Merge pull request #390 from chrislxj/master

fix BGC restart inconsisntent bug

include/define.h

@@ -56,8 +56,10 @@
 
 !    Conflicts :  only used when LULC_IGBP_PFT is defined.
 #ifndef LULC_IGBP_PFT
+#ifndef LULC_IGBP_PC
 #undef BGC
 #endif
+#endif
 ! 7.1 If defined, CROP model is used
 #define CROP
 !    Conflicts : only used when BGC is defined

main/BGC/MOD_BGC_Vars_TimeVariables.F90

@@ -970,6 +970,7 @@ SUBROUTINE WRITE_BGCTimeVariables (file_restart)
       CALL ncio_write_vector (file_restart, 'sminn_vr             ', 'soil' ,   nl_soil, 'patch', landpatch, sminn_vr    )
       CALL ncio_write_vector (file_restart, 'smin_no3_vr          ', 'soil' ,   nl_soil, 'patch', landpatch, smin_no3_vr )
       CALL ncio_write_vector (file_restart, 'smin_nh4_vr          ', 'soil' ,   nl_soil, 'patch', landpatch, smin_nh4_vr )
+      CALL ncio_write_vector (file_restart, 'lag_npp              ', 'patch', landpatch, lag_npp              )
 
       IF(DEF_USE_NITRIF)THEN
          CALL ncio_write_vector (file_restart, 'tCONC_O2_UNSAT       ', 'soil'  ,   nl_soil, 'patch', landpatch, tconc_o2_unsat)
@@ -1132,6 +1133,7 @@ SUBROUTINE READ_BGCTimeVariables (file_restart)
       CALL ncio_read_vector (file_restart, 'sminn_vr             ',   nl_soil, landpatch, sminn_vr   )
       CALL ncio_read_vector (file_restart, 'smin_no3_vr          ',   nl_soil, landpatch, smin_no3_vr)
       CALL ncio_read_vector (file_restart, 'smin_nh4_vr          ',   nl_soil, landpatch, smin_nh4_vr)
+      CALL ncio_read_vector (file_restart, 'lag_npp              ', landpatch, lag_npp, defval =1.0  )
 
       IF(DEF_USE_NITRIF)THEN
          CALL ncio_read_vector (file_restart, 'tCONC_O2_UNSAT       ',   nl_soil, landpatch, tconc_o2_unsat         )

main/BGC/MOD_BGC_Veg_NutrientCompetition.F90

@@ -149,8 +149,9 @@ SUBROUTINE calc_plant_nutrient_competition_CLM45_default(i,ps,pe,npcropmin)
          IF (gpp_p(m) > 0.0_r8) THEN
             downreg_p(m) = excess_cflux_p(m)/gpp_p(m)
             psn_to_cpool_p(m) = psn_to_cpool_p(m) * (1._r8 - downreg_p(m))
-
-	 ENDIF
+         ELSE
+            downreg_p(m) = 0._r8
+         ENDIF
 
          ! calculate the amount of new leaf C dictated by these allocation
          ! decisions, and calculate the daily fluxes of C and N to current

main/CoLM.F90

@@ -125,10 +125,10 @@ PROGRAM CoLM
    integer :: e_year, e_month, e_day, e_seconds, e_julian
    integer :: p_year, p_month, p_day, p_seconds, p_julian
    integer :: lc_year, lai_year
-   integer :: month, mday, year_p, month_p, mday_p
+   integer :: month, mday, year_p, month_p, mday_p, month_prev, mday_prev
    integer :: spinup_repeat, istep
 
-   type(timestamp) :: ststamp, itstamp, etstamp, ptstamp
+   type(timestamp) :: ststamp, itstamp, etstamp, ptstamp, time_prev
 
    integer*8 :: start_time, end_time, c_per_sec, time_used
 !-----------------------------------------------------------------------
@@ -326,7 +326,7 @@ PROGRAM CoLM
 
 #ifdef BGC
       IF (DEF_USE_NITRIF) THEN
-         CALL init_nitrif_data (sdate)
+         CALL init_nitrif_data (ststamp)
       ENDIF
 
       IF (DEF_NDEP_FREQUENCY==1)THEN ! Initial annual ndep data readin
@@ -386,7 +386,15 @@ PROGRAM CoLM
          IF(DEF_USE_OZONEDATA)THEN
             CALL update_Ozone_data(itstamp, deltim)
          ENDIF
+
 #ifdef BGC
+         IF(DEF_USE_NITRIF) THEN
+            time_prev = itstamp + int(-deltim)
+            CALL julian2monthday(time_prev%year,time_prev%day,month_prev,mday_prev)
+            if(month_p /= month_prev)then
+               CALL update_nitrif_data (month_p)
+            end if
+         ENDIF
          IF(DEF_USE_FIRE)THEN
             CALL update_lightning_data (itstamp, deltim)
          ENDIF
@@ -407,11 +415,6 @@ PROGRAM CoLM
          CALL julian2monthday (jdate(1), jdate(2), month, mday)
 
 #ifdef BGC
-         IF(DEF_USE_NITRIF) THEN
-            IF (month /= month_p) THEN
-               CALL update_nitrif_data (month)
-            ENDIF
-         ENDIF
 
          IF (DEF_NDEP_FREQUENCY==1)THEN ! Read Annual Ndep data
             IF (jdate(1) /= year_p) THEN

main/MOD_NitrifData.F90

@@ -20,7 +20,7 @@ MODULE MOD_NitrifData
 
 CONTAINS
 
-   SUBROUTINE init_nitrif_data (idate)
+   SUBROUTINE init_nitrif_data (time)
 
 !-----------------------------------------------------------------------
 ! !DESCRIPTION:
@@ -35,7 +35,7 @@ SUBROUTINE init_nitrif_data (idate)
    USE MOD_LandPatch
    IMPLICIT NONE
 
-   integer, intent(in) :: idate(3)
+   type(timestamp), intent(in) :: time
 
    ! Local Variables
    character(len=256) :: file_nitrif
@@ -54,7 +54,7 @@ SUBROUTINE init_nitrif_data (idate)
       IF (allocated(lon)) deallocate(lon)
       IF (allocated(lat)) deallocate(lat)
 
-      CALL julian2monthday (idate(1), idate(2), month, mday)
+      CALL julian2monthday (time%year, time%day, month, mday)
 
       CALL update_nitrif_data (month)
 

run/scripts/SummaryTest.bash

@@ -8,14 +8,15 @@ Help()
 
    echo "!----------------------------------------------------------------------------!"
    echo 'Syntax: ./SummaryTest.bash -n $TestPath/$TestName [-f $TestLists][-i $Varlist]'
+   echo '        [-t $TestType]'
    echo "!----------------------------------------------------------------------------!"
    echo options:
    echo "-n The Path and Name of the test working folder"
    echo '-f (Optional) The list of switches of all test cases, if $TestLists '
    echo '   is absent, use $ROOT/run/script/TestLists as the default test list. '
    echo '-i Specify the summary item of the test restuls:' 
    echo '   1)CreateCase;	2)Compile;	3)Submit_Mksrfdata;'
-   echo '   4)Submit_Mkinidata;	5)Submit_Case'
+   echo '   4)Submit_Mkinidata;	5)Submit_Case;  6)Sugmit_Restart;   7)RestartMatch'
    echo '-h display command information'
 }
 
@@ -30,7 +31,7 @@ SummaryTest()
       exit
    fi
    if [ "$3" == "All" ];then
-      Varlist="CreateCase Compile Submit_Mksrfdata Submit_Mkinidata Submit_Case"
+      Varlist="CreateCase Compile Submit_Mksrfdata Submit_Mkinidata Submit_Case Submit_Restart RestartMatch"
    fi
 
 TestCaseLists=$2

run/scripts/create_test

@@ -8,6 +8,7 @@ Help()
 
    echo "!-----------------------------------------------------------------------!"
    echo 'Syntax: ./create_test -n $TestPath/$TestName [-f $TestLists][-m $Mode]'
+   echo '        [-t $TestType]'
    echo "!-----------------------------------------------------------------------!"
    echo options:
    echo "-n The Path and Name of the test working folder"
@@ -22,6 +23,9 @@ Help()
    echo '      $TestPath/$TestName '
    echo '   4) RunNoMkSrf: create_test will follow $TestLists to run without make'
    echo '      surface data for all test cases under $TestPath/$TestName '
+   echo '-t (Optional) Type of the test: '
+   echo '   1) SMS: Smoke test, normally run model under different configuration'
+   echo '   2) RES: Restart test, run model from restart file to check their consistency'
    echo '-h display command information'
 }
 

share/MOD_Namelist.F90

@@ -727,13 +727,13 @@ MODULE MOD_Namelist
       logical :: sum_irrig_count                  = .true.
 
       logical :: ndep_to_sminn                    = .true.
-      logical :: CONC_O2_UNSAT                    = .true.
-      logical :: O2_DECOMP_DEPTH_UNSAT            = .true.
-      logical :: abm                              = .true.
-      logical :: gdp                              = .true.
-      logical :: peatf                            = .true.
-      logical :: hdm                              = .true.
-      logical :: lnfm                             = .true.
+      logical :: CONC_O2_UNSAT                    = .false.
+      logical :: O2_DECOMP_DEPTH_UNSAT            = .false.
+      logical :: abm                              = .false.
+      logical :: gdp                              = .false.
+      logical :: peatf                            = .false.
+      logical :: hdm                              = .false.
+      logical :: lnfm                             = .false.
 
       logical :: leafcCap                         = .false.
       logical :: leafc_storageCap                 = .false.
@@ -1928,6 +1928,10 @@ SUBROUTINE sync_hist_vars (set_defaults)
       ENDIF
 #endif
       CALL sync_hist_vars_one (DEF_hist_vars%ndep_to_sminn                   , set_defaults)
+      IF(DEF_USE_NITRIF)THEN
+         CALL sync_hist_vars_one (DEF_hist_vars%CONC_O2_UNSAT                , set_defaults)
+         CALL sync_hist_vars_one (DEF_hist_vars%O2_DECOMP_DEPTH_UNSAT        , set_defaults)
+      ENDIF
       IF(DEF_USE_FIRE)THEN
          CALL sync_hist_vars_one (DEF_hist_vars%abm                          , set_defaults)
          CALL sync_hist_vars_one (DEF_hist_vars%gdp                          , set_defaults)

share/MOD_TimeManager.F90

@@ -114,7 +114,7 @@ FUNCTION addsec(tstamp, sec)
 
       addsec = tstamp
       addsec%sec = addsec%sec + sec
-      IF (addsec%sec > 86400) THEN
+      DO WHILE (addsec%sec > 86400) 
          addsec%sec = addsec%sec - 86400
          IF( isleapyear(addsec%year) ) THEN
             maxday = 366
@@ -126,7 +126,20 @@ FUNCTION addsec(tstamp, sec)
             addsec%year = addsec%year + 1
             addsec%day = 1
          ENDIF
-      ENDIF
+      ENDDO
+      DO WHILE (addsec%sec <= 0)
+         addsec%sec = addsec%sec + 86400
+         IF( isleapyear(addsec%year-1) )THEN
+            maxday = 366
+         ELSE
+            maxday = 365
+         ENDIF
+         addsec%day = addsec%day - 1
+         IF(addsec%day <= 0) THEN
+            addsec%year = addsec%year - 1
+            addsec%day = maxday
+         ENDIF
+      ENDDO
       RETURN
 
    END FUNCTION addsec