)
+call write_data('RESTART/stirring.res.nc', 'stir_imag', aimag(s_stir), spectral_domain)
+call random_seed(get=seed)
+call write_data('RESTART/stirring.res.nc', 'ran_nmbr_seed', seed, no_domain=.true.)
+
+deallocate(wave_mask, s_stir, localize, g_stir_sqr)
+module_is_initialized = .false.
+
+end subroutine stirring_end
+!================================================================================================================================
+
+end module stirring_mod
diff --git a/src/atmos_spectral_shallow/atmosphere.F90 b/src/atmos_spectral_shallow/atmosphere.F90
new file mode 100644
index 000000000..3b59b37fb
--- /dev/null
+++ b/src/atmos_spectral_shallow/atmosphere.F90
@@ -0,0 +1,279 @@
+Module atmosphere_mod
+
+!-----------------------------------------------------------------------
+!                   GNU General Public License                        
+!                                                                      
+! This program is free software; you can redistribute it and/or modify it and  
+! are expected to follow the terms of the GNU General Public License  
+! as published by the Free Software Foundation; either version 2 of   
+! the License, or (at your option) any later version.                 
+!                                                                      
+! This program is distributed in the hope that it will be useful, but WITHOUT    
+! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  
+! or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public    
+! License for more details.                                           
+!                                                                      
+! For the full text of the GNU General Public License,                
+! write to: Free Software Foundation, Inc.,                           
+!           675 Mass Ave, Cambridge, MA 02139, USA.                   
+! or see:   http://www.gnu.org/licenses/gpl.html                      
+!-----------------------------------------------------------------------
+
+!=========================================================================
+
+use     fms_mod, only: open_namelist_file,   &
+                       open_restart_file,    &
+                       file_exist,           &
+                       check_nml_error,      &
+                       error_mesg,           &
+                       FATAL, WARNING,       &
+                       write_version_number, &
+                       mpp_pe,               &
+                       mpp_root_pe,          &
+                       close_file,           &
+                       stdlog
+
+use     mpp_mod, only: mpp_max
+
+use     constants_mod, only: radius_earth => radius, &
+                             omega_earth  => omega
+
+use      transforms_mod,  only : get_deg_lon,               &
+                                 get_deg_lat,               &
+                                 get_grid_boundaries,       &
+                                 get_grid_domain,           &
+                                 get_spec_domain,           &
+                                 area_weighted_global_mean, &
+                                 atmosphere_domain
+
+use    time_manager_mod,  only : time_type,      &
+                                 set_time,       &
+                                 get_time,       &
+                                 interval_alarm, &
+                                 operator(+),    &
+                                 operator(<),    &
+                                 operator(==)
+
+use shallow_dynamics_mod,  only : shallow_dynamics_init,    &
+                                  shallow_dynamics,         &
+                                  shallow_dynamics_end,     &
+                                  dynamics_type
+    
+use shallow_physics_mod, only : shallow_physics_init, &
+                                shallow_physics,      &
+                                shallow_physics_end,  &
+                                phys_type
+
+use shallow_diagnostics_mod,  only : shallow_diagnostics_init,   &
+                                     shallow_diagnostics
+
+
+!========================================================================
+implicit none
+private
+!========================================================================
+
+! version information 
+!========================================================================
+character(len=128) :: version = '$Id: atmosphere.F90,v 14.0 2007/03/15 22:13:18 fms Exp $'
+character(len=128) :: tagname = '$Name: siena_201207 $'
+!========================================================================
+
+public :: atmosphere_init, &
+          atmosphere,      &
+          atmosphere_end,  &
+          atmosphere_domain
+
+!========================================================================
+
+integer, parameter :: num_time_levels = 2
+
+integer         :: unit, seconds, days
+integer         :: pe, npes
+integer         :: previous, current, future
+logical         :: root
+
+integer         :: dt_integer
+real            :: dt_real
+type(time_type) :: dt_time_type, Time_init, Time_step
+
+real :: delta_t   ! = 2*dt_real for leapfrog step
+
+integer, dimension(2) :: axes  
+
+type(phys_type),     save :: Phys
+type(dynamics_type), save :: Dyn
+
+integer :: is, ie, js, je, ms, me, ns, ne
+integer :: num_lon, num_lat
+integer, dimension(4) :: axis_id         ! axes identifiers 
+
+logical :: module_is_initialized =.false.
+
+
+integer :: print_interval
+! namelist 
+!========================================================================
+namelist /atmosphere_nml/ print_interval
+!========================================================================
+
+contains
+!=======================================================================
+
+subroutine atmosphere_init(Time_init_in, Time, Time_step_in)
+
+type (time_type), intent(in) :: Time_init_in, Time, Time_step_in
+
+integer :: i, j, n, nn, ierr, io, unit
+integer :: nlon, nlat
+
+pe   = mpp_pe()
+root = (pe == mpp_root_pe())
+
+Time_step = Time_step_in
+call get_time(Time_step, seconds, days)
+dt_integer   = 86400*days + seconds
+dt_real      = float(dt_integer)
+dt_time_type = Time_step
+Time_init    = Time_init_in
+
+! read the namelist
+
+if (file_exist('input.nml')) then
+  unit = open_namelist_file ()
+  ierr=1
+  do while (ierr /= 0)
+    read  (unit, nml=atmosphere_nml, iostat=io, end=10)
+    ierr = check_nml_error (io, 'atmosphere_nml')
+  enddo
+  10 call close_file (unit)
+endif
+call write_version_number(version, tagname)
+if (root) write (stdlog(), nml=atmosphere_nml)
+
+call shallow_dynamics_init (Dyn, Time, Time_init)    
+
+call get_grid_domain(is,ie,js,je)
+call get_spec_domain(ms,me,ns,ne)
+ 
+num_lon = Dyn%num_lon
+num_lat = Dyn%num_lat
+
+nlon = ie+1-is  ! size of grid on each processor
+nlat = je+1-js
+
+call shallow_physics_init(Phys)
+call shallow_diagnostics_init(Time, num_lon, num_lat)
+
+if(Time == Time_init) then
+  previous = 1
+  current  = 1
+else
+  previous = 1  
+  current  = 2
+endif
+
+module_is_initialized = .true.
+
+return
+end subroutine atmosphere_init
+
+!=====================================================================
+
+subroutine atmosphere(Time)
+
+type (time_type), intent(in) :: Time
+integer :: day, second, dt
+
+
+if(.not.module_is_initialized) then
+  call error_mesg('atmosphere', &
+                  'atmosphere_init has not been called', FATAL)
+end if
+
+call get_time(Time_step, second, day)
+dt = second + 86400*day
+
+Dyn%Tend%u   = 0.0
+Dyn%Tend%v   = 0.0
+Dyn%Tend%h   = 0.0
+if(Dyn%grid_tracer) Dyn%Tend%tr  = 0.0
+if(Dyn%spec_tracer) Dyn%Tend%trs = 0.0
+
+if(Time == Time_init) then
+  delta_t = dt_real
+  future = 2
+else
+  delta_t = 2.0*dt_real
+  future = previous
+endif
+
+call shallow_physics(Time,                                 &
+                     Dyn%Tend%u, Dyn%Tend%v, Dyn%Tend%h,   &
+                     Dyn%Grid%u, Dyn%Grid%v, Dyn%Grid%h,   &
+                     delta_t, previous, current,           &
+                     Phys)
+
+call shallow_dynamics(Time, Time_init, &
+                      Dyn, previous, current, future, delta_t) 
+     
+previous   = current
+current    = future
+
+call shallow_diagnostics (Time+Time_step, Dyn%Grid, Phys, current) 
+
+call get_time(Time+Time_step, second, day)
+if(mod(second+86400*day, print_interval) < dt)  &
+   call global_diag(second, day, current)
+
+return
+end subroutine atmosphere
+
+!=======================================================================================
+
+subroutine global_diag(second, day, current)
+
+integer, intent(in) :: second, day, current
+
+real    :: enstrophy, div_squared, max_Froude
+real, dimension(size(Dyn%Grid%u,1), size(Dyn%Grid%u,2)) :: speed
+
+enstrophy = &
+area_weighted_global_mean(Dyn%grid%vor(:,:,current)*Dyn%grid%vor(:,:,current))
+
+div_squared = &
+area_weighted_global_mean(Dyn%grid%div(:,:,current)*Dyn%grid%div(:,:,current))
+
+speed = Dyn%Grid%u(:,:,current)*Dyn%Grid%u(:,:,current) +&
+        Dyn%Grid%v(:,:,current)*Dyn%Grid%v(:,:,current)
+max_Froude = maxval(speed/Dyn%Grid%h(:,:,current))
+call mpp_max(max_Froude)
+
+if(root) then
+  write(*,1000) day, second, enstrophy, div_squared, max_Froude
+end if
+1000 format(1x, 'day =',i6,2x,'second =', i6, &
+    2x,'enstrophy = ',e13.6,3x,'div_squared = ',e13.6, 3x, &
+    'max_Froude = ', e10.3)
+
+return
+end subroutine global_diag
+
+!===============================================================================
+subroutine atmosphere_end
+
+if(.not.module_is_initialized) then
+  call error_mesg('atmosphere_end', &
+                  'atmosphere_init has not been called.', FATAL)
+end if
+
+call shallow_physics_end (Phys)
+call shallow_dynamics_end (Dyn, previous, current)
+
+module_is_initialized = .false.
+
+return
+end subroutine atmosphere_end
+
+!=======================================================================================
+end module atmosphere_mod
diff --git a/src/atmos_spectral_shallow/atmosphere.html b/src/atmos_spectral_shallow/atmosphere.html
new file mode 100644
index 000000000..13e269faf
--- /dev/null
+++ b/src/atmos_spectral_shallow/atmosphere.html
@@ -0,0 +1,164 @@
+
+module atmosphere_mod
+
+
+

+
+
module atmosphere_mod

+
+
+
+     Contact: Isaac Held
+     Reviewers: Peter Phillipps
+

+
+
+
+

+
OVERVIEW

+
+
+   A spectral transform model for the shallow water equations on the sphere
+

+
+
+
+

+
DESCRIPTION

+
+
+   Integrates the shallow water equations for hydrostatic flow in a thin layer
+   of homogeneous fluid on the sphere, using the spectral transform technique.
+   Also allows for the inclusion of a passive tracer advected by the 
+   spectral advection algorithm as the vorticity, and a gridpoint tracer 
+   advected with a finite volume algorithm on the transform grid.  
+   The default experiment is forced by a "monsoonal" mass source, starting
+   from a state of rest.
+   
+   For a full description of the model and algorithms used, see shallow.ps
+
+   The interfaces in this module are the generic intefaces required by the
+   main program that can be used to drive various idealized atmospheric
+   models within FMS. Model resolution and related parameters are set in
+   namelists within the modules shallow_xxx.
+

+
+
+
+

+
OTHER MODULES USED

+
+
+     fms_mod
+     constants_mod
+     transforms_mod
+     time_manager_mod
+     diag_manager_mod
+     shallow_dynamics_mod
+     shallow_physics_mod
+     shallow_diagnostics_mod
+

+
+
+
+

+
PUBLIC INTERFACE

+
+
+  use atmosphere_mod [,only: atmosphere_init,       
+                             atmosphere,
+			     atmosphere_end]
+

+
+
+
+

+
PUBLIC DATA

+
+
+  There are no public data types
+

+
+
+
+

+
PUBLIC ROUTINES

+
+
+subroutine atmosphere_init. Initializes the model.
+subroutine atmosphere.      Integrates forward one time step
+subroutine atmosphere_end.  Terminates model, cleaning up memory and finalizing diagnostics.
+
+
+
+ subroutine atmosphere_init(Time_init, Time, Time_step)
+
+   input:
+
+   type(time_type) :: Time_init -- Initial model time
+
+   type(time_type) :: Time      -- Model time
+
+   type(time_type) :: Time_step -- Time step
+
+   When Time=Time_init, the first time step is a forward
+   step rather than leap frog because a cold start is assumed.
+
+   The FMS main program that runs the solo atmospheric models
+   obtains Time_init from the diag_table and Time from its namelist.
+       
+
+

+
+
+  subroutine atmosphere(Time)
+
+    input:
+ 
+    type(time_type) :: Time -- Model time
+      
+    Integrates forward one time step
+
+
+

+ 
+   subroutine atmosphere_end
+   
+    No calling arguments.  
+      
+    Terminates model, cleaning up memory and finalizing diagnostics
+
+

+

+
+
+
NAMELIST

+
+
+&atmosphere_nml
+
+   print_interval, integer : time interval in seconds 
+   between prints of global mean energy and enstrophy to standard output
+

+
+
+
+

+
ERROR MESSAGES

+
+
+  Fatal error message if subroutine atmosphere or atmosphere_end
+  is called prior to atmosphere_init.
+

+
+
+

+
+
diff --git a/src/atmos_spectral_shallow/shallow.pdf b/src/atmos_spectral_shallow/shallow.pdf
new file mode 100644
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diff --git a/src/atmos_spectral_shallow/shallow_diagnostics.F90 b/src/atmos_spectral_shallow/shallow_diagnostics.F90
new file mode 100644
index 000000000..b8dc52f68
--- /dev/null
+++ b/src/atmos_spectral_shallow/shallow_diagnostics.F90
@@ -0,0 +1,139 @@
+
+module shallow_diagnostics_mod
+
+!-----------------------------------------------------------------------
+!                   GNU General Public License                        
+!                                                                      
+! This program is free software; you can redistribute it and/or modify it and  
+! are expected to follow the terms of the GNU General Public License  
+! as published by the Free Software Foundation; either version 2 of   
+! the License, or (at your option) any later version.                 
+!                                                                      
+! This program is distributed in the hope that it will be useful, but WITHOUT    
+! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  
+! or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public    
+! License for more details.                                           
+!                                                                      
+! For the full text of the GNU General Public License,                
+! write to: Free Software Foundation, Inc.,                           
+!           675 Mass Ave, Cambridge, MA 02139, USA.                   
+! or see:   http://www.gnu.org/licenses/gpl.html                      
+!-----------------------------------------------------------------------
+
+use              fms_mod, only: write_version_number
+
+use       transforms_mod, only: get_grid_boundaries, &
+                                get_deg_lon,         &
+                                get_deg_lat,         &
+                                get_grid_domain,     &
+                                get_spec_domain,     & 
+                                grid_domain
+
+use     diag_manager_mod, only: diag_axis_init, &
+                                register_diag_field, &
+                                register_static_field, &
+                                send_data
+
+use     time_manager_mod, only: time_type, &
+                                get_time
+
+
+use shallow_physics_mod,  only:  phys_type
+use shallow_dynamics_mod, only:  grid_type
+
+
+implicit none
+private
+
+public :: shallow_diagnostics_init, &
+          shallow_diagnostics
+
+character(len=84), parameter :: version = '$Id: shallow_diagnostics.F90,v 10.0 2003/10/24 22:01:02 fms Exp $'
+character(len=84), parameter :: tagname = '$Name: siena_201207 $'
+character(len=8) :: axiset   = 'shallow'
+character(len=84) :: mod_name = 'shallow_diagnostics'
+
+logical :: module_is_initialized = .false.
+
+integer :: id_vor, id_stream, id_pv, id_u, id_v, id_div, id_h, id_trs, id_tr
+
+integer :: is, ie, js, je
+
+contains
+
+!-----------------------------------------------------------------------------------------------------------------
+subroutine shallow_diagnostics_init(Time, lon_max, lat_max)
+
+type(time_type), intent(in) :: Time
+integer, intent(in) :: lon_max, lat_max
+
+real, dimension(lon_max  ) :: lon
+real, dimension(lon_max+1) :: lonb
+real, dimension(lat_max  ) :: lat
+real, dimension(lat_max+1) :: latb
+
+integer, dimension(2) :: axis_2d
+
+integer :: log_unit, id_lonb, id_lon, id_latb, id_lat
+integer :: namelist_unit, ierr, io
+real    :: rad_to_deg
+logical :: used
+
+call write_version_number(version, tagname)
+
+call get_grid_domain(is, ie, js, je)
+
+rad_to_deg = 45./atan(1.)
+call get_grid_boundaries(lonb,latb,global=.true.)
+call get_deg_lon(lon)
+call get_deg_lat(lat)
+
+id_lonb=diag_axis_init('lonb', rad_to_deg*lonb, 'degrees_E', 'x', 'longitude edges', set_name=axiset, Domain2=grid_domain)
+id_latb=diag_axis_init('latb', rad_to_deg*latb, 'degrees_N', 'y', 'latitude edges',  set_name=axiset, Domain2=grid_domain)
+id_lon =diag_axis_init('lon', lon, 'degrees_E', 'x', 'longitude', set_name=axiset, Domain2=grid_domain, edges=id_lonb)
+id_lat =diag_axis_init('lat', lat, 'degrees_N', 'y', 'latitude',  set_name=axiset, Domain2=grid_domain, edges=id_latb)
+
+axis_2d(1) = id_lon
+axis_2d(2) = id_lat
+
+id_u      = register_diag_field(mod_name, 'ucomp' , axis_2d, Time, 'u_wind'              , 'm/s'      ) 
+id_v      = register_diag_field(mod_name, 'vcomp' , axis_2d, Time, 'v_wind'              , 'm/s'      ) 
+id_vor    = register_diag_field(mod_name, 'vor'   , axis_2d, Time, 'relative vorticity'  , '1/s'      )
+id_div    = register_diag_field(mod_name, 'div'   , axis_2d, Time, 'divergence'          , '1/s'      )
+id_h      = register_diag_field(mod_name, 'h'     , axis_2d, Time, 'geopotential'        , 'm2/s2'    )
+id_pv     = register_diag_field(mod_name, 'pv'    , axis_2d, Time, 'potential vorticity' , 's/m2'     )
+id_stream = register_diag_field(mod_name, 'stream', axis_2d, Time, 'streamfunction'      , 'm^2/s'    )
+id_trs    = register_diag_field(mod_name, 'trs'   , axis_2d, Time, 'spectral tracer'     , 'none'     )
+id_tr     = register_diag_field(mod_name, 'tr'    , axis_2d, Time, 'grid tracer'         , 'none'     )
+
+module_is_initialized = .true.
+
+return
+end subroutine shallow_diagnostics_init
+
+!--------------------------------------------------------------------------------------------
+
+subroutine shallow_diagnostics(Time, Grid, Phys, time_index)
+
+type(time_type), intent(in) :: Time
+type(phys_type), intent(in) :: Phys
+type(grid_type), intent(in) :: Grid
+integer,         intent(in) :: time_index
+
+logical :: used
+   
+if(id_u       > 0) used = send_data(id_u      , Grid%u       (:,:, time_index)     , time)
+if(id_v       > 0) used = send_data(id_v      , Grid%v       (:,:, time_index)     , time)
+if(id_vor     > 0) used = send_data(id_vor    , Grid%vor     (:,:, time_index)     , time)
+if(id_div     > 0) used = send_data(id_div    , Grid%div     (:,:, time_index)     , time)
+if(id_h       > 0) used = send_data(id_h      , Grid%h       (:,:, time_index)     , time)
+if(id_pv      > 0) used = send_data(id_pv     , Grid%pv      (:,:)                 , time)
+if(id_stream  > 0) used = send_data(id_stream , Grid%stream  (:,:)                 , time)
+if(id_tr      > 0) used = send_data(id_tr     , Grid%tr      (:,:, time_index)     , time)
+if(id_trs     > 0) used = send_data(id_trs    , Grid%trs     (:,:, time_index)     , time)
+
+return
+end subroutine shallow_diagnostics
+!--------------------------------------------------------------------------------------------
+
+end module shallow_diagnostics_mod
diff --git a/src/atmos_spectral_shallow/shallow_diagnostics.html b/src/atmos_spectral_shallow/shallow_diagnostics.html
new file mode 100644
index 000000000..65db99f52
--- /dev/null
+++ b/src/atmos_spectral_shallow/shallow_diagnostics.html
@@ -0,0 +1,150 @@
+
+module shallow_diagnostics_mod
+
+
+

+
+
+
module shallow_diagnostics_mod

+
+
+
+     Contact: Isaac Held
+     Reviewers: Peter Phillipps
+
+

+
+
+
+

+
OVERVIEW

+
+
+
+   The diagnostics module for the model that solves the shallow water
+   equation on the sphere  
+   
+

+
+
+
+

+
DESCRIPTION

+
+
+
+   Using the diagnostics manager, creates output files for the shallow model.
+   Variables currently available for output are
+       zonal wind 
+       meridional wind 
+       relative vorticity
+       absolute vorticity
+       streamfunction
+       spectral tracer in grid domain
+       grid tracer
+       
+   Whether or not these fields are actually output, the location of the 
+   output, the frequency of output, whether or not the output is averaged
+   in time or an instantaneous snapshot, is controlled by a 
+   diag_table file utilized by the diagnostics manager module
+       
+   One can add other diagnostics by following the (somewhat convoluted)
+       pattern within the program
+
+
+

+
+
+
+

+
OTHER MODULES USED

+
+
+
+     diag_manaager_mod
+     transforms_mod
+     time_manager_mod
+     shallow_dynamics_mod
+     shallow_physics_mod
+
+

+
+
+
+

+
PUBLIC INTERFACE

+
+
+
+  use shallow_diagnostics_mod [,only: shallow_diagnostics_init,       
+                                         shallow_diagnostics]
+                                
+

+
+
+
+
+

+
PUBLIC ROUTINES

+
+
+
+subroutine  shallow_diagnostics_init
+subroutine  shallow_diagnostics
+
+
+
+
+ subroutine shallow_diagnostics_init(Time, num_lon, num_lat)
+ 
+   type(time_type)    , intent(in)     :: Time
+         current time 
+   integer, intent(in) :: num_lon, num_lat
+      num_lon = number of longitudes in global domain
+      num_lat = number of latitudes in global domain
+         
+
+   Initializes module
+
+
+
+

+
+
+
+  subroutine shallow_diagnostics (Time, Grid, Phys, time_index)
+  
+    type(time_type), intent(in) :: Time
+    type(phys_type), intent(in) :: Phys
+    type(grid_type), intent(in) :: Grid
+    integer,         intent(in) :: time_index
+    
+    phys_type is defined in shallow_physics_mod; ;
+       
+    grid_type is defined in shallow_dynamics_mod: 
+      Grid contains all of the fields to be output
+      
+    many of the grid fields in grid_type are dimensioned (lon, lat, time_index)
+     where time_index = 1 or 2 -- the two time levels needed to update the
+     state of the model using a leapfrog step are toggled between (:,:,1)
+     and (:,:,2).  The input time_index (which must equal either 1 or 2) 
+     determines which of these two fields is output)
+     
+     (this is confusing -- the calling program needs to know what has
+      been placed in which slot -- it would be better to store this 
+      information within the data type)
+ 
+
+
+
+

+
+
+
diff --git a/src/atmos_spectral_shallow/shallow_dynamics.F90 b/src/atmos_spectral_shallow/shallow_dynamics.F90
new file mode 100644
index 000000000..543e37230
--- /dev/null
+++ b/src/atmos_spectral_shallow/shallow_dynamics.F90
@@ -0,0 +1,607 @@
+module shallow_dynamics_mod
+
+!-----------------------------------------------------------------------
+!                   GNU General Public License                        
+!                                                                      
+! This program is free software; you can redistribute it and/or modify it and  
+! are expected to follow the terms of the GNU General Public License  
+! as published by the Free Software Foundation; either version 2 of   
+! the License, or (at your option) any later version.                 
+!                                                                      
+! This program is distributed in the hope that it will be useful, but WITHOUT    
+! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  
+! or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public    
+! License for more details.                                           
+!                                                                      
+! For the full text of the GNU General Public License,                
+! write to: Free Software Foundation, Inc.,                           
+!           675 Mass Ave, Cambridge, MA 02139, USA.                   
+! or see:   http://www.gnu.org/licenses/gpl.html                      
+!-----------------------------------------------------------------------
+
+use               fms_mod, only: open_namelist_file,   &
+                                 open_restart_file,    &
+                                 file_exist,           &
+                                 check_nml_error,      &
+                                 error_mesg,           &
+                                 FATAL,                &
+                                 write_version_number, &
+                                 mpp_pe,               &
+                                 mpp_root_pe,          &
+                                 read_data,            &
+                                 write_data,           &
+                                 set_domain,           &
+                                 close_file,           &
+                                 stdlog
+
+use    time_manager_mod,  only : time_type,      &
+                                 get_time,       &
+                                 operator(==),   &
+                                 operator(-)
+
+use       constants_mod,  only : radius, omega
+
+use         transforms_mod, only: transforms_init,         transforms_end,          &
+                                  get_grid_boundaries,     horizontal_advection,    &
+                                  trans_spherical_to_grid, trans_grid_to_spherical, &  
+                                  compute_laplacian,       get_eigen_laplacian,     &
+                                  get_sin_lat,             get_cos_lat,             &
+                                  get_deg_lon,             get_deg_lat,             &
+                                  get_grid_domain,         get_spec_domain,         &
+                                  spectral_domain,         grid_domain,             &
+                                  vor_div_from_uv_grid,    uv_grid_from_vor_div
+
+use   spectral_damping_mod, only: spectral_damping_init,   compute_spectral_damping
+
+use           leapfrog_mod, only: leapfrog
+
+use       fv_advection_mod, only : fv_advection_init, a_grid_horiz_advection
+
+!======================================================================================
+implicit none
+private
+!======================================================================================
+
+public :: shallow_dynamics_init, shallow_dynamics, shallow_dynamics_end, &
+          dynamics_type, grid_type, spectral_type, tendency_type
+
+
+! version information 
+!===================================================================
+character(len=128) :: version = '$Id: shallow_dynamics.F90,v 10.0 2003/10/24 22:01:02 fms Exp $'
+character(len=128) :: tagname = '$Name: siena_201207 $'
+!===================================================================
+
+type grid_type
+   real, pointer, dimension(:,:,:) :: u=>NULL(), v=>NULL(), vor=>NULL(), div=>NULL(), h=>NULL(), trs=>NULL(), tr=>NULL()
+   real, pointer, dimension(:,:)   :: stream=>NULL(), pv=>NULL()
+end type
+type spectral_type
+   complex, pointer, dimension(:,:,:) :: vor=>NULL(), div=>NULL(), h=>NULL(), trs=>NULL()
+end type
+type tendency_type
+   real, pointer, dimension(:,:) :: u=>NULL(), v=>NULL(), h=>NULL(), trs=>NULL(), tr=>NULL()
+end type
+type dynamics_type
+   type(grid_type)     :: grid
+   type(spectral_type) :: spec
+   type(tendency_type) :: tend
+   integer             :: num_lon, num_lat
+   logical             :: grid_tracer, spec_tracer
+end type
+
+
+
+integer, parameter :: num_time_levels = 2
+
+integer :: is, ie, js, je, ms, me, ns, ne
+
+logical :: module_is_initialized = .false.
+
+real,  allocatable, dimension(:) :: sin_lat, cos_lat, rad_lat, deg_lat, deg_lon, &
+                                    coriolis
+
+real,  allocatable, dimension(:,:) :: eigen
+
+integer :: pe, npes
+
+
+! namelist parameters with default values
+
+integer :: num_lon            = 256 
+integer :: num_lat            = 128
+integer :: num_fourier        = 85
+integer :: num_spherical      = 86
+integer :: fourier_inc         = 1
+! (these define a standard T85 model)
+
+logical :: check_fourier_imag = .false.
+logical :: south_to_north     = .true.
+logical :: triang_trunc   = .true.
+
+real    :: robert_coeff        = 0.04
+real    :: robert_coeff_tracer = 0.04
+real    :: longitude_origin    = 0.0
+
+character(len=64) :: damping_option = 'resolution_dependent'
+integer :: damping_order       = 4
+real    :: damping_coeff       = 1.e-04
+real    :: h_0                 = 3.e04
+
+logical :: spec_tracer      = .true.
+logical :: grid_tracer      = .true.
+
+real, dimension(2) :: valid_range_v = (/-1.e3,1.e3/)
+
+namelist /shallow_dynamics_nml/ check_fourier_imag,          &
+                          south_to_north, triang_trunc,      &
+                          num_lon, num_lat, num_fourier,     &
+                          num_spherical, fourier_inc,        &
+                          longitude_origin, damping_option,  &
+                          damping_order,     damping_coeff,  &
+                          robert_coeff, robert_coeff_tracer, &
+                          h_0, spec_tracer, grid_tracer,     &
+                          valid_range_v
+
+contains
+
+!=======================================================================================
+
+subroutine shallow_dynamics_init (Dyn,  Time, Time_init)
+
+type(dynamics_type), intent(inout)  :: Dyn
+type(time_type)    , intent(in)     :: Time, Time_init
+
+integer :: i, j
+
+real,    allocatable, dimension(:)   :: glon_bnd, glat_bnd
+real :: xx, yy, dd
+
+integer  :: ierr, io, unit
+logical  :: root
+
+! < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > 
+
+call write_version_number (version, tagname)
+
+pe   =  mpp_pe()
+root = (pe == mpp_root_pe())
+
+if (file_exist('input.nml')) then
+  unit = open_namelist_file ()
+  ierr=1
+  do while (ierr /= 0)
+    read  (unit, nml=shallow_dynamics_nml, iostat=io, end=10)
+    ierr = check_nml_error (io, 'shallow_dynamics_nml')
+  enddo
+  10 call close_file (unit)
+endif
+
+if (root) write (stdlog(), nml=shallow_dynamics_nml)
+
+call transforms_init(radius, num_lat, num_lon, num_fourier, fourier_inc, num_spherical, &
+         south_to_north=south_to_north,   &
+         triang_trunc=triang_trunc,       &
+         longitude_origin=longitude_origin       )
+
+call get_grid_domain(is,ie,js,je)
+call get_spec_domain(ms,me,ns,ne)
+
+Dyn%num_lon = num_lon
+Dyn%num_lat = num_lat
+Dyn%spec_tracer  = spec_tracer
+Dyn%grid_tracer  = grid_tracer
+
+allocate (sin_lat   (js:je))
+allocate (cos_lat   (js:je))
+allocate (deg_lat   (js:je))
+allocate (deg_lon   (is:ie))
+allocate (coriolis  (js:je))
+
+call get_deg_lon (deg_lon)
+call get_deg_lat (deg_lat)
+call get_sin_lat (sin_lat)
+call get_cos_lat (cos_lat)
+
+allocate (glon_bnd  (num_lon + 1))
+allocate (glat_bnd  (num_lat + 1))
+call get_grid_boundaries (glon_bnd, glat_bnd, global=.true.)
+
+coriolis = 2*omega*sin_lat
+
+call spectral_damping_init(damping_coeff, damping_order, damping_option, num_fourier, num_spherical, 1, 0., 0., 0.)
+
+allocate(eigen(ms:me,ns:ne))
+call get_eigen_laplacian(eigen)
+
+allocate (Dyn%spec%vor (ms:me, ns:ne, num_time_levels))
+allocate (Dyn%spec%div (ms:me, ns:ne, num_time_levels))
+allocate (Dyn%spec%h   (ms:me, ns:ne, num_time_levels))
+
+allocate (Dyn%grid%u   (is:ie, js:je, num_time_levels))
+allocate (Dyn%grid%v   (is:ie, js:je, num_time_levels))
+allocate (Dyn%grid%vor (is:ie, js:je, num_time_levels))
+allocate (Dyn%grid%div (is:ie, js:je, num_time_levels))
+allocate (Dyn%grid%h   (is:ie, js:je, num_time_levels))
+
+allocate (Dyn%tend%u        (is:ie, js:je))
+allocate (Dyn%tend%v        (is:ie, js:je))
+allocate (Dyn%tend%h        (is:ie, js:je))
+allocate (Dyn%grid%stream   (is:ie, js:je))
+allocate (Dyn%grid%pv       (is:ie, js:je))
+
+call fv_advection_init(num_lon, num_lat, glat_bnd, 360./float(fourier_inc))
+if(Dyn%grid_tracer) then
+  allocate(Dyn%Grid%tr (is:ie, js:je, num_time_levels))
+  allocate(Dyn%Tend%tr (is:ie, js:je))
+endif
+
+if(Dyn%spec_tracer) then
+  allocate(Dyn%Grid%trs (is:ie, js:je, num_time_levels))
+  allocate(Dyn%Tend%trs (is:ie, js:je))
+  allocate(Dyn%Spec%trs (ms:me, ns:ne, num_time_levels))
+endif
+
+if(Time == Time_init) then
+
+  Dyn%Grid%vor(:,:,1) = 0.0
+  Dyn%Grid%div(:,:,1) = 0.0
+  Dyn%Grid%h  (:,:,1) = h_0
+    
+  call trans_grid_to_spherical(Dyn%Grid%vor(:,:,1), Dyn%Spec%vor(:,:,1))
+  call trans_grid_to_spherical(Dyn%Grid%div(:,:,1), Dyn%Spec%div(:,:,1))
+  call trans_grid_to_spherical(Dyn%Grid%h  (:,:,1), Dyn%Spec%h  (:,:,1))
+
+  call uv_grid_from_vor_div   (Dyn%Spec%vor(:,:,1), Dyn%Spec%div(:,:,1),  &
+                               Dyn%Grid%u  (:,:,1), Dyn%Grid%v  (:,:,1))
+  
+  if(Dyn%grid_tracer) then
+    Dyn%Grid%tr = 0.0
+    do j = js, je
+      if(deg_lat(j) > 10.0 .and. deg_lat(j) < 20.0) Dyn%Grid%tr(:,j,1) =  1.0
+      if(deg_lat(j) > 70.0 )                        Dyn%Grid%tr(:,j,1) = -1.0
+    end do
+  endif
+  
+  if(Dyn%spec_tracer) then
+    Dyn%Grid%trs = 0.0
+    do j = js, je
+      if(deg_lat(j) > 10.0 .and. deg_lat(j) < 20.0) Dyn%Grid%trs(:,j,1) =  1.0
+      if(deg_lat(j) > 70.0 )                        Dyn%Grid%trs(:,j,1) = -1.0
+    end do
+    call trans_grid_to_spherical(Dyn%Grid%trs(:,:,1), Dyn%Spec%trs(:,:,1))
+  endif
+  
+else
+
+  call read_restart(Dyn)
+  
+endif
+
+module_is_initialized = .true.
+
+return
+end subroutine shallow_dynamics_init
+
+!========================================================================================
+
+subroutine shallow_dynamics(Time, Time_init, Dyn, previous, current, future, delta_t)
+
+type(time_type)    , intent(in)    :: Time, Time_init
+type(dynamics_type), intent(inout) :: Dyn
+integer, intent(in   )  :: previous, current, future
+real,    intent(in   )  :: delta_t
+
+! < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < >
+
+complex, dimension(ms:me, ns:ne)  :: dt_vors, dt_divs, dt_hs, stream, bs, work
+real,    dimension(is:ie, js:je)  :: vorg, bg, h_future, h_dt, dt_vorg
+integer :: j
+
+! < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > 
+
+if(.not.module_is_initialized) then
+  call error_mesg('shallow_dynamics','dynamics has not been initialized ', FATAL)
+endif
+
+
+do j = js,je
+  vorg(:,j) = Dyn%Grid%vor(:,j,current) + coriolis(j) 
+end do
+Dyn%Tend%u = Dyn%Tend%u + vorg*Dyn%Grid%v(:,:,current)
+Dyn%Tend%v = Dyn%Tend%v - vorg*Dyn%Grid%u(:,:,current)
+
+call vor_div_from_uv_grid (Dyn%Tend%u, Dyn%Tend%v, dt_vors, dt_divs)
+
+call horizontal_advection (Dyn%Spec%h(:,:,current),   &
+         Dyn%Grid%u(:,:,current), Dyn%Grid%v(:,:,current), Dyn%Tend%h)
+
+Dyn%Tend%h = Dyn%Tend%h - Dyn%Grid%h(:,:,current)*Dyn%Grid%div(:,:,current)
+
+call trans_grid_to_spherical (Dyn%Tend%h, dt_hs)
+
+bg = (Dyn%Grid%h(:,:,current) + &
+   0.5*(Dyn%Grid%u(:,:,current)**2 + Dyn%Grid%v(:,:,current)**2))
+
+call trans_grid_to_spherical(bg, bs)
+dt_divs = dt_divs - compute_laplacian(bs)
+
+call implicit_correction (dt_divs, dt_hs, Dyn%Spec%div, Dyn%Spec%h, &
+                            delta_t, previous, current)
+
+call compute_spectral_damping(Dyn%Spec%vor(:,:,previous), dt_vors, delta_t)
+call compute_spectral_damping(Dyn%Spec%div(:,:,previous), dt_divs, delta_t)
+call compute_spectral_damping(Dyn%Spec%h  (:,:,previous), dt_hs  , delta_t)
+
+call leapfrog(Dyn%Spec%vor , dt_vors  , previous, current, future, delta_t, robert_coeff)
+call leapfrog(Dyn%Spec%div , dt_divs  , previous, current, future, delta_t, robert_coeff)
+call leapfrog(Dyn%Spec%h   , dt_hs    , previous, current, future, delta_t, robert_coeff)
+
+call trans_spherical_to_grid(Dyn%Spec%vor(:,:,future), Dyn%Grid%vor(:,:,future))
+call trans_spherical_to_grid(Dyn%Spec%div(:,:,future), Dyn%Grid%div(:,:,future))
+  
+
+call uv_grid_from_vor_div  (Dyn%Spec%vor (:,:,future),  Dyn%Spec%div(:,:,future), &
+                            Dyn%Grid%u   (:,:,future),  Dyn%Grid%v  (:,:,future))
+
+call trans_spherical_to_grid (Dyn%Spec%h (:,:,future),  Dyn%Grid%h(:,:,future))
+
+if(minval(Dyn%Grid%v) < valid_range_v(1) .or. maxval(Dyn%Grid%v) > valid_range_v(2)) then
+  call error_mesg('shallow_dynamics','meridional wind out of valid range', FATAL)
+endif
+
+if(Dyn%spec_tracer) call update_spec_tracer(Dyn%Spec%trs, Dyn%Grid%trs, Dyn%Tend%trs, &
+                         Dyn%Grid%u, Dyn%Grid%v, previous, current, future, delta_t)
+
+if(Dyn%grid_tracer) call update_grid_tracer(Dyn%Grid%tr, Dyn%Tend%tr, &
+                         Dyn%Grid%u, Dyn%Grid%v, previous, current, future, delta_t)
+
+
+!  for diagnostics
+
+stream = compute_laplacian(Dyn%Spec%vor(:,:,current), -1) ! for diagnostic purposes
+call trans_spherical_to_grid(stream, Dyn%grid%stream)
+
+Dyn%Grid%pv = vorg/Dyn%Grid%h(:,:,current)
+
+return
+end subroutine shallow_dynamics
+!================================================================================
+
+subroutine implicit_correction(dt_divs, dt_hs, divs, hs, delta_t, previous, current)
+
+complex, intent(inout), dimension(ms:,ns:)   :: dt_divs, dt_hs
+complex, intent(in),    dimension(ms:,ns:,:) :: divs, hs
+real   , intent(in)                          :: delta_t
+integer, intent(in)                          :: previous, current
+
+real :: xi, mu, mu2
+
+xi    = 0.5 ! centered implicit   (for backwards implicit, set xi = 1.0)
+
+mu  = xi*delta_t
+mu2 = mu*mu
+
+dt_hs   = dt_hs + h_0*(divs(:,:,current) - divs(:,:,previous))
+dt_divs = dt_divs - eigen*(hs(:,:,current) - hs(:,:,previous))
+
+dt_divs = (dt_divs + mu*eigen*dt_hs)/(1.0 + mu2*eigen*h_0)
+dt_hs   =  dt_hs - mu*h_0*dt_divs
+
+return
+end subroutine implicit_correction 
+
+!===================================================================================
+
+subroutine update_spec_tracer(tr_spec, tr_grid, dt_tr, ug, vg, &
+                              previous, current, future, delta_t)
+
+complex, intent(inout), dimension(ms:me, ns:ne, num_time_levels) :: tr_spec
+real   , intent(inout), dimension(is:ie, js:je, num_time_levels) :: tr_grid
+real   , intent(inout), dimension(is:ie, js:je                 ) :: dt_tr
+real   , intent(in   ), dimension(is:ie, js:je, num_time_levels) :: ug, vg  
+real   , intent(in   )  :: delta_t
+integer, intent(in   )  :: previous, current, future
+
+complex, dimension(ms:me, ns:ne) :: dt_trs
+
+call horizontal_advection     (tr_spec(:,:,current), ug(:,:,current), vg(:,:,current), dt_tr)
+call trans_grid_to_spherical  (dt_tr, dt_trs)
+call compute_spectral_damping (tr_spec(:,:,previous), dt_trs, delta_t)
+call leapfrog                 (tr_spec, dt_trs, previous, current, future, delta_t, robert_coeff)
+call trans_spherical_to_grid  (tr_spec(:,:,future), tr_grid(:,:,future))
+
+return
+end subroutine update_spec_tracer
+!==========================================================================
+
+subroutine update_grid_tracer(tr_grid, dt_tr_grid, ug, vg, &
+                              previous, current, future, delta_t)
+
+real   , intent(inout), dimension(is:ie, js:je, num_time_levels) :: tr_grid
+real   , intent(inout), dimension(is:ie, js:je                 ) :: dt_tr_grid
+real   , intent(in   ), dimension(is:ie, js:je, num_time_levels) :: ug, vg
+
+real   , intent(in   )  :: delta_t
+integer, intent(in   )  :: previous, current, future
+
+real, dimension(is:ie,js:je) :: tr_current, tr_future
+
+tr_future = tr_grid(:,:,previous) + delta_t*dt_tr_grid
+dt_tr_grid = 0.0
+call a_grid_horiz_advection (ug(:,:,current), vg(:,:,current), tr_future, delta_t, dt_tr_grid)
+tr_future = tr_future + delta_t*dt_tr_grid
+tr_current = tr_grid(:,:,current) + &
+    robert_coeff_tracer*(tr_grid(:,:,previous) + tr_future - 2.0*tr_grid(:,:,current))
+tr_grid(:,:,current) = tr_current
+tr_grid(:,:,future)  = tr_future
+
+return
+end subroutine update_grid_tracer
+
+!==========================================================================
+
+subroutine read_restart(Dyn)
+
+type(dynamics_type), intent(inout)  :: Dyn
+
+integer :: unit, m, n, nt
+real, dimension(ms:me, ns:ne) :: real_part, imag_part
+
+if(file_exist('INPUT/shallow_dynamics.res.nc')) then
+  do nt = 1, 2
+    call read_data('INPUT/shallow_dynamics.res.nc', 'vors_real', real_part, spectral_domain, timelevel=nt)
+    call read_data('INPUT/shallow_dynamics.res.nc', 'vors_imag', imag_part, spectral_domain, timelevel=nt)
+    do n=ns,ne
+      do m=ms,me
+        Dyn%Spec%vor(m,n,nt) = cmplx(real_part(m,n),imag_part(m,n))
+      end do
+    end do
+    call read_data('INPUT/shallow_dynamics.res.nc', 'divs_real', real_part, spectral_domain, timelevel=nt)
+    call read_data('INPUT/shallow_dynamics.res.nc', 'divs_imag', imag_part, spectral_domain, timelevel=nt)
+    do n=ns,ne
+      do m=ms,me
+        Dyn%Spec%div(m,n,nt) = cmplx(real_part(m,n),imag_part(m,n))
+      end do
+    end do
+    call read_data('INPUT/shallow_dynamics.res.nc', 'hs_real', real_part, spectral_domain, timelevel=nt)
+    call read_data('INPUT/shallow_dynamics.res.nc', 'hs_imag', imag_part, spectral_domain, timelevel=nt)
+    do n=ns,ne
+      do m=ms,me
+        Dyn%Spec%h(m,n,nt) = cmplx(real_part(m,n),imag_part(m,n))
+      end do
+    end do
+    if(Dyn%spec_tracer) then
+      call read_data('INPUT/shallow_dynamics.res.nc', 'trs_real', real_part, spectral_domain, timelevel=nt)
+      call read_data('INPUT/shallow_dynamics.res.nc', 'trs_imag', imag_part, spectral_domain, timelevel=nt)
+      do n=ns,ne
+        do m=ms,me
+          Dyn%Spec%trs(m,n,nt) = cmplx(real_part(m,n),imag_part(m,n))
+        end do
+      end do
+    endif
+    call read_data('INPUT/shallow_dynamics.res.nc', 'u',   Dyn%Grid%u  (:,:,nt), grid_domain, timelevel=nt)
+    call read_data('INPUT/shallow_dynamics.res.nc', 'v',   Dyn%Grid%v  (:,:,nt), grid_domain, timelevel=nt)
+    call read_data('INPUT/shallow_dynamics.res.nc', 'vor', Dyn%Grid%vor(:,:,nt), grid_domain, timelevel=nt)
+    call read_data('INPUT/shallow_dynamics.res.nc', 'div', Dyn%Grid%div(:,:,nt), grid_domain, timelevel=nt)
+    call read_data('INPUT/shallow_dynamics.res.nc', 'h',   Dyn%Grid%h  (:,:,nt), grid_domain, timelevel=nt)
+    if(Dyn%spec_tracer) then
+      call read_data('INPUT/shallow_dynamics.res.nc', 'trs', Dyn%Grid%trs(:,:,nt), grid_domain, timelevel=nt)
+    endif
+    if(Dyn%grid_tracer) then
+      call read_data('INPUT/shallow_dynamics.res.nc', 'tr', Dyn%Grid%tr(:,:,nt), grid_domain, timelevel=nt)
+    endif
+  end do
+else if(file_exist('INPUT/shallow_dynamics.res')) then
+  unit = open_restart_file(file='INPUT/shallow_dynamics.res',action='read')
+
+  do nt = 1, 2
+    call set_domain(spectral_domain)
+    call read_data(unit,Dyn%Spec%vor(:,:, nt))
+    call read_data(unit,Dyn%Spec%div(:,:, nt))
+    call read_data(unit,Dyn%Spec%h  (:,:, nt))
+    if(Dyn%spec_tracer) call read_data(unit,Dyn%Spec%trs(:,:, nt))
+
+    call set_domain(grid_domain)
+    call read_data(unit,Dyn%Grid%u   (:,:, nt))
+    call read_data(unit,Dyn%Grid%v   (:,:, nt))
+    call read_data(unit,Dyn%Grid%vor (:,:, nt))
+    call read_data(unit,Dyn%Grid%div (:,:, nt))
+    call read_data(unit,Dyn%Grid%h   (:,:, nt))
+    if(Dyn%spec_tracer) call read_data(unit,Dyn%Grid%trs(:,:, nt))
+    if(Dyn%grid_tracer) call read_data(unit,Dyn%Grid%tr (:,:, nt))
+    
+  end do
+  call close_file(unit)
+  
+else
+    call error_mesg('read_restart', 'restart does not exist', FATAL)
+endif
+  
+return
+end subroutine read_restart
+
+!====================================================================
+
+subroutine write_restart(Dyn, previous, current)
+
+type(dynamics_type), intent(in)  :: Dyn
+integer, intent(in) :: previous, current
+
+integer :: unit, nt, nn
+
+do nt = 1, 2
+  if(nt == 1) nn = previous
+  if(nt == 2) nn = current
+  call write_data('RESTART/shallow_dynamics.res.nc', 'vors_real',  real(Dyn%Spec%vor(:,:,nn)), spectral_domain)
+  call write_data('RESTART/shallow_dynamics.res.nc', 'vors_imag', aimag(Dyn%Spec%vor(:,:,nn)), spectral_domain)
+  call write_data('RESTART/shallow_dynamics.res.nc', 'divs_real',  real(Dyn%Spec%div(:,:,nn)), spectral_domain)
+  call write_data('RESTART/shallow_dynamics.res.nc', 'divs_imag', aimag(Dyn%Spec%div(:,:,nn)), spectral_domain)
+  call write_data('RESTART/shallow_dynamics.res.nc', 'hs_real',    real(Dyn%Spec%h  (:,:,nn)), spectral_domain)
+  call write_data('RESTART/shallow_dynamics.res.nc', 'hs_imag',   aimag(Dyn%Spec%h  (:,:,nn)), spectral_domain)
+  if(Dyn%spec_tracer) then
+    call write_data('RESTART/shallow_dynamics.res.nc', 'trs_real',  real(Dyn%Spec%trs(:,:,nn)), spectral_domain)
+    call write_data('RESTART/shallow_dynamics.res.nc', 'trs_imag', aimag(Dyn%Spec%trs(:,:,nn)), spectral_domain)
+  endif
+  call write_data('RESTART/shallow_dynamics.res.nc', 'u',   Dyn%Grid%u  (:,:,nn), grid_domain)
+  call write_data('RESTART/shallow_dynamics.res.nc', 'v',   Dyn%Grid%v  (:,:,nn), grid_domain)
+  call write_data('RESTART/shallow_dynamics.res.nc', 'vor', Dyn%Grid%vor(:,:,nn), grid_domain)
+  call write_data('RESTART/shallow_dynamics.res.nc', 'div', Dyn%Grid%div(:,:,nn), grid_domain)
+  call write_data('RESTART/shallow_dynamics.res.nc', 'h',   Dyn%Grid%h  (:,:,nn), grid_domain)
+  if(Dyn%spec_tracer) then
+    call write_data('RESTART/shallow_dynamics.res.nc', 'trs', Dyn%Grid%trs(:,:,nn), grid_domain)
+  endif
+  if(Dyn%grid_tracer) then
+    call write_data('RESTART/shallow_dynamics.res.nc', 'tr', Dyn%Grid%tr(:,:,nn), grid_domain)
+  endif
+enddo
+
+!unit = open_restart_file(file='RESTART/shallow_dynamics.res', action='write')
+
+!do n = 1, 2
+!  if(n == 1) nn = previous
+!  if(n == 2) nn = current
+!  
+!  call set_domain(spectral_domain)
+!  call write_data(unit,Dyn%Spec%vor(:,:, nn))
+!  call write_data(unit,Dyn%Spec%div(:,:, nn))
+!  call write_data(unit,Dyn%Spec%h  (:,:, nn))
+!  if(Dyn%spec_tracer) call write_data(unit,Dyn%Spec%trs(:,:, nn))
+!
+!  call set_domain(grid_domain)
+!  call write_data(unit,Dyn%Grid%u   (:,:, nn))
+!  call write_data(unit,Dyn%Grid%v   (:,:, nn))
+!  call write_data(unit,Dyn%Grid%vor (:,:, nn))
+!  call write_data(unit,Dyn%Grid%div (:,:, nn))
+!  call write_data(unit,Dyn%Grid%h   (:,:, nn))
+!  if(Dyn%spec_tracer) call write_data(unit,Dyn%Grid%trs(:,:, nn))
+!  if(Dyn%grid_tracer) call write_data(unit,Dyn%Grid%tr (:,:, nn))
+!  
+!end do
+
+!call close_file(unit)
+
+end subroutine write_restart
+
+!====================================================================
+
+subroutine shallow_dynamics_end (Dyn, previous, current)
+
+type(dynamics_type), intent(inout)  :: Dyn
+integer, intent(in) :: previous, current
+
+if(.not.module_is_initialized) then
+  call error_mesg('shallow_dynamics_end','dynamics has not been initialized ', FATAL)
+endif
+
+call write_restart (Dyn, previous, current)
+
+call transforms_end
+
+module_is_initialized = .false.
+
+return
+end subroutine shallow_dynamics_end
+!===================================================================================
+
+end module shallow_dynamics_mod
diff --git a/src/atmos_spectral_shallow/shallow_dynamics.html b/src/atmos_spectral_shallow/shallow_dynamics.html
new file mode 100644
index 000000000..600933a30
--- /dev/null
+++ b/src/atmos_spectral_shallow/shallow_dynamics.html
@@ -0,0 +1,370 @@
+
+module shallow_dynamics_mod
+
+
+

+
+
+
module shallow_dynamics_mod

+
+
+
+     Contact: Isaac Held
+     Reviewers: Peter Phillipps
+
+

+
+
+
+

+
OVERVIEW

+
+
+
+   The dynamical core of the spectral transform model for 
+   the shallow water equations on the sphere.  
+   
+

+
+
+
+

+
DESCRIPTION

+
+
+
+   Integrates the shallow water equation for hydrostatic flow of a homgeoneous,
+   incompressible fluid on the
+   sphere using the spectral transform technique.  Also allows for the
+   inclusion of a passive tracer advected by the the spectral advection
+   algorithm, and a gridpoint tracer advected with a finite
+   volume  algorithm on the transform grid.  Thinking of the model as one of
+   the upper tropopsheric flow, the default experiment involves relaxation of 
+   the geopotential to an "equilibrium value" with maxima (whose amplitude
+   and shape are controlled from the namelist) along the equator and in the 
+   subtropicals.
+
+   For a full description of the model and algorithms used, see 
+     shallow.ps 
+   
+   For higher level routines for running this shallow water model,
+   see  atmosphere_mod 
+
+
+

+
+
+
+

+
OTHER MODULES USED

+
+
+
+     fms_mod
+     constants_mod
+     time_manager_mod
+     transforms_mod
+     spectral_damping_mod
+     leapfrog_mod
+     fv_advection_mod
+
+

+
+
+
+

+
PUBLIC INTERFACE

+
+
+
+  use shallow_dynamics_mod [,only: shallow_dynamics_init,       
+                                   shallow_dynamics,
+			           shallow_dynamics_end,
+                                   dynamics_type,
+				   grid_type,
+				   spectral_type,
+				   tendency_type]
+                                
+

+
+
+
+

+
PUBLIC DATA

+
+
+     
+

+ 
+
+type grid_type
+   real, pointer, dimension(:,:,:) :: u, v, vor, div, h, trs, tr
+   real, pointer, dimension(:,:)   :: stream, pv
+end type
+
+   allocated space for grid fields
+
+   (:,:,:) => (lon, lat, time_level)
+   (:,:)   => (lon, lat)
+      (lon, lat) on local computational domain
+      time_level stores the two time levels needed for the
+          leapfrog step
+   
+   u      -- eastward velocity (m/s)
+   v      -- northward velocity (m/s)
+   vor    -- vorticity (1/s)
+   div    -- divergence (1/s)
+   h      -- geopotential (m^2/s^2)
+   trs    -- tracer advected spectrally
+   tr     -- tracer advected on grid
+   pv     -- (f + vor)/h, where f = 2*omega*sin(lat) (s/m^2)
+   stream -- streamfunction (m^2/s) at current time
+   
+ 
+ 
+ 

+ 
+ 
+type spectral_type
+   complex, pointer, dimension(:,:,:) :: vor, div, h, trs
+end type
+
+   allocated space for spectral fields
+   
+      (:,:,:) => (zonal, meridional, time_level)
+
+   vor -- spectral vorticity
+   div -- spectral divergence
+   h   -- spectral geopotential
+   trs -- spectral tracer
+
+ 

+ 
+ 
+type tendency_type
+    real, pointer, dimension(:,:) :: u, v, h, trs, tr
+end type
+
+   allocated space for accumulating tendencies, d/dt, in grid space, 
+           for prognostic variables
+   
+      (:,:,:) => (lon, lat)
+
+ 

+ 
+ 
+type dynamics_type
+   type(grid_type)     :: grid
+   type(spectral_type) :: spec
+   type(tendency_type) :: tend
+   integer             :: num_lon, num_lat  ! size of global domain
+   logical             :: grid_tracer, spec_tracer 
+end type
+
+   grid_tracer = .true. => tracer with gridpoint advection is beign integrated
+   similarly for spec_tracer
+ 
+ 

+ 
+

+
+
+
+

+
PUBLIC ROUTINES

+
+
+
+subroutine  shallow_dynamics_init
+subroutine  shallow _dynamics
+subroutine  shallow_dynamics_end
+type (grid_type)
+type (spectral_type)
+type (tendency_type)
+type (dynamics_type)
+
+
+
+
+
+ subroutine shallow_dynamics_init(Dyn,  Time, Time_init)
+ 
+   type(dynamics_type), intent(inout)  :: Dyn
+         type containing all dynamical fields and related information
+	 (see type (dynamics_type))
+	 
+   type(time_type)    , intent(in)     :: Time, Time_init
+         current time and time at which integeration began
+	 time_type defined by time_manager_mod
+         
+
+   Initializes the module;
+   Reads restart from 'INPUT/shallow_dynamics.res' if Time = Time_init;
+     otherwise uses default initial conditions
+
+
+
+

+
+
+
+  subroutine shallow_dynamics &
+     (Time, Time_init, Dyn, previous, current, future, delta_t)
+ 
+     type(time_type)    , intent(inout)  :: Time, Time_init
+     type(dynamics_type), intent(inout)  :: Dyn
+     integer            , intent(in   )  :: previous, current, future
+     real               , intent(in   )  :: delta_t
+      
+     previous, current and future = 1 or 2
+       these integers refer to the third dimension of the 
+         three-dimensional fields in Dyn
+       the fields at time t - delta_t are assumed to be in (:,:,previous)
+       the fields at time t           are assumed to be in (:,:,current)
+       the fields at time t + delta_t are placed        in (:,:,future)
+          overwriting whatever is already there
+
+     delta_t = time step in seconds
+     
+     updates dynamical fields by one time step
+
+
+
+

+
+ 
+   subroutine shallow_dynamics_end(Dyn, previous, current)
+   
+     type(dynamics_type), intent(inout)  :: Dyn
+     integer, intent(in) :: previous, current
+   
+      
+    Terminates module; 
+     writes restart file to 'RESTART/shallow_dynamics.res'
+    
+    
+
+
+

+

+
+
+
+

+
NAMELIST

+
+
+
+&shallow_dynamics_nml
+
+  integer :: num_lat            = 128  
+        number of latitudes in global grid
+       
+  integer :: num_lon            = 256
+        number of longitudes in global grid
+        should equal 2*num_lat for Triangular truncation
+  
+  integer :: num_fourier        = 85
+        the retained fourier wavenumber are n*fourier_inc, where
+        n ranges from 0 to num_fourier
+	 
+  integer :: num_spherical      = 86
+        the maximum number of meridional modes for any zonal wavenumber
+        for triangular truncation, set num_spherical = num_fourier +1
+         
+  integer :: fourier_inc        = 1
+        creates a "sector" model if fourier_inc > 1; integration domain is
+	(360 degrees longitude)/fourier_inc
+	
+  (the default values listed above define a standard T85 model)
+
+  logical :: check_fourier_imag = .false.
+        if true, checks to see if fields to be transformed to grid 
+	domain have zero imaginary part to their zonally symmetric
+	modes; useful for debugging
+	
+  logical :: south_to_north     = .true.
+        true => grid runs from south to north
+	false => grid runs from north to south
+	
+  logical :: triangular_trunc   = .true.
+        true  => shape of truncation is triangular
+	false => shape of truncation is rhomboidal
+
+  real    :: robert_coeff       = 0.04
+        x(current) => (1-2r)*x(current) + r*(x(future)+x(previous))
+	where r = robert_coeff (non-dimensional)
+	
+  real    :: robert_coeff_tracer       = 0.04
+        (same as robert_coeff, but for grid tracer)
+	
+  real    :: longitude_origin   = 0.0
+        longitude of first longitude, in degrees
+	(if you want the westgern boundary of first grid boc to be at 
+         0.0, set longitude_origin = 0.5*360./float(num_lon))
+	 
+  integer :: damping_option     = 'resolution_dependent'
+  integer :: damping_order      = 4
+  real    :: damping_coeff      = 1.e-04
+  
+        damping = nu*(del^2)^n where n = damping order
+	damping_option = 'resolution_dependent' or 'resolution_independent'
+	  = 'resolution_dependent' => nu is set so that the damping rate for the 
+	        mode (m=0,n=num_spherical-1) equals damping_coeff (in 1/s)
+	        For triangular truncation, damping_coeff is then the 
+	        rate of damping of the highest retained mode
+	     
+	  = 'resolution_independent' => nu = damping_coef
+	  
+  real    :: h_0  = 3.e04
+          (m^2)/(s^2) 
+          the initial condition is a state of rest with geopotential = h_0
+	  (h_0 is also used to determine the part of the divergence equation
+	   that is integrated implicitly)
+	
+  logical :: spec_tracer      = .true.
+  logical :: grid_tracer      = .true.
+       spec_tracer = true => a passive tracer is carried that is advected
+          spectrally, with the same algorithm as the vorticity
+       grid_tracer = ture => a passive tracer is carried that is advected
+          on the spectral transform grid by a finite-volume algorithm
+	  (see  shallow.ps )
+       Both tracers can be carried simultaeneously
+	  
+  real, dimension(2) :: valid_range_v = -1000., 1000.
+        A valid range for meridional wind. Model terminates if meridional wind
+	goes outside the valid range. Allows model to terminate gracefully when,
+	for example, the model becomes numerically unstable.
+
+

+
+
+
+

+
ERROR MESSAGES

+
+
+
+   "Dynamics has not been initialized"
+      -- shallow_dynamics_init must be called before any other
+         routines in the module are called
+	 
+   "restart does not exist" 
+      -- Time is not equal to Time_init at initalization, but the file
+          'INPUT/shallow_dynamics.res' does not exit 
+	 
+
+

+
+
+
+

+
+
diff --git a/src/atmos_spectral_shallow/shallow_physics.F90 b/src/atmos_spectral_shallow/shallow_physics.F90
new file mode 100644
index 000000000..8f8896d2e
--- /dev/null
+++ b/src/atmos_spectral_shallow/shallow_physics.F90
@@ -0,0 +1,232 @@
+module shallow_physics_mod
+
+!-----------------------------------------------------------------------
+!                   GNU General Public License                        
+!                                                                      
+! This program is free software; you can redistribute it and/or modify it and  
+! are expected to follow the terms of the GNU General Public License  
+! as published by the Free Software Foundation; either version 2 of   
+! the License, or (at your option) any later version.                 
+!                                                                      
+! This program is distributed in the hope that it will be useful, but WITHOUT    
+! ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  
+! or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public    
+! License for more details.                                           
+!                                                                      
+! For the full text of the GNU General Public License,                
+! write to: Free Software Foundation, Inc.,                           
+!           675 Mass Ave, Cambridge, MA 02139, USA.                   
+! or see:   http://www.gnu.org/licenses/gpl.html                      
+!-----------------------------------------------------------------------
+
+use               fms_mod, only: open_namelist_file,   &
+                                 open_restart_file,    &
+                                 file_exist,           &
+                                 check_nml_error,      &
+                                 error_mesg,           &
+                                 FATAL, WARNING,       &
+                                 write_version_number, &
+                                 mpp_pe,               &
+                                 mpp_root_pe,          &
+                                 fms_init, fms_end,    &
+                                 read_data,            &
+                                 write_data,           &
+                                 set_domain,           &
+                                 close_file,           &
+                                 stdlog
+
+use         transforms_mod, only: get_sin_lat, get_cos_lat,  &
+                                  get_deg_lon, get_deg_lat,  &
+                                  get_wts_lat, &
+                                  get_grid_domain, get_spec_domain, &
+                                  grid_domain
+
+use       time_manager_mod, only: time_type
+
+!========================================================================
+implicit none
+private
+!========================================================================
+
+public :: shallow_physics_init,    &
+          shallow_physics,         &
+          shallow_physics_end,     &
+          phys_type
+
+
+! version information 
+!========================================================================
+character(len=128) :: version = '$Id: shallow_physics.F90,v 10.0 2003/10/24 22:01:02 fms Exp $'
+character(len=128) :: tagname = '$Name: siena_201207 $'
+!========================================================================
+
+type phys_type
+   real, pointer, dimension(:,:)   :: empty=>NULL()
+end type
+
+logical :: module_is_initialized = .false.
+
+integer :: is, ie, js, je
+
+integer :: pe
+logical :: root
+
+real, allocatable, dimension(:) :: rad_lat, deg_lat, deg_lon, &
+         sin_lat, cos_lat, wts_lat
+
+real, allocatable, dimension(:,:) :: h_eq
+
+real    :: kappa_m, kappa_t
+
+
+
+! namelist 
+!========================================================================
+
+real    :: fric_damp_time  = -20.0
+real    :: therm_damp_time = -10.0
+real    :: del_h           = 1.e04
+real    :: h_0             = 3.e04
+real    :: h_amp           = 2.e04
+real    :: h_lon           =  90.0
+real    :: h_lat           =  25.0
+real    :: h_width         =  15.0
+real    :: h_itcz          = 1.e05
+real    :: itcz_width      =  4.0
+
+namelist /shallow_physics_nml/ fric_damp_time, therm_damp_time, del_h, h_0, &
+                               h_amp, h_lon, h_lat, h_width, &
+                               itcz_width, h_itcz
+!========================================================================
+
+contains
+
+!========================================================================
+
+subroutine shallow_physics_init(Phys) 
+
+type(phys_type), intent(inout) :: Phys
+
+integer :: i, j, unit, ierr, io
+
+real :: xx, yy, dd
+
+call write_version_number(version, tagname)
+
+pe = mpp_pe()
+root = (pe == mpp_root_pe())
+
+! read the namelist
+
+if (file_exist('input.nml')) then
+  unit = open_namelist_file ()
+  ierr=1
+  do while (ierr /= 0)
+    read  (unit, nml=shallow_physics_nml, iostat=io, end=10)
+    ierr = check_nml_error (io, 'shallow_physics_nml')
+  enddo
+  10 call close_file (unit)
+endif
+
+if(fric_damp_time  < 0.0)  fric_damp_time = -  fric_damp_time*86400
+if(therm_damp_time < 0.0) therm_damp_time = - therm_damp_time*86400
+
+kappa_m = 0.0
+kappa_t = 0.0
+if( fric_damp_time .ne. 0.0) kappa_m = 1./fric_damp_time
+if(therm_damp_time .ne. 0.0) kappa_t = 1./therm_damp_time
+
+call get_grid_domain(is,ie,js,je)
+
+allocate ( rad_lat      (js:je) )
+allocate ( deg_lat      (js:je) )
+allocate ( sin_lat      (js:je) )
+allocate ( cos_lat      (js:je) )
+allocate ( wts_lat      (js:je) )
+allocate ( deg_lon      (is:ie) )
+allocate ( h_eq   (is:ie,js:je) )
+
+call get_wts_lat(wts_lat)
+call get_deg_lat(deg_lat)
+call get_deg_lon(deg_lon)
+rad_lat = deg_lat*atan(1.)/45. 
+sin_lat = sin(rad_lat)
+cos_lat = cos(rad_lat)
+
+
+do j = js, je
+  do i = is, ie
+     xx = (deg_lon(i) - h_lon)/(h_width*2.0)
+     yy = (deg_lat(j) - h_lat)/h_width
+     dd =  xx*xx + yy*yy
+     h_eq(i,j) = h_0 + h_amp*max(1.e-10, exp(-dd))
+  end do
+end do
+
+do j = js, je
+  yy = deg_lat(j)/itcz_width
+  dd = yy*yy
+  h_eq(:,j) = h_eq(:,j) + h_itcz*exp(-dd)
+end do 
+
+!if(file_exist('INPUT/shallow_physics.res')) then
+!  unit = open_restart_file(file='INPUT/shallow_physics.res',action='read')
+!  call set_domain(grid_domain)
+!  call close_file(unit)
+!else
+
+!endif
+
+module_is_initialized = .true.
+
+return
+end subroutine shallow_physics_init
+
+!=======================================================================
+
+subroutine shallow_physics(Time, dt_ug, dt_vg, dt_hg, ug, vg, hg,   &
+                             delta_t, previous, current, Phys)
+
+real, intent(inout),  dimension(is:ie, js:je)    :: dt_ug, dt_vg, dt_hg
+real, intent(in)   ,  dimension(is:ie, js:je, 2) :: ug, vg, hg
+
+real   , intent(in)  :: delta_t
+integer, intent(in)  :: previous, current
+
+type(time_type), intent(in)    :: Time
+type(phys_type), intent(inout) :: Phys
+
+dt_ug = dt_ug - kappa_m*ug(:,:,previous)
+dt_vg = dt_vg - kappa_m*vg(:,:,previous)
+dt_hg = dt_hg - kappa_t*(hg(:,:,previous) - h_eq)
+
+
+return
+end subroutine shallow_physics
+
+!======================================================================
+
+subroutine shallow_physics_end(Phys)
+
+type(phys_type), intent(in) :: Phys
+
+integer :: unit
+
+if(.not.module_is_initialized) then
+  call error_mesg('shallow_physics_end','physics has not been initialized ', FATAL)
+endif
+
+!unit = open_restart_file(file='RESTART/shallow_physics.res', action='write')
+
+!call set_domain(grid_domain)
+
+!call close_file(unit)
+
+module_is_initialized = .false.
+
+return
+end subroutine shallow_physics_end
+
+!======================================================================
+
+end module shallow_physics_mod
diff --git a/src/atmos_spectral_shallow/shallow_physics.html b/src/atmos_spectral_shallow/shallow_physics.html
new file mode 100644
index 000000000..d3ad34980
--- /dev/null
+++ b/src/atmos_spectral_shallow/shallow_physics.html
@@ -0,0 +1,210 @@
+
+module shallow_physics_mod
+
+
+

+
+
+
module shallow_physics_mod

+
+
+
+     Contact: Isaac Held
+     Reviewers: Peter Phillipps
+
+

+
+
+
+

+
OVERVIEW

+
+
+
+   A module that allows one to add processes that act in the grid domain
+   to the dynamics of the shallow model on the sphere
+   
+

+
+
+
+

+
DESCRIPTION

+
+
+
+   A module that allows one to add processes that act in the grid domain
+   to the dynamics of the shallow model on the sphere.  Currently adds
+   a relaxation to a specified  "equilibrium geopotential" and relaxes
+   the winds to zero
+

+
+
+
+

+
OTHER MODULES USED

+
+
+
+     fms_mod
+     transforms_mod
+     time_manager_mod
+
+

+
+
+
+

+
PUBLIC INTERFACE

+
+
+
+  use shallow_physics_mod [,only: shallow_physics_init,       
+                                         shallow_physics,
+					 shallow_physics_end,
+					 phys_type]
+                                
+

+
+
+
+

+
PUBLIC DATA

+
+
+     
+

+ 
+
+type phys_type
+   real, pointer, dimension(:,:)   :: empty
+end type
+
+  fields from physics module made available for diagnostics
+  
+ 

+ 
+
+

+
+
+
+

+
PUBLIC ROUTINES

+
+
+
+subroutine  shallow_physics_init
+subroutine  shallow_physics
+subroutine  shallow_physics_end
+type(phys_type)
+
+
+
+
+
+ subroutine shallow_physics_init(Phys)
+ 
+   type(phys_type)    , intent(inout)     :: Phys
+  
+ 
+   Initializes module
+
+
+
+

+
+
+
+  subroutine shallow_physics (Time, dt_ug, dt_vg, dt_hg, ug, vg, hg,   &
+                             delta_t, previous, current, Phys)
+
+      real, intent(inout),  dimension(:,:)    :: dt_ug, dt_vg, dt_hg
+      
+         the u, v and geopotential tendencies onto which tendencies due to 
+	    the grid-point physics are added (m/(s^2) for dt_ug, dt_vg; 
+	    (m^2)/(s^3) for dt_hg)
+	 
+      real, intent(in)   ,  dimension(:,:, 2) :: ug, vg, hg
+         the grid zonal and meridional velocities (m/s) and
+	 geopotential (m^2/s^2)
+	 the third index is the time-index used in the leapfrog step
+
+      real   , intent(in)  :: delta_t  
+         time step (s)
+	 
+      integer, intent(in)  :: previous, current
+         = 1 or 2
+	 ug(:,:,previous) is the velocity at t-delta_t
+	 ug(:,:,current ) is the velocity at t
+
+      type(time_type), intent(in)    :: Time
+      type(phys_type), intent(inout) :: Phys
+ 
+
+
+
+

+
+
+
+  subroutine shallow_physics_end (Phys)
+
+      type(phys_type), intent(inout) :: Phys
+ 
+
+
+

+

+
+
+
+
+

+
NAMELIST

+
+
+
+&shallow_physics_nml
+
+real    :: fric_damp_time  = -20.0
+           rate at which ua nd v are relaxed to zero (seconds)
+           (if negative, units are days instead -- negative sign is ignored) 
+      
+real    :: therm_damp_time = -10.0
+           rate at which geopotential is relaxed to h_eq
+	   (units as above)
+
+real    :: h_0             = 3.e04  (m^2/s^2)
+real    :: h_amp           = 2.e04  (m^2/s^2)
+real    :: h_lon           =  90.0  degrees
+real    :: h_lat           =  25.0  degrees
+real    :: h_width         =  15.0  degrees
+real    :: h_itcz          = 1.e05  (m^2/s^2)
+real    :: itcz_width      =  4.0   degrees
+
+           h_eq is defined as
+	   h_0 + h_amp*exp(-r^2) + h_itcz*exp(-d^2)
+	   
+	   where r^2 = xx^2 + yy^2
+	      xx = (lon - h_lon)/(2*h_width)
+	      yy = (lat - h_lat)/h_width
+	      
+	   and d = lat/itcz_width
+	  
+
+

+
+
+
+

+
+
+

From dea4afda3d3062edb3a80332d17542543c18ce4c Mon Sep 17 00:00:00 2001
From: sit23 
Date: Tue, 14 May 2019 16:29:41 +0100
Subject: [PATCH 02/24] Copied example input and diag file entries into test
 case, and set up shallow code base again.

---
 .../shallow_water/shallow_water_test.py       | 107 ++++++++++++++++++
 src/extra/python/isca/__init__.py             |   2 +-
 src/extra/python/isca/codebase.py             |  10 +-
 3 files changed, 113 insertions(+), 6 deletions(-)
 create mode 100644 exp/test_cases/shallow_water/shallow_water_test.py

diff --git a/exp/test_cases/shallow_water/shallow_water_test.py b/exp/test_cases/shallow_water/shallow_water_test.py
new file mode 100644
index 000000000..b2d20f8a4
--- /dev/null
+++ b/exp/test_cases/shallow_water/shallow_water_test.py
@@ -0,0 +1,107 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+NCORES = 8
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+exp = Experiment('shallow_test_experiment', codebase=cb)
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+
+
+exp.diag_table = diag
+
+#Empty the run directory ready to run
+exp.clear_rundir()
+
+#Define values for the 'core' namelist
+exp.namelist = namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml'
+   'print_memory_usage':True,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 256,
+   'num_lat'             : 128,
+   'num_fourier'         : 85,
+   'num_spherical'       : 86,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : .true.,
+   'spec_tracer'         : .true.,
+   'robert_coeff'        : 0.04
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  : -50.0,
+   'therm_damp_time' : -10.0,
+   'del_h'           :  2.e04,
+   'h_0'             :  3.e04,
+   'h_amp'           :  1.e05,
+   'h_lon'           :  90.0,
+   'h_lat'           :  25.0,
+   'h_width'         :  15.0,
+   'itcz_width'      :  4.0,
+   'h_itcz'          :  4.e04,
+   },
+})
+
+#Lets do a run!
+if __name__=="__main__":
+    exp.run(1, use_restart=False, num_cores=NCORES)
+    for i in range(2,121):
+        exp.run(i, num_cores=NCORES)
diff --git a/src/extra/python/isca/__init__.py b/src/extra/python/isca/__init__.py
index 495c24e12..1ab4fe8e5 100644
--- a/src/extra/python/isca/__init__.py
+++ b/src/extra/python/isca/__init__.py
@@ -77,4 +77,4 @@ def emit(self, event, *args, **kwargs):
 
 
 from isca.experiment import Experiment, DiagTable, Namelist, FailedRunError
-from isca.codebase import IscaCodeBase, DryCodeBase, GreyCodeBase #, ShallowCodeBase
+from isca.codebase import IscaCodeBase, DryCodeBase, GreyCodeBase, ShallowCodeBase
diff --git a/src/extra/python/isca/codebase.py b/src/extra/python/isca/codebase.py
index b9863999f..8cd57b27a 100644
--- a/src/extra/python/isca/codebase.py
+++ b/src/extra/python/isca/codebase.py
@@ -303,8 +303,8 @@ class DryCodeBase(GreyCodeBase):
 
 
 
-# class ShallowCodeBase(CodeBase):
-#     """The Shallow Water Equations.
-#     """
-#     name = 'shallow'
-#     executable_name = 'shallow.x'
+class ShallowCodeBase(CodeBase):
+    """The Shallow Water Equations.
+    """
+    name = 'shallow'
+    executable_name = 'shallow.x'

From a5a6c8e0cc3916110771a8147b7f5138eee0b597 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Tue, 14 May 2019 16:47:42 +0100
Subject: [PATCH 03/24] updated experiment to get it to run, and updated
 leapfrog and damping options in shallow water to get in line with Isca
 modifications.

---
 .../shallow_water/shallow_water_test.py         |  9 +++++----
 src/atmos_spectral_shallow/shallow_dynamics.F90 | 17 ++++++++++-------
 2 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/exp/test_cases/shallow_water/shallow_water_test.py b/exp/test_cases/shallow_water/shallow_water_test.py
index b2d20f8a4..53359d36c 100644
--- a/exp/test_cases/shallow_water/shallow_water_test.py
+++ b/exp/test_cases/shallow_water/shallow_water_test.py
@@ -54,6 +54,7 @@
      'minutes': 0,
      'seconds': 0,
      'dt_atmos': 1200,
+     'calendar': 'no_calendar',
     },
 
  'atmosphere_nml':{
@@ -65,7 +66,7 @@
    'fileset_write': 'single'
     },
 
- 'fms_nml'
+ 'fms_nml':{
    'print_memory_usage':True,
    'domains_stack_size': 200000,
     },
@@ -80,9 +81,9 @@
    'damping_order'       : 4,
    'damping_coeff'       : 1.e-04,
    'h_0'                 : 3.e04,
-   'grid_tracer'         : .true.,
-   'spec_tracer'         : .true.,
-   'robert_coeff'        : 0.04
+   'grid_tracer'         : True,
+   'spec_tracer'         : True,
+   'robert_coeff'        : 0.04,
    'robert_coeff_tracer' : 0.04,
     },
 
diff --git a/src/atmos_spectral_shallow/shallow_dynamics.F90 b/src/atmos_spectral_shallow/shallow_dynamics.F90
index 543e37230..98f674084 100644
--- a/src/atmos_spectral_shallow/shallow_dynamics.F90
+++ b/src/atmos_spectral_shallow/shallow_dynamics.F90
@@ -112,7 +112,8 @@ module shallow_dynamics_mod
 integer :: num_lat            = 128
 integer :: num_fourier        = 85
 integer :: num_spherical      = 86
-integer :: fourier_inc         = 1
+integer :: fourier_inc        = 1
+integer :: cutoff_wn          = 30
 ! (these define a standard T85 model)
 
 logical :: check_fourier_imag = .false.
@@ -122,6 +123,7 @@ module shallow_dynamics_mod
 real    :: robert_coeff        = 0.04
 real    :: robert_coeff_tracer = 0.04
 real    :: longitude_origin    = 0.0
+real    :: raw_filter_coeff    = 1.0
 
 character(len=64) :: damping_option = 'resolution_dependent'
 integer :: damping_order       = 4
@@ -141,7 +143,8 @@ module shallow_dynamics_mod
                           damping_order,     damping_coeff,  &
                           robert_coeff, robert_coeff_tracer, &
                           h_0, spec_tracer, grid_tracer,     &
-                          valid_range_v
+                          valid_range_v, cutoff_wn,          &
+                          raw_filter_coeff
 
 contains
 
@@ -209,7 +212,7 @@ subroutine shallow_dynamics_init (Dyn,  Time, Time_init)
 
 coriolis = 2*omega*sin_lat
 
-call spectral_damping_init(damping_coeff, damping_order, damping_option, num_fourier, num_spherical, 1, 0., 0., 0.)
+call spectral_damping_init(damping_coeff, damping_order, damping_option, cutoff_wn, num_fourier, num_spherical, 1, 0., 0., 0.)
 
 allocate(eigen(ms:me,ns:ne))
 call get_eigen_laplacian(eigen)
@@ -333,9 +336,9 @@ subroutine shallow_dynamics(Time, Time_init, Dyn, previous, current, future, del
 call compute_spectral_damping(Dyn%Spec%div(:,:,previous), dt_divs, delta_t)
 call compute_spectral_damping(Dyn%Spec%h  (:,:,previous), dt_hs  , delta_t)
 
-call leapfrog(Dyn%Spec%vor , dt_vors  , previous, current, future, delta_t, robert_coeff)
-call leapfrog(Dyn%Spec%div , dt_divs  , previous, current, future, delta_t, robert_coeff)
-call leapfrog(Dyn%Spec%h   , dt_hs    , previous, current, future, delta_t, robert_coeff)
+call leapfrog(Dyn%Spec%vor , dt_vors  , previous, current, future, delta_t, robert_coeff, raw_filter_coeff)
+call leapfrog(Dyn%Spec%div , dt_divs  , previous, current, future, delta_t, robert_coeff, raw_filter_coeff)
+call leapfrog(Dyn%Spec%h   , dt_hs    , previous, current, future, delta_t, robert_coeff, raw_filter_coeff)
 
 call trans_spherical_to_grid(Dyn%Spec%vor(:,:,future), Dyn%Grid%vor(:,:,future))
 call trans_spherical_to_grid(Dyn%Spec%div(:,:,future), Dyn%Grid%div(:,:,future))
@@ -408,7 +411,7 @@ subroutine update_spec_tracer(tr_spec, tr_grid, dt_tr, ug, vg, &
 call horizontal_advection     (tr_spec(:,:,current), ug(:,:,current), vg(:,:,current), dt_tr)
 call trans_grid_to_spherical  (dt_tr, dt_trs)
 call compute_spectral_damping (tr_spec(:,:,previous), dt_trs, delta_t)
-call leapfrog                 (tr_spec, dt_trs, previous, current, future, delta_t, robert_coeff)
+call leapfrog                 (tr_spec, dt_trs, previous, current, future, delta_t, robert_coeff, raw_filter_coeff)
 call trans_spherical_to_grid  (tr_spec(:,:,future), tr_grid(:,:,future))
 
 return

From bd7df0686d49b62af7d24bbc395c5ae3ac0ad5a3 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Tue, 14 May 2019 17:15:33 +0100
Subject: [PATCH 04/24] Integrated barotropic vorticity equation into Isca
 framework too. Needed same fixes as shallow dynamics.

---
 .../barotropic_vor_eq_stirring_test.py        | 116 ++++++++++++++++++
 .../barotropic_vor_eq_test.py                 | 100 +++++++++++++++
 .../barotropic_dynamics.F90                   |  11 +-
 src/extra/python/isca/__init__.py             |   2 +-
 src/extra/python/isca/codebase.py             |   6 +
 5 files changed, 230 insertions(+), 5 deletions(-)
 create mode 100644 exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_stirring_test.py
 create mode 100644 exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_test.py

diff --git a/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_stirring_test.py b/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_stirring_test.py
new file mode 100644
index 000000000..e03867687
--- /dev/null
+++ b/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_stirring_test.py
@@ -0,0 +1,116 @@
+import os
+
+import numpy as np
+
+from isca import BarotropicCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+NCORES = 8
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = BarotropicCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+exp = Experiment('barotropic_stirring_test_experiment', codebase=cb)
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('barotropic_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'vor', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'pv', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'stream', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'trs', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'tr', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'eddy_vor', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'delta_u', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+
+exp.diag_table = diag
+
+#Empty the run directory ready to run
+exp.clear_rundir()
+
+#Define values for the 'core' namelist
+exp.namelist = namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':True,
+   'domains_stack_size': 200000,
+    },
+
+ 'barotropic_dynamics_nml':{
+   'triang_trunc'   : True,
+   'num_lat'        : 128,
+   'num_lon'        : 256,
+   'num_fourier'    : 85,
+   'num_spherical'  : 86,
+   'fourier_inc'    : 1,
+   'damping_option' : 'resolution_dependent',
+   'damping_order'  : 2,
+   'damping_coeff'  : 1.157E-4,
+   'damping_coeff_r': 1.929E-6,
+   'grid_tracer'    : True,
+   'spec_tracer'    : True,
+   'm_0'            : 6,
+   'zeta_0'         : 0.0,
+   'eddy_lat'       : 45.0,
+   'eddy_width'     : 10.0,
+   'robert_coeff'   : 0.04,
+   'initial_zonal_wind' : 'zero',
+    },
+
+ 'barotropic_physics_nml':{
+   },
+
+ 'stirring_nml': {
+   'decay_time':172800,
+   'amplitude':3.e-11,
+   'lat0':45.,
+   'lon0':180.,
+   'widthy':12.,
+   'widthx':45.,
+   'B':1.0,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+    exp.run(1, use_restart=False, num_cores=NCORES)
+    for i in range(2,121):
+        exp.run(i, num_cores=NCORES)
diff --git a/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_test.py b/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_test.py
new file mode 100644
index 000000000..fec772b66
--- /dev/null
+++ b/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_test.py
@@ -0,0 +1,100 @@
+import os
+
+import numpy as np
+
+from isca import BarotropicCodebase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+NCORES = 8
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = BarotropicCodebase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+exp = Experiment('barotropic_test_experiment', codebase=cb)
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('barotropic_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'vor', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'pv', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'stream', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'trs', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'tr', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'eddy_vor', time_avg=True)
+diag.add_field('barotropic_diagnostics', 'delta_u', time_avg=True)
+
+exp.diag_table = diag
+
+#Empty the run directory ready to run
+exp.clear_rundir()
+
+#Define values for the 'core' namelist
+exp.namelist = namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':True,
+   'domains_stack_size': 200000,
+    },
+
+ 'barotropic_dynamics_nml':{
+   'triang_trunc'   : True,
+   'num_lat'        : 128,
+   'num_lon'        : 256,
+   'num_fourier'    : 85,
+   'num_spherical'  : 86,
+   'fourier_inc'    : 1,
+   'damping_option' : 'resolution_dependent',
+   'damping_order'  : 4,
+   'damping_coeff'  : 1.e-04,
+   'grid_tracer'    : True,
+   'spec_tracer'    : True,
+   'm_0'            : 4,
+   'zeta_0'         : 8.e-05,
+   'eddy_lat'       : 45.0,
+   'eddy_width'     : 15.0,
+   'robert_coeff'   : 0.04,
+    },
+
+ 'barotropic_physics_nml':{
+   },
+})
+
+#Lets do a run!
+if __name__=="__main__":
+    exp.run(1, use_restart=False, num_cores=NCORES)
+    for i in range(2,121):
+        exp.run(i, num_cores=NCORES)
diff --git a/src/atmos_spectral_barotropic/barotropic_dynamics.F90 b/src/atmos_spectral_barotropic/barotropic_dynamics.F90
index 07922fdbc..64be9cd8d 100644
--- a/src/atmos_spectral_barotropic/barotropic_dynamics.F90
+++ b/src/atmos_spectral_barotropic/barotropic_dynamics.F90
@@ -122,6 +122,7 @@ module barotropic_dynamics_mod
 
 real    :: robert_coeff       = 0.04
 real    :: longitude_origin   = 0.0
+real    :: raw_filter_coeff   = 1.0
 
 character(len=64) :: damping_option = 'resolution_dependent'
 integer :: damping_order      = 4
@@ -141,6 +142,7 @@ module barotropic_dynamics_mod
 integer :: num_fourier        = 85
 integer :: num_spherical      = 86
 integer :: fourier_inc        = 1
+integer :: cutoff_wn          = 30
 
 real, dimension(2) :: valid_range_v = (/-1.e3,1.e3/)
 character(len=64) :: initial_zonal_wind = 'two_jets'
@@ -154,7 +156,8 @@ module barotropic_dynamics_mod
                                  damping_coeff_r,   robert_coeff,      &
                                  spec_tracer, grid_tracer,             &
                                  eddy_lat, eddy_width, zeta_0, m_0,    &
-                                 valid_range_v, initial_zonal_wind
+                                 valid_range_v, initial_zonal_wind,    &
+                                 cutoff_wn
 
 contains
 
@@ -231,7 +234,7 @@ subroutine barotropic_dynamics_init (Dyn, Time, Time_init, dt_real, id_lon, id_l
 rad_lat = deg_lat*atan(1.0)/45.0
 rad_lon = deg_lon*atan(1.0)/45.0
 
-call spectral_damping_init(damping_coeff, damping_order, damping_option, num_fourier, num_spherical, 1, 0., 0., 0., &
+call spectral_damping_init(damping_coeff, damping_order, damping_option, cutoff_wn, num_fourier, num_spherical, 1, 0., 0., 0., &
                            damping_coeff_r=damping_coeff_r)
 call stirring_init(dt_real, Time, id_lon, id_lat, id_lonb, id_latb)
 
@@ -363,7 +366,7 @@ subroutine barotropic_dynamics(Time, Time_init, Dyn, previous, current, future,
 
 call stirring(Time, dt_vors)
 
-call leapfrog(Dyn%Spec%vor , dt_vors  , previous, current, future, delta_t, robert_coeff)
+call leapfrog(Dyn%Spec%vor , dt_vors  , previous, current, future, delta_t, robert_coeff, raw_filter_coeff)
 
 call trans_spherical_to_grid(Dyn%Spec%vor(:,:,future), Dyn%Grid%vor(:,:,future))
   
@@ -404,7 +407,7 @@ subroutine update_spec_tracer(tr_spec, tr_grid, dt_tr, ug, vg, &
 call horizontal_advection     (tr_spec(:,:,current), ug(:,:,current), vg(:,:,current), dt_tr)
 call trans_grid_to_spherical  (dt_tr, dt_trs)
 call compute_spectral_damping (tr_spec(:,:,previous), dt_trs, delta_t)
-call leapfrog                 (tr_spec, dt_trs, previous, current, future, delta_t, robert_coeff)
+call leapfrog                 (tr_spec, dt_trs, previous, current, future, delta_t, robert_coeff, raw_filter_coeff)
 call trans_spherical_to_grid  (tr_spec(:,:,future), tr_grid(:,:,future))
 
 return
diff --git a/src/extra/python/isca/__init__.py b/src/extra/python/isca/__init__.py
index 1ab4fe8e5..6573fdf85 100644
--- a/src/extra/python/isca/__init__.py
+++ b/src/extra/python/isca/__init__.py
@@ -77,4 +77,4 @@ def emit(self, event, *args, **kwargs):
 
 
 from isca.experiment import Experiment, DiagTable, Namelist, FailedRunError
-from isca.codebase import IscaCodeBase, DryCodeBase, GreyCodeBase, ShallowCodeBase
+from isca.codebase import IscaCodeBase, DryCodeBase, GreyCodeBase, ShallowCodeBase, BarotropicCodebase
diff --git a/src/extra/python/isca/codebase.py b/src/extra/python/isca/codebase.py
index 8cd57b27a..d29f661dc 100644
--- a/src/extra/python/isca/codebase.py
+++ b/src/extra/python/isca/codebase.py
@@ -308,3 +308,9 @@ class ShallowCodeBase(CodeBase):
     """
     name = 'shallow'
     executable_name = 'shallow.x'
+
+class BarotropicCodebase(CodeBase):
+    """The Barotropic vorticity equations.
+    """
+    name = 'barotropic'
+    executable_name = 'barotropic_isca.x'
\ No newline at end of file

From 4c22f20c342c753c6470514566d21fc20d5827dd Mon Sep 17 00:00:00 2001
From: sit23 
Date: Tue, 14 May 2019 17:18:04 +0100
Subject: [PATCH 05/24] Fixed small typo in barotropic codebase object.

---
 .../barotropic_vorticity_equation/barotropic_vor_eq_test.py   | 4 ++--
 src/extra/python/isca/__init__.py                             | 2 +-
 src/extra/python/isca/codebase.py                             | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_test.py b/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_test.py
index fec772b66..01cdcc687 100644
--- a/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_test.py
+++ b/exp/test_cases/barotropic_vorticity_equation/barotropic_vor_eq_test.py
@@ -2,13 +2,13 @@
 
 import numpy as np
 
-from isca import BarotropicCodebase, DiagTable, Experiment, Namelist, GFDL_BASE
+from isca import BarotropicCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
 
 NCORES = 8
 base_dir = os.path.dirname(os.path.realpath(__file__))
 # a CodeBase can be a directory on the computer,
 # useful for iterative development
-cb = BarotropicCodebase.from_directory(GFDL_BASE)
+cb = BarotropicCodeBase.from_directory(GFDL_BASE)
 
 # or it can point to a specific git repo and commit id.
 # This method should ensure future, independent, reproducibility of results.
diff --git a/src/extra/python/isca/__init__.py b/src/extra/python/isca/__init__.py
index 6573fdf85..cd9e8af1b 100644
--- a/src/extra/python/isca/__init__.py
+++ b/src/extra/python/isca/__init__.py
@@ -77,4 +77,4 @@ def emit(self, event, *args, **kwargs):
 
 
 from isca.experiment import Experiment, DiagTable, Namelist, FailedRunError
-from isca.codebase import IscaCodeBase, DryCodeBase, GreyCodeBase, ShallowCodeBase, BarotropicCodebase
+from isca.codebase import IscaCodeBase, DryCodeBase, GreyCodeBase, ShallowCodeBase, BarotropicCodeBase
diff --git a/src/extra/python/isca/codebase.py b/src/extra/python/isca/codebase.py
index d29f661dc..8ce9b35b7 100644
--- a/src/extra/python/isca/codebase.py
+++ b/src/extra/python/isca/codebase.py
@@ -309,7 +309,7 @@ class ShallowCodeBase(CodeBase):
     name = 'shallow'
     executable_name = 'shallow.x'
 
-class BarotropicCodebase(CodeBase):
+class BarotropicCodeBase(CodeBase):
     """The Barotropic vorticity equations.
     """
     name = 'barotropic'

From 717a94abe0bed959dc7b9e8e5929ac645edea675 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 16 May 2019 10:11:41 +0100
Subject: [PATCH 06/24] Rewrite of stirring module to retain functionality, but
 to get rid of it defining grid for output. This should make it possible to
 use stirring in the shallow water model.

---
 src/atmos_spectral_barotropic/atmosphere.F90  |  6 +++-
 .../barotropic_diagnostics.F90                | 28 +++++++++++++++++--
 .../barotropic_dynamics.F90                   |  6 ++--
 src/atmos_spectral_barotropic/stirring.F90    |  9 +-----
 4 files changed, 33 insertions(+), 16 deletions(-)

diff --git a/src/atmos_spectral_barotropic/atmosphere.F90 b/src/atmos_spectral_barotropic/atmosphere.F90
index 40a01ebb1..6b878fe98 100644
--- a/src/atmos_spectral_barotropic/atmosphere.F90
+++ b/src/atmos_spectral_barotropic/atmosphere.F90
@@ -63,6 +63,9 @@ module atmosphere_mod
 use  barotropic_diagnostics_mod, only: barotropic_diagnostics_init,   &
                                        barotropic_diagnostics
 
+use                stirring_mod, only: stirring_init
+
+
 !========================================================================
 implicit none
 private
@@ -142,7 +145,7 @@ subroutine atmosphere_init(Time_init_in, Time, Time_step_in)
 call write_version_number(version, tagname)
 if (root) write (stdlog(), nml=atmosphere_nml)
 
-call barotropic_dynamics_init (Dyn, Time, Time_init, dt_real, id_lon, id_lat, id_lonb, id_latb)
+call barotropic_dynamics_init (Dyn, Time, Time_init, dt_real)
 
 call get_grid_domain(is,ie,js,je)
 call get_spec_domain(ms,me,ns,ne)
@@ -155,6 +158,7 @@ subroutine atmosphere_init(Time_init_in, Time, Time_step_in)
 
 call barotropic_physics_init(Phys)
 call barotropic_diagnostics_init(Time, num_lon, num_lat, id_lon, id_lat, id_lonb, id_latb)
+call stirring_init(dt_real, Time, id_lon, id_lat, id_lonb, id_latb)
 
 if(Time == Time_init) then
   previous = 1
diff --git a/src/atmos_spectral_barotropic/barotropic_diagnostics.F90 b/src/atmos_spectral_barotropic/barotropic_diagnostics.F90
index 69cfc096e..fa632893a 100644
--- a/src/atmos_spectral_barotropic/barotropic_diagnostics.F90
+++ b/src/atmos_spectral_barotropic/barotropic_diagnostics.F90
@@ -28,11 +28,15 @@ module barotropic_diagnostics_mod
 use       transforms_mod, only: get_grid_domain,     &
                                 get_spec_domain,     & 
                                 grid_domain,         &
-                                trans_spherical_to_grid
+                                trans_spherical_to_grid, &
+                                get_deg_lon,         & 
+                                get_deg_lat,         &
+                                get_grid_boundaries
 
 use     diag_manager_mod, only: register_diag_field, &
                                 register_static_field, &
-                                send_data
+                                send_data,             &
+                                diag_axis_init
 
 use     time_manager_mod, only: time_type, &
                                 get_time
@@ -63,10 +67,18 @@ module barotropic_diagnostics_mod
 subroutine barotropic_diagnostics_init(Time, lon_max, lat_max, id_lon, id_lat, id_lonb, id_latb)
 
 type(time_type), intent(in) :: Time
-integer, intent(in) :: lon_max, lat_max, id_lon, id_lat, id_lonb, id_latb
+integer, intent(in) :: lon_max, lat_max
+integer, intent(out):: id_lon, id_lat, id_lonb, id_latb
+
+real, dimension(lon_max  ) :: lon
+real, dimension(lon_max+1) :: lonb
+real, dimension(lat_max  ) :: lat
+real, dimension(lat_max+1) :: latb
 
 integer, dimension(2) :: axis_2d
 
+real :: rad_to_deg
+
 integer :: log_unit
 integer :: namelist_unit, ierr, io
 logical :: used
@@ -76,6 +88,16 @@ subroutine barotropic_diagnostics_init(Time, lon_max, lat_max, id_lon, id_lat, i
 call get_grid_domain(is, ie, js, je)
 call get_spec_domain(ms, me, ns, ne)
 
+call get_deg_lon(lon)          
+call get_deg_lat(lat)
+call get_grid_boundaries(lonb,latb,global=.true.)
+
+rad_to_deg = 45./atan(1.)
+id_lonb=diag_axis_init('lonb', rad_to_deg*lonb, 'degrees_E', 'x', 'longitude edges', set_name=axiset, Domain2=grid_domain)
+id_latb=diag_axis_init('latb', rad_to_deg*latb, 'degrees_N', 'y', 'latitude edges',  set_name=axiset, Domain2=grid_domain)
+id_lon =diag_axis_init('lon', lon, 'degrees_E', 'x', 'longitude', set_name=axiset, Domain2=grid_domain, edges=id_lonb)
+id_lat =diag_axis_init('lat', lat, 'degrees_N', 'y', 'latitude',  set_name=axiset, Domain2=grid_domain, edges=id_latb)
+
 axis_2d(1) = id_lon
 axis_2d(2) = id_lat 
 
diff --git a/src/atmos_spectral_barotropic/barotropic_dynamics.F90 b/src/atmos_spectral_barotropic/barotropic_dynamics.F90
index 64be9cd8d..ac18b6127 100644
--- a/src/atmos_spectral_barotropic/barotropic_dynamics.F90
+++ b/src/atmos_spectral_barotropic/barotropic_dynamics.F90
@@ -61,7 +61,7 @@ module barotropic_dynamics_mod
 use       fv_advection_mod, only: fv_advection_init, &
                                   a_grid_horiz_advection
 
-use           stirring_mod, only: stirring_init, stirring, stirring_end
+use           stirring_mod, only: stirring, stirring_end
 
 !===============================================================================================
 implicit none
@@ -163,12 +163,11 @@ module barotropic_dynamics_mod
 
 !===============================================================================================
 
-subroutine barotropic_dynamics_init (Dyn, Time, Time_init, dt_real, id_lon, id_lat, id_lonb, id_latb)
+subroutine barotropic_dynamics_init (Dyn, Time, Time_init, dt_real)
 
 type(dynamics_type), intent(inout)  :: Dyn
 type(time_type)    , intent(in)     :: Time, Time_init
 real, intent(in) :: dt_real
-integer, intent(out) :: id_lon, id_lat, id_lonb, id_latb
 
 integer :: i, j
 
@@ -236,7 +235,6 @@ subroutine barotropic_dynamics_init (Dyn, Time, Time_init, dt_real, id_lon, id_l
 
 call spectral_damping_init(damping_coeff, damping_order, damping_option, cutoff_wn, num_fourier, num_spherical, 1, 0., 0., 0., &
                            damping_coeff_r=damping_coeff_r)
-call stirring_init(dt_real, Time, id_lon, id_lat, id_lonb, id_latb)
 
 allocate (Dyn%spec%vor (ms:me, ns:ne, num_time_levels))
 allocate (Dyn%grid%u   (is:ie, js:je, num_time_levels))
diff --git a/src/atmos_spectral_barotropic/stirring.F90 b/src/atmos_spectral_barotropic/stirring.F90
index 04bdfc280..88aad46a8 100644
--- a/src/atmos_spectral_barotropic/stirring.F90
+++ b/src/atmos_spectral_barotropic/stirring.F90
@@ -77,7 +77,7 @@ module stirring_mod
 subroutine stirring_init(dt, Time, id_lon, id_lat, id_lonb, id_latb)
 real, intent(in) :: dt
 type(time_type), intent(in) :: Time
-integer, intent(out) :: id_lon, id_lat, id_lonb, id_latb
+integer, intent(in) :: id_lon, id_lat, id_lonb, id_latb
 real :: xx, kk, rad_to_deg
 integer :: i,j,m,n,ierr,io,unit,lon_max,lat_max
 real, allocatable, dimension(:) :: ampx, ampy, lon, lat, lonb, latb
@@ -108,13 +108,6 @@ subroutine stirring_init(dt, Time, id_lon, id_lat, id_lonb, id_latb)
 
 call get_deg_lon(lon)          
 call get_deg_lat(lat)
-call get_grid_boundaries(lonb,latb,global=.true.)
-
-rad_to_deg = 180./pi
-id_lonb=diag_axis_init('lonb', rad_to_deg*lonb, 'degrees_E', 'x', 'longitude edges', set_name='barotropic', Domain2=grid_domain)
-id_latb=diag_axis_init('latb', rad_to_deg*latb, 'degrees_N', 'y', 'latitude edges',  set_name='barotropic', Domain2=grid_domain)
-id_lon =diag_axis_init('lon', lon, 'degrees_E', 'x', 'longitude', set_name='barotropic', Domain2=grid_domain, edges=id_lonb)
-id_lat =diag_axis_init('lat', lat, 'degrees_N', 'y', 'latitude',  set_name='barotropic', Domain2=grid_domain, edges=id_latb)
 
 module_is_initialized = .true.
 if(amplitude == 0.0) return ! stirring does nothing more unless amplitude is non-zero

From 2f6acc087a84ebd6531cd1d5692e79645928136a Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 16 May 2019 10:20:05 +0100
Subject: [PATCH 07/24] Updated shallow code to include stirring, but thanks to
 rewrite of stirring, we can output stirring variables from within shallow
 water framework.

---
 src/atmos_spectral_shallow/atmosphere.F90          |  8 +++++---
 src/atmos_spectral_shallow/shallow_diagnostics.F90 |  5 +++--
 src/atmos_spectral_shallow/shallow_dynamics.F90    | 10 ++++++++--
 3 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/src/atmos_spectral_shallow/atmosphere.F90 b/src/atmos_spectral_shallow/atmosphere.F90
index 3b59b37fb..7336f9b72 100644
--- a/src/atmos_spectral_shallow/atmosphere.F90
+++ b/src/atmos_spectral_shallow/atmosphere.F90
@@ -67,6 +67,7 @@ Module atmosphere_mod
 use shallow_diagnostics_mod,  only : shallow_diagnostics_init,   &
                                      shallow_diagnostics
 
+use                stirring_mod, only: stirring_init
 
 !========================================================================
 implicit none
@@ -124,7 +125,7 @@ subroutine atmosphere_init(Time_init_in, Time, Time_step_in)
 
 type (time_type), intent(in) :: Time_init_in, Time, Time_step_in
 
-integer :: i, j, n, nn, ierr, io, unit
+integer :: i, j, n, nn, ierr, io, unit, id_lon, id_lat, id_lonb, id_latb
 integer :: nlon, nlat
 
 pe   = mpp_pe()
@@ -151,7 +152,7 @@ subroutine atmosphere_init(Time_init_in, Time, Time_step_in)
 call write_version_number(version, tagname)
 if (root) write (stdlog(), nml=atmosphere_nml)
 
-call shallow_dynamics_init (Dyn, Time, Time_init)    
+call shallow_dynamics_init (Dyn, Time, Time_init, dt_real)    
 
 call get_grid_domain(is,ie,js,je)
 call get_spec_domain(ms,me,ns,ne)
@@ -163,7 +164,8 @@ subroutine atmosphere_init(Time_init_in, Time, Time_step_in)
 nlat = je+1-js
 
 call shallow_physics_init(Phys)
-call shallow_diagnostics_init(Time, num_lon, num_lat)
+call shallow_diagnostics_init(Time, num_lon, num_lat, id_lon, id_lat, id_lonb, id_latb)
+call stirring_init(dt_real, Time, id_lon, id_lat, id_lonb, id_latb)
 
 if(Time == Time_init) then
   previous = 1
diff --git a/src/atmos_spectral_shallow/shallow_diagnostics.F90 b/src/atmos_spectral_shallow/shallow_diagnostics.F90
index b8dc52f68..e0fd0052a 100644
--- a/src/atmos_spectral_shallow/shallow_diagnostics.F90
+++ b/src/atmos_spectral_shallow/shallow_diagnostics.F90
@@ -62,10 +62,11 @@ module shallow_diagnostics_mod
 contains
 
 !-----------------------------------------------------------------------------------------------------------------
-subroutine shallow_diagnostics_init(Time, lon_max, lat_max)
+subroutine shallow_diagnostics_init(Time, lon_max, lat_max, id_lon, id_lat, id_lonb, id_latb)
 
 type(time_type), intent(in) :: Time
 integer, intent(in) :: lon_max, lat_max
+integer, intent(out):: id_lon, id_lat, id_lonb, id_latb
 
 real, dimension(lon_max  ) :: lon
 real, dimension(lon_max+1) :: lonb
@@ -74,7 +75,7 @@ subroutine shallow_diagnostics_init(Time, lon_max, lat_max)
 
 integer, dimension(2) :: axis_2d
 
-integer :: log_unit, id_lonb, id_lon, id_latb, id_lat
+integer :: log_unit
 integer :: namelist_unit, ierr, io
 real    :: rad_to_deg
 logical :: used
diff --git a/src/atmos_spectral_shallow/shallow_dynamics.F90 b/src/atmos_spectral_shallow/shallow_dynamics.F90
index 98f674084..eacbfc159 100644
--- a/src/atmos_spectral_shallow/shallow_dynamics.F90
+++ b/src/atmos_spectral_shallow/shallow_dynamics.F90
@@ -57,6 +57,8 @@ module shallow_dynamics_mod
 
 use       fv_advection_mod, only : fv_advection_init, a_grid_horiz_advection
 
+use           stirring_mod, only : stirring, stirring_end
+
 !======================================================================================
 implicit none
 private
@@ -150,17 +152,18 @@ module shallow_dynamics_mod
 
 !=======================================================================================
 
-subroutine shallow_dynamics_init (Dyn,  Time, Time_init)
+subroutine shallow_dynamics_init (Dyn,  Time, Time_init, dt_real)
 
 type(dynamics_type), intent(inout)  :: Dyn
 type(time_type)    , intent(in)     :: Time, Time_init
+real               , intent(in)     :: dt_real
 
 integer :: i, j
 
 real,    allocatable, dimension(:)   :: glon_bnd, glat_bnd
 real :: xx, yy, dd
 
-integer  :: ierr, io, unit
+integer  :: ierr, io, unit, id_lon, id_lat, id_lonb, id_latb
 logical  :: root
 
 ! < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > < > 
@@ -336,6 +339,8 @@ subroutine shallow_dynamics(Time, Time_init, Dyn, previous, current, future, del
 call compute_spectral_damping(Dyn%Spec%div(:,:,previous), dt_divs, delta_t)
 call compute_spectral_damping(Dyn%Spec%h  (:,:,previous), dt_hs  , delta_t)
 
+call stirring(Time, dt_vors)
+
 call leapfrog(Dyn%Spec%vor , dt_vors  , previous, current, future, delta_t, robert_coeff, raw_filter_coeff)
 call leapfrog(Dyn%Spec%div , dt_divs  , previous, current, future, delta_t, robert_coeff, raw_filter_coeff)
 call leapfrog(Dyn%Spec%h   , dt_hs    , previous, current, future, delta_t, robert_coeff, raw_filter_coeff)
@@ -600,6 +605,7 @@ subroutine shallow_dynamics_end (Dyn, previous, current)
 call write_restart (Dyn, previous, current)
 
 call transforms_end
+call stirring_end
 
 module_is_initialized = .false.
 

From 6c696ee3c208bc1a4db138bd3c7dba4457a8348b Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 16 May 2019 10:23:39 +0100
Subject: [PATCH 08/24] Remove needless string definitions.

---
 src/atmos_spectral_barotropic/stirring.F90 | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/atmos_spectral_barotropic/stirring.F90 b/src/atmos_spectral_barotropic/stirring.F90
index 88aad46a8..7ceafdb82 100644
--- a/src/atmos_spectral_barotropic/stirring.F90
+++ b/src/atmos_spectral_barotropic/stirring.F90
@@ -53,8 +53,6 @@ module stirring_mod
 integer, allocatable, dimension(:)   :: seed        ! random number seed
 real ::  astir, bstir
 integer :: num_steps, num_fourier, num_spherical, nseed
-character(len=8)  :: axiset   = 'barotropic'
-character(len=84) :: mod_name = 'barotropic_diagnostics'
 
 logical :: module_is_initialized = .false.
 

From 993966c732a603b51a07fd99b5a276b1e8a3707e Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 16 May 2019 11:16:02 +0100
Subject: [PATCH 09/24] Adding comments to stirring file to point out origin.

---
 .../shallow_water_stirring_test.py            | 126 ++++++++++++++++++
 src/atmos_spectral_barotropic/stirring.F90    |   2 +-
 2 files changed, 127 insertions(+), 1 deletion(-)
 create mode 100644 exp/test_cases/shallow_water/shallow_water_stirring_test.py

diff --git a/exp/test_cases/shallow_water/shallow_water_stirring_test.py b/exp/test_cases/shallow_water/shallow_water_stirring_test.py
new file mode 100644
index 000000000..d6571c2c1
--- /dev/null
+++ b/exp/test_cases/shallow_water/shallow_water_stirring_test.py
@@ -0,0 +1,126 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+NCORES = 8
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+exp = Experiment('shallow_stirring_test_experiment', codebase=cb)
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+
+exp.diag_table = diag
+
+#Empty the run directory ready to run
+exp.clear_rundir()
+
+#Define values for the 'core' namelist
+exp.namelist = namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':True,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 256,
+   'num_lat'             : 128,
+   'num_fourier'         : 85,
+   'num_spherical'       : 86,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : True,
+   'spec_tracer'         : True,
+   'robert_coeff'        : 0.04,
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  : -50.0,
+   'therm_damp_time' : -10.0,
+   'del_h'           :  2.e04,
+   'h_0'             :  3.e04,
+   'h_amp'           :  1.e05,
+   'h_lon'           :  90.0,
+   'h_lat'           :  25.0,
+   'h_width'         :  15.0,
+   'itcz_width'      :  4.0,
+   'h_itcz'          :  4.e04,
+   },
+
+#The below stirring parameters are those of Vallis et al 2004 DOI: 10.1175/1520-0469(2004)061<0264:AMASDM>2.0.CO;2
+#They have a decorrelation time set by 'decay_time', chosen to be 2 days by default. The forcing is also localised in
+#latitude and longitude, with the centre of the forcing set by lat0 and lon0, and the width of the gaussians set by 
+#'widthy and widthx'. B sets the variation in longitude, with ampx = 1 + B*exp(-xx/widthx**2)
+
+ 'stirring_nml': {
+   'decay_time':172800,
+   'amplitude':3.e-13,
+   'lat0':45.,
+   'lon0':180.,
+   'widthy':12.,
+   'widthx':45.,
+   'B':1.0,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+    exp.run(1, use_restart=False, num_cores=NCORES)
+    for i in range(2,122):
+        exp.run(i, num_cores=NCORES)
diff --git a/src/atmos_spectral_barotropic/stirring.F90 b/src/atmos_spectral_barotropic/stirring.F90
index 7ceafdb82..687fb81f9 100644
--- a/src/atmos_spectral_barotropic/stirring.F90
+++ b/src/atmos_spectral_barotropic/stirring.F90
@@ -210,7 +210,7 @@ subroutine stirring(Time, dt_vors)
 if(ms == 0 .and. ns == 0) then
   new_stirring(0,0)=cmplx(0.0,0.0) ! A non-zero global mean is introduced by the grid space computation, but we don't want it.
 endif
-s_stir = bstir*s_stir + new_stirring
+s_stir = bstir*s_stir + new_stirring !This is equation A.6 in Vallis et al 2004 - DOI:10.1175/1520-0469(2004)061<0264:AMASDM>2.0.CO;2
 
 dt_vors = dt_vors + s_stir
 call trans_spherical_to_grid(s_stir,g_stir)

From 4693d72a31bf6286422c370f9a4d2912b509b0a1 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 16 May 2019 14:12:44 +0100
Subject: [PATCH 10/24] Making the wavenumber range of the forcing a namelist
 parameter set.

---
 src/atmos_spectral_barotropic/stirring.F90 | 27 ++++++++++++++--------
 1 file changed, 18 insertions(+), 9 deletions(-)

diff --git a/src/atmos_spectral_barotropic/stirring.F90 b/src/atmos_spectral_barotropic/stirring.F90
index 687fb81f9..7de10c3f1 100644
--- a/src/atmos_spectral_barotropic/stirring.F90
+++ b/src/atmos_spectral_barotropic/stirring.F90
@@ -62,12 +62,16 @@ module stirring_mod
 public :: stirring_init, stirring, stirring_end
 
 real :: decay_time=2*86400, amplitude=0.0, lat0=45., widthy=12.
+logical :: do_localize=.true.!Default true to allow forcing to be localized in physical space. Set to false to have forcing everywhere.
 
 ! Set B to a non-zero value for stirring that has zonal structure.
 ! The strength of the stirring at latitude=lat0 is: amplitude*(1.0 + B*exp(-.5*((lon-lon0)/widthx)**2))
-real :: lon0=180., B=0.0, widthx=45. ! widthx
+real :: lon0=180., B=0.0, widthx=45., C=1.0 ! widthx
+integer :: n_total_forcing_max = 15 !total wavenumbers LESS THAN this number will be forced
+integer :: n_total_forcing_min = 9 !total wavenumbers GREATER THAN this number will be forced
+integer :: zonal_forcing_min = 3 !Zonal wavenumbers GREATER THAN this number will be forced, subject to total wavenumber constraints
 
-namelist / stirring_nml / decay_time, amplitude, lat0, lon0, widthy, widthx, B
+namelist / stirring_nml / decay_time, amplitude, lat0, lon0, widthy, widthx, B, do_localize, n_total_forcing_max, n_total_forcing_min, zonal_forcing_min
 
 contains
 
@@ -123,9 +127,9 @@ subroutine stirring_init(dt, Time, id_lon, id_lat, id_lonb, id_latb)
 allocate(g_stir_sqr(is:ie,js:je)); g_stir_sqr = 0.0
 
 ! wave_mask is .true. when  (m+n > 9) .and. (m+n < 15) .and. (m > 3)
-do m=4,14
+do m=(zonal_forcing_min+1),(n_total_forcing_max-1)
   if(m >= ms .and. m <= me) then
-    do n=10-m,14-m
+    do n=(n_total_forcing_min+1)-m,(n_total_forcing_max-1)-m
       if(n >= ns .and. n <= ne) then
         wave_mask(m,n) = .true.
       endif
@@ -146,11 +150,16 @@ subroutine stirring_init(dt, Time, id_lon, id_lat, id_lonb, id_latb)
 do j=js,je
   ampy(j) = exp(-.5*((lat(j)-lat0)/widthy)**2)
 enddo
-do j=js,je
-do i=is,ie
-  localize(i,j) = ampx(i)*ampy(j)
-enddo
-enddo
+if (do_localize) then
+    do j=js,je
+        do i=is,ie
+            localize(i,j) = ampx(i)*ampy(j)
+        enddo
+    enddo
+else
+    localize = 1.0
+endif
+
 deallocate(ampx, ampy)
 
 num_steps = 0

From f8fcd5c1fa9f34c93d4bcffac15ef70ced110c59 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 16 May 2019 14:13:08 +0100
Subject: [PATCH 11/24] Trying to make scott and polvani 2007 esque flows.

---
 ...shallow_water_small_scale_stirring_test.py | 151 ++++++++++++++++++
 ...iant_planet_shallow_water_stirring_test.py | 148 +++++++++++++++++
 2 files changed, 299 insertions(+)
 create mode 100644 exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py
 create mode 100644 exp/shallow_water_giant_planet/giant_planet_shallow_water_stirring_test.py

diff --git a/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py b/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py
new file mode 100644
index 000000000..a45007b8b
--- /dev/null
+++ b/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py
@@ -0,0 +1,151 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+import pdb
+
+NCORES = 8
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+diag.add_file('atmos_daily', 1, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+
+
+#Empty the run directory ready to run
+
+#Define values for the 'core' namelist
+namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':False,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 512,
+   'num_lat'             : 256,
+   'num_fourier'         : 170,
+   'num_spherical'       : 171,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : False,
+   'spec_tracer'         : False,
+   'robert_coeff'        : 0.04,
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  :  0.0,
+   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
+   'h_amp'           :  0.,
+   'h_itcz'          :  0.,
+   },
+
+ 'stirring_nml': {
+   'B':0.0,
+   'do_localize': False,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    for number_ld_in_radius_units in [10.]:
+
+        exp = Experiment('giant_shallow_stirring_test_experiment_uniform_small_scale_stirring_mk3', codebase=cb)
+
+        exp.diag_table = diag 
+        exp.namelist = namelist 
+        exp.clear_rundir()
+
+        rotation_period = ((9.*3600.)+55.*60 + 30.)
+        omega = 2.*np.pi/ rotation_period
+        radius = 69911e3
+        grav = 24.79
+
+        # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
+
+        equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
+        equilibrium_depth = equilibrium_geopotential/grav
+
+        exp.update_namelist({
+            'shallow_dynamics_nml':{
+                'h_0': equilibrium_geopotential
+            },
+            'shallow_physics_nml': {
+                'h_0': equilibrium_geopotential, 
+                'therm_damp_time' : rotation_period * 1., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
+            },
+            'constants_nml': {
+                'omega': omega,
+                'radius': radius,
+            },
+            'stirring_nml': {
+                'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
+                'amplitude':3.e-13,
+                'n_total_forcing_max': 45,
+                'n_total_forcing_min': 39,
+
+            },
+
+        })
+
+        exp.run(1, use_restart=False, num_cores=NCORES)
+        for i in range(2,122):
+            exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/giant_planet_shallow_water_stirring_test.py b/exp/shallow_water_giant_planet/giant_planet_shallow_water_stirring_test.py
new file mode 100644
index 000000000..fa19bc3c5
--- /dev/null
+++ b/exp/shallow_water_giant_planet/giant_planet_shallow_water_stirring_test.py
@@ -0,0 +1,148 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+import pdb
+
+NCORES = 8
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+diag.add_file('atmos_daily', 1, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+
+
+#Empty the run directory ready to run
+
+#Define values for the 'core' namelist
+namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':False,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 512,
+   'num_lat'             : 256,
+   'num_fourier'         : 170,
+   'num_spherical'       : 171,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : False,
+   'spec_tracer'         : False,
+   'robert_coeff'        : 0.04,
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  :  0.0,
+   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
+   'h_amp'           :  0.,
+   'h_itcz'          :  0.,
+   },
+
+ 'stirring_nml': {
+   'B':0.0,
+   'do_localize': False,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    for number_ld_in_radius_units in [10.]:
+
+        exp = Experiment('giant_shallow_stirring_test_experiment_uniform_stirring_mk3', codebase=cb)
+
+        exp.diag_table = diag 
+        exp.namelist = namelist 
+        exp.clear_rundir()
+
+        rotation_period = ((9.*3600.)+55.*60 + 30.)
+        omega = 2.*np.pi/ rotation_period
+        radius = 69911e3
+        grav = 24.79
+
+        # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
+
+        equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
+        equilibrium_depth = equilibrium_geopotential/grav
+
+        exp.update_namelist({
+            'shallow_dynamics_nml':{
+                'h_0': equilibrium_geopotential
+            },
+            'shallow_physics_nml': {
+                'h_0': equilibrium_geopotential, 
+                'therm_damp_time' : rotation_period * 1., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
+            },
+            'constants_nml': {
+                'omega': omega,
+                'radius': radius,
+            },
+            'stirring_nml': {
+                'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
+                'amplitude':3.e-13,
+            },
+
+        })
+
+        exp.run(1, use_restart=False, num_cores=NCORES)
+        for i in range(2,122):
+            exp.run(i, num_cores=NCORES)

From a2796269c0530356a675bee8cecdaf12ee7aad5f Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 16 May 2019 14:15:51 +0100
Subject: [PATCH 12/24] Adding missing model files that I forgot to commit.
 These are necessary for compilation of new codes.

---
 src/extra/model/barotropic/field_table |   0
 src/extra/model/barotropic/path_names  | 138 +++++++++++++++++++++++++
 src/extra/model/shallow/path_names     | 138 +++++++++++++++++++++++++
 3 files changed, 276 insertions(+)
 create mode 100644 src/extra/model/barotropic/field_table
 create mode 100644 src/extra/model/barotropic/path_names
 create mode 100644 src/extra/model/shallow/path_names

diff --git a/src/extra/model/barotropic/field_table b/src/extra/model/barotropic/field_table
new file mode 100644
index 000000000..e69de29bb
diff --git a/src/extra/model/barotropic/path_names b/src/extra/model/barotropic/path_names
new file mode 100644
index 000000000..e7c619d86
--- /dev/null
+++ b/src/extra/model/barotropic/path_names
@@ -0,0 +1,138 @@
+atmos_solo/atmos_model.F90
+atmos_spectral_barotropic/atmosphere.F90
+atmos_spectral_barotropic/barotropic_diagnostics.F90
+atmos_spectral_barotropic/barotropic_dynamics.F90
+atmos_spectral_barotropic/barotropic_physics.F90
+atmos_spectral_barotropic/stirring.F90
+atmos_spectral/model/fv_advection.F90
+atmos_spectral/model/leapfrog.F90
+atmos_spectral/model/spectral_damping.F90
+atmos_spectral/tools/gauss_and_legendre.F90
+atmos_spectral/tools/grid_fourier.F90
+atmos_spectral/tools/spec_mpp.F90
+atmos_spectral/tools/spherical.F90
+atmos_spectral/tools/spherical_fourier.F90
+atmos_spectral/tools/transforms.F90
+shared/constants/constants.F90
+shared/diag_manager/diag_axis.F90
+shared/diag_manager/diag_data.F90
+shared/diag_manager/diag_grid.F90
+shared/diag_manager/diag_manager.F90
+shared/diag_manager/diag_output.F90
+shared/diag_manager/diag_table.F90
+shared/diag_manager/diag_util.F90
+shared/fft/fft99.F90
+shared/fft/fft.F90
+shared/field_manager/field_manager.F90
+shared/field_manager/fm_util.F90
+shared/field_manager/parse.inc
+shared/fms/fms.F90
+shared/fms/fms_io.F90
+shared/fms/read_data_2d.inc
+shared/fms/read_data_3d.inc
+shared/fms/read_data_4d.inc
+shared/fms/test_fms_io.F90
+shared/fms/write_data.inc
+shared/include/fms_platform.h
+shared/memutils/memuse.c
+shared/memutils/memutils.F90
+shared/mosaic/constant.h
+shared/mosaic/create_xgrid.c
+shared/mosaic/create_xgrid.h
+shared/mosaic/gradient_c2l.c
+shared/mosaic/gradient_c2l.h
+shared/mosaic/gradient.F90
+shared/mosaic/grid.F90
+shared/mosaic/interp.c
+shared/mosaic/interp.h
+shared/mosaic/mosaic.F90
+shared/mosaic/mosaic_util.c
+shared/mosaic/mosaic_util.h
+shared/mosaic/read_mosaic.c
+shared/mosaic/read_mosaic.h
+shared/mpp/affinity.c
+shared/mpp/include/mpp_chksum.h
+shared/mpp/include/mpp_chksum_int.h
+shared/mpp/include/mpp_chksum_scalar.h
+shared/mpp/include/mpp_comm.inc
+shared/mpp/include/mpp_comm_mpi.inc
+shared/mpp/include/mpp_comm_nocomm.inc
+shared/mpp/include/mpp_comm_sma.inc
+shared/mpp/include/mpp_data_mpi.inc
+shared/mpp/include/mpp_data_nocomm.inc
+shared/mpp/include/mpp_data_sma.inc
+shared/mpp/include/mpp_define_nest_domains.inc
+shared/mpp/include/mpp_do_check.h
+shared/mpp/include/mpp_do_checkV.h
+shared/mpp/include/mpp_do_get_boundary.h
+shared/mpp/include/mpp_do_global_field.h
+shared/mpp/include/mpp_domains_comm.inc
+shared/mpp/include/mpp_domains_define.inc
+shared/mpp/include/mpp_domains_misc.inc
+shared/mpp/include/mpp_domains_reduce.inc
+shared/mpp/include/mpp_domains_util.inc
+shared/mpp/include/mpp_do_redistribute.h
+shared/mpp/include/mpp_do_update_ad.h
+shared/mpp/include/mpp_do_update.h
+shared/mpp/include/mpp_do_update_nest.h
+shared/mpp/include/mpp_do_update_nonblock.h
+shared/mpp/include/mpp_do_updateV_ad.h
+shared/mpp/include/mpp_do_updateV.h
+shared/mpp/include/mpp_do_updateV_nonblock.h
+shared/mpp/include/mpp_error_a_a.h
+shared/mpp/include/mpp_error_a_s.h
+shared/mpp/include/mpp_error_s_a.h
+shared/mpp/include/mpp_error_s_s.h
+shared/mpp/include/mpp_gather.h
+shared/mpp/include/mpp_get_boundary.h
+shared/mpp/include/mpp_global_field.h
+shared/mpp/include/mpp_global_reduce.h
+shared/mpp/include/mpp_global_sum_ad.h
+shared/mpp/include/mpp_global_sum.h
+shared/mpp/include/mpp_global_sum_tl.h
+shared/mpp/include/mpp_io_connect.inc
+shared/mpp/include/mpp_io_misc.inc
+shared/mpp/include/mpp_io_read.inc
+shared/mpp/include/mpp_io_util.inc
+shared/mpp/include/mpp_io_write.inc
+shared/mpp/include/mpp_read_2Ddecomp.h
+shared/mpp/include/mpp_reduce_mpi.h
+shared/mpp/include/mpp_reduce_nocomm.h
+shared/mpp/include/mpp_reduce_sma.h
+shared/mpp/include/mpp_sum.inc
+shared/mpp/include/mpp_sum_mpi.h
+shared/mpp/include/mpp_sum_nocomm.h
+shared/mpp/include/mpp_sum_sma.h
+shared/mpp/include/mpp_transmit.inc
+shared/mpp/include/mpp_transmit_mpi.h
+shared/mpp/include/mpp_transmit_nocomm.h
+shared/mpp/include/mpp_transmit_sma.h
+shared/mpp/include/mpp_update_domains2D_ad.h
+shared/mpp/include/mpp_update_domains2D.h
+shared/mpp/include/mpp_update_domains2D_nonblock.h
+shared/mpp/include/mpp_update_nest_domains.h
+shared/mpp/include/mpp_util.inc
+shared/mpp/include/mpp_util_mpi.inc
+shared/mpp/include/mpp_util_nocomm.inc
+shared/mpp/include/mpp_util_sma.inc
+shared/mpp/include/mpp_write_2Ddecomp.h
+shared/mpp/include/mpp_write.h
+shared/mpp/include/system_clock.h
+shared/mpp/mpp_data.F90
+shared/mpp/mpp_domains.F90
+shared/mpp/mpp.F90
+shared/mpp/mpp_io.F90
+shared/mpp/mpp_memutils.F90
+shared/mpp/mpp_parameter.F90
+shared/mpp/mpp_pset.F90
+shared/mpp/mpp_utilities.F90
+shared/mpp/nsclock.c
+shared/mpp/test_mpp_domains.F90
+shared/mpp/test_mpp.F90
+shared/mpp/test_mpp_io.F90
+shared/mpp/test_mpp_pset.F90
+shared/mpp/threadloc.c
+shared/platform/platform.F90
+shared/time_manager/get_cal_time.F90
+shared/time_manager/time_manager.F90
+shared/tracer_manager/tracer_manager.F90
diff --git a/src/extra/model/shallow/path_names b/src/extra/model/shallow/path_names
new file mode 100644
index 000000000..14f1c56f1
--- /dev/null
+++ b/src/extra/model/shallow/path_names
@@ -0,0 +1,138 @@
+atmos_solo/atmos_model.F90
+atmos_spectral/model/fv_advection.F90
+atmos_spectral/model/leapfrog.F90
+atmos_spectral/model/spectral_damping.F90
+atmos_spectral_shallow/atmosphere.F90
+atmos_spectral_shallow/shallow_diagnostics.F90
+atmos_spectral_shallow/shallow_dynamics.F90
+atmos_spectral_shallow/shallow_physics.F90
+atmos_spectral_barotropic/stirring.F90
+atmos_spectral/tools/gauss_and_legendre.F90
+atmos_spectral/tools/grid_fourier.F90
+atmos_spectral/tools/spec_mpp.F90
+atmos_spectral/tools/spherical.F90
+atmos_spectral/tools/spherical_fourier.F90
+atmos_spectral/tools/transforms.F90
+shared/constants/constants.F90
+shared/diag_manager/diag_axis.F90
+shared/diag_manager/diag_data.F90
+shared/diag_manager/diag_grid.F90
+shared/diag_manager/diag_manager.F90
+shared/diag_manager/diag_output.F90
+shared/diag_manager/diag_table.F90
+shared/diag_manager/diag_util.F90
+shared/fft/fft99.F90
+shared/fft/fft.F90
+shared/field_manager/field_manager.F90
+shared/field_manager/fm_util.F90
+shared/field_manager/parse.inc
+shared/fms/fms.F90
+shared/fms/fms_io.F90
+shared/fms/read_data_2d.inc
+shared/fms/read_data_3d.inc
+shared/fms/read_data_4d.inc
+shared/fms/test_fms_io.F90
+shared/fms/write_data.inc
+shared/include/fms_platform.h
+shared/memutils/memuse.c
+shared/memutils/memutils.F90
+shared/mosaic/constant.h
+shared/mosaic/create_xgrid.c
+shared/mosaic/create_xgrid.h
+shared/mosaic/gradient_c2l.c
+shared/mosaic/gradient_c2l.h
+shared/mosaic/gradient.F90
+shared/mosaic/grid.F90
+shared/mosaic/interp.c
+shared/mosaic/interp.h
+shared/mosaic/mosaic.F90
+shared/mosaic/mosaic_util.c
+shared/mosaic/mosaic_util.h
+shared/mosaic/read_mosaic.c
+shared/mosaic/read_mosaic.h
+shared/mpp/affinity.c
+shared/mpp/include/mpp_chksum.h
+shared/mpp/include/mpp_chksum_int.h
+shared/mpp/include/mpp_chksum_scalar.h
+shared/mpp/include/mpp_comm.inc
+shared/mpp/include/mpp_comm_mpi.inc
+shared/mpp/include/mpp_comm_nocomm.inc
+shared/mpp/include/mpp_comm_sma.inc
+shared/mpp/include/mpp_data_mpi.inc
+shared/mpp/include/mpp_data_nocomm.inc
+shared/mpp/include/mpp_data_sma.inc
+shared/mpp/include/mpp_define_nest_domains.inc
+shared/mpp/include/mpp_do_check.h
+shared/mpp/include/mpp_do_checkV.h
+shared/mpp/include/mpp_do_get_boundary.h
+shared/mpp/include/mpp_do_global_field.h
+shared/mpp/include/mpp_domains_comm.inc
+shared/mpp/include/mpp_domains_define.inc
+shared/mpp/include/mpp_domains_misc.inc
+shared/mpp/include/mpp_domains_reduce.inc
+shared/mpp/include/mpp_domains_util.inc
+shared/mpp/include/mpp_do_redistribute.h
+shared/mpp/include/mpp_do_update_ad.h
+shared/mpp/include/mpp_do_update.h
+shared/mpp/include/mpp_do_update_nest.h
+shared/mpp/include/mpp_do_update_nonblock.h
+shared/mpp/include/mpp_do_updateV_ad.h
+shared/mpp/include/mpp_do_updateV.h
+shared/mpp/include/mpp_do_updateV_nonblock.h
+shared/mpp/include/mpp_error_a_a.h
+shared/mpp/include/mpp_error_a_s.h
+shared/mpp/include/mpp_error_s_a.h
+shared/mpp/include/mpp_error_s_s.h
+shared/mpp/include/mpp_gather.h
+shared/mpp/include/mpp_get_boundary.h
+shared/mpp/include/mpp_global_field.h
+shared/mpp/include/mpp_global_reduce.h
+shared/mpp/include/mpp_global_sum_ad.h
+shared/mpp/include/mpp_global_sum.h
+shared/mpp/include/mpp_global_sum_tl.h
+shared/mpp/include/mpp_io_connect.inc
+shared/mpp/include/mpp_io_misc.inc
+shared/mpp/include/mpp_io_read.inc
+shared/mpp/include/mpp_io_util.inc
+shared/mpp/include/mpp_io_write.inc
+shared/mpp/include/mpp_read_2Ddecomp.h
+shared/mpp/include/mpp_reduce_mpi.h
+shared/mpp/include/mpp_reduce_nocomm.h
+shared/mpp/include/mpp_reduce_sma.h
+shared/mpp/include/mpp_sum.inc
+shared/mpp/include/mpp_sum_mpi.h
+shared/mpp/include/mpp_sum_nocomm.h
+shared/mpp/include/mpp_sum_sma.h
+shared/mpp/include/mpp_transmit.inc
+shared/mpp/include/mpp_transmit_mpi.h
+shared/mpp/include/mpp_transmit_nocomm.h
+shared/mpp/include/mpp_transmit_sma.h
+shared/mpp/include/mpp_update_domains2D_ad.h
+shared/mpp/include/mpp_update_domains2D.h
+shared/mpp/include/mpp_update_domains2D_nonblock.h
+shared/mpp/include/mpp_update_nest_domains.h
+shared/mpp/include/mpp_util.inc
+shared/mpp/include/mpp_util_mpi.inc
+shared/mpp/include/mpp_util_nocomm.inc
+shared/mpp/include/mpp_util_sma.inc
+shared/mpp/include/mpp_write_2Ddecomp.h
+shared/mpp/include/mpp_write.h
+shared/mpp/include/system_clock.h
+shared/mpp/mpp_data.F90
+shared/mpp/mpp_domains.F90
+shared/mpp/mpp.F90
+shared/mpp/mpp_io.F90
+shared/mpp/mpp_memutils.F90
+shared/mpp/mpp_parameter.F90
+shared/mpp/mpp_pset.F90
+shared/mpp/mpp_utilities.F90
+shared/mpp/nsclock.c
+shared/mpp/test_mpp_domains.F90
+shared/mpp/test_mpp.F90
+shared/mpp/test_mpp_io.F90
+shared/mpp/test_mpp_pset.F90
+shared/mpp/threadloc.c
+shared/platform/platform.F90
+shared/time_manager/get_cal_time.F90
+shared/time_manager/time_manager.F90
+shared/tracer_manager/tracer_manager.F90

From e74e5c0d9c28ac7933570c711d74dc3a72f5638f Mon Sep 17 00:00:00 2001
From: sit23 
Date: Fri, 17 May 2019 17:02:59 +0100
Subject: [PATCH 13/24] Added ability to do deep velocities, I think. Seems
 reasonable. Now testing.

---
 .../shallow_diagnostics.F90                   |  4 +++-
 .../shallow_dynamics.F90                      | 20 ++++++++++++++-----
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/src/atmos_spectral_shallow/shallow_diagnostics.F90 b/src/atmos_spectral_shallow/shallow_diagnostics.F90
index e0fd0052a..447cf64aa 100644
--- a/src/atmos_spectral_shallow/shallow_diagnostics.F90
+++ b/src/atmos_spectral_shallow/shallow_diagnostics.F90
@@ -55,7 +55,7 @@ module shallow_diagnostics_mod
 
 logical :: module_is_initialized = .false.
 
-integer :: id_vor, id_stream, id_pv, id_u, id_v, id_div, id_h, id_trs, id_tr
+integer :: id_vor, id_stream, id_pv, id_u, id_v, id_div, id_h, id_trs, id_tr, id_d_geopot
 
 integer :: is, ie, js, je
 
@@ -106,6 +106,7 @@ subroutine shallow_diagnostics_init(Time, lon_max, lat_max, id_lon, id_lat, id_l
 id_stream = register_diag_field(mod_name, 'stream', axis_2d, Time, 'streamfunction'      , 'm^2/s'    )
 id_trs    = register_diag_field(mod_name, 'trs'   , axis_2d, Time, 'spectral tracer'     , 'none'     )
 id_tr     = register_diag_field(mod_name, 'tr'    , axis_2d, Time, 'grid tracer'         , 'none'     )
+id_d_geopot = register_diag_field(mod_name, 'deep_geopot', axis_2d, Time, 'deep_geopot'  , 'm2/s2')
 
 module_is_initialized = .true.
 
@@ -132,6 +133,7 @@ subroutine shallow_diagnostics(Time, Grid, Phys, time_index)
 if(id_stream  > 0) used = send_data(id_stream , Grid%stream  (:,:)                 , time)
 if(id_tr      > 0) used = send_data(id_tr     , Grid%tr      (:,:, time_index)     , time)
 if(id_trs     > 0) used = send_data(id_trs    , Grid%trs     (:,:, time_index)     , time)
+if(id_d_geopot > 0) used = send_data(id_d_geopot, Grid%deep_geopot (:,:)             , time)
 
 return
 end subroutine shallow_diagnostics
diff --git a/src/atmos_spectral_shallow/shallow_dynamics.F90 b/src/atmos_spectral_shallow/shallow_dynamics.F90
index eacbfc159..79946cf0a 100644
--- a/src/atmos_spectral_shallow/shallow_dynamics.F90
+++ b/src/atmos_spectral_shallow/shallow_dynamics.F90
@@ -39,7 +39,7 @@ module shallow_dynamics_mod
                                  operator(==),   &
                                  operator(-)
 
-use       constants_mod,  only : radius, omega
+use       constants_mod,  only : radius, omega, DEG_TO_RAD
 
 use         transforms_mod, only: transforms_init,         transforms_end,          &
                                   get_grid_boundaries,     horizontal_advection,    &
@@ -76,7 +76,7 @@ module shallow_dynamics_mod
 
 type grid_type
    real, pointer, dimension(:,:,:) :: u=>NULL(), v=>NULL(), vor=>NULL(), div=>NULL(), h=>NULL(), trs=>NULL(), tr=>NULL()
-   real, pointer, dimension(:,:)   :: stream=>NULL(), pv=>NULL()
+   real, pointer, dimension(:,:)   :: stream=>NULL(), pv=>NULL(), deep_geopot=>NULL()
 end type
 type spectral_type
    complex, pointer, dimension(:,:,:) :: vor=>NULL(), div=>NULL(), h=>NULL(), trs=>NULL()
@@ -132,6 +132,9 @@ module shallow_dynamics_mod
 real    :: damping_coeff       = 1.e-04
 real    :: h_0                 = 3.e04
 
+real    :: u_deep_mag          = 0.
+real    :: n_merid_deep_flow   = 3.
+
 logical :: spec_tracer      = .true.
 logical :: grid_tracer      = .true.
 
@@ -146,7 +149,8 @@ module shallow_dynamics_mod
                           robert_coeff, robert_coeff_tracer, &
                           h_0, spec_tracer, grid_tracer,     &
                           valid_range_v, cutoff_wn,          &
-                          raw_filter_coeff
+                          raw_filter_coeff,                  &
+                          u_deep_mag, n_merid_deep_flow
 
 contains
 
@@ -235,6 +239,8 @@ subroutine shallow_dynamics_init (Dyn,  Time, Time_init, dt_real)
 allocate (Dyn%tend%h        (is:ie, js:je))
 allocate (Dyn%grid%stream   (is:ie, js:je))
 allocate (Dyn%grid%pv       (is:ie, js:je))
+allocate (Dyn%grid%deep_geopot(is:ie, js:je))
+
 
 call fv_advection_init(num_lon, num_lat, glat_bnd, 360./float(fourier_inc))
 if(Dyn%grid_tracer) then
@@ -248,6 +254,10 @@ subroutine shallow_dynamics_init (Dyn,  Time, Time_init, dt_real)
   allocate(Dyn%Spec%trs (ms:me, ns:ne, num_time_levels))
 endif
 
+do i = is, ie 
+    Dyn%grid%deep_geopot(i, js:je) = -2.*omega * u_deep_mag * radius * (1./(1.-n_merid_deep_flow**2.))*(-cos(n_merid_deep_flow*DEG_TO_RAD*deg_lat(js:je))*cos(DEG_TO_RAD*deg_lat(js:je)) - n_merid_deep_flow * (sin(n_merid_deep_flow*DEG_TO_RAD*deg_lat(js:je))*sin(DEG_TO_RAD*deg_lat(js:je))-sin(n_merid_deep_flow*(2.*atan(1.)))))
+enddo
+
 if(Time == Time_init) then
 
   Dyn%Grid%vor(:,:,1) = 0.0
@@ -326,7 +336,7 @@ subroutine shallow_dynamics(Time, Time_init, Dyn, previous, current, future, del
 
 call trans_grid_to_spherical (Dyn%Tend%h, dt_hs)
 
-bg = (Dyn%Grid%h(:,:,current) + &
+bg = (Dyn%Grid%h(:,:,current) + Dyn%grid%deep_geopot(:,:) + &
    0.5*(Dyn%Grid%u(:,:,current)**2 + Dyn%Grid%v(:,:,current)**2))
 
 call trans_grid_to_spherical(bg, bs)
@@ -370,7 +380,7 @@ subroutine shallow_dynamics(Time, Time_init, Dyn, previous, current, future, del
 stream = compute_laplacian(Dyn%Spec%vor(:,:,current), -1) ! for diagnostic purposes
 call trans_spherical_to_grid(stream, Dyn%grid%stream)
 
-Dyn%Grid%pv = vorg/Dyn%Grid%h(:,:,current)
+Dyn%Grid%pv = vorg/(Dyn%Grid%h(:,:,current)+Dyn%grid%deep_geopot(:,:))
 
 return
 end subroutine shallow_dynamics

From 172087f14c844ee6c2e798d833757a1f1e5744fa Mon Sep 17 00:00:00 2001
From: sit23 
Date: Fri, 31 May 2019 10:07:09 +0100
Subject: [PATCH 14/24] Updaing shallow water code to better account for deep
 velocities in ics and in PV definition, which I previously modified
 incorrectly.

---
 .../shallow_diagnostics.F90                   | 45 +++++++++++++++++--
 .../shallow_dynamics.F90                      | 12 +++--
 2 files changed, 50 insertions(+), 7 deletions(-)

diff --git a/src/atmos_spectral_shallow/shallow_diagnostics.F90 b/src/atmos_spectral_shallow/shallow_diagnostics.F90
index 447cf64aa..ce485758b 100644
--- a/src/atmos_spectral_shallow/shallow_diagnostics.F90
+++ b/src/atmos_spectral_shallow/shallow_diagnostics.F90
@@ -27,7 +27,8 @@ module shallow_diagnostics_mod
                                 get_deg_lat,         &
                                 get_grid_domain,     &
                                 get_spec_domain,     & 
-                                grid_domain
+                                grid_domain,         &
+                                area_weighted_global_mean
 
 use     diag_manager_mod, only: diag_axis_init, &
                                 register_diag_field, &
@@ -55,7 +56,7 @@ module shallow_diagnostics_mod
 
 logical :: module_is_initialized = .false.
 
-integer :: id_vor, id_stream, id_pv, id_u, id_v, id_div, id_h, id_trs, id_tr, id_d_geopot
+integer :: id_vor, id_stream, id_pv, id_u, id_v, id_div, id_h, id_trs, id_tr, id_d_geopot, id_u_sqd, id_v_sqd, id_h_sqd, id_u_sqd_mean, id_v_sqd_mean, id_h_sqd_mean, id_ekin
 
 integer :: is, ie, js, je
 
@@ -102,12 +103,22 @@ subroutine shallow_diagnostics_init(Time, lon_max, lat_max, id_lon, id_lat, id_l
 id_vor    = register_diag_field(mod_name, 'vor'   , axis_2d, Time, 'relative vorticity'  , '1/s'      )
 id_div    = register_diag_field(mod_name, 'div'   , axis_2d, Time, 'divergence'          , '1/s'      )
 id_h      = register_diag_field(mod_name, 'h'     , axis_2d, Time, 'geopotential'        , 'm2/s2'    )
-id_pv     = register_diag_field(mod_name, 'pv'    , axis_2d, Time, 'potential vorticity' , 's/m2'     )
+id_pv     = register_diag_field(mod_name, 'pv_corrected'    , axis_2d, Time, 'potential vorticity' , 's/m2'     )
 id_stream = register_diag_field(mod_name, 'stream', axis_2d, Time, 'streamfunction'      , 'm^2/s'    )
 id_trs    = register_diag_field(mod_name, 'trs'   , axis_2d, Time, 'spectral tracer'     , 'none'     )
 id_tr     = register_diag_field(mod_name, 'tr'    , axis_2d, Time, 'grid tracer'         , 'none'     )
 id_d_geopot = register_diag_field(mod_name, 'deep_geopot', axis_2d, Time, 'deep_geopot'  , 'm2/s2')
 
+id_u_sqd      = register_diag_field(mod_name, 'ucomp_sqd' , axis_2d, Time, 'u_wind_sqd'              , 'm^2/s^2'      ) 
+id_v_sqd      = register_diag_field(mod_name, 'vcomp_sqd' , axis_2d, Time, 'v_wind_sqd'              , 'm^2/s^2'      ) 
+id_h_sqd      = register_diag_field(mod_name, 'h_sqd'     , axis_2d, Time, 'geopotential_sqd'        , 'm4/s4'    )
+
+id_u_sqd_mean      = register_diag_field(mod_name, 'ucomp_sqd_mean' , Time, 'u_wind_sqd_mean'              , 'm^2/s^2'      ) 
+id_v_sqd_mean      = register_diag_field(mod_name, 'vcomp_sqd_mean' , Time, 'v_wind_sqd_mean'              , 'm^2/s^2'      ) 
+id_h_sqd_mean      = register_diag_field(mod_name, 'h_sqd_mean'     , Time, 'geopotential_sqd_mean'        , 'm4/s4'    )
+
+id_ekin      = register_diag_field(mod_name, 'e_kin' , Time, 'kinetic_energy'              , 'm^2/s^2'      ) 
+
 module_is_initialized = .true.
 
 return
@@ -135,6 +146,34 @@ subroutine shallow_diagnostics(Time, Grid, Phys, time_index)
 if(id_trs     > 0) used = send_data(id_trs    , Grid%trs     (:,:, time_index)     , time)
 if(id_d_geopot > 0) used = send_data(id_d_geopot, Grid%deep_geopot (:,:)             , time)
 
+if (id_u_sqd > 0) then
+    used = send_data(id_u_sqd      , Grid%u       (:,:, time_index)**2     , time)
+endif
+
+if (id_v_sqd > 0) then
+    used = send_data(id_v_sqd      , Grid%v       (:,:, time_index)**2     , time)
+endif
+
+if (id_h_sqd > 0) then
+    used = send_data(id_h_sqd      , Grid%h       (:,:, time_index)**2     , time)
+endif
+
+if (id_u_sqd_mean > 0) then
+    used = send_data(id_u_sqd_mean      , area_weighted_global_mean(Grid%u       (:,:, time_index)**2)     , time)
+endif
+
+if (id_v_sqd_mean > 0) then
+    used = send_data(id_v_sqd_mean      , area_weighted_global_mean(Grid%v       (:,:, time_index)**2)     , time)
+endif
+
+if (id_h_sqd_mean > 0) then
+    used = send_data(id_h_sqd_mean      , area_weighted_global_mean(Grid%h       (:,:, time_index)**2)     , time)
+endif
+
+if (id_ekin > 0) then
+    used = send_data(id_ekin      , 0.5*(area_weighted_global_mean(Grid%u       (:,:, time_index)**2) + area_weighted_global_mean(Grid%v       (:,:, time_index)**2))     , time)
+endif
+
 return
 end subroutine shallow_diagnostics
 !--------------------------------------------------------------------------------------------
diff --git a/src/atmos_spectral_shallow/shallow_dynamics.F90 b/src/atmos_spectral_shallow/shallow_dynamics.F90
index 79946cf0a..8953ca662 100644
--- a/src/atmos_spectral_shallow/shallow_dynamics.F90
+++ b/src/atmos_spectral_shallow/shallow_dynamics.F90
@@ -49,7 +49,8 @@ module shallow_dynamics_mod
                                   get_deg_lon,             get_deg_lat,             &
                                   get_grid_domain,         get_spec_domain,         &
                                   spectral_domain,         grid_domain,             &
-                                  vor_div_from_uv_grid,    uv_grid_from_vor_div
+                                  vor_div_from_uv_grid,    uv_grid_from_vor_div,    &
+                                  area_weighted_global_mean
 
 use   spectral_damping_mod, only: spectral_damping_init,   compute_spectral_damping
 
@@ -165,7 +166,7 @@ subroutine shallow_dynamics_init (Dyn,  Time, Time_init, dt_real)
 integer :: i, j
 
 real,    allocatable, dimension(:)   :: glon_bnd, glat_bnd
-real :: xx, yy, dd
+real :: xx, yy, dd, deep_geopot_global_mean
 
 integer  :: ierr, io, unit, id_lon, id_lat, id_lonb, id_latb
 logical  :: root
@@ -258,11 +259,14 @@ subroutine shallow_dynamics_init (Dyn,  Time, Time_init, dt_real)
     Dyn%grid%deep_geopot(i, js:je) = -2.*omega * u_deep_mag * radius * (1./(1.-n_merid_deep_flow**2.))*(-cos(n_merid_deep_flow*DEG_TO_RAD*deg_lat(js:je))*cos(DEG_TO_RAD*deg_lat(js:je)) - n_merid_deep_flow * (sin(n_merid_deep_flow*DEG_TO_RAD*deg_lat(js:je))*sin(DEG_TO_RAD*deg_lat(js:je))-sin(n_merid_deep_flow*(2.*atan(1.)))))
 enddo
 
+deep_geopot_global_mean = area_weighted_global_mean(Dyn%grid%deep_geopot(:,:))
+Dyn%grid%deep_geopot(:,:) = Dyn%grid%deep_geopot(:,:)-deep_geopot_global_mean
+
 if(Time == Time_init) then
 
   Dyn%Grid%vor(:,:,1) = 0.0
   Dyn%Grid%div(:,:,1) = 0.0
-  Dyn%Grid%h  (:,:,1) = h_0
+  Dyn%Grid%h  (:,:,1) = h_0 - Dyn%grid%deep_geopot(:,:)
     
   call trans_grid_to_spherical(Dyn%Grid%vor(:,:,1), Dyn%Spec%vor(:,:,1))
   call trans_grid_to_spherical(Dyn%Grid%div(:,:,1), Dyn%Spec%div(:,:,1))
@@ -380,7 +384,7 @@ subroutine shallow_dynamics(Time, Time_init, Dyn, previous, current, future, del
 stream = compute_laplacian(Dyn%Spec%vor(:,:,current), -1) ! for diagnostic purposes
 call trans_spherical_to_grid(stream, Dyn%grid%stream)
 
-Dyn%Grid%pv = vorg/(Dyn%Grid%h(:,:,current)+Dyn%grid%deep_geopot(:,:))
+Dyn%Grid%pv = vorg/(Dyn%Grid%h(:,:,current))
 
 return
 end subroutine shallow_dynamics

From de1f769f32623a424ea193af9882b0a67cf73e46 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Fri, 31 May 2019 10:08:11 +0100
Subject: [PATCH 15/24] First lot of experiments for poster. Run at T170 and
 forced at small-ish scale.

---
 ...et_shallow_water_deep_velocity_test_mk1.py | 166 +++++++++++++++++
 ...ter_deep_velocity_test_mk1_vary_damping.py | 169 +++++++++++++++++
 ...et_shallow_water_deep_velocity_test_mk1.py | 167 +++++++++++++++++
 ...et_shallow_water_deep_velocity_test_mk2.py | 170 ++++++++++++++++++
 ...shallow_water_small_scale_stirring_test.py |  14 +-
 5 files changed, 679 insertions(+), 7 deletions(-)
 create mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
 create mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1_vary_damping.py
 create mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk1.py
 create mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk2.py

diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
new file mode 100644
index 000000000..56d419739
--- /dev/null
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
@@ -0,0 +1,166 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+import pdb
+
+NCORES = 16
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+# diag.add_file('atmos_daily', 1, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv_corrected', time_avg=True)
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h_sqd_mean', time_avg=True)
+
+#Empty the run directory ready to run
+
+#Define values for the 'core' namelist
+namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':False,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 512,
+   'num_lat'             : 256,
+   'num_fourier'         : 170,
+   'num_spherical'       : 171,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : False,
+   'spec_tracer'         : False,
+   'robert_coeff'        : 0.04,
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  :  0.0,
+   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
+   'h_amp'           :  0.,
+   'h_itcz'          :  0.,
+   },
+
+ 'stirring_nml': {
+   'B':0.0,
+   'do_localize': False,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    for ld_value in [10.0, 0.1, 0.05, 0.01]:
+
+        for u_deep_mag_val in [50., 0.]:
+
+            if u_deep_mag_val!=0.:
+                u_deep_merid_arr = [3, 11, 19, 26]
+            else:
+                u_deep_merid_arr = [3]
+
+            for u_deep_merid in u_deep_merid_arr:
+
+                exp = Experiment('giant_planet_fixed_deep_ics_forced_no_rad_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid)), codebase=cb)
+
+                exp.diag_table = diag 
+                exp.namelist = namelist 
+                exp.clear_rundir()
+
+                rotation_period = ((9.*3600.)+55.*60 + 30.)
+                omega = 2.*np.pi/ rotation_period
+                radius = 69911e3
+                grav = 24.79
+                number_ld_in_radius_units = ld_value
+
+                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
+
+                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
+                equilibrium_depth = equilibrium_geopotential/grav
+
+                exp.update_namelist({
+                    'shallow_dynamics_nml':{
+                        'h_0': equilibrium_geopotential,
+                        'u_deep_mag'   : u_deep_mag_val,
+                        'n_merid_deep_flow': u_deep_merid,                    
+                    },
+                    'shallow_physics_nml': {
+                        'h_0': equilibrium_geopotential, 
+                        'therm_damp_time' : rotation_period * 0., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
+                    },
+                    'constants_nml': {
+                        'omega': omega,
+                        'radius': radius,
+                    },
+                    'stirring_nml': {
+                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
+                        'amplitude':3.e-13,
+                        'n_total_forcing_max': 85,
+                        'n_total_forcing_min': 79,
+
+                    },
+
+                })
+
+                exp.run(1, use_restart=False, num_cores=NCORES)
+                for i in range(2,361):
+                    exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1_vary_damping.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1_vary_damping.py
new file mode 100644
index 000000000..c2335a0be
--- /dev/null
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1_vary_damping.py
@@ -0,0 +1,169 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+import pdb
+
+NCORES = 16
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+# diag.add_file('atmos_daily', 1, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv_correct', time_avg=True)
+
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h_sqd_mean', time_avg=True)
+
+#Empty the run directory ready to run
+
+#Define values for the 'core' namelist
+namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':False,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 512,
+   'num_lat'             : 256,
+   'num_fourier'         : 170,
+   'num_spherical'       : 171,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : False,
+   'spec_tracer'         : False,
+   'robert_coeff'        : 0.04,
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  :  0.0,
+   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
+   'h_amp'           :  0.,
+   'h_itcz'          :  0.,
+   },
+
+ 'stirring_nml': {
+   'B':0.0,
+   'do_localize': False,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    for ld_value in [0.1]:
+
+        for u_deep_mag_val in [0., 50.]:
+
+            if u_deep_mag_val!=0.:
+                u_deep_merid_arr = [3, 11, 19, 26]
+            else:
+                u_deep_merid_arr = [3]
+
+            for u_deep_merid in u_deep_merid_arr:
+
+                for damping_time_rot in [1000., 10000.]: #, 0., 100., Also want to do these, but can alias existing runs for them
+
+                        exp = Experiment('giant_planet_fixed_deep_ics_forced_rad_damping_'+str(damping_time_rot)+'_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid)), codebase=cb)
+
+                        exp.diag_table = diag 
+                        exp.namelist = namelist 
+                        exp.clear_rundir()
+
+                        rotation_period = ((9.*3600.)+55.*60 + 30.)
+                        omega = 2.*np.pi/ rotation_period
+                        radius = 69911e3
+                        grav = 24.79
+                        number_ld_in_radius_units = ld_value
+
+                        # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
+
+                        equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
+                        equilibrium_depth = equilibrium_geopotential/grav
+
+                        exp.update_namelist({
+                            'shallow_dynamics_nml':{
+                                'h_0': equilibrium_geopotential,
+                                'u_deep_mag'   : u_deep_mag_val,
+                                'n_merid_deep_flow': u_deep_merid,                    
+                            },
+                            'shallow_physics_nml': {
+                                'h_0': equilibrium_geopotential, 
+                                'therm_damp_time' : rotation_period * damping_time_rot, #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
+                            },
+                            'constants_nml': {
+                                'omega': omega,
+                                'radius': radius,
+                            },
+                            'stirring_nml': {
+                                'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
+                                'amplitude':3.e-13,
+                                'n_total_forcing_max': 85,
+                                'n_total_forcing_min': 79,
+
+                            },
+
+                        })
+
+                        exp.run(1, use_restart=False, num_cores=NCORES)
+                        for i in range(2,721):
+                            exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk1.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk1.py
new file mode 100644
index 000000000..0d5ce04b4
--- /dev/null
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk1.py
@@ -0,0 +1,167 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+import pdb
+
+NCORES = 16
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+# diag.add_file('atmos_daily', 1, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
+
+
+#Empty the run directory ready to run
+
+#Define values for the 'core' namelist
+namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':False,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 512,
+   'num_lat'             : 256,
+   'num_fourier'         : 170,
+   'num_spherical'       : 171,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : False,
+   'spec_tracer'         : False,
+   'robert_coeff'        : 0.04,
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  :  0.0,
+   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
+   'h_amp'           :  0.,
+   'h_itcz'          :  0.,
+   },
+
+ 'stirring_nml': {
+   'B':0.0,
+   'do_localize': False,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    for ld_value in [10.0]:
+        for u_deep_mag_val in [50.,]:
+        #for u_deep_mag_val in [-50.]:
+
+            if u_deep_mag_val!=0.:
+                u_deep_merid_arr = [3,]
+            else:
+                u_deep_merid_arr = [3]
+
+            #u_deep_merid_arr = [3]
+
+            for u_deep_merid in u_deep_merid_arr:
+
+                exp = Experiment('giant_planet_shallow_water_deep_velocity_test_mk2_no_forcing_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid)), codebase=cb)
+
+                exp.diag_table = diag 
+                exp.namelist = namelist 
+                exp.clear_rundir()
+
+                rotation_period = ((9.*3600.)+55.*60 + 30.)
+                omega = 2.*np.pi/ rotation_period
+                radius = 69911e3
+                grav = 24.79
+                number_ld_in_radius_units = ld_value
+
+                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
+
+                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
+                equilibrium_depth = equilibrium_geopotential/grav
+
+                exp.update_namelist({
+                    'shallow_dynamics_nml':{
+                        'h_0': equilibrium_geopotential,
+                        'u_deep_mag'   : u_deep_mag_val,
+                        'n_merid_deep_flow': u_deep_merid,                    
+                    },
+                    'shallow_physics_nml': {
+                        'h_0': equilibrium_geopotential, 
+                        'therm_damp_time' : rotation_period * 100., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
+                    },
+                    'constants_nml': {
+                        'omega': omega,
+                        'radius': radius,
+                    },
+                    'stirring_nml': {
+                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
+                        'amplitude':0.,
+                        'n_total_forcing_max': 85,
+                        'n_total_forcing_min': 79,
+
+                    },
+
+                })
+
+                exp.run(1, use_restart=False, num_cores=NCORES)
+                for i in range(2,2101):
+                    exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk2.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk2.py
new file mode 100644
index 000000000..711b2c34b
--- /dev/null
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk2.py
@@ -0,0 +1,170 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+import pdb
+
+NCORES = 16
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+# diag.add_file('atmos_daily', 1, 'days', time_units='days')
+# diag.add_file('atmos_timestep', 1200, 'seconds', time_units='days')
+
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
+
+
+
+#Empty the run directory ready to run
+
+#Define values for the 'core' namelist
+namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 1200,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':False,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 512,
+   'num_lat'             : 256,
+   'num_fourier'         : 170,
+   'num_spherical'       : 171,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : False,
+   'spec_tracer'         : False,
+   'robert_coeff'        : 0.04,
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  :  0.0,
+   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
+   'h_amp'           :  0.,
+   'h_itcz'          :  0.,
+   },
+
+ 'stirring_nml': {
+   'B':0.0,
+   'do_localize': False,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    for ld_value in [0.1, 10.0]:
+        # for u_deep_mag_val in [50., 0., 25.]:
+        for u_deep_mag_val in [50., 0.]:
+
+            # if u_deep_mag_val!=0.:
+            #     u_deep_merid_arr = [3, 11, 19, 26]
+            # else:
+            #     u_deep_merid_arr = [3]
+
+            u_deep_merid_arr = [3]
+
+            for u_deep_merid in u_deep_merid_arr:
+
+                exp = Experiment('giant_planet_shallow_water_deep_velocity_test_mk8_no_forcing_no_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid)), codebase=cb)
+
+                exp.diag_table = diag 
+                exp.namelist = namelist 
+                exp.clear_rundir()
+
+                rotation_period = ((9.*3600.)+55.*60 + 30.)
+                omega = 2.*np.pi/ rotation_period
+                radius = 69911e3
+                grav = 24.79
+                number_ld_in_radius_units = ld_value
+
+                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
+
+                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
+                equilibrium_depth = equilibrium_geopotential/grav
+
+                exp.update_namelist({
+                    'shallow_dynamics_nml':{
+                        'h_0': equilibrium_geopotential,
+                        'u_deep_mag'   : u_deep_mag_val,
+                        'n_merid_deep_flow': u_deep_merid,                    
+                    },
+                    'shallow_physics_nml': {
+                        'h_0': equilibrium_geopotential, 
+                        'therm_damp_time' : 0.
+                    },
+                    'constants_nml': {
+                        'omega': omega,
+                        'radius': radius,
+                    },
+                    'stirring_nml': {
+                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
+                        'amplitude':0.,
+                        'n_total_forcing_max': 85,
+                        'n_total_forcing_min': 79,
+
+                    },
+
+                })
+
+                exp.run(1, use_restart=False, num_cores=NCORES)
+                for i in range(2,121):
+                    exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py b/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py
index a45007b8b..14c4b323c 100644
--- a/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py
+++ b/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py
@@ -6,7 +6,7 @@
 
 import pdb
 
-NCORES = 8
+NCORES = 16
 base_dir = os.path.dirname(os.path.realpath(__file__))
 # a CodeBase can be a directory on the computer,
 # useful for iterative development
@@ -106,9 +106,9 @@
 #Lets do a run!
 if __name__=="__main__":
 
-    for number_ld_in_radius_units in [10.]:
+    for number_ld_in_radius_units in [0.1]:
 
-        exp = Experiment('giant_shallow_stirring_test_experiment_uniform_small_scale_stirring_mk3', codebase=cb)
+        exp = Experiment('giant_shallow_stirring_test_experiment_uniform_smaller_120_scale_stirring_mk3_longer_damping_ld_'+str(number_ld_in_radius_units), codebase=cb)
 
         exp.diag_table = diag 
         exp.namelist = namelist 
@@ -130,7 +130,7 @@
             },
             'shallow_physics_nml': {
                 'h_0': equilibrium_geopotential, 
-                'therm_damp_time' : rotation_period * 1., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
+                'therm_damp_time' : rotation_period * 10000., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
             },
             'constants_nml': {
                 'omega': omega,
@@ -139,13 +139,13 @@
             'stirring_nml': {
                 'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
                 'amplitude':3.e-13,
-                'n_total_forcing_max': 45,
-                'n_total_forcing_min': 39,
+                'n_total_forcing_max': 125,
+                'n_total_forcing_min': 119,
 
             },
 
         })
 
         exp.run(1, use_restart=False, num_cores=NCORES)
-        for i in range(2,122):
+        for i in range(2,121):
             exp.run(i, num_cores=NCORES)

From c09ad56ad00ceb7c6cc1d259a68edc2054347d8f Mon Sep 17 00:00:00 2001
From: sit23 
Date: Tue, 18 Jun 2019 19:05:55 +0100
Subject: [PATCH 16/24] Updating outputs for energy diagnostics.

---
 ...et_shallow_water_deep_velocity_test_mk1.py | 23 ++++--
 .../shallow_diagnostics.F90                   | 72 ++++++++++++++++++-
 .../shallow_dynamics.F90                      |  9 ++-
 3 files changed, 96 insertions(+), 8 deletions(-)

diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
index 56d419739..fe65deba8 100644
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
@@ -49,6 +49,14 @@
 diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
 diag.add_field('shallow_diagnostics', 'h_sqd_mean', time_avg=True)
 
+diag.add_field('shallow_diagnostics', 'e_kin_density', time_avg=True)
+diag.add_field('shallow_diagnostics', 'eq_geopot', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_kin_real_units', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_pot_real_units', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_tot_real_units', time_avg=True)
+diag.add_field('shallow_diagnostics', 'u_rms', time_avg=True)
+
+
 #Empty the run directory ready to run
 
 #Define values for the 'core' namelist
@@ -109,18 +117,22 @@
 #Lets do a run!
 if __name__=="__main__":
 
-    for ld_value in [10.0, 0.1, 0.05, 0.01]:
+    # for ld_value in [10.0, 0.1, 0.05, 0.01]:
+    for ld_value in [0.05,]:
 
-        for u_deep_mag_val in [50., 0.]:
+
+        for u_deep_mag_val in [50.]:
 
             if u_deep_mag_val!=0.:
-                u_deep_merid_arr = [3, 11, 19, 26]
+                u_deep_merid_arr = [27]
+                # u_deep_merid_arr = [5,7,9]
+
             else:
                 u_deep_merid_arr = [3]
 
             for u_deep_merid in u_deep_merid_arr:
 
-                exp = Experiment('giant_planet_fixed_deep_ics_forced_no_rad_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid)), codebase=cb)
+                exp = Experiment('giant_planet_fixed_deep_ics_forced_no_rad_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid))+'_energy_outputs_3', codebase=cb)
 
                 exp.diag_table = diag 
                 exp.namelist = namelist 
@@ -141,7 +153,8 @@
                     'shallow_dynamics_nml':{
                         'h_0': equilibrium_geopotential,
                         'u_deep_mag'   : u_deep_mag_val,
-                        'n_merid_deep_flow': u_deep_merid,                    
+                        'n_merid_deep_flow': u_deep_merid,         
+                        # 'u_upper_mag_init':  u_deep_mag_val,
                     },
                     'shallow_physics_nml': {
                         'h_0': equilibrium_geopotential, 
diff --git a/src/atmos_spectral_shallow/shallow_diagnostics.F90 b/src/atmos_spectral_shallow/shallow_diagnostics.F90
index ce485758b..7a8cbed09 100644
--- a/src/atmos_spectral_shallow/shallow_diagnostics.F90
+++ b/src/atmos_spectral_shallow/shallow_diagnostics.F90
@@ -56,7 +56,7 @@ module shallow_diagnostics_mod
 
 logical :: module_is_initialized = .false.
 
-integer :: id_vor, id_stream, id_pv, id_u, id_v, id_div, id_h, id_trs, id_tr, id_d_geopot, id_u_sqd, id_v_sqd, id_h_sqd, id_u_sqd_mean, id_v_sqd_mean, id_h_sqd_mean, id_ekin
+integer :: id_vor, id_stream, id_pv, id_u, id_v, id_div, id_h, id_trs, id_tr, id_d_geopot, id_u_sqd, id_v_sqd, id_h_sqd, id_u_sqd_mean, id_v_sqd_mean, id_h_sqd_mean, id_ekin, id_ekin_density, id_eq_geopot, id_e_kin_real_units, id_e_pot_real_units, id_e_tot_real_units, id_u_rms
 
 integer :: is, ie, js, je
 
@@ -118,6 +118,14 @@ subroutine shallow_diagnostics_init(Time, lon_max, lat_max, id_lon, id_lat, id_l
 id_h_sqd_mean      = register_diag_field(mod_name, 'h_sqd_mean'     , Time, 'geopotential_sqd_mean'        , 'm4/s4'    )
 
 id_ekin      = register_diag_field(mod_name, 'e_kin' , Time, 'kinetic_energy'              , 'm^2/s^2'      ) 
+id_ekin_density = register_diag_field(mod_name, 'e_kin_density' , Time, 'kinetic_energy_density'              , 'm^3/s^2'      ) 
+
+id_eq_geopot = register_diag_field(mod_name, 'eq_geopot' , Time, 'equilibrium_geopotential'              , 'm^2/s^2'      ) 
+id_e_kin_real_units = register_diag_field(mod_name, 'e_kin_real_units' , Time, 'e_kin_real_units'              , 'J/kg'      ) 
+id_e_pot_real_units = register_diag_field(mod_name, 'e_pot_real_units' , Time, 'e_pot_real_units'              , 'J/kg'      ) 
+id_e_tot_real_units = register_diag_field(mod_name, 'e_tot_real_units' , Time, 'e_tot_real_units'              , 'J/kg'      ) 
+
+id_u_rms = register_diag_field(mod_name, 'u_rms' , Time, 'r_rms'              , 'm/s'      ) 
 
 module_is_initialized = .true.
 
@@ -133,6 +141,8 @@ subroutine shallow_diagnostics(Time, Grid, Phys, time_index)
 type(grid_type), intent(in) :: Grid
 integer,         intent(in) :: time_index
 
+real :: e_kin_real_units, e_pot_real_units, e_tot_real_units, eq_geopot
+
 logical :: used
    
 if(id_u       > 0) used = send_data(id_u      , Grid%u       (:,:, time_index)     , time)
@@ -174,6 +184,66 @@ subroutine shallow_diagnostics(Time, Grid, Phys, time_index)
     used = send_data(id_ekin      , 0.5*(area_weighted_global_mean(Grid%u       (:,:, time_index)**2) + area_weighted_global_mean(Grid%v       (:,:, time_index)**2))     , time)
 endif
 
+if (id_ekin_density > 0) then
+    used = send_data(id_ekin_density      , 0.5*(area_weighted_global_mean(Grid%h       (:,:, time_index)*(Grid%u       (:,:, time_index)**2)) + area_weighted_global_mean(Grid%h       (:,:, time_index)*(Grid%v       (:,:, time_index)**2)))     , time)
+endif
+
+eq_geopot = 0.
+e_kin_real_units = 0.
+e_pot_real_units = 0.
+
+if (id_eq_geopot > 0) then
+
+    eq_geopot = area_weighted_global_mean(Grid%h       (:,:, time_index))
+    used = send_data(id_eq_geopot      , eq_geopot,  time)
+
+endif
+
+
+if (id_e_kin_real_units > 0) then
+
+    if (eq_geopot == 0.) eq_geopot = area_weighted_global_mean(Grid%h       (:,:, time_index))
+
+    e_kin_real_units = 0.5*(area_weighted_global_mean(Grid%h       (:,:, time_index)*(Grid%u       (:,:, time_index)**2)) + area_weighted_global_mean(Grid%h       (:,:, time_index)*(Grid%v       (:,:, time_index)**2))) / eq_geopot
+
+    used = send_data(id_e_kin_real_units      , e_kin_real_units,  time)
+
+endif
+
+if (id_e_pot_real_units > 0) then
+
+    if (eq_geopot == 0.) eq_geopot = area_weighted_global_mean(Grid%h       (:,:, time_index))
+
+    e_pot_real_units = 0.5*(area_weighted_global_mean(Grid%h       (:,:, time_index)**2.)) / eq_geopot
+
+    used = send_data(id_e_pot_real_units      , e_pot_real_units,  time)
+
+endif
+
+if (id_e_tot_real_units > 0) then
+
+    if (eq_geopot == 0.) eq_geopot = area_weighted_global_mean(Grid%h       (:,:, time_index))
+
+    if (e_kin_real_units == 0.) then
+        e_kin_real_units = 0.5*(area_weighted_global_mean(Grid%h       (:,:, time_index)*(Grid%u       (:,:, time_index)**2)) + area_weighted_global_mean(Grid%h       (:,:, time_index)*(Grid%v       (:,:, time_index)**2))) / eq_geopot
+    endif
+
+    if (e_pot_real_units == 0.) then 
+        e_pot_real_units = 0.5*(area_weighted_global_mean(Grid%h       (:,:, time_index)**2.)) / eq_geopot
+    endif
+
+    e_tot_real_units = e_kin_real_units + e_pot_real_units
+
+    used = send_data(id_e_tot_real_units      , e_tot_real_units,  time)
+
+endif
+
+if (id_u_rms > 0) then
+
+    used = send_data(id_u_rms      , (area_weighted_global_mean(Grid%u       (:,:, time_index)**2) + area_weighted_global_mean(Grid%v       (:,:, time_index)**2))**0.5,  time)
+
+endif
+
 return
 end subroutine shallow_diagnostics
 !--------------------------------------------------------------------------------------------
diff --git a/src/atmos_spectral_shallow/shallow_dynamics.F90 b/src/atmos_spectral_shallow/shallow_dynamics.F90
index 8953ca662..67ce5b3e8 100644
--- a/src/atmos_spectral_shallow/shallow_dynamics.F90
+++ b/src/atmos_spectral_shallow/shallow_dynamics.F90
@@ -135,6 +135,7 @@ module shallow_dynamics_mod
 
 real    :: u_deep_mag          = 0.
 real    :: n_merid_deep_flow   = 3.
+real    :: u_upper_mag_init    = 0.
 
 logical :: spec_tracer      = .true.
 logical :: grid_tracer      = .true.
@@ -151,7 +152,8 @@ module shallow_dynamics_mod
                           h_0, spec_tracer, grid_tracer,     &
                           valid_range_v, cutoff_wn,          &
                           raw_filter_coeff,                  &
-                          u_deep_mag, n_merid_deep_flow
+                          u_deep_mag, n_merid_deep_flow,     &
+                          u_upper_mag_init
 
 contains
 
@@ -264,7 +266,10 @@ subroutine shallow_dynamics_init (Dyn,  Time, Time_init, dt_real)
 
 if(Time == Time_init) then
 
-  Dyn%Grid%vor(:,:,1) = 0.0
+  do i = is, ie   
+    Dyn%Grid%vor(i,js:je,1) = -((u_upper_mag_init * n_merid_deep_flow)/radius) * sin(DEG_to_RAD * deg_lat(js:je))
+  enddo
+
   Dyn%Grid%div(:,:,1) = 0.0
   Dyn%Grid%h  (:,:,1) = h_0 - Dyn%grid%deep_geopot(:,:)
     

From c1a3f2af8c6d75cb92a2fd7277a62ae34e94a5fe Mon Sep 17 00:00:00 2001
From: sit23 
Date: Sat, 29 Jun 2019 22:21:21 +0100
Subject: [PATCH 17/24] Updated experiments.

---
 ...w_water_deep_velocity_test_mk1_high_res.py | 175 ++++++++++++++++++
 ...w_water_deep_velocity_test_mk1_high_res.py | 175 ++++++++++++++++++
 2 files changed, 350 insertions(+)
 create mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
 create mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/part_2/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py

diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
new file mode 100644
index 000000000..5772107da
--- /dev/null
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
@@ -0,0 +1,175 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+import pdb
+
+NCORES = 32
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+# diag.add_file('atmos_daily', 1, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv_corrected', time_avg=True)
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h_sqd_mean', time_avg=True)
+
+diag.add_field('shallow_diagnostics', 'e_kin_density', time_avg=True)
+diag.add_field('shallow_diagnostics', 'eq_geopot', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_kin_real_units', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_pot_real_units', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_tot_real_units', time_avg=True)
+diag.add_field('shallow_diagnostics', 'u_rms', time_avg=True)
+
+#Empty the run directory ready to run
+
+#Define values for the 'core' namelist
+namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 600,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':False,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 1024,
+   'num_lat'             : 512,
+   'num_fourier'         : 341,
+   'num_spherical'       : 342,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : False,
+   'spec_tracer'         : False,
+   'robert_coeff'        : 0.04,
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  :  0.0,
+   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
+   'h_amp'           :  0.,
+   'h_itcz'          :  0.,
+   },
+
+ 'stirring_nml': {
+   'B':0.0,
+   'do_localize': False,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    for forcing_amplitude in [7.5, 5., 10.]:
+
+        for damping_time in [ 10000., 1000., 100000.]:
+            u_deep_mag_val = 50.
+
+            if u_deep_mag_val!=0.:
+                u_deep_merid_arr = [27]
+            else:
+                u_deep_merid_arr = [3]
+
+            for u_deep_merid in u_deep_merid_arr:
+
+                ld_value = 0.025
+                exp = Experiment('high_res_small_forcing_giant_planet_fixed_deep_ics_forced_'+str(damping_time)+'_rad_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid))+'_strong_forcing_'+str(forcing_amplitude), codebase=cb)
+
+                exp.diag_table = diag 
+                exp.namelist = namelist 
+                exp.clear_rundir()
+
+                rotation_period = ((9.*3600.)+55.*60 + 30.)
+                omega = 2.*np.pi/ rotation_period
+                radius = 69911e3
+                grav = 24.79
+                number_ld_in_radius_units = ld_value
+
+                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
+
+                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
+                equilibrium_depth = equilibrium_geopotential/grav
+
+                exp.update_namelist({
+                    'shallow_dynamics_nml':{
+                        'h_0': equilibrium_geopotential,
+                        'u_deep_mag'   : u_deep_mag_val,
+                        'n_merid_deep_flow': u_deep_merid,                    
+                    },
+                    'shallow_physics_nml': {
+                        'h_0': equilibrium_geopotential, 
+                        'therm_damp_time' : rotation_period * damping_time, #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
+                    },
+                    'constants_nml': {
+                        'omega': omega,
+                        'radius': radius,
+                    },
+                    'stirring_nml': {
+                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
+                        'amplitude':3.e-13*forcing_amplitude,
+                        'n_total_forcing_max': 170,
+                        'n_total_forcing_min': 164,
+
+                    },
+
+                })
+
+                exp.run(1, use_restart=False, num_cores=NCORES, multi_node=True)
+                for i in range(2,721):
+                    exp.run(i, num_cores=NCORES, multi_node=True)
diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/part_2/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/part_2/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
new file mode 100644
index 000000000..2c6a8f028
--- /dev/null
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/part_2/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
@@ -0,0 +1,175 @@
+import os
+
+import numpy as np
+
+from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
+
+import pdb
+
+NCORES = 32
+base_dir = os.path.dirname(os.path.realpath(__file__))
+# a CodeBase can be a directory on the computer,
+# useful for iterative development
+cb = ShallowCodeBase.from_directory(GFDL_BASE)
+
+# or it can point to a specific git repo and commit id.
+# This method should ensure future, independent, reproducibility of results.
+# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
+
+# compilation depends on computer specific settings.  The $GFDL_ENV
+# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
+# is used to load the correct compilers.  The env file is always loaded from
+# $GFDL_BASE and not the checked out git repo.
+
+cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
+
+# create an Experiment object to handle the configuration of model parameters
+# and output diagnostics
+
+#Tell model how to write diagnostics
+diag = DiagTable()
+diag.add_file('atmos_monthly', 30, 'days', time_units='days')
+# diag.add_file('atmos_daily', 1, 'days', time_units='days')
+
+#Tell model which diagnostics to write
+diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'div', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
+diag.add_field('shallow_diagnostics', 'pv_corrected', time_avg=True)
+diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
+diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
+# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
+diag.add_field('stirring_mod', 'stirring', time_avg=True)
+# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
+diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
+diag.add_field('shallow_diagnostics', 'h_sqd_mean', time_avg=True)
+
+diag.add_field('shallow_diagnostics', 'e_kin_density', time_avg=True)
+diag.add_field('shallow_diagnostics', 'eq_geopot', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_kin_real_units', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_pot_real_units', time_avg=True)
+diag.add_field('shallow_diagnostics', 'e_tot_real_units', time_avg=True)
+diag.add_field('shallow_diagnostics', 'u_rms', time_avg=True)
+
+#Empty the run directory ready to run
+
+#Define values for the 'core' namelist
+namelist = Namelist({
+    'main_nml':{
+     'days'   : 30,
+     'hours'  : 0,
+     'minutes': 0,
+     'seconds': 0,
+     'dt_atmos': 600,
+     'calendar': 'no_calendar',
+    },
+
+ 'atmosphere_nml':{
+   'print_interval': 86400,
+    },
+
+'fms_io_nml':{
+   'threading_write' :'single',
+   'fileset_write': 'single'
+    },
+
+ 'fms_nml':{
+   'print_memory_usage':False,
+   'domains_stack_size': 200000,
+    },
+
+ 'shallow_dynamics_nml':{
+   'num_lon'             : 1024,
+   'num_lat'             : 512,
+   'num_fourier'         : 341,
+   'num_spherical'       : 342,
+   'fourier_inc'         : 1,
+   'damping_option'      : 'resolution_dependent',
+   'damping_order'       : 4,
+   'damping_coeff'       : 1.e-04,
+   'h_0'                 : 3.e04,
+   'grid_tracer'         : False,
+   'spec_tracer'         : False,
+   'robert_coeff'        : 0.04,
+   'robert_coeff_tracer' : 0.04,
+    },
+
+ 'shallow_physics_nml':{
+   'fric_damp_time'  :  0.0,
+   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
+   'h_amp'           :  0.,
+   'h_itcz'          :  0.,
+   },
+
+ 'stirring_nml': {
+   'B':0.0,
+   'do_localize': False,
+   },
+
+})
+
+#Lets do a run!
+if __name__=="__main__":
+
+    for forcing_amplitude in [ 10.]:
+
+        for damping_time in [ 10000., 1000., 100000.]:
+            u_deep_mag_val = 50.
+
+            if u_deep_mag_val!=0.:
+                u_deep_merid_arr = [27]
+            else:
+                u_deep_merid_arr = [3]
+
+            for u_deep_merid in u_deep_merid_arr:
+
+                ld_value = 0.025
+                exp = Experiment('high_res_small_forcing_giant_planet_fixed_deep_ics_forced_'+str(damping_time)+'_rad_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid))+'_strong_forcing_'+str(forcing_amplitude), codebase=cb)
+
+                exp.diag_table = diag 
+                exp.namelist = namelist 
+                exp.clear_rundir()
+
+                rotation_period = ((9.*3600.)+55.*60 + 30.)
+                omega = 2.*np.pi/ rotation_period
+                radius = 69911e3
+                grav = 24.79
+                number_ld_in_radius_units = ld_value
+
+                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
+
+                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
+                equilibrium_depth = equilibrium_geopotential/grav
+
+                exp.update_namelist({
+                    'shallow_dynamics_nml':{
+                        'h_0': equilibrium_geopotential,
+                        'u_deep_mag'   : u_deep_mag_val,
+                        'n_merid_deep_flow': u_deep_merid,                    
+                    },
+                    'shallow_physics_nml': {
+                        'h_0': equilibrium_geopotential, 
+                        'therm_damp_time' : rotation_period * damping_time, #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
+                    },
+                    'constants_nml': {
+                        'omega': omega,
+                        'radius': radius,
+                    },
+                    'stirring_nml': {
+                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
+                        'amplitude':3.e-13*forcing_amplitude,
+                        'n_total_forcing_max': 170,
+                        'n_total_forcing_min': 164,
+
+                    },
+
+                })
+
+                exp.run(1, use_restart=False, num_cores=NCORES, multi_node=True)
+                for i in range(2,721):
+                    exp.run(i, num_cores=NCORES, multi_node=True)

From 4e46f2ce6011e952f4eb441b41040964822ea94e Mon Sep 17 00:00:00 2001
From: sit23 
Date: Tue, 2 Jul 2019 14:43:47 +0100
Subject: [PATCH 18/24] Ignorning supercomputer log files.

---
 .gitignore | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 89b27824a..a414eda46 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,4 +26,6 @@ src/extra/python/scripts/*.nc
 src/extra/python/scripts/archived/
 mima_pz.txt
 test/.cache
-test/results.xml
\ No newline at end of file
+test/results.xml
+*.sh.e*
+*.sh.o*

From f1cc51d60631154c87ee718be4d0f4dd6c2668d3 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Tue, 2 Jul 2019 14:54:52 +0100
Subject: [PATCH 19/24] Adding diagnostics for momentum budget.

---
 src/atmos_spectral_shallow/shallow_diagnostics.F90 | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/atmos_spectral_shallow/shallow_diagnostics.F90 b/src/atmos_spectral_shallow/shallow_diagnostics.F90
index 7a8cbed09..3ea5dc0a8 100644
--- a/src/atmos_spectral_shallow/shallow_diagnostics.F90
+++ b/src/atmos_spectral_shallow/shallow_diagnostics.F90
@@ -56,7 +56,7 @@ module shallow_diagnostics_mod
 
 logical :: module_is_initialized = .false.
 
-integer :: id_vor, id_stream, id_pv, id_u, id_v, id_div, id_h, id_trs, id_tr, id_d_geopot, id_u_sqd, id_v_sqd, id_h_sqd, id_u_sqd_mean, id_v_sqd_mean, id_h_sqd_mean, id_ekin, id_ekin_density, id_eq_geopot, id_e_kin_real_units, id_e_pot_real_units, id_e_tot_real_units, id_u_rms
+integer :: id_vor, id_stream, id_pv, id_u, id_v, id_div, id_h, id_trs, id_tr, id_d_geopot, id_u_sqd, id_v_sqd, id_h_sqd, id_u_sqd_mean, id_v_sqd_mean, id_h_sqd_mean, id_ekin, id_ekin_density, id_eq_geopot, id_e_kin_real_units, id_e_pot_real_units, id_e_tot_real_units, id_u_rms, id_vcomp_vor, id_ucomp_vcomp
 
 integer :: is, ie, js, je
 
@@ -127,6 +127,10 @@ subroutine shallow_diagnostics_init(Time, lon_max, lat_max, id_lon, id_lat, id_l
 
 id_u_rms = register_diag_field(mod_name, 'u_rms' , Time, 'r_rms'              , 'm/s'      ) 
 
+id_vcomp_vor    = register_diag_field(mod_name, 'vcomp_vor'   , axis_2d, Time, 'vcomp * relative vorticity'  , 'm/s^2'      )
+
+id_ucomp_vcomp    = register_diag_field(mod_name, 'ucomp_vcomp'   , axis_2d, Time, 'ucomp * vcomp'  , 'm^2/s^2'      )
+
 module_is_initialized = .true.
 
 return
@@ -244,6 +248,10 @@ subroutine shallow_diagnostics(Time, Grid, Phys, time_index)
 
 endif
 
+
+if(id_vcomp_vor       > 0) used = send_data(id_vcomp_vor      , Grid%v       (:,:, time_index) * Grid%vor       (:,:, time_index)     , time)
+if(id_ucomp_vcomp     > 0) used = send_data(id_ucomp_vcomp    , Grid%u     (:,:, time_index) * Grid%v     (:,:, time_index)    , time)
+
 return
 end subroutine shallow_diagnostics
 !--------------------------------------------------------------------------------------------

From ee7394d7b9283eb141742b05e07a0f3b48752740 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 18 Jul 2019 15:06:45 +0100
Subject: [PATCH 20/24] Added daily output for more useful diagnostics.

---
 ...t_planet_shallow_water_deep_velocity_test_mk1_high_res.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
index 5772107da..b512fec67 100644
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
@@ -29,7 +29,7 @@
 #Tell model how to write diagnostics
 diag = DiagTable()
 diag.add_file('atmos_monthly', 30, 'days', time_units='days')
-# diag.add_file('atmos_daily', 1, 'days', time_units='days')
+#diag.add_file('atmos_daily', 1, 'days', time_units='days')
 
 #Tell model which diagnostics to write
 diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
@@ -41,6 +41,9 @@
 diag.add_field('shallow_diagnostics', 'pv_corrected', time_avg=True)
 diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
 diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp_vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'ucomp_vcomp', time_avg=True)
+
 # diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
 # diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
 diag.add_field('stirring_mod', 'stirring', time_avg=True)

From bee23e085fe10c0fa4ae494563069410b3af592a Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 18 Jul 2019 15:09:17 +0100
Subject: [PATCH 21/24] Adding momentum budget analysis outputs.

---
 .../giant_planet_shallow_water_deep_velocity_test_mk1.py   | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
index fe65deba8..40c853e40 100644
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
@@ -41,6 +41,9 @@
 diag.add_field('shallow_diagnostics', 'pv_corrected', time_avg=True)
 diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
 diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
+diag.add_field('shallow_diagnostics', 'vcomp_vor', time_avg=True)
+diag.add_field('shallow_diagnostics', 'ucomp_vcomp', time_avg=True)
+
 # diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
 # diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
 diag.add_field('stirring_mod', 'stirring', time_avg=True)
@@ -124,7 +127,7 @@
         for u_deep_mag_val in [50.]:
 
             if u_deep_mag_val!=0.:
-                u_deep_merid_arr = [27]
+                u_deep_merid_arr = [23]
                 # u_deep_merid_arr = [5,7,9]
 
             else:
@@ -175,5 +178,5 @@
                 })
 
                 exp.run(1, use_restart=False, num_cores=NCORES)
-                for i in range(2,361):
+                for i in range(2,481):
                     exp.run(i, num_cores=NCORES)

From cbca8c77abe3adb65ce09ff479a1b93b6e8eb5a3 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Fri, 7 Feb 2020 09:11:16 +0000
Subject: [PATCH 22/24] parameter updates.

---
 ..._planet_shallow_water_deep_velocity_test_mk1_high_res.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
index b512fec67..c7af1d59c 100644
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
+++ b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
@@ -119,9 +119,9 @@
 #Lets do a run!
 if __name__=="__main__":
 
-    for forcing_amplitude in [7.5, 5., 10.]:
+    for forcing_amplitude in [7.5]:
 
-        for damping_time in [ 10000., 1000., 100000.]:
+        for damping_time in [ 100000.]:
             u_deep_mag_val = 50.
 
             if u_deep_mag_val!=0.:
@@ -174,5 +174,5 @@
                 })
 
                 exp.run(1, use_restart=False, num_cores=NCORES, multi_node=True)
-                for i in range(2,721):
+                for i in range(721,841):
                     exp.run(i, num_cores=NCORES, multi_node=True)

From bb15cef1f0443c852a0cccec72e230e434ec6460 Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 19 Mar 2020 08:49:02 +0000
Subject: [PATCH 23/24] Update shallow code to include vortex migration
 experiments.

---
 .../scripts/run_plevel.py                     |  17 +--
 .../shallow_dynamics.F90                      |  65 +++++++++-
 .../remove_certain_restart_and_data_files.py  | 111 ++++++++++--------
 3 files changed, 130 insertions(+), 63 deletions(-)

diff --git a/postprocessing/plevel_interpolation/scripts/run_plevel.py b/postprocessing/plevel_interpolation/scripts/run_plevel.py
index 294ecb53a..6b6b9bfe7 100644
--- a/postprocessing/plevel_interpolation/scripts/run_plevel.py
+++ b/postprocessing/plevel_interpolation/scripts/run_plevel.py
@@ -7,11 +7,12 @@
 import subprocess
 
 start_time=time.time()
-base_dir='/scratch/sit204/Data_2013/'
-exp_name_list = ['no_ice_flux_lhe_exps_q_flux_hadgem_anoms_3']
+base_dir='/disca/share/sit204/data_from_isca_cpu/cssp_perturb_exps/anoms/'
+#exp_name_list = ['soc_ga3_files_smooth_topo_fftw_mk1_fresh_compile_long', 'soc_ga3_files_smooth_topo_old_fft_mk2_long']
+exp_name_list = [f'soc_ga3_do_simple_false_cmip_o3_bucket_perturbed_ens_{f}' for f in range(100, 200)]
 avg_or_daily_list=['monthly']
-start_file=287
-end_file=288
+start_file=1
+end_file=1
 nfiles=(end_file-start_file)+1
 
 do_extra_averaging=False #If true, then 6hourly data is averaged into daily data using cdo
@@ -44,7 +45,7 @@
     var_names['timestep']='-a'
     var_names['6hourly']='ucomp slp height vor t_surf vcomp omega'
     var_names['daily']='ucomp slp height vor t_surf vcomp omega temp'
-    file_suffix='_interp_new_height_temp'
+    file_suffix='_interp_new_height_temp_not_below_ground'
 
 elif level_set=='ssw_diagnostics':
     plevs['6hourly']=' -p "1000 10000"'
@@ -66,10 +67,12 @@
 
             number_prefix=''
 
-            if n+start_file < 100:
+            if n+start_file < 1000:
                 number_prefix='0'
-            if n+start_file < 10:
+            if n+start_file < 100:
                 number_prefix='00'
+            if n+start_file < 10:
+                number_prefix = '000'
 
             nc_file_in = base_dir+'/'+exp_name+'/run'+number_prefix+str(n+start_file)+'/atmos_'+avg_or_daily+'.nc'
             nc_file_out = out_dir+'/'+exp_name+'/run'+number_prefix+str(n+start_file)+'/atmos_'+avg_or_daily+file_suffix+'.nc'
diff --git a/src/atmos_spectral_shallow/shallow_dynamics.F90 b/src/atmos_spectral_shallow/shallow_dynamics.F90
index 67ce5b3e8..7ba1ec3f8 100644
--- a/src/atmos_spectral_shallow/shallow_dynamics.F90
+++ b/src/atmos_spectral_shallow/shallow_dynamics.F90
@@ -140,6 +140,18 @@ module shallow_dynamics_mod
 logical :: spec_tracer      = .true.
 logical :: grid_tracer      = .true.
 
+!Options for injecting an initial vortex pair
+real    :: lon_centre_init_cyc = 0.
+real    :: lat_centre_init_cyc = 60.
+real    :: lon_centre_init_acyc = 180.
+real    :: lat_centre_init_acyc = 60.
+real    :: init_vortex_radius_deg = 5.
+real    :: init_vortex_vor_f = 0.5
+real    :: init_vortex_h_h_0 = 0.1
+logical :: add_initial_vortex_pair = .false.
+logical :: add_initial_vortex_as_height = .true.
+
+
 real, dimension(2) :: valid_range_v = (/-1.e3,1.e3/)
 
 namelist /shallow_dynamics_nml/ check_fourier_imag,          &
@@ -153,7 +165,17 @@ module shallow_dynamics_mod
                           valid_range_v, cutoff_wn,          &
                           raw_filter_coeff,                  &
                           u_deep_mag, n_merid_deep_flow,     &
-                          u_upper_mag_init
+                          u_upper_mag_init,                  &
+                          lon_centre_init_cyc,               &
+                          lat_centre_init_cyc,               &
+                          lon_centre_init_acyc,              &
+                          lat_centre_init_acyc,              &                          
+                          init_vortex_radius_deg,            &
+                          init_vortex_vor_f,                 &
+                          init_vortex_h_h_0,                 &
+                          add_initial_vortex_pair,           &
+                          add_initial_vortex_as_height                 
+
 
 contains
 
@@ -168,7 +190,7 @@ subroutine shallow_dynamics_init (Dyn,  Time, Time_init, dt_real)
 integer :: i, j
 
 real,    allocatable, dimension(:)   :: glon_bnd, glat_bnd
-real :: xx, yy, dd, deep_geopot_global_mean
+real :: xx, yy, dd, deep_geopot_global_mean, radius_loc_cyc, radius_loc_acyc
 
 integer  :: ierr, io, unit, id_lon, id_lat, id_lonb, id_latb
 logical  :: root
@@ -266,12 +288,45 @@ subroutine shallow_dynamics_init (Dyn,  Time, Time_init, dt_real)
 
 if(Time == Time_init) then
 
+    Dyn%Grid%div(:,:,1) = 0.0
+    Dyn%Grid%h  (:,:,1) = h_0 - Dyn%grid%deep_geopot(:,:)
+
   do i = is, ie   
     Dyn%Grid%vor(i,js:je,1) = -((u_upper_mag_init * n_merid_deep_flow)/radius) * sin(DEG_to_RAD * deg_lat(js:je))
-  enddo
 
-  Dyn%Grid%div(:,:,1) = 0.0
-  Dyn%Grid%h  (:,:,1) = h_0 - Dyn%grid%deep_geopot(:,:)
+    if (add_initial_vortex_pair) then
+
+        do j=js, je
+
+            radius_loc_cyc = ((min((deg_lon(i)-lon_centre_init_cyc)**2., (deg_lon(i)-lon_centre_init_cyc-360.)**2.)+(deg_lat(j)-lat_centre_init_cyc)**2.)**0.5)/init_vortex_radius_deg
+            radius_loc_acyc = ((min((deg_lon(i)-lon_centre_init_acyc)**2., (deg_lon(i)-lon_centre_init_acyc-360.)**2.)+(deg_lat(j)-lat_centre_init_acyc)**2.)**0.5)/init_vortex_radius_deg            
+
+
+            if(radius_loc_cyc.le.1.0 .and. radius_loc_acyc.le.1.0) then
+                call error_mesg('shallow_dynamics','Cannot initialise cyclone and anticyclone in same grid box ', FATAL)
+            endif
+
+            if(add_initial_vortex_as_height) then
+                if (radius_loc_cyc.le.2.0) then
+                    Dyn%Grid%h(i,j,1) = Dyn%Grid%h(i,j,1) + init_vortex_h_h_0 * -h_0 * exp(-radius_loc_cyc**2.)
+                elseif (radius_loc_acyc.le.2.0) then 
+                    Dyn%Grid%h(i,j,1) = Dyn%Grid%h(i,j,1) + init_vortex_h_h_0 * h_0 * exp(-radius_loc_acyc**2.)
+                endif
+            else
+                if (radius_loc_cyc.le.1.0) then
+                    Dyn%Grid%vor(i,j,1) = init_vortex_vor_f * 2.*omega
+                elseif (radius_loc_acyc.le.1.0) then 
+                    Dyn%Grid%vor(i,j,1) = init_vortex_vor_f * -2.*omega
+                endif
+
+            endif
+
+        enddo
+        
+
+    endif
+
+  enddo
     
   call trans_grid_to_spherical(Dyn%Grid%vor(:,:,1), Dyn%Spec%vor(:,:,1))
   call trans_grid_to_spherical(Dyn%Grid%div(:,:,1), Dyn%Spec%div(:,:,1))
diff --git a/src/extra/python/scripts/remove_certain_restart_and_data_files.py b/src/extra/python/scripts/remove_certain_restart_and_data_files.py
index 98d658a95..582a05c9c 100644
--- a/src/extra/python/scripts/remove_certain_restart_and_data_files.py
+++ b/src/extra/python/scripts/remove_certain_restart_and_data_files.py
@@ -1,6 +1,7 @@
 import sh
 import os
 import pdb
+from glob import glob
 
 P = os.path.join
 
@@ -12,11 +13,15 @@ def __init__(self, basedir, workdir, datadir, exp_name):
         self.expname = exp_name
 
 
-def create_exp_object(exp_name):
+def create_exp_object(exp_name, data_directory=None):
+
+    if data_directory is None:
+        datadir = os.environ['GFDL_DATA']
+    else:
+        datadir = data_directory
 
-    basedir = os.environ['GFDL_BASE']
     workdir = os.environ['GFDL_WORK']
-    datadir = os.environ['GFDL_DATA']
+    basedir = os.environ['GFDL_BASE']
     expname = '/'+exp_name+'/'
 
     exp_object = temporary_exp_object(basedir, workdir, datadir, exp_name)
@@ -24,34 +29,42 @@ def create_exp_object(exp_name):
     return exp_object
 
 
-def keep_only_certain_restart_files(exp_object, max_num_files, interval=12):
+# def keep_only_certain_restart_files(exp_object, max_num_files, interval=12):
 
-    #        sh.ls(sh.glob(P(self.workdir,'restarts','res_*.cpio'))) #TODO get max_num_files calculated in line, rather than a variable to pass.
+#     #        sh.ls(sh.glob(P(self.workdir,'restarts','res_*.cpio'))) #TODO get max_num_files calculated in line, rather than a variable to pass.
 
-            #First defines a list of ALL the restart file numbers
-        files_to_remove=list(range(0,max_num_files))
+#             #First defines a list of ALL the restart file numbers
+#         files_to_remove=list(range(0,max_num_files))
 
-            #Then defines a list of the ones we want to KEEP
-        files_to_keep  =list(range(0,max_num_files,interval)) 
+#             #Then defines a list of the ones we want to KEEP
+#         files_to_keep  =list(range(0,max_num_files,interval)) 
 
-            #Then we remove the files we want to keep from the list of all files, giving a list of those we wish to remove
-        for x in files_to_keep:
-               files_to_remove.remove(x) 
+#             #Then we remove the files we want to keep from the list of all files, giving a list of those we wish to remove
+#         for x in files_to_keep:
+#                files_to_remove.remove(x) 
 
-            #Then we remove them.
-        for entry in files_to_remove:
-            try:
-                sh.rm(P(exp_object.workdir,exp_object.expname,'restarts','res_'+str(entry)+'.cpio'))
-#                 print P(exp_object.workdir,exp_object.expname,'restarts','res_'+str(entry)+'.cpio')
+#             #Then we remove them.
+#         for entry in files_to_remove:
+#             try:
+#                 sh.rm(P(exp_object.workdir,exp_object.expname,'restarts','res_'+str(entry)+'.cpio'))
+# #                 print P(exp_object.workdir,exp_object.expname,'restarts','res_'+str(entry)+'.cpio')
 
-            except sh.ErrorReturnCode_1:
-                pass
-#                 print 'Tried to remove some restart files, but number '+str(entry)+' does not exist'
+#             except sh.ErrorReturnCode_1:
+#                 pass
+# #                 print 'Tried to remove some restart files, but number '+str(entry)+' does not exist'
                 
-def keep_only_certain_restart_files_data_dir(exp_object, max_num_files, interval=12):
+def keep_only_certain_restart_files_data_dir(exp_object, max_num_files=None, interval=12):
 
     #        sh.ls(sh.glob(P(self.workdir,'restarts','res_*.cpio'))) #TODO get max_num_files calculated in line, rather than a variable to pass.
 
+        if max_num_files is None:
+            month_list = glob(P(exp_object.datadir,exp_object.expname, 'restarts')+'/res*.tar.gz')
+            if len(month_list)==0:
+                return
+            else:
+                final_month = month_list[-1].split('/res')
+            max_num_files = int(final_month[-1].split('.tar.gz')[0])
+
             #First defines a list of ALL the restart file numbers
         files_to_remove=list(range(0,max_num_files))
 
@@ -62,13 +75,27 @@ def keep_only_certain_restart_files_data_dir(exp_object, max_num_files, interval
         for x in files_to_keep:
                files_to_remove.remove(x) 
 
+        first_to_be_removed = True
+        number_removed = 0
+        number_not_removed = 0
             #Then we remove them.
-        for entry in files_to_remove:
+        for entry in files_to_remove[1:-1]:
             try:
-                sh.rm(P(exp_object.datadir,exp_object.expname,'run%03d' % entry,'INPUT','res'))
-#                 print 'would be removing ' + P(exp_object.datadir,exp_object.expname,'run'+str(entry),'INPUT','res')
+                file_to_remove = P(exp_object.datadir,exp_object.expname, 'restarts', 'res%04d.tar.gz' % entry)
+                if os.path.isfile(file_to_remove) and first_to_be_removed:
+                    first_to_be_removed=False
+                    number_not_removed+=1
+                    # print('would have removed '+file_to_remove+' but wanted to make sure not to delete the first restart')
+                else:
+                    sh.rm(file_to_remove)
+                    number_removed+=1
+                    # print('have removed ' + file_to_remove)
             except sh.ErrorReturnCode_1:
+                number_not_removed+=1                
+                # print('could not remove ' + file_to_remove)
                 pass
+        print(P(exp_object.datadir,exp_object.expname), 'number removed '+str(number_removed), 'number not removed '+str(number_not_removed))
+                
 #                 print 'Tried to remove some restart files, but number '+str(entry)+' does not exist'                
 
 def keep_only_certain_daily_data_uninterp(exp_object, max_num_files, interval=None, file_name = 'atmos_daily.nc'):
@@ -88,8 +115,8 @@ def keep_only_certain_daily_data_uninterp(exp_object, max_num_files, interval=No
             #Then we remove them.
         for entry in files_to_remove:           
             try:
-                sh.rm(P(exp_object.datadir,exp_object.expname,'run%03d' % entry,file_name))
-                print(('Removed '+P(exp_object.datadir,exp_object.expname,'run%03d' % entry,file_name)))        
+                sh.rm(P(exp_object.datadir,exp_object.expname,'run%04d' % entry,file_name))
+                print(('Removed '+P(exp_object.datadir,exp_object.expname,'run%04d' % entry,file_name)))        
             except sh.ErrorReturnCode_1:
                 pass
 #                 print 'Tried to remove some atmos_daily files, but number '+str(entry)+' does not exist'
@@ -98,36 +125,18 @@ def keep_only_certain_daily_data_uninterp(exp_object, max_num_files, interval=No
             
 if __name__=="__main__":
 
-    max_num_files_input = 325
+    max_num_files_input = None
     
-#     exp_name_list=['simple_continents_post_princeton_qflux_anoms_'+str(x) for x in range(31,32)]
-
-#     exp_name_list=['aquaplanet_qflux_anoms_'+str(x) for x in [12,18,23,32,8]]
-
-#     exp_name_list = ['simple_continents_post_princeton_qflux_control_1','simple_continents_post_princeton_fixed_sst_1', 'simple_continents_post_princeton_qflux_control_nod_1', 'simple_continents_post_princeton_qflux_control_scf_1']
-#     
-#     exp_name_list = ['annual_mean_ice_princeton_qflux_control_matrix_qflux_2017_code_1', 'annual_mean_ice_post_princeton_fixed_sst_1', 'annual_mean_ice_princeton_fixed_sst_1'] 
-# 
-#     exp_name_list.extend(['annual_mean_ice_post_princeton_fixed_sst_el_nino_1'])
-
-#     exp_name_list = ['simple_continents_post_princeton_qflux_control_1']
-
-#     exp_name_list = ['annual_mean_ice_princeton_qflux_control_1']#, 'annual_mean_ice_post_princeton_qflux_control_1']
-
-#     exp_name_list = ['annual_mean_ice_post_princeton_fixed_sst_TEST_1', 'annual_mean_ice_princeton_qflux_control_matrix_qflux_1']
-
-#     exp_name_list.extend(['simple_continents_post_princeton_fixed_sst_1'])
-
-#     exp_name_list = ['giant_drag_exp_chai_values_without_dc_bug_latest_1']
-#     exp_name_list = ['aquaplanet_qflux_control_1']
+    # exp_name_list = ['']
+    exp_name_list = glob('/disca/share/sit204/data_isca_from_gv5/frierson_post_soc_fix_*/')
     
-    exp_name_list = ['giant_drag_exp_chai_values_with_dc_bug_latest_start_to_finish_1', 'giant_drag_exp_chai_values_without_dc_bug_latest_start_to_finish_1']
     
     for exp_name_input in exp_name_list:    
-        temp_obj = create_exp_object(exp_name_input)
-        keep_only_certain_restart_files(temp_obj, max_num_files_input)
+        print('Percentage progress through list:'+str(exp_name_list.index(exp_name_input)/len(exp_name_list)))
+        temp_obj = create_exp_object(exp_name_input, data_directory='/disca/share/sit204/data_from_isca_cpu/')
+        # keep_only_certain_restart_files(temp_obj, max_num_files_input)
         keep_only_certain_restart_files_data_dir(temp_obj, max_num_files_input)
-        keep_only_certain_daily_data_uninterp(temp_obj, max_num_files_input, file_name = 'fms_moist.x')
+        # keep_only_certain_daily_data_uninterp(temp_obj, max_num_files_input, file_name = 'fms_moist.x')
 #         keep_only_certain_daily_data_uninterp(temp_obj, max_num_files_input)
 
     
\ No newline at end of file

From d706b3407f103732c818c010f4abf447c6614efc Mon Sep 17 00:00:00 2001
From: sit23 
Date: Thu, 10 Dec 2020 17:53:17 +0000
Subject: [PATCH 24/24] Removing unecessary experiment files.

---
 ...et_shallow_water_deep_velocity_test_mk1.py | 182 ------------------
 ...ter_deep_velocity_test_mk1_vary_damping.py | 169 ----------------
 ...w_water_deep_velocity_test_mk1_high_res.py | 178 -----------------
 ...w_water_deep_velocity_test_mk1_high_res.py | 175 -----------------
 ...et_shallow_water_deep_velocity_test_mk1.py | 167 ----------------
 ...et_shallow_water_deep_velocity_test_mk2.py | 170 ----------------
 ...shallow_water_small_scale_stirring_test.py | 151 ---------------
 ...iant_planet_shallow_water_stirring_test.py | 148 --------------
 8 files changed, 1340 deletions(-)
 delete mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
 delete mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1_vary_damping.py
 delete mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
 delete mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/part_2/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
 delete mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk1.py
 delete mode 100644 exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk2.py
 delete mode 100644 exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py
 delete mode 100644 exp/shallow_water_giant_planet/giant_planet_shallow_water_stirring_test.py

diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
deleted file mode 100644
index 40c853e40..000000000
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1.py
+++ /dev/null
@@ -1,182 +0,0 @@
-import os
-
-import numpy as np
-
-from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
-
-import pdb
-
-NCORES = 16
-base_dir = os.path.dirname(os.path.realpath(__file__))
-# a CodeBase can be a directory on the computer,
-# useful for iterative development
-cb = ShallowCodeBase.from_directory(GFDL_BASE)
-
-# or it can point to a specific git repo and commit id.
-# This method should ensure future, independent, reproducibility of results.
-# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
-
-# compilation depends on computer specific settings.  The $GFDL_ENV
-# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
-# is used to load the correct compilers.  The env file is always loaded from
-# $GFDL_BASE and not the checked out git repo.
-
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
-# create an Experiment object to handle the configuration of model parameters
-# and output diagnostics
-
-#Tell model how to write diagnostics
-diag = DiagTable()
-diag.add_file('atmos_monthly', 30, 'days', time_units='days')
-# diag.add_file('atmos_daily', 1, 'days', time_units='days')
-
-#Tell model which diagnostics to write
-diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'div', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv_corrected', time_avg=True)
-diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
-diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp_vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'ucomp_vcomp', time_avg=True)
-
-# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
-diag.add_field('stirring_mod', 'stirring', time_avg=True)
-# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
-diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h_sqd_mean', time_avg=True)
-
-diag.add_field('shallow_diagnostics', 'e_kin_density', time_avg=True)
-diag.add_field('shallow_diagnostics', 'eq_geopot', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_kin_real_units', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_pot_real_units', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_tot_real_units', time_avg=True)
-diag.add_field('shallow_diagnostics', 'u_rms', time_avg=True)
-
-
-#Empty the run directory ready to run
-
-#Define values for the 'core' namelist
-namelist = Namelist({
-    'main_nml':{
-     'days'   : 30,
-     'hours'  : 0,
-     'minutes': 0,
-     'seconds': 0,
-     'dt_atmos': 1200,
-     'calendar': 'no_calendar',
-    },
-
- 'atmosphere_nml':{
-   'print_interval': 86400,
-    },
-
-'fms_io_nml':{
-   'threading_write' :'single',
-   'fileset_write': 'single'
-    },
-
- 'fms_nml':{
-   'print_memory_usage':False,
-   'domains_stack_size': 200000,
-    },
-
- 'shallow_dynamics_nml':{
-   'num_lon'             : 512,
-   'num_lat'             : 256,
-   'num_fourier'         : 170,
-   'num_spherical'       : 171,
-   'fourier_inc'         : 1,
-   'damping_option'      : 'resolution_dependent',
-   'damping_order'       : 4,
-   'damping_coeff'       : 1.e-04,
-   'h_0'                 : 3.e04,
-   'grid_tracer'         : False,
-   'spec_tracer'         : False,
-   'robert_coeff'        : 0.04,
-   'robert_coeff_tracer' : 0.04,
-    },
-
- 'shallow_physics_nml':{
-   'fric_damp_time'  :  0.0,
-   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
-   'h_amp'           :  0.,
-   'h_itcz'          :  0.,
-   },
-
- 'stirring_nml': {
-   'B':0.0,
-   'do_localize': False,
-   },
-
-})
-
-#Lets do a run!
-if __name__=="__main__":
-
-    # for ld_value in [10.0, 0.1, 0.05, 0.01]:
-    for ld_value in [0.05,]:
-
-
-        for u_deep_mag_val in [50.]:
-
-            if u_deep_mag_val!=0.:
-                u_deep_merid_arr = [23]
-                # u_deep_merid_arr = [5,7,9]
-
-            else:
-                u_deep_merid_arr = [3]
-
-            for u_deep_merid in u_deep_merid_arr:
-
-                exp = Experiment('giant_planet_fixed_deep_ics_forced_no_rad_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid))+'_energy_outputs_3', codebase=cb)
-
-                exp.diag_table = diag 
-                exp.namelist = namelist 
-                exp.clear_rundir()
-
-                rotation_period = ((9.*3600.)+55.*60 + 30.)
-                omega = 2.*np.pi/ rotation_period
-                radius = 69911e3
-                grav = 24.79
-                number_ld_in_radius_units = ld_value
-
-                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
-
-                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
-                equilibrium_depth = equilibrium_geopotential/grav
-
-                exp.update_namelist({
-                    'shallow_dynamics_nml':{
-                        'h_0': equilibrium_geopotential,
-                        'u_deep_mag'   : u_deep_mag_val,
-                        'n_merid_deep_flow': u_deep_merid,         
-                        # 'u_upper_mag_init':  u_deep_mag_val,
-                    },
-                    'shallow_physics_nml': {
-                        'h_0': equilibrium_geopotential, 
-                        'therm_damp_time' : rotation_period * 0., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
-                    },
-                    'constants_nml': {
-                        'omega': omega,
-                        'radius': radius,
-                    },
-                    'stirring_nml': {
-                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
-                        'amplitude':3.e-13,
-                        'n_total_forcing_max': 85,
-                        'n_total_forcing_min': 79,
-
-                    },
-
-                })
-
-                exp.run(1, use_restart=False, num_cores=NCORES)
-                for i in range(2,481):
-                    exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1_vary_damping.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1_vary_damping.py
deleted file mode 100644
index c2335a0be..000000000
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/giant_planet_shallow_water_deep_velocity_test_mk1_vary_damping.py
+++ /dev/null
@@ -1,169 +0,0 @@
-import os
-
-import numpy as np
-
-from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
-
-import pdb
-
-NCORES = 16
-base_dir = os.path.dirname(os.path.realpath(__file__))
-# a CodeBase can be a directory on the computer,
-# useful for iterative development
-cb = ShallowCodeBase.from_directory(GFDL_BASE)
-
-# or it can point to a specific git repo and commit id.
-# This method should ensure future, independent, reproducibility of results.
-# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
-
-# compilation depends on computer specific settings.  The $GFDL_ENV
-# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
-# is used to load the correct compilers.  The env file is always loaded from
-# $GFDL_BASE and not the checked out git repo.
-
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
-# create an Experiment object to handle the configuration of model parameters
-# and output diagnostics
-
-#Tell model how to write diagnostics
-diag = DiagTable()
-diag.add_file('atmos_monthly', 30, 'days', time_units='days')
-# diag.add_file('atmos_daily', 1, 'days', time_units='days')
-
-#Tell model which diagnostics to write
-diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'div', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv_correct', time_avg=True)
-
-diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
-diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
-diag.add_field('stirring_mod', 'stirring', time_avg=True)
-# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
-diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h_sqd_mean', time_avg=True)
-
-#Empty the run directory ready to run
-
-#Define values for the 'core' namelist
-namelist = Namelist({
-    'main_nml':{
-     'days'   : 30,
-     'hours'  : 0,
-     'minutes': 0,
-     'seconds': 0,
-     'dt_atmos': 1200,
-     'calendar': 'no_calendar',
-    },
-
- 'atmosphere_nml':{
-   'print_interval': 86400,
-    },
-
-'fms_io_nml':{
-   'threading_write' :'single',
-   'fileset_write': 'single'
-    },
-
- 'fms_nml':{
-   'print_memory_usage':False,
-   'domains_stack_size': 200000,
-    },
-
- 'shallow_dynamics_nml':{
-   'num_lon'             : 512,
-   'num_lat'             : 256,
-   'num_fourier'         : 170,
-   'num_spherical'       : 171,
-   'fourier_inc'         : 1,
-   'damping_option'      : 'resolution_dependent',
-   'damping_order'       : 4,
-   'damping_coeff'       : 1.e-04,
-   'h_0'                 : 3.e04,
-   'grid_tracer'         : False,
-   'spec_tracer'         : False,
-   'robert_coeff'        : 0.04,
-   'robert_coeff_tracer' : 0.04,
-    },
-
- 'shallow_physics_nml':{
-   'fric_damp_time'  :  0.0,
-   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
-   'h_amp'           :  0.,
-   'h_itcz'          :  0.,
-   },
-
- 'stirring_nml': {
-   'B':0.0,
-   'do_localize': False,
-   },
-
-})
-
-#Lets do a run!
-if __name__=="__main__":
-
-    for ld_value in [0.1]:
-
-        for u_deep_mag_val in [0., 50.]:
-
-            if u_deep_mag_val!=0.:
-                u_deep_merid_arr = [3, 11, 19, 26]
-            else:
-                u_deep_merid_arr = [3]
-
-            for u_deep_merid in u_deep_merid_arr:
-
-                for damping_time_rot in [1000., 10000.]: #, 0., 100., Also want to do these, but can alias existing runs for them
-
-                        exp = Experiment('giant_planet_fixed_deep_ics_forced_rad_damping_'+str(damping_time_rot)+'_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid)), codebase=cb)
-
-                        exp.diag_table = diag 
-                        exp.namelist = namelist 
-                        exp.clear_rundir()
-
-                        rotation_period = ((9.*3600.)+55.*60 + 30.)
-                        omega = 2.*np.pi/ rotation_period
-                        radius = 69911e3
-                        grav = 24.79
-                        number_ld_in_radius_units = ld_value
-
-                        # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
-
-                        equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
-                        equilibrium_depth = equilibrium_geopotential/grav
-
-                        exp.update_namelist({
-                            'shallow_dynamics_nml':{
-                                'h_0': equilibrium_geopotential,
-                                'u_deep_mag'   : u_deep_mag_val,
-                                'n_merid_deep_flow': u_deep_merid,                    
-                            },
-                            'shallow_physics_nml': {
-                                'h_0': equilibrium_geopotential, 
-                                'therm_damp_time' : rotation_period * damping_time_rot, #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
-                            },
-                            'constants_nml': {
-                                'omega': omega,
-                                'radius': radius,
-                            },
-                            'stirring_nml': {
-                                'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
-                                'amplitude':3.e-13,
-                                'n_total_forcing_max': 85,
-                                'n_total_forcing_min': 79,
-
-                            },
-
-                        })
-
-                        exp.run(1, use_restart=False, num_cores=NCORES)
-                        for i in range(2,721):
-                            exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
deleted file mode 100644
index c7af1d59c..000000000
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
+++ /dev/null
@@ -1,178 +0,0 @@
-import os
-
-import numpy as np
-
-from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
-
-import pdb
-
-NCORES = 32
-base_dir = os.path.dirname(os.path.realpath(__file__))
-# a CodeBase can be a directory on the computer,
-# useful for iterative development
-cb = ShallowCodeBase.from_directory(GFDL_BASE)
-
-# or it can point to a specific git repo and commit id.
-# This method should ensure future, independent, reproducibility of results.
-# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
-
-# compilation depends on computer specific settings.  The $GFDL_ENV
-# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
-# is used to load the correct compilers.  The env file is always loaded from
-# $GFDL_BASE and not the checked out git repo.
-
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
-# create an Experiment object to handle the configuration of model parameters
-# and output diagnostics
-
-#Tell model how to write diagnostics
-diag = DiagTable()
-diag.add_file('atmos_monthly', 30, 'days', time_units='days')
-#diag.add_file('atmos_daily', 1, 'days', time_units='days')
-
-#Tell model which diagnostics to write
-diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'div', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv_corrected', time_avg=True)
-diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
-diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp_vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'ucomp_vcomp', time_avg=True)
-
-# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
-diag.add_field('stirring_mod', 'stirring', time_avg=True)
-# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
-diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h_sqd_mean', time_avg=True)
-
-diag.add_field('shallow_diagnostics', 'e_kin_density', time_avg=True)
-diag.add_field('shallow_diagnostics', 'eq_geopot', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_kin_real_units', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_pot_real_units', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_tot_real_units', time_avg=True)
-diag.add_field('shallow_diagnostics', 'u_rms', time_avg=True)
-
-#Empty the run directory ready to run
-
-#Define values for the 'core' namelist
-namelist = Namelist({
-    'main_nml':{
-     'days'   : 30,
-     'hours'  : 0,
-     'minutes': 0,
-     'seconds': 0,
-     'dt_atmos': 600,
-     'calendar': 'no_calendar',
-    },
-
- 'atmosphere_nml':{
-   'print_interval': 86400,
-    },
-
-'fms_io_nml':{
-   'threading_write' :'single',
-   'fileset_write': 'single'
-    },
-
- 'fms_nml':{
-   'print_memory_usage':False,
-   'domains_stack_size': 200000,
-    },
-
- 'shallow_dynamics_nml':{
-   'num_lon'             : 1024,
-   'num_lat'             : 512,
-   'num_fourier'         : 341,
-   'num_spherical'       : 342,
-   'fourier_inc'         : 1,
-   'damping_option'      : 'resolution_dependent',
-   'damping_order'       : 4,
-   'damping_coeff'       : 1.e-04,
-   'h_0'                 : 3.e04,
-   'grid_tracer'         : False,
-   'spec_tracer'         : False,
-   'robert_coeff'        : 0.04,
-   'robert_coeff_tracer' : 0.04,
-    },
-
- 'shallow_physics_nml':{
-   'fric_damp_time'  :  0.0,
-   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
-   'h_amp'           :  0.,
-   'h_itcz'          :  0.,
-   },
-
- 'stirring_nml': {
-   'B':0.0,
-   'do_localize': False,
-   },
-
-})
-
-#Lets do a run!
-if __name__=="__main__":
-
-    for forcing_amplitude in [7.5]:
-
-        for damping_time in [ 100000.]:
-            u_deep_mag_val = 50.
-
-            if u_deep_mag_val!=0.:
-                u_deep_merid_arr = [27]
-            else:
-                u_deep_merid_arr = [3]
-
-            for u_deep_merid in u_deep_merid_arr:
-
-                ld_value = 0.025
-                exp = Experiment('high_res_small_forcing_giant_planet_fixed_deep_ics_forced_'+str(damping_time)+'_rad_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid))+'_strong_forcing_'+str(forcing_amplitude), codebase=cb)
-
-                exp.diag_table = diag 
-                exp.namelist = namelist 
-                exp.clear_rundir()
-
-                rotation_period = ((9.*3600.)+55.*60 + 30.)
-                omega = 2.*np.pi/ rotation_period
-                radius = 69911e3
-                grav = 24.79
-                number_ld_in_radius_units = ld_value
-
-                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
-
-                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
-                equilibrium_depth = equilibrium_geopotential/grav
-
-                exp.update_namelist({
-                    'shallow_dynamics_nml':{
-                        'h_0': equilibrium_geopotential,
-                        'u_deep_mag'   : u_deep_mag_val,
-                        'n_merid_deep_flow': u_deep_merid,                    
-                    },
-                    'shallow_physics_nml': {
-                        'h_0': equilibrium_geopotential, 
-                        'therm_damp_time' : rotation_period * damping_time, #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
-                    },
-                    'constants_nml': {
-                        'omega': omega,
-                        'radius': radius,
-                    },
-                    'stirring_nml': {
-                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
-                        'amplitude':3.e-13*forcing_amplitude,
-                        'n_total_forcing_max': 170,
-                        'n_total_forcing_min': 164,
-
-                    },
-
-                })
-
-                exp.run(1, use_restart=False, num_cores=NCORES, multi_node=True)
-                for i in range(721,841):
-                    exp.run(i, num_cores=NCORES, multi_node=True)
diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/part_2/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/part_2/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
deleted file mode 100644
index 2c6a8f028..000000000
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/high_res/smaller_forcing/tuned_galperin_forcing/part_2/giant_planet_shallow_water_deep_velocity_test_mk1_high_res.py
+++ /dev/null
@@ -1,175 +0,0 @@
-import os
-
-import numpy as np
-
-from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
-
-import pdb
-
-NCORES = 32
-base_dir = os.path.dirname(os.path.realpath(__file__))
-# a CodeBase can be a directory on the computer,
-# useful for iterative development
-cb = ShallowCodeBase.from_directory(GFDL_BASE)
-
-# or it can point to a specific git repo and commit id.
-# This method should ensure future, independent, reproducibility of results.
-# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
-
-# compilation depends on computer specific settings.  The $GFDL_ENV
-# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
-# is used to load the correct compilers.  The env file is always loaded from
-# $GFDL_BASE and not the checked out git repo.
-
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
-# create an Experiment object to handle the configuration of model parameters
-# and output diagnostics
-
-#Tell model how to write diagnostics
-diag = DiagTable()
-diag.add_file('atmos_monthly', 30, 'days', time_units='days')
-# diag.add_file('atmos_daily', 1, 'days', time_units='days')
-
-#Tell model which diagnostics to write
-diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'div', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv_corrected', time_avg=True)
-diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
-diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
-diag.add_field('stirring_mod', 'stirring', time_avg=True)
-# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
-diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h_sqd_mean', time_avg=True)
-
-diag.add_field('shallow_diagnostics', 'e_kin_density', time_avg=True)
-diag.add_field('shallow_diagnostics', 'eq_geopot', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_kin_real_units', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_pot_real_units', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_tot_real_units', time_avg=True)
-diag.add_field('shallow_diagnostics', 'u_rms', time_avg=True)
-
-#Empty the run directory ready to run
-
-#Define values for the 'core' namelist
-namelist = Namelist({
-    'main_nml':{
-     'days'   : 30,
-     'hours'  : 0,
-     'minutes': 0,
-     'seconds': 0,
-     'dt_atmos': 600,
-     'calendar': 'no_calendar',
-    },
-
- 'atmosphere_nml':{
-   'print_interval': 86400,
-    },
-
-'fms_io_nml':{
-   'threading_write' :'single',
-   'fileset_write': 'single'
-    },
-
- 'fms_nml':{
-   'print_memory_usage':False,
-   'domains_stack_size': 200000,
-    },
-
- 'shallow_dynamics_nml':{
-   'num_lon'             : 1024,
-   'num_lat'             : 512,
-   'num_fourier'         : 341,
-   'num_spherical'       : 342,
-   'fourier_inc'         : 1,
-   'damping_option'      : 'resolution_dependent',
-   'damping_order'       : 4,
-   'damping_coeff'       : 1.e-04,
-   'h_0'                 : 3.e04,
-   'grid_tracer'         : False,
-   'spec_tracer'         : False,
-   'robert_coeff'        : 0.04,
-   'robert_coeff_tracer' : 0.04,
-    },
-
- 'shallow_physics_nml':{
-   'fric_damp_time'  :  0.0,
-   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
-   'h_amp'           :  0.,
-   'h_itcz'          :  0.,
-   },
-
- 'stirring_nml': {
-   'B':0.0,
-   'do_localize': False,
-   },
-
-})
-
-#Lets do a run!
-if __name__=="__main__":
-
-    for forcing_amplitude in [ 10.]:
-
-        for damping_time in [ 10000., 1000., 100000.]:
-            u_deep_mag_val = 50.
-
-            if u_deep_mag_val!=0.:
-                u_deep_merid_arr = [27]
-            else:
-                u_deep_merid_arr = [3]
-
-            for u_deep_merid in u_deep_merid_arr:
-
-                ld_value = 0.025
-                exp = Experiment('high_res_small_forcing_giant_planet_fixed_deep_ics_forced_'+str(damping_time)+'_rad_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid))+'_strong_forcing_'+str(forcing_amplitude), codebase=cb)
-
-                exp.diag_table = diag 
-                exp.namelist = namelist 
-                exp.clear_rundir()
-
-                rotation_period = ((9.*3600.)+55.*60 + 30.)
-                omega = 2.*np.pi/ rotation_period
-                radius = 69911e3
-                grav = 24.79
-                number_ld_in_radius_units = ld_value
-
-                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
-
-                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
-                equilibrium_depth = equilibrium_geopotential/grav
-
-                exp.update_namelist({
-                    'shallow_dynamics_nml':{
-                        'h_0': equilibrium_geopotential,
-                        'u_deep_mag'   : u_deep_mag_val,
-                        'n_merid_deep_flow': u_deep_merid,                    
-                    },
-                    'shallow_physics_nml': {
-                        'h_0': equilibrium_geopotential, 
-                        'therm_damp_time' : rotation_period * damping_time, #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
-                    },
-                    'constants_nml': {
-                        'omega': omega,
-                        'radius': radius,
-                    },
-                    'stirring_nml': {
-                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
-                        'amplitude':3.e-13*forcing_amplitude,
-                        'n_total_forcing_max': 170,
-                        'n_total_forcing_min': 164,
-
-                    },
-
-                })
-
-                exp.run(1, use_restart=False, num_cores=NCORES, multi_node=True)
-                for i in range(2,721):
-                    exp.run(i, num_cores=NCORES, multi_node=True)
diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk1.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk1.py
deleted file mode 100644
index 0d5ce04b4..000000000
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk1.py
+++ /dev/null
@@ -1,167 +0,0 @@
-import os
-
-import numpy as np
-
-from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
-
-import pdb
-
-NCORES = 16
-base_dir = os.path.dirname(os.path.realpath(__file__))
-# a CodeBase can be a directory on the computer,
-# useful for iterative development
-cb = ShallowCodeBase.from_directory(GFDL_BASE)
-
-# or it can point to a specific git repo and commit id.
-# This method should ensure future, independent, reproducibility of results.
-# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
-
-# compilation depends on computer specific settings.  The $GFDL_ENV
-# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
-# is used to load the correct compilers.  The env file is always loaded from
-# $GFDL_BASE and not the checked out git repo.
-
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
-# create an Experiment object to handle the configuration of model parameters
-# and output diagnostics
-
-#Tell model how to write diagnostics
-diag = DiagTable()
-diag.add_file('atmos_monthly', 30, 'days', time_units='days')
-# diag.add_file('atmos_daily', 1, 'days', time_units='days')
-
-#Tell model which diagnostics to write
-diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'div', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
-diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
-diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
-diag.add_field('stirring_mod', 'stirring', time_avg=True)
-# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
-diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
-
-
-#Empty the run directory ready to run
-
-#Define values for the 'core' namelist
-namelist = Namelist({
-    'main_nml':{
-     'days'   : 30,
-     'hours'  : 0,
-     'minutes': 0,
-     'seconds': 0,
-     'dt_atmos': 1200,
-     'calendar': 'no_calendar',
-    },
-
- 'atmosphere_nml':{
-   'print_interval': 86400,
-    },
-
-'fms_io_nml':{
-   'threading_write' :'single',
-   'fileset_write': 'single'
-    },
-
- 'fms_nml':{
-   'print_memory_usage':False,
-   'domains_stack_size': 200000,
-    },
-
- 'shallow_dynamics_nml':{
-   'num_lon'             : 512,
-   'num_lat'             : 256,
-   'num_fourier'         : 170,
-   'num_spherical'       : 171,
-   'fourier_inc'         : 1,
-   'damping_option'      : 'resolution_dependent',
-   'damping_order'       : 4,
-   'damping_coeff'       : 1.e-04,
-   'h_0'                 : 3.e04,
-   'grid_tracer'         : False,
-   'spec_tracer'         : False,
-   'robert_coeff'        : 0.04,
-   'robert_coeff_tracer' : 0.04,
-    },
-
- 'shallow_physics_nml':{
-   'fric_damp_time'  :  0.0,
-   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
-   'h_amp'           :  0.,
-   'h_itcz'          :  0.,
-   },
-
- 'stirring_nml': {
-   'B':0.0,
-   'do_localize': False,
-   },
-
-})
-
-#Lets do a run!
-if __name__=="__main__":
-
-    for ld_value in [10.0]:
-        for u_deep_mag_val in [50.,]:
-        #for u_deep_mag_val in [-50.]:
-
-            if u_deep_mag_val!=0.:
-                u_deep_merid_arr = [3,]
-            else:
-                u_deep_merid_arr = [3]
-
-            #u_deep_merid_arr = [3]
-
-            for u_deep_merid in u_deep_merid_arr:
-
-                exp = Experiment('giant_planet_shallow_water_deep_velocity_test_mk2_no_forcing_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid)), codebase=cb)
-
-                exp.diag_table = diag 
-                exp.namelist = namelist 
-                exp.clear_rundir()
-
-                rotation_period = ((9.*3600.)+55.*60 + 30.)
-                omega = 2.*np.pi/ rotation_period
-                radius = 69911e3
-                grav = 24.79
-                number_ld_in_radius_units = ld_value
-
-                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
-
-                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
-                equilibrium_depth = equilibrium_geopotential/grav
-
-                exp.update_namelist({
-                    'shallow_dynamics_nml':{
-                        'h_0': equilibrium_geopotential,
-                        'u_deep_mag'   : u_deep_mag_val,
-                        'n_merid_deep_flow': u_deep_merid,                    
-                    },
-                    'shallow_physics_nml': {
-                        'h_0': equilibrium_geopotential, 
-                        'therm_damp_time' : rotation_period * 100., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
-                    },
-                    'constants_nml': {
-                        'omega': omega,
-                        'radius': radius,
-                    },
-                    'stirring_nml': {
-                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
-                        'amplitude':0.,
-                        'n_total_forcing_max': 85,
-                        'n_total_forcing_min': 79,
-
-                    },
-
-                })
-
-                exp.run(1, use_restart=False, num_cores=NCORES)
-                for i in range(2,2101):
-                    exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk2.py b/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk2.py
deleted file mode 100644
index 711b2c34b..000000000
--- a/exp/shallow_water_giant_planet/first_param_sweep_deep_velocities/no_forcing_giant_planet_shallow_water_deep_velocity_test_mk2.py
+++ /dev/null
@@ -1,170 +0,0 @@
-import os
-
-import numpy as np
-
-from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
-
-import pdb
-
-NCORES = 16
-base_dir = os.path.dirname(os.path.realpath(__file__))
-# a CodeBase can be a directory on the computer,
-# useful for iterative development
-cb = ShallowCodeBase.from_directory(GFDL_BASE)
-
-# or it can point to a specific git repo and commit id.
-# This method should ensure future, independent, reproducibility of results.
-# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
-
-# compilation depends on computer specific settings.  The $GFDL_ENV
-# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
-# is used to load the correct compilers.  The env file is always loaded from
-# $GFDL_BASE and not the checked out git repo.
-
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
-# create an Experiment object to handle the configuration of model parameters
-# and output diagnostics
-
-#Tell model how to write diagnostics
-diag = DiagTable()
-diag.add_file('atmos_monthly', 30, 'days', time_units='days')
-# diag.add_file('atmos_daily', 1, 'days', time_units='days')
-# diag.add_file('atmos_timestep', 1200, 'seconds', time_units='days')
-
-
-#Tell model which diagnostics to write
-diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'div', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
-diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
-diag.add_field('shallow_diagnostics', 'deep_geopot', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
-diag.add_field('stirring_mod', 'stirring', time_avg=True)
-# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
-diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
-diag.add_field('shallow_diagnostics', 'e_kin', time_avg=True)
-
-
-
-#Empty the run directory ready to run
-
-#Define values for the 'core' namelist
-namelist = Namelist({
-    'main_nml':{
-     'days'   : 30,
-     'hours'  : 0,
-     'minutes': 0,
-     'seconds': 0,
-     'dt_atmos': 1200,
-     'calendar': 'no_calendar',
-    },
-
- 'atmosphere_nml':{
-   'print_interval': 86400,
-    },
-
-'fms_io_nml':{
-   'threading_write' :'single',
-   'fileset_write': 'single'
-    },
-
- 'fms_nml':{
-   'print_memory_usage':False,
-   'domains_stack_size': 200000,
-    },
-
- 'shallow_dynamics_nml':{
-   'num_lon'             : 512,
-   'num_lat'             : 256,
-   'num_fourier'         : 170,
-   'num_spherical'       : 171,
-   'fourier_inc'         : 1,
-   'damping_option'      : 'resolution_dependent',
-   'damping_order'       : 4,
-   'damping_coeff'       : 1.e-04,
-   'h_0'                 : 3.e04,
-   'grid_tracer'         : False,
-   'spec_tracer'         : False,
-   'robert_coeff'        : 0.04,
-   'robert_coeff_tracer' : 0.04,
-    },
-
- 'shallow_physics_nml':{
-   'fric_damp_time'  :  0.0,
-   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
-   'h_amp'           :  0.,
-   'h_itcz'          :  0.,
-   },
-
- 'stirring_nml': {
-   'B':0.0,
-   'do_localize': False,
-   },
-
-})
-
-#Lets do a run!
-if __name__=="__main__":
-
-    for ld_value in [0.1, 10.0]:
-        # for u_deep_mag_val in [50., 0., 25.]:
-        for u_deep_mag_val in [50., 0.]:
-
-            # if u_deep_mag_val!=0.:
-            #     u_deep_merid_arr = [3, 11, 19, 26]
-            # else:
-            #     u_deep_merid_arr = [3]
-
-            u_deep_merid_arr = [3]
-
-            for u_deep_merid in u_deep_merid_arr:
-
-                exp = Experiment('giant_planet_shallow_water_deep_velocity_test_mk8_no_forcing_no_damping_ld_'+str(ld_value)+'_udeep_mag_'+str(u_deep_mag_val)+'_u_deep_merid_'+str(int(u_deep_merid)), codebase=cb)
-
-                exp.diag_table = diag 
-                exp.namelist = namelist 
-                exp.clear_rundir()
-
-                rotation_period = ((9.*3600.)+55.*60 + 30.)
-                omega = 2.*np.pi/ rotation_period
-                radius = 69911e3
-                grav = 24.79
-                number_ld_in_radius_units = ld_value
-
-                # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
-
-                equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
-                equilibrium_depth = equilibrium_geopotential/grav
-
-                exp.update_namelist({
-                    'shallow_dynamics_nml':{
-                        'h_0': equilibrium_geopotential,
-                        'u_deep_mag'   : u_deep_mag_val,
-                        'n_merid_deep_flow': u_deep_merid,                    
-                    },
-                    'shallow_physics_nml': {
-                        'h_0': equilibrium_geopotential, 
-                        'therm_damp_time' : 0.
-                    },
-                    'constants_nml': {
-                        'omega': omega,
-                        'radius': radius,
-                    },
-                    'stirring_nml': {
-                        'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
-                        'amplitude':0.,
-                        'n_total_forcing_max': 85,
-                        'n_total_forcing_min': 79,
-
-                    },
-
-                })
-
-                exp.run(1, use_restart=False, num_cores=NCORES)
-                for i in range(2,121):
-                    exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py b/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py
deleted file mode 100644
index 14c4b323c..000000000
--- a/exp/shallow_water_giant_planet/giant_planet_shallow_water_small_scale_stirring_test.py
+++ /dev/null
@@ -1,151 +0,0 @@
-import os
-
-import numpy as np
-
-from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
-
-import pdb
-
-NCORES = 16
-base_dir = os.path.dirname(os.path.realpath(__file__))
-# a CodeBase can be a directory on the computer,
-# useful for iterative development
-cb = ShallowCodeBase.from_directory(GFDL_BASE)
-
-# or it can point to a specific git repo and commit id.
-# This method should ensure future, independent, reproducibility of results.
-# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
-
-# compilation depends on computer specific settings.  The $GFDL_ENV
-# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
-# is used to load the correct compilers.  The env file is always loaded from
-# $GFDL_BASE and not the checked out git repo.
-
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
-# create an Experiment object to handle the configuration of model parameters
-# and output diagnostics
-
-#Tell model how to write diagnostics
-diag = DiagTable()
-diag.add_file('atmos_monthly', 30, 'days', time_units='days')
-diag.add_file('atmos_daily', 1, 'days', time_units='days')
-
-#Tell model which diagnostics to write
-diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'div', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
-diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
-diag.add_field('stirring_mod', 'stirring', time_avg=True)
-# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
-diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
-
-
-#Empty the run directory ready to run
-
-#Define values for the 'core' namelist
-namelist = Namelist({
-    'main_nml':{
-     'days'   : 30,
-     'hours'  : 0,
-     'minutes': 0,
-     'seconds': 0,
-     'dt_atmos': 1200,
-     'calendar': 'no_calendar',
-    },
-
- 'atmosphere_nml':{
-   'print_interval': 86400,
-    },
-
-'fms_io_nml':{
-   'threading_write' :'single',
-   'fileset_write': 'single'
-    },
-
- 'fms_nml':{
-   'print_memory_usage':False,
-   'domains_stack_size': 200000,
-    },
-
- 'shallow_dynamics_nml':{
-   'num_lon'             : 512,
-   'num_lat'             : 256,
-   'num_fourier'         : 170,
-   'num_spherical'       : 171,
-   'fourier_inc'         : 1,
-   'damping_option'      : 'resolution_dependent',
-   'damping_order'       : 4,
-   'damping_coeff'       : 1.e-04,
-   'h_0'                 : 3.e04,
-   'grid_tracer'         : False,
-   'spec_tracer'         : False,
-   'robert_coeff'        : 0.04,
-   'robert_coeff_tracer' : 0.04,
-    },
-
- 'shallow_physics_nml':{
-   'fric_damp_time'  :  0.0,
-   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
-   'h_amp'           :  0.,
-   'h_itcz'          :  0.,
-   },
-
- 'stirring_nml': {
-   'B':0.0,
-   'do_localize': False,
-   },
-
-})
-
-#Lets do a run!
-if __name__=="__main__":
-
-    for number_ld_in_radius_units in [0.1]:
-
-        exp = Experiment('giant_shallow_stirring_test_experiment_uniform_smaller_120_scale_stirring_mk3_longer_damping_ld_'+str(number_ld_in_radius_units), codebase=cb)
-
-        exp.diag_table = diag 
-        exp.namelist = namelist 
-        exp.clear_rundir()
-
-        rotation_period = ((9.*3600.)+55.*60 + 30.)
-        omega = 2.*np.pi/ rotation_period
-        radius = 69911e3
-        grav = 24.79
-
-        # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
-
-        equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
-        equilibrium_depth = equilibrium_geopotential/grav
-
-        exp.update_namelist({
-            'shallow_dynamics_nml':{
-                'h_0': equilibrium_geopotential
-            },
-            'shallow_physics_nml': {
-                'h_0': equilibrium_geopotential, 
-                'therm_damp_time' : rotation_period * 10000., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
-            },
-            'constants_nml': {
-                'omega': omega,
-                'radius': radius,
-            },
-            'stirring_nml': {
-                'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
-                'amplitude':3.e-13,
-                'n_total_forcing_max': 125,
-                'n_total_forcing_min': 119,
-
-            },
-
-        })
-
-        exp.run(1, use_restart=False, num_cores=NCORES)
-        for i in range(2,121):
-            exp.run(i, num_cores=NCORES)
diff --git a/exp/shallow_water_giant_planet/giant_planet_shallow_water_stirring_test.py b/exp/shallow_water_giant_planet/giant_planet_shallow_water_stirring_test.py
deleted file mode 100644
index fa19bc3c5..000000000
--- a/exp/shallow_water_giant_planet/giant_planet_shallow_water_stirring_test.py
+++ /dev/null
@@ -1,148 +0,0 @@
-import os
-
-import numpy as np
-
-from isca import ShallowCodeBase, DiagTable, Experiment, Namelist, GFDL_BASE
-
-import pdb
-
-NCORES = 8
-base_dir = os.path.dirname(os.path.realpath(__file__))
-# a CodeBase can be a directory on the computer,
-# useful for iterative development
-cb = ShallowCodeBase.from_directory(GFDL_BASE)
-
-# or it can point to a specific git repo and commit id.
-# This method should ensure future, independent, reproducibility of results.
-# cb = DryCodeBase.from_repo(repo='https://github.com/isca/isca', commit='isca1.1')
-
-# compilation depends on computer specific settings.  The $GFDL_ENV
-# environment variable is used to determine which `$GFDL_BASE/src/extra/env` file
-# is used to load the correct compilers.  The env file is always loaded from
-# $GFDL_BASE and not the checked out git repo.
-
-cb.compile()  # compile the source code to working directory $GFDL_WORK/codebase
-
-# create an Experiment object to handle the configuration of model parameters
-# and output diagnostics
-
-#Tell model how to write diagnostics
-diag = DiagTable()
-diag.add_file('atmos_monthly', 30, 'days', time_units='days')
-diag.add_file('atmos_daily', 1, 'days', time_units='days')
-
-#Tell model which diagnostics to write
-diag.add_field('shallow_diagnostics', 'ucomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vcomp', time_avg=True)
-diag.add_field('shallow_diagnostics', 'vor', time_avg=True)
-diag.add_field('shallow_diagnostics', 'div', time_avg=True)
-diag.add_field('shallow_diagnostics', 'h', time_avg=True)
-diag.add_field('shallow_diagnostics', 'pv', time_avg=True)
-diag.add_field('shallow_diagnostics', 'stream', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'trs', time_avg=True)
-# diag.add_field('shallow_diagnostics', 'tr', time_avg=True)
-diag.add_field('stirring_mod', 'stirring', time_avg=True)
-# diag.add_field('stirring_mod', 'stirring_amp', time_avg=True)
-diag.add_field('stirring_mod', 'stirring_sqr', time_avg=True)
-
-
-#Empty the run directory ready to run
-
-#Define values for the 'core' namelist
-namelist = Namelist({
-    'main_nml':{
-     'days'   : 30,
-     'hours'  : 0,
-     'minutes': 0,
-     'seconds': 0,
-     'dt_atmos': 1200,
-     'calendar': 'no_calendar',
-    },
-
- 'atmosphere_nml':{
-   'print_interval': 86400,
-    },
-
-'fms_io_nml':{
-   'threading_write' :'single',
-   'fileset_write': 'single'
-    },
-
- 'fms_nml':{
-   'print_memory_usage':False,
-   'domains_stack_size': 200000,
-    },
-
- 'shallow_dynamics_nml':{
-   'num_lon'             : 512,
-   'num_lat'             : 256,
-   'num_fourier'         : 170,
-   'num_spherical'       : 171,
-   'fourier_inc'         : 1,
-   'damping_option'      : 'resolution_dependent',
-   'damping_order'       : 4,
-   'damping_coeff'       : 1.e-04,
-   'h_0'                 : 3.e04,
-   'grid_tracer'         : False,
-   'spec_tracer'         : False,
-   'robert_coeff'        : 0.04,
-   'robert_coeff_tracer' : 0.04,
-    },
-
- 'shallow_physics_nml':{
-   'fric_damp_time'  :  0.0,
-   'h_0'             :  3.e04, #Scott and Polvani begin with L_D_polar = 10 radii in size, i.e. depth of 9,910 metres.
-   'h_amp'           :  0.,
-   'h_itcz'          :  0.,
-   },
-
- 'stirring_nml': {
-   'B':0.0,
-   'do_localize': False,
-   },
-
-})
-
-#Lets do a run!
-if __name__=="__main__":
-
-    for number_ld_in_radius_units in [10.]:
-
-        exp = Experiment('giant_shallow_stirring_test_experiment_uniform_stirring_mk3', codebase=cb)
-
-        exp.diag_table = diag 
-        exp.namelist = namelist 
-        exp.clear_rundir()
-
-        rotation_period = ((9.*3600.)+55.*60 + 30.)
-        omega = 2.*np.pi/ rotation_period
-        radius = 69911e3
-        grav = 24.79
-
-        # Model uses geopotential as its height co-ordinate. So depth is h_0/grav.
-
-        equilibrium_geopotential = (2.*number_ld_in_radius_units*omega*radius)**2.
-        equilibrium_depth = equilibrium_geopotential/grav
-
-        exp.update_namelist({
-            'shallow_dynamics_nml':{
-                'h_0': equilibrium_geopotential
-            },
-            'shallow_physics_nml': {
-                'h_0': equilibrium_geopotential, 
-                'therm_damp_time' : rotation_period * 1., #Thermal damping time in Scott and Polvani is 1 rotation period (v_l = 1)
-            },
-            'constants_nml': {
-                'omega': omega,
-                'radius': radius,
-            },
-            'stirring_nml': {
-                'decay_time':10.*rotation_period, #Scott and Polvani use decorrelation time of 10 planetary rotations - i.e. a long time for Jupiter. 
-                'amplitude':3.e-13,
-            },
-
-        })
-
-        exp.run(1, use_restart=False, num_cores=NCORES)
-        for i in range(2,122):
-            exp.run(i, num_cores=NCORES)