Dev merge eclm with FruitTree and WinterCrops all at once

.github/ISSUE_TEMPLATE/01_bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Report a problem with the code
+
+---
+
+### Brief summary of bug
+
+[Give a one or two sentence summary. This could be the same as the issue title if you feel that is a sufficient summary.]
+
+### General bug information
+
+**CTSM version you are using:** [output of `git describe`]
+
+**Does this bug cause significantly incorrect results in the model's science?** [Yes / No]
+
+**Configurations affected:** [Fill this in if known.]
+
+### Details of bug
+
+[Fill in details here.]
+
+### Important details of your setup / configuration so we can reproduce the bug
+
+[Specify anything relevant: the compset, resolution, machine, compiler, any xml or namelist changes, etc. You don't have to repeat anything that you have already noted above.]
+
+### Important output or errors that show the problem
+
+[Fill this in with anything relevant that you haven't already noted; if there is nothing to add, delete this section.]

.github/ISSUE_TEMPLATE/02_support_needed.md

@@ -0,0 +1,36 @@
+---
+name: Support needed for model use
+about: Ask for help with using CTSM
+
+---
+
+### NOTE: Be sure to read the relevant documentation and user forums
+
+We have limited staff and ability to provide support. Here are some resources that might provide help:
+- User's Guide: https://escomp.github.io/ctsm-docs/doc/build/html/users_guide/index.html
+- CLM Forum: https://bb.cgd.ucar.edu/forums/land-modeling-clm
+- README files amongst the source code
+- GitHub CTSM issues: https://github.com/escomp/ctsm/issues/
+- Also make sure this issue is unique to CTSM and not really an issue with CESM or CIME
+
+### Details of support request
+
+[Fill in details here.]
+
+### Important details of your setup / configuration so we can better assist you
+
+**CTSM version you are using:** [output of `git describe`]
+
+**Have you made any modifications to code, xml files, etc.?** [Yes / No]
+
+[If Yes: Please point us to your modifications. However: In general we can NOT support problems with modified code. Try to show the problem without modifications.]
+
+**If you are having problems with a specific case: Is your case on a machine accessible to most CTSM developers (e.g., an NCAR machine)?** [Yes / No]
+
+If Yes:
+
+- Location of case directory: [Fill this in]
+
+- Location of run directory: [Fill this in]
+
+[If No: Please make sure you have included all important input and output needed to understand your issue, either by pasting it into the issue text, or by attaching relevant files. However: We are less likely to be able to reproduce your problem if the issue is NOT on an NCAR machine.]

.github/ISSUE_TEMPLATE/03_science_discussion.md

@@ -0,0 +1,7 @@
+---
+name: Science discussion
+about: We encourage the use of issues to discuss CTSM science developments
+
+---
+
+

.github/ISSUE_TEMPLATE/04_other.md

@@ -0,0 +1,7 @@
+---
+name: Other
+about: Other issues (enhancement, cleanup, documentation, etc.)
+
+---
+
+

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,20 @@
+### Description of changes
+
+### Specific notes
+
+Contributors other than yourself, if any:
+
+CTSM Issues Fixed (include github issue #):
+
+Are answers expected to change (and if so in what way)?
+
+Any User Interface Changes (namelist or namelist defaults changes)?
+
+Testing performed, if any:
+(List what testing you did to show your changes worked as expected)
+(This can be manual testing or running of the different test suites)
+(Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide)
+(aux_clm on cheyenne for gnu/pgi and hobart for gnu/pgi/nag is the standard for tags on master)
+
+**NOTE: Be sure to check your Coding style against the standard:**
+https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines

src/clm5/biogeochem/CNBalanceCheckMod.F90

@@ -105,6 +105,7 @@ subroutine BeginCNBalance(this, bounds, num_soilc, filter_soilc, &
        c = filter_soilc(fc)
        col_begcb(c) = totcolc(c)
        col_begnb(c) = totcoln(c)
+
     end do
 
     end associate
@@ -161,10 +162,9 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
 
          ! calculate the total column-level carbon storage, for mass conservation check
          col_endcb(c) = totcolc(c)
-
          ! calculate total column-level inputs
          col_cinputs = gpp(c)
-
+         
          ! calculate total column-level outputs
          ! er = ar + hr, col_fire_closs includes patch-level fire losses
          col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c) + &
@@ -181,7 +181,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, &
 
          ! subtract leaching flux
          col_coutputs = col_coutputs - som_c_leached(c)
-
+         
          ! calculate the total column-level carbon balance error for this time step
          col_errcb(c) = (col_cinputs - col_coutputs)*dt - &
               (col_endcb(c) - col_begcb(c))

src/clm5/biogeochem/CNCIsoFluxMod.F90

@@ -135,7 +135,7 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp,         &
            iso_cnveg_cf%frootc_to_litter_patch              , cnveg_cf%frootc_to_litter_patch, &
            iso_cnveg_cs%frootc_patch                        , cnveg_cs%frootc_patch, &
            num_soilp                                        , filter_soilp, 1._r8, 0, isotope)
-
+ 
       call CIsoFluxCalc(&
            iso_cnveg_cf%livestemc_to_deadstemc_patch        , cnveg_cf%livestemc_to_deadstemc_patch, &
            iso_cnveg_cs%livestemc_patch                     , cnveg_cs%livestemc_patch, &
@@ -414,6 +414,17 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp,         &
               iso_cnveg_cs%totvegc_patch                       , cnveg_cs%totvegc_patch, &
               num_soilp                                        , filter_soilp, 1._r8, 0, isotope)
 
+         call CIsoFluxCalc(&
+              iso_cnveg_cf%crop_seedc_to_froot_patch            , cnveg_cf%crop_seedc_to_froot_patch, &
+              iso_cnveg_cs%totvegc_patch                       , cnveg_cs%totvegc_patch, &
+              num_soilp                                        , filter_soilp, 1._r8, 0, isotope)
+
+         call CIsoFluxCalc(&
+              iso_cnveg_cf%crop_seedc_to_deadstem_patch        , cnveg_cf%crop_seedc_to_deadstem_patch, &
+              iso_cnveg_cs%totvegc_patch                       , cnveg_cs%totvegc_patch, &
+              num_soilp                                        , filter_soilp, 1._r8, 0, isotope)
+
+
          call CIsoFluxCalc(&
               iso_cnveg_cf%grain_curmr_patch                   , cnveg_cf%grain_curmr_patch, &
               iso_cnveg_cs%cpool_patch                         , cnveg_cs%cpool_patch, &
@@ -1222,7 +1233,7 @@ subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, &
                           + frootc_to_litter(p) * fr_fcel(ivt(p)) * wtcol(p) * froot_prof(p,j)
                      phenology_c_to_litr_lig_c(c,j) = phenology_c_to_litr_lig_c(c,j) &
                           + frootc_to_litter(p) * fr_flig(ivt(p)) * wtcol(p) * froot_prof(p,j)
-
+                     
 !DML
                      if (ivt(p) >= npcropmin) then ! add livestemc to litter
                         ! stem litter carbon fluxes
@@ -1492,7 +1503,6 @@ subroutine CNCIsoHarvestPftToColumn (num_soilc, filter_soilc, &
                            hrv_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j)
                       harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + &
                            hrv_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j)
-
                       ! storage harvest mortality carbon fluxes
                       harvest_c_to_litr_met_c(c,j)      = harvest_c_to_litr_met_c(c,j)      + &
                            hrv_leafc_storage_to_litter(p)      * wtcol(p) * leaf_prof(p,j)