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Cleanup time-managers and move to clocks

Ideal engineering time: 14 days
Estimate of code lines: 5k, 500 scripts
Actual: 11.7k CAM, 9k csm_share, 1.5k clm, 1k esmf_wrf_timemgr, .1 scripts
Actual total: 23.5k
16 weeks
150lpd
2 weeks vacation, Breckenridge and ESMF meeting

Use chghilevtimemgr_clm3_expa_61 branch for CLM (changes lnd_comp_mct.F90, drivers program_csm.F90, program_off.F90 stays same, time_manager.F90 stays same).
Pass in sync_clock from top level to atm, lnd, ice, ocn components
Get rid of nlend, and rstwr except in ???_comp.F90 files. ???_comp_mct.F90 set these based on the SyncClock passed into them.
Leave comctl and comsol as it is.
Pass in SyncClock and CCSMInit to readnamelist and use them to set the relevent values.
Remove alarm in restart use SyncClock and restart alarm methods.
Leave clock on restart file – but on restart compare with SyncClock and make sure times are in sync.
Use Sync clock to get start and ref times.
Remove ic_ymd and ic_tod – not needed anymore.
Remove order of dependence of CAM and CLM namelists
Change cam namelist to cam_inparm and CLM to clm_inparm
Change CCSM scripts for namelist change.
Remove get_clock and get_curr_ESMF_Time methods from time_manager – not needed.
Remove public attribute and ranting and raving from tm_clock declaration in time_manager.
Remove tm_aqua_planet from time_manager, ccsminparm sets this by setting perpetual_run and perpetual_ymd appropriately at the top level.
Remove input namelist (other than dtime) from time_manager.
timemgr_init redone to be based off of input sync_clock set at top level.
Brian E. will move calculation of dtime based on resolution from build-namelist to inside of dynamics code.
Set top level driver information from seq_ccsm namelist pass to sub-components.
ccsm_inparm:
- case_desc
- case_name
- start_type
- archive_dir
- mss_irt
- mss_wpass
- brnch_retain_casename
timemgr_inparm:
- calendar
- stop_noption
- stop_n
- stop_tod
- stop_ymd
- stop_tod
- stop_final_ymd
- restart_noption
- restart_n
- start_ymd ! MUST BE SET!
- start_tod ! Defaults to zero
- ref_ymd
- ref_tod
- perpetual_run
- perpetual_ymd
- atm_cpl_dt ! MUST BE SET! coupling frequency of atm to surface AND for now must equal camexp dtime
- orb_obliq
- orb_eccen
- orb_mvelp
- orb_iyear_AD
- atm_ideal_phys
- atm_adiabatic
- aqua_planet ! If aqua_planet is set, perpetual_ymd is also set to 3/21
Change build_namelist to also create ccsminparm namelist
Add initial method to shr_timemgr_mod to create sync_clock and to create a new clock from the sync_clock with a different dtime.
Initialization method in time_manager creates it's internal tm_clock based on the input sync_clock with it's own dtime.

Definition part of seq_ccsm_mct.F90.
Top clock/InitInfo level initialization...

  !
   ! Initialize Initialization Information and clock setup objects
   !
   call shr_inputInfo_setDefaults( CCSMInit )
   call shr_inputInfo_readNL( NLFileName, LogPrint=masterproc, MPICom=mpicom, &
                              MasterTask=masterproc, CCSMInitOut=CCSMInit )
   ! Get Perpetual run mode (in case aqua_planet mode is set)
   call shr_inputInfo_get( CCSMInit, perpetual_run=perpetual_run, perpetual_ymd=perpetual_ymd )
   call shr_timeMgr_setDefaults( ClockSetup, perpetual_run, perpetual_ymd )
   call shr_timeMgr_readNL( NLFileName, LogPrint=masterproc, MPICom=mpicom, &
                            MasterTask=masterproc, SetupOut=ClockSetup )
   ! If a startup type
   if ( .not. shr_InputInfo_IsRestart( CCSMInit ) )then
      ! Setup the clock and check that the ClockSetup object is valid
      call shr_timeMgr_setupClock( ClockSetup, LogPrint=masterproc,               &
                                   desc="Sequential CCSM with MCT Master Clock",  &
                                   ClockOut=SyncClock )
   ! Else if a continue or branch type
   else
      ! Read in restart file
      call shr_inputInfo_readRPointer( MPICom, masterproc, CCSMInit, rest_file )
      call shr_inputInfo_readRestart(  rest_file, MPICom=mpicom, LogPrint=masterproc, &
                                       MasterTask=masterproc, CCSMInitOut=CCSMInit )
   end if

Component Initialization calls..

  !
   ! Figure out which components will run
   !
   atm_present = shr_inputInfo_runModel( CCSMInit, 'atm' )
   lnd_present = shr_inputInfo_runModel( CCSMInit, 'lnd' )
   ocn_present = shr_inputInfo_runModel( CCSMInit, 'ocn' )
   ice_present = shr_inputInfo_runModel( CCSMInit, 'ice' )
   !
   ! Initialization of phase 1 of cam and surface components
   !
   if ( atm_present ) call atm_init1_mct( gsMap_atm, a2x_a, x2a_a, CCSMInit, SyncClock )
   if ( lnd_present ) call lnd_init_mct ( gsMap_lnd, x2l_l, l2x_l, CCSMInit, SyncClock )
   if ( ocn_present ) call ocn_init_mct ( gsMap_ocn, x2o_o, o2x_o, CCSMInit, SyncClock )
   if ( ice_present ) call ice_init_mct ( gsMap_ice, x2i_i, i2x_i, CCSMInit, SyncClock )

Atm initialization

    subroutine atm_init1( shr_ccsm_init, atm_in, &
                          atm_out, CCSMInit, syncClock )
     type(shr_inputInfo_InitType), intent(IN) :: CCSMInit
     type(shr_timemgr_clockType), intent(IN) :: sync_clock
     call timemgr_init( syncClock )
.
.
.
     module time_manager
     type(shr_timemgr_clockType) :: tm_clock  ! Local instance of clock for CAM
     subroutine timemgr_init( sync_clock )
.    tm_clock = shr_timemgr_SetupFromClock( dtime, sync_clock )
.
.

con_cam.F90

call ccsm_seq_timer_init()
call shr_msg_stdio('atm')
call cpl_interface_init(cpl_fields_atmname,mpicom)
call spmdinit ()
call ccsm_seq_printlogheader()    ! Print Model heading and copyright message
call ccsmini1( sync_clock )  !  Get orbital information from coupler to put in sync_clock
call shr_ccsm_input_nl( unit=5, ccsm_initdata, sync_clock, &
                                            log_print=masterproc )
call atm_init(          ccsm_initdata, atm_in, atm_out, sync_clock)
call ccsmini2(           ccsm_initdata, atm_in,          sync_clock )
do while ( .not. shr_timemgr_is_last_step( sync_clock ) )
   call atm_run1(       atm_in, atm_out )
   call ccsm_run(       atm_in, atm_out, sync_clock )
   call atm_run2(       atm_in, atm_out )
   call atm_run3(       atm_out )
   call atm_run4(       atm_in, atm_out , sync_clock)
   call shr_timemgr_advance_timestep( sync_clock )
end do
dall atm_final(         atm_in, atm_out )
call ccsmfin(    )
call cpl_interface_finalize(cpl_fields_atmname)

Example input namelist:

&ccsm_inparm
 case_name              = 'camrun'
 start_type             = "initial"
/
&timemgr_inparm
 atm_cpl_dt             = 1800
 iyear_ad               = 1950
 restart_nmonths        = 1
 start_type             = "initial"
 start_ymd              = 901
 stop_ndays             = 1
/
&cam_inparm
 absems_data            = '/fs/cgd/csm/inputdata/atm/cam/rad/abs_ems_factors_fastvx.c030508.nc'
 aeroptics              = '/fs/cgd/csm/inputdata/atm/cam/rad/AerosolOptics_c050419.nc'
 bnd_topo               = '/fs/cgd/csm/inputdata/atm/cam/topo/USGS-gtopo30_32x64_c050520.nc'
 bndtvaer               = '/fs/cgd/csm/inputdata/atm/cam/rad/AerosolMass_V_32x64_clim_c031022.nc'
 bndtvo         = '/fs/cgd/csm/inputdata/atm/cam/ozone/pcmdio3.r8.64x1_L60_clim_c970515.nc'
 bndtvs         = '/fs/cgd/csm/inputdata/atm/cam/sst/sst_HadOIBl_bc_32x64_clim_c030228.nc'
 ncdata         = '/fs/cgd/csm/inputdata/atm/cam/inic/gaus/cami_0000-09-01_32x64_L26_c030918.nc'
/
&clm_inparm
 fpftcon                = '/fs/cgd/csm/inputdata/lnd/clm2/pftdata/pft-physiology-cn16.c040719'
 fsurdat                = '/fs/cgd/csm/inputdata/lnd/clm2/srfdata/cam/clms_3.1_32x64_c050523.nc'
/

CCSM input namelist:

&ccsm_inparm
 case_name              = 'csmrun'
 start_type             = "continue"
 restart_pfile          = "./ccsm.csmrun.rpointer"
/
&timemgr_inparm
 atm_cpl_dt             = 3600
 start_ymd              = 901
 stop_nyears           = 9999
/
&cam_inparm
 absems_data            = '/fs/cgd/csm/inputdata/atm/cam/rad/abs_ems_factors_fastvx.c030508.nc'
 aeroptics              = '/fs/cgd/csm/inputdata/atm/cam/rad/AerosolOptics_c050419.nc'
 bnd_topo               = '/fs/cgd/csm/inputdata/atm/cam/topo/USGS-gtopo30_32x64_c050520.nc'
 bndtvaer               = '/fs/cgd/csm/inputdata/atm/cam/rad/AerosolMass_V_32x64_clim_c031022.nc'
 bndtvo         = '/fs/cgd/csm/inputdata/atm/cam/ozone/pcmdio3.r8.64x1_L60_clim_c970515.nc'
 bndtvs         = '/fs/cgd/csm/inputdata/atm/cam/sst/sst_HadOIBl_bc_32x64_clim_c030228.nc'
 dtime          = 1800
 ncdata         = '/fs/cgd/csm/inputdata/atm/cam/inic/gaus/cami_0000-09-01_32x64_L26_c030918.nc'
/

Note:
In the creation of the cam namelist ncdata takes into account what the start date is set to. If dates don't agree – then it may not be able to create the needed input datasets.