Difference between revisions of "Adding dH/dt module"
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Now we stop adding/editing things for a minute and type '''make''' to rebuild and make sure we haven't broken the code yet. If you get a successful build, then proceed to '''Step 2'''. | Now we stop adding/editing things for a minute and type '''make''' to rebuild and make sure we haven't broken the code yet. If you get a successful build, then proceed to '''Step 2'''. | ||
Revision as of 14:55, 13 August 2009
Contents |
Overview
This page contains step-by-step instructions for adding a new module to Glimmer-CISM. In this case, the module is a first-order, upwinding advection scheme for mass transport (dH/dt) using velocities calculated from a higher-order dynamics model. The procedure, however, is generic and could apply to adding almost any module. The goal here is not to get lost in the details of the upwinding scheme (we'll provide the code for that later) but rather to understand the steps for adding a module in an incremental, structured way that allows you to track small errors and fix them at each step.
- To go directly to some exercises using the higher-order dynamics and the evolution scheme, go to Ice Sheet Evolution Experiments.
- For mathematical background on upwinded transport, consult the Solving the equation for thickness evolution pages.
Step 0
We first need to download the code, configure it, and check that we can get a successful initial build (presumably we've done that already if you've been able to do the higher-order test suite exercises). If not, then type the following from within the highest level directory containing the source code:
./bootstrap ./configure --with-netcdf=/path/to_netcdf !!! Note: specify your own path to netCDF libs here !!! make
Step 1
In step 1, we will create a module containing "empty" subroutines and add this module to the build.
Create a module fo_upwind_advect.F90 that contains the necessary subroutines. For now, these will just be "stubs", which we will fill in later.
module fo_upwind_advect ! subroutines for mass advection scheme based on 1st order upwinding contains !---------------------------------------------------------------------- subroutine fo_upwind_advect_init( ) ! initialization for 1st-order upwinding mass advection end subroutine fo_upwind_advect_init !---------------------------------------------------------------------- subroutine fo_upwind_advect_final( ) ! finalization for 1st-order upwinding mass advection end subroutine fo_upwind_advect_final !---------------------------------------------------------------------- subroutine fo_upwind_advect_driver( ) ! driver for 1st-order upwind mass advection end subroutine fo_upwind_advect_driver !---------------------------------------------------------------------- subroutine fo_upwind_advect_main( ) ! 1st-order upwinding mass advection end subroutine fo_upwind_advect_main !---------------------------------------------------------------------- end module fo_upwind_advect
Add this new module to the build by editing Makefile.am in src/fortran/ ...
libglide_a_SOURCES = glide.F90 glide_setup.F90 glide_types.F90 glide_temp.F90 \ glide_bwater.F90 glide_deriv.F90 xls.F90 ice3d_lib.F90 \ glide_velo_higher.F90 glide_thck.F90 glide_velo.F90 \ glide_mask.F90 glide_stop.F90 glide_io.F90 \ glide_nc_custom.F90 isostasy.F90 isostasy_el.F90\ isostasy_setup.F90 isostasy_types.F90 glide_lithot.F90\ glide_lithot3d.F90 glide_lithot1d.F90 glide_profile.F90\ glide_diagnostics.F90 glissade.F90 glissade_remap.F90\ glissade_velo.F90 glissade_constants.F90 glide_vertint.F90\ glide_thckmask.F90 glide_nonlin.F90 glide_grids.F90\ glam.F90 glam_strs2.F90 glam_thck_ppm.F90\ remap_advection.F90 remap_glamutils.F90 glide_ground.F90
becomes ...
libglide_a_SOURCES = glide.F90 glide_setup.F90 glide_types.F90 glide_temp.F90 \ glide_bwater.F90 glide_deriv.F90 xls.F90 ice3d_lib.F90 \ glide_velo_higher.F90 glide_thck.F90 glide_velo.F90 \ glide_mask.F90 glide_stop.F90 glide_io.F90 \ glide_nc_custom.F90 isostasy.F90 isostasy_el.F90\ isostasy_setup.F90 isostasy_types.F90 glide_lithot.F90\ glide_lithot3d.F90 glide_lithot1d.F90 glide_profile.F90\ glide_diagnostics.F90 glissade.F90 glissade_remap.F90\ glissade_velo.F90 glissade_constants.F90 glide_vertint.F90\ glide_thckmask.F90 glide_nonlin.F90 glide_grids.F90\ glam.F90 glam_strs2.F90 glam_thck_ppm.F90\ remap_advection.F90 remap_glamutils.F90 glide_ground.F90 \ ! CHANGED LAST TWO LINES fo_upwind_advect.F90
[Note: the comment in the 2nd to last line may cause a problem for make.] Now we stop adding/editing things for a minute and type make to rebuild and make sure we haven't broken the code yet. If you get a successful build, then proceed to Step 2.
Step 2
In step 2, we will do some minor updates to other parts of the code so that there is an option to call our 1st order upwinding scheme when we want to evolve the ice thickness (that is, rather than using some other scheme).
In glide_types.F90, add the following to the transport scheme options around line 100 ...
integer, parameter :: EVOL_PSEUDO_DIFF = 0 integer, parameter :: EVOL_ADI = 1 integer, parameter :: EVOL_DIFFUSION = 2 integer, parameter :: EVOL_INC_REMAP = 3 integer, parameter :: EVOL_FO_UPWIND = 4 ! ADDED THIS LINE
... similarly, update some lines around 207 for documentation ...
!*FD Thickness evolution method: !*FD \begin{description} !*FD \item[0] Pseudo-diffusion approach !*FD \item[2] Diffusion approach (also calculates velocities) !*FD \item[3] Incremental remapping !*FD \item[4] 1st-order upwinding scheme ! ADDED THIS LINE !*FD \end{description}
In glide_setup.F90, around line 475, change ...
character(len=*), dimension(0:4), parameter :: evolution = (/ & ! CHANGED 0:3 TO 0:4 'pseudo-diffusion ', & 'ADI scheme ', & 'iterated diffusion ', & 'remap thickness ', & '1st order upwind ' /) ! ADDED THIS LINE
Time to type make again and check for a successful build. If so, proceed to Step 3.
Step 3
Now we will add use statements, if constructs, and dummy calls to the advection subroutines from the appropriate places in the code. Hence, we are setting up all the necessary structure to call the subroutines but are not passing any arguments to them yet (nor are they actually doing anything yet).
In glide.F90, add the following use statement to subroutine glide_initialise ...
use glam_strs2, only : glam_velo_fordsiapstr_init use remap_glamutils, only : horizontal_remap_init use fo_upwind_advect, only : fo_upwind_advect_init ! ADDED
Now add if construct and call to the initialization stub in fo_upwind_advect_mod.F90, around line 190 of glide.F90, just after the if construct for EVOL_INC_REMAP ...
if (model%options%whichevol== EVOL_FO_UPWIND ) then call fo_upwind_advect_init( ) end if
In glide_stop.F90, add the following to the use statements ...
module glide_stop use glide_types use glimmer_log use remap_glamutils use fo_upwind_advect, only : fo_upwind_advect_final ! ADDED
Add the necessary if construct to glide_stop.F90 around line 150, as we did with the initialization routine ...
if (model%options%whichevol== EVOL_FO_UPWIND ) then call fo_upwind_advect_final( ) endif
Finally, update the use statements in glide.F90 around line 340, and the case construct for ice sheet evolution, around line 380, so that the 1st order upwinding subroutines can be called ...
use glide_thck use glide_velo use glide_ground use glide_setup use glide_temp use glide_mask use isostasy use glam, only: inc_remap_driver use fo_upwind_advect, only: fo_upwind_advect_driver ! ADDED
... and add a call to the driver routine to the case construct (passing no args yet) ...
case(EVOL_FO_UPWIND) ! Use first order upwind scheme for mass transport call fo_upwind_advect_driver( )
Make sure to place it BEFORE the existing "end select" statement!
Type make again and check for a successful build. If so, proceed to Step 4.
Step 4
At this point we've done nothing but build the necessary structures in the code. Now we will start filling in the subroutines with the necessary variable definitions. We'll follow this by passing arguments and, if everything still works, we can actually start to do something w/ those arguments within the subroutines themselves.
Note that, in practice, one doesn't always know ahead of time exactly what variables are needed within a particular subroutine, and there is some trial and error while figuring it out. Here, we'll assume we've thought this out really well ahead of time and we know exactly what we need to do before we ever started writing the code (like punch-card programmers of old), in which case we know exactly which arguments are needed when we start.
First, we'll fill out the rest of the "driver" subroutine, which has two parts, (1) calling the higher-order dynamics subroutines run_ho_diagnostic to get the appropriate velocity fields and, (2) calling fo_upwind_advect_main, which uses those velocity fields, the thickness field, and then moves mass around to calculate a new thickness field. In subroutine fo_upwind_advect_driver we add the following ...
subroutine fo_upwind_advect_driver( model ) ! ADDED ARG ! driver routine for the 1st order, upwind mass transport scheme type(glide_global_type), intent(inout) :: model ! ADDED call run_ho_diagnostic(model) ! ADDED CALL AND ARG call fo_upwind_advect_main( ) ...
Note that we also passed the model in to the driver and gave "model" a type definition. We also need to add the appropriate use statements for "model" and to access the higher-order dynamics routines, which we'll do below.
Next, add argument definitions to the main subroutine in fo_upwind_advect.F90 ...
subroutine fo_upwind_advect_main( thck, stagthck, acab, dt, uflx, vflx, ewn, nsn, dew, dns ) ! CHANGED ! 1st-order upwinding mass advection implicit none ! ADDED real (kind = dp), intent(in) :: dt ! time step (sec) real (kind = dp), dimension(:,:), intent(inout) :: thck ! thickness on normal grid (m) real (kind = dp), dimension(:,:), intent(in) :: stagthck ! thickness on staggered grid (m) real (kind = sp), dimension(:,:), intent(in) :: acab ! surf mass balance (accum/ablation) (m/sec) real (kind = dp), dimension(:,:), intent(in) :: uflx, vflx ! flux in x,y directions (m^2/sec) real (kind = dp), intent(in) :: dew, dns ! grid spacing in x,y directions (m) integer, intent(in) :: ewn, nsn ! no. of grid points in x,y directions real (kind = dp) :: He, Hw, Hn, Hs, ue, uw, vn, vs ! ADDED integer :: ew, ns end subroutine fo_upwind_advect_main
Because these definitions require kind "dp", we need to add a use statment at the start of the module. We've also added the necessary use statement for accessing "model" and the higher-order dynamics subroutines (from above) and a few more we'll use later on ...
module fo_upwind_advect ! subroutines for mass advection scheme based on 1st order upwinding ! ADDED use glimmer_paramets, only: sp, dp, len0, thk0, tim0, vel0, tim0, acc0, scyr ! scales for swapping between dim and non-dim vars use glide_types use glide_velo_higher private public :: fo_upwind_advect_init, fo_upwind_advect_driver, fo_upwind_advect_final ... etc ...
To avoid someone mucking around with variables in the module that we don't want them to touch, we've also added the "private" and "public" statements; the only parts of the module that can be accessed from outside are through calls to the three "public" subroutines.
The arguments that we defined above in fo_upwind_advect_main need to be passed in from the driver routine fo_upwind_advect_driver to the subroutine that does all of the work, fo_upwind_advect_main. To do this, we must access them from the derived type "model". The entire driver subroutine then becomes ...
subroutine fo_upwind_advect_driver( model ) ! driver routine for the 1st order, upwind mass transport scheme type(glide_global_type), intent(inout) :: model call run_ho_diagnostic(model) ! get velocities and fluxes from HO dynamic subroutines call fo_upwind_advect_main( model%geometry%thck, model%geomderv%stagthck, & model%climate%acab, model%numerics%dt, & model%velocity_hom%uflx,model%velocity_hom%vflx, & model%general%ewn, model%general%nsn, & model%numerics%dew, model%numerics%dns ) end subroutine fo_upwind_advect_driver
Finally, we pass the derived type "model" during the call to the driver subroutine in glide.F90 ...
case(EVOL_FO_UPWIND) ! Use first order upwind scheme for mass transport call fo_upwind_advect_driver( model ) ! ADDED ARGUMENT end select
Type make again and check for a successful build. If so, proceed to Step 5.
Step 5
Now let's fill in the init and finalization subroutines in fo_upwind_advect.F90. This takes some thought ahead of time and might require a bit of trial and error. Again, for now we'll assume that we've thought this out really well ahead of time and we know exactly what we need.
First, declare any other necessary variables at the start of the module fo_upwind_advection.F90. Here, these are the allocatable work arrays that we'll use in fo_upwind_advect_main. The beginning of the module becomes ...
module fo_upwind_advect !---------------------------------------------------------------------- ! init, finalize, and driver subroutines for mass advection based on 1st order upwinding use glimmer_paramets, only: sp, dp, len0, thk0, tim0, vel0, tim0, acc0, scyr use glide_types use glide_velo_higher private public :: fo_upwind_advect_init, fo_upwind_advect_driver, fo_upwind_advect_final ! allocatable work arrays ! ADDED real (kind = dp), allocatable, dimension(:,:) :: & ubar, vbar, & ubar_grid, vbar_grid, & flux_net, thck_grid, & mask, thck_old contains ... etc ...
Now change the initialization and finalization subroutines ...
subroutine fo_upwind_advect_init( ewn, nsn ) ! ADDED ARGS HERE ! initialization for 1st-order upwinding mass advection implicit none ! ADDED integer, intent(in) :: ewn, nsn ! horizontal grid dimensions ! ADDED TYPE DEF integer :: errstat ! ADDED FOR ERROR HANDLING ! allocate work arrays ! ADDED THESE allocate( ubar(ewn-1,nsn-1), stat=errstat ); ubar = 0.0_dp allocate( vbar(ewn-1,nsn-1), stat=errstat ); vbar = 0.0_dp allocate( ubar_grid(ewn+1,nsn+1), stat=errstat ); ubar_grid = 0.0_dp allocate( vbar_grid(ewn+1,nsn+1), stat=errstat ); vbar_grid = 0.0_dp allocate( thck_grid(ewn+2,nsn+2), stat=errstat ); thck_grid = 0.0_dp allocate( flux_net(ewn,nsn), stat=errstat ); flux_net = 0.0_dp allocate( mask(ewn,nsn), stat=errstat ); mask = 0.0_dp allocate( thck_old(ewn,nsn), stat=errstat ); thck_old = 0.0_dp if ( errstat /= 0 ) then ! ADDED FOR ERROR HANDLING print *, 'error: allocation in fo_upwind_advect failed!' stop end if end subroutine fo_upwind_advect_init
Note that ewn, nsn are passed in above, so we need to make sure they are passed from the main code where this call sits. In glide.F90 we have ...
call fo_upwind_advect_init( model%general%ewn, model%general%nsn ) ! ADDED ARGS
As with the initialization subroutine, we add deallocation statements for work arrays in the finalization subroutine ...
subroutine fo_upwind_advect_final( ) ! finalization for 1st-order upwinding mass advection implicit none ! ADDED ! deallocate work arrays ! ADDED THESE if( allocated( ubar ) ) deallocate( ubar ) if( allocated( vbar ) ) deallocate( vbar ) if( allocated( ubar_grid ) ) deallocate( ubar_grid ) if( allocated( vbar_grid ) ) deallocate( vbar_grid ) if( allocated( thck_grid ) ) deallocate( thck_grid ) if( allocated( flux_net ) ) deallocate( flux_net ) if( allocated( mask ) ) deallocate( mask ) if( allocated( thck_old ) ) deallocate( thck_old ) end subroutine fo_upwind_advect_final
Type make again and check for a successful build. If so, proceed to Step 6.
Step 6
Now we are actually ready to do something ... that is, fill in the guts of the new subroutine, where the thickness evolution calculation takes place. Rather than have you figure out how to code up the 1st-order upwinding scheme on your own, we'll provide you with the chunk of code to do that (below), noting that the details of the calculation scheme are discussed HERE.
! ---------------------------------- subroutine fo_upwind_advect_main( thck, stagthck, acab, dt, uflx, vflx, ewn, nsn, dew, dns ) ! 1st-order upwinding mass advection that uses a finite-volume like scheme for ! mass conservation. Velocities from the staggered grid (B-grid) are averaged onto the ! faces of the non-staggered grid (i.e. faces of the grid where scalers like thickness live). ! Thus, the averaged velocities exist on a C-grid, allowing mass transport to be treated ! in a finite-volume manner; depth averaged velocities give the fluxes out of each cell ! centered on a thickness point and the thickness advected is chosen according to upwinding. ! ! Note that this works at the calving front because a non-zero staggered thickness there ! defines the velocities there. These velocites can be used to define the velocity at ! the face of the last non-zero thickness cell (on the normal grid) which corresponds to ! the location of the calving front. implicit none real (kind = dp), intent(in) :: dt real (kind = dp), dimension(:,:), intent(inout) :: thck real (kind = dp), dimension(:,:), intent(in) :: stagthck real (kind = sp), dimension(:,:), intent(in) :: acab real (kind = dp), dimension(:,:), intent(in) :: uflx, vflx real (kind = dp), intent(in) :: dew, dns integer, intent(in) :: ewn, nsn real (kind = dp) :: He, Hw, Hn, Hs, ue, uw, vn, vs ! upwinding variables and interface velocities integer :: ew, ns where( stagthck > 0.0_dp ) ! calculate the depth-ave velocities ubar = uflx / stagthck vbar = vflx / stagthck end where where( thck > 0.0_dp ) ! mask for eventually removing flux outside of the original domain mask = 1.0_dp ! (i.e. stuff that moves past the calving front goes away) else where mask = 0.0_dp end where thck_old = thck ! save the old thickness for debugging purposes ! fill in the interior values on the extended velocity grid (extended B-grid) ubar_grid(2:ewn,2:nsn) = ubar vbar_grid(2:ewn,2:nsn) = vbar ! fill in the interior values on the extended thickness grid thck_grid(2:ewn+1,2:nsn+1) = thck(:,:) ! calculate the interface velocities from the extended B-grid, then use upwinding ! criterion to advect thickness in or out of cells (NOTE that parts of this could ! probably be vectorized at some point) do ns = 1, nsn do ew = 1, ewn ! interface depth-ave velocities ue = ( ubar_grid(ew+1,ns+1) + ubar_grid(ew+1,ns) ) / 2.0d0 uw = ( ubar_grid(ew,ns+1) + ubar_grid(ew,ns) ) / 2.0d0 vn = ( vbar_grid(ew,ns+1) + vbar_grid(ew+1,ns+1) ) / 2.0d0 vs = ( vbar_grid(ew,ns) + vbar_grid(ew+1,ns) ) / 2.0d0 ! choose thickness to advect based on upwinding if( ue > 0.0d0 )then He = - thck_grid(ew+1,ns+1) ! negative signs necessary so that flux to the east else ! results in mass loss in this volume (and vice versa) He = - thck_grid(ew+2,ns+1) end if if( uw > 0.0d0 )then Hw = thck_grid(ew,ns+1) else Hw = thck_grid(ew+1,ns+1) end if if( vn > 0.0d0 )then Hn = - thck_grid(ew+1,ns+1) ! negative signs here as above for ue, and He else Hn = - thck_grid(ew+1,ns+2) end if if( vs > 0.0d0 )then Hs = thck_grid(ew+1,ns) else Hs = thck_grid(ew+1,ns+1) end if ! net flux into/out of each cell flux_net(ew,ns) = ( ue*He*dns + uw*Hw*dns + vn*Hn*dew + vs*Hs*dew ) end do end do thck = thck_old + ( 1 / (dns * dew) * flux_net ) * dt + (acab * dt) ! debugging print *, ' ' print *, 'net volume change = ', sum( (thck-thck_old)*mask )*thk0 *dew*dns*len0**2 print *, 'net calving flux = ', sum( thck * (1.0d0-mask) )*thk0*dew*dns*len0**2 print *, '(for the confined shelf experiment, the above two should sum to ~0)' print *, 'mean accum/ablat rate = ', sum( acab * mask ) / sum(mask) / (dt*tim0) * scyr print *, 'mean dH/dt = ', sum( (thck-thck_old)*mask )*thk0 / sum(mask) / (dt*tim0) * scyr print *, 'sum of flux change (should be ~0) = ', sum( flux_net*vel0*thk0*len0 ) print *, ' ' ! pause thck = thck * mask ! remove any mass advected outside of initial domain where( thck < 0.0_dp ) ! gaurd against thickness going negative thck = 0.0_dp end where end subroutine fo_upwind_advect_main ! ----------------------------------
Ice Sheet Evolution
At this point, if you have one final successful build, we should be ready to use the code to actually evolve the ice sheet thickness. To try some simple test cases with the higher-order model and ice sheet evolution using the 1st-order scheme, go here:
