Update Time Manager (#566)

* Initial refactor of time manager
- nyr, month, mday, sec are the new time manager prognostic variables
- time is renamed to timesec and is a diagnostic, not prognostic variable
- remove time_forc, was not needed or being used anyway
- refactor ice_calendar, use calendar_type to define calendar after initialization
- add several new subroutines to ice_calendar including
  - advance_time = handles advancing the model a timestep
  - calendar_compute_elapsed_days = compute elapsed days since 0000-01-01
  - calendar_compute_days_between = compute days between two yyyy-mm-dd dates
  - calendar_set_date_from_timesecs = support conversion of timesecs to date for binary restarts
  - calendar = same behavior as old method, just no more argument
- add month_init, day_init, sec_init, and npt_unit to namelist
- this is bit-for-bit with f5f487f on cheyenne with full test suite, manual checks of log files
  were done to verify.  restart files are not identical due to changes in files saved
- old restarts should be backwards compatible
- to advance the model a timestep, call advance_time() or update nyr, month, mday, sec and call calendar().
  subroutine calendar() will adjust the date values as needed (for instance, adding a million seconds to sec).

* Add unit test for calendar

* refactor ice_calendar and update calchk unit test

* update calchk unit test

* update compare scripts to support unit tests

* Add calc_timesteps to compute timesteps from npt and npt_unit
Modify set_nml.run* to use new npt_unit and npt
Add calc_timesteps test to calchk unit test
Update standalone model to call calc_timesteps during initialization
  and after restarts are read

* Update JRA55_data implementation
Update computation of fyear to support cycling correctly with new definition on nyr
Modify restart run lengths to be days instead of timesteps
Add debugging to ice_forcing.F90
Add timer for forcing

* clean up merge from master and recent changes

* update documentation and add timer to serial ice_timers.F90

* Update CICE for coupling with RASM with new time manager

- Update drivers/mct/cesm1/CICE_InitMod.F90 and CICE_RunMod.F90
  - use advance_timestep
  - get rid of use of time variable, shift to nyr, month, mday, sec
  - update calendar call
  - update usage of year_init
- Add section in user guide about coupling with new time manager
- Fix stuff unrelated to time manager
  - Fix bug in wght_file diagnostic in ice_domain.F90, was written before defined
  - Fix bug in bathymetry settings when max kmt is greater than hardcoded 40 levels
  - Add a few missing namelist variables recently added to documentation

* clean up old code

* update documentation

* update ice_calendar comments

* update time manager documentation in dg_dynamics

* update history restart documentation

* Update prognostic calendar variables to myear, mmonth, mday, msec.

They were nyr, month, mday, sec.  The "m" in front means model and it
creates more unique names in the source code than year, month, day, sec
which can be hard to grep for because there are so many matches.

cice.setup

@@ -1094,7 +1094,7 @@ cd ${testname_base}
 source ./cice.settings
 if (\${dobuild} == true) then
    if (\${doreuse} == true) then
-     set ciceexe = "../ciceexe.\${ICE_ENVNAME}.\${ICE_COMMDIR}.\${ICE_BLDDEBUG}.\${ICE_THREADED}.\${ICE_IOTYPE}"
+     set ciceexe = "../ciceexe.\${ICE_TARGET}.\${ICE_ENVNAME}.\${ICE_COMMDIR}.\${ICE_BLDDEBUG}.\${ICE_THREADED}.\${ICE_IOTYPE}"
      ./cice.build --exe \${ciceexe}
      if !(-e \${ciceexe}) cp -p \${ICE_RUNDIR}/cice \${ciceexe}
    else

cicecore/cicedynB/analysis/ice_history.F90

@@ -1713,7 +1713,7 @@ subroutine accum_hist (dt)
       use ice_domain_size, only: nfsd
       use ice_grid, only: tmask, lmask_n, lmask_s, dxu, dyu
       use ice_calendar, only: new_year, write_history, &
-                              write_ic, time, histfreq, nstreams, month, &
+                              write_ic, timesecs, histfreq, nstreams, mmonth, &
                               new_month
       use ice_dyn_eap, only: a11, a12, e11, e12, e22, s11, s12, s22, &
           yieldstress11, yieldstress12, yieldstress22
@@ -1864,7 +1864,7 @@ subroutine accum_hist (dt)
            avgct(ns) = avgct(ns) + c1
 !           if (avgct(ns) == c1) time_beg(ns) = (time-dt)/int(secday)
            if (avgct(ns) == c1) then
-              time_beg(ns) = (time-dt)/int(secday)
+              time_beg(ns) = (timesecs-dt)/int(secday)
               time_beg(ns) = real(time_beg(ns),kind=real_kind)
            endif
          endif
@@ -3966,7 +3966,7 @@ subroutine accum_hist (dt)
         enddo                   ! iblk
         !$OMP END PARALLEL DO
 
-        time_end(ns) = time/int(secday)
+        time_end(ns) = timesecs/int(secday)
         time_end(ns) = real(time_end(ns),kind=real_kind)
 
       !---------------------------------------------------------------
@@ -4057,7 +4057,7 @@ subroutine accum_hist (dt)
             enddo
          endif                  ! new_year
 
-         if ( (month .eq. 7) .and. new_month ) then 
+         if ( (mmonth .eq. 7) .and. new_month ) then 
             do j=jlo,jhi
             do i=ilo,ihi
                ! reset SH Jul 1

cicecore/cicedynB/analysis/ice_history_shared.F90

@@ -653,9 +653,9 @@ module ice_history_shared
 
       subroutine construct_filename(ncfile,suffix,ns)
 
-      use ice_calendar, only: sec, nyr, month, daymo,  &
+      use ice_calendar, only: msec, myear, mmonth, daymo,  &
                               mday, write_ic, histfreq, histfreq_n, &
-                              year_init, new_year, new_month, new_day, &
+                              new_year, new_month, new_day, &
                               dt
       use ice_restart_shared, only: lenstr
 
@@ -667,12 +667,12 @@ subroutine construct_filename(ncfile,suffix,ns)
       character (len=1) :: cstream
       character(len=*), parameter :: subname = '(construct_filename)'
 
-        iyear = nyr + year_init - 1 ! set year_init=1 in ice_in to get iyear=nyr
-        imonth = month
+        iyear = myear
+        imonth = mmonth
         iday = mday
-        isec = sec - dt
+        isec = msec - dt
 
-        if (write_ic) isec = sec
+        if (write_ic) isec = msec
         ! construct filename
         if (write_ic) then
            write(ncfile,'(a,a,i4.4,a,i2.2,a,i2.2,a,i5.5,a,a)')  &
@@ -688,7 +688,7 @@ subroutine construct_filename(ncfile,suffix,ns)
            imonth = 12
            iday = daymo(imonth)
           elseif (new_month) then
-           imonth = month - 1
+           imonth = mmonth - 1
            iday = daymo(imonth)
           elseif (new_day) then
            iday = iday - 1
@@ -703,7 +703,7 @@ subroutine construct_filename(ncfile,suffix,ns)
          if (histfreq(ns) == '1') then ! instantaneous, write every dt
            write(ncfile,'(a,a,i4.4,a,i2.2,a,i2.2,a,i5.5,a,a)')  &
             history_file(1:lenstr(history_file))//trim(cstream),'_inst.', &
-             iyear,'-',imonth,'-',iday,'-',sec,'.',suffix
+             iyear,'-',imonth,'-',iday,'-',msec,'.',suffix
 
          elseif (hist_avg) then    ! write averaged data
 
@@ -714,7 +714,7 @@ subroutine construct_filename(ncfile,suffix,ns)
           elseif (histfreq(ns) == 'h'.or.histfreq(ns) == 'H') then ! hourly
            write(ncfile,'(a,a,i2.2,a,i4.4,a,i2.2,a,i2.2,a,i5.5,a,a)')  &
             history_file(1:lenstr(history_file))//trim(cstream),'_', &
-             histfreq_n(ns),'h.',iyear,'-',imonth,'-',iday,'-',sec,'.',suffix
+             histfreq_n(ns),'h.',iyear,'-',imonth,'-',iday,'-',msec,'.',suffix
           elseif (histfreq(ns) == 'm'.or.histfreq(ns) == 'M') then ! monthly
            write(ncfile,'(a,a,i4.4,a,i2.2,a,a)')  &
             history_file(1:lenstr(history_file))//trim(cstream),'.', &
@@ -728,7 +728,7 @@ subroutine construct_filename(ncfile,suffix,ns)
          else                     ! instantaneous with histfreq > dt
            write(ncfile,'(a,a,i4.4,a,i2.2,a,i2.2,a,i5.5,a,a)')  &
             history_file(1:lenstr(history_file)),'_inst.', &
-             iyear,'-',imonth,'-',iday,'-',sec,'.',suffix
+             iyear,'-',imonth,'-',iday,'-',msec,'.',suffix
          endif
         endif