Merge pull request #7 from rgknox/logging-experiments

merge logging experiments up to master
NGEET · Jan 30, 2018 · b4d0b92 · b4d0b92
2 parents f260503 + 0eb71d9
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,44 @@
+<!--- Provide a general summary of your changes in the Title above -->
+
+### Description:
+<!--- Describe your changes in detail -->
+<!--- please add issue number if one exists -->
+
+### Collaborators:
+<!--- List names of collaborators or people who have interacted -->
+<!--- in bringing about this set of changes -->
+<!--- consultation, discussions, etc. -->
+
+### Expectation of Answer Changes:
+<!--- Please describe under what conditions, if any, -->
+<!--- the model is expected to generated different answers -->
+<!--- from the master version of the code -->
+
+
+### Checklist:
+<!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
+<!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
+- [ ] My change requires a change to the documentation.
+- [ ] I have updated the in-code documentation AND wiki accordingly.
+- [ ] I have read the [**CONTRIBUTING**](https://github.com/rgknox/fates/blob/rgknox-new-PR-template/CONTRIBUTING.md) document.
+- [ ] FATES PASS/FAIL regression tests were run
+- [ ] If answers were expected to change, evaluation was performed and provided
+
+
+### Test Results:
+<!--- Non-trivial changes require the PASS/FAIL regression tests. -->
+<!--- If changes to code are NOT expected to change answers, tests must -->
+<!--- be run against a baseline. -->
+
+FATES-CLM (or) HLM test hash-tag:
+
+FATES-CLM (or) HLM baseline hash-tag:
+
+FATES baseline hash-tag:
+
+Test Output:
+
+<!--- paste in test results here -->
+
+
+<!--this template is from https://www.talater.com/open-source-templates/#/page/99--> 
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,52 @@
+# How to contribute
+
+Thank you for considering contributing to the development of FATES. There are a few guidelines that we need contributions to follow.
+
+## Read and Understand the FATES license:
+
+https://github.com/NGEET/fates/blob/master/LICENSE.txt
+
+## If working with unreleased code, please read the use policy that governs the developer repository:
+
+https://github.com/NGEET/fates/wiki/Use-and-distribution-policy-for-fates-developer-repository
+
+## Getting Started
+
+Those who wish to contribute code to FATES must have those changes integrated through the developer repository NGEET/fates.  Changes that make it to public releases must go through this repository first, as well.  Here are some basic first steps.
+
+* All developers should create a fork of the NGEET/fates repository into their personal space on github
+* Follow the developer work-flow described here: https://github.com/NGEET/fates/wiki/FATES-Development-Workflow
+* Each set of changes should have its own feature branch that encapsulates your desired changes, following the conventions outlined here: https://github.com/NGEET/fates/wiki/Feature-Branch-Naming-Convention
+* The work-flow will lead you eventually to submit a Pull-Request to NGEET/fates:master, please follow the template in the Pull Request and communicate as best you can if you are unsure how to fill out the text
+* It is best to create an issue to describe the work you are undertaking prior to starting.  This helps the community sync with your efforts, prevents duplication of efforts, and science is not done in a vaccuum!
+* Expect peers to interact, help, discuss and eventually approve your submission (pull-request)
+
+
+## Things to Remember
+
+* Make commits in logical units (i.e. group changes)
+* Changes that are submitted should be limited to 1 single feature (i.e. don't submit changes to the radiation code and the nutrient cycle simultaneous, pick one thing)
+* Check for unnecessary whitespace with `git diff --check` before committing
+* We have no standard protocol for commit messages, but try to make them meaningful, concise and succinct.
+* You will most likely have to test (see workflow above), see: https://github.com/NGEET/fates/wiki/Testing-Protocols
+
+
+## Coding Practices and Style
+
+Please refer to the FATES style guide: https://github.com/NGEET/fates/wiki/Coding-Practices-and-Style-Guide
+
+
+## Trivial Changes
+
+If changes are trivial, it's possible testing will not be required. Conversations via the Pull Request will address if tests are not needed
+
+## Documentation
+
+Yes please!  If you are creating new code, fixing existing code, anything.  Please add comments in the code itself.  Please also follow the style guide for comments.  Also, please create and/or modify existing wiki documentation.  You may be asked to add documtation prior to having a pull-request approved.
+
+
+## Additional Resources
+
+* [General GitHub documentation](https://help.github.com/)
+* [GitHub pull request documentation](https://help.github.com/articles/creating-a-pull-request/)
+* [FATES Wiki](https://github.com/NGEET/fates/wiki)
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,6 +1,6 @@
 Functionally Assembled Terrestrial Ecosystem Simulator (“FATES”)
 
-Copyright (c) 2016-2017, The Regents of the University of California, through Lawrence
+Copyright (c) 2016-2018, The Regents of the University of California, through Lawrence
 Berkeley National Laboratory, University Corporation for Atmospheric Research, Los Alamos
 National Security, LLC (LANS), as operator of Los Alamos National Laboratory (LANL), and
 President and Fellows of Harvard College. All rights reserved.

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # NGEE-T fates repository
 ------------------------------
 
-This is the developer repository of the Next Generation Ecosystem Experiment Tropics’ (NGEE-T) model: the Functionally Assembled Terrestrial Ecosystem Simulator (FATES).
+This is the developer repository of the Next Generation Ecosystem Experiment Tropics’ (NGEE-T) model: the Functionally Assembled Terrestrial Ecosystem Simulator (FATES). (https://github.com/NGEET/fates)
 
 For more information on the FATES model, see our wiki:  https://github.com/NGEET/fates/wiki
 
@@ -20,3 +20,5 @@ http://www.cesm.ucar.edu/
 The NGEE-T project maintains a mirror of CLM.  That software system will automatically pull in the FATES software, and is where most users should go to clone the code:
 
 https://github.com/NGEET/fates-clm
+
+
diff --git a/biogeochem/EDCanopyStructureMod.F90 b/biogeochem/EDCanopyStructureMod.F90
@@ -8,8 +8,10 @@ module EDCanopyStructureMod
   use FatesConstantsMod     , only : r8 => fates_r8
   use FatesGlobals          , only : fates_log
   use EDPftvarcon           , only : EDPftvarcon_inst
-  use EDGrowthFunctionsMod  , only : c_area
+  use FatesAllometryMod     , only : carea_allom
   use EDCohortDynamicsMod   , only : copy_cohort, terminate_cohorts, fuse_cohorts
+  use EDCohortDynamicsMod   , only : tree_lai
+  use EDCohortDynamicsMod   , only : tree_sai
   use EDtypesMod            , only : ed_site_type, ed_patch_type, ed_cohort_type, ncwd
   use EDTypesMod            , only : nclmax
   use EDTypesMod            , only : nlevleaf
@@ -317,7 +319,9 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr)
          rankordered_area_sofar = 0.0_r8
          currentCohort => currentPatch%tallest 
          do while (associated(currentCohort))
-            currentCohort%c_area = c_area(currentCohort)
+
+            call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)
+
             if(arealayer > currentPatch%area.and.currentCohort%canopy_layer == i_lyr)then
                if (ED_val_comp_excln .ge. 0.0_r8 ) then
                   ! normal (stochastic) case. weight cohort demotion by inverse size to a constant power
@@ -443,9 +447,10 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr)
                         currentCohort%n = 0.0_r8
                         currentCohort%c_area = 0._r8
                      else  
-                        currentCohort%c_area = c_area(currentCohort)       
+                        call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)
                      endif
-                     copyc%c_area = c_area(copyc)
+
+                     call carea_allom(copyc%dbh,copyc%n,currentSite%spread,copyc%pft,copyc%c_area)
 
 
                      !----------- Insert copy into linked list ------------------------!                         
@@ -517,7 +522,7 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr)
                         currentCohort%c_area = 0._r8
 
                      else  
-                        currentCohort%c_area = c_area(currentCohort)       
+                        call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)
                      endif
 
                   endif ! matches: if (cc_loss < currentCohort%c_area)then
@@ -619,8 +624,7 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)
             do while (associated(currentCohort))            
                if(currentCohort%canopy_layer == i_lyr+1)then !look at the cohorts in the canopy layer below... 
                   currentCohort%canopy_layer = i_lyr   
-                  currentCohort%c_area = c_area(currentCohort)
-
+                  call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)
                   ! keep track of number and biomass of promoted cohort
                   currentSite%promotion_rate(currentCohort%size_class) = &
                         currentSite%promotion_rate(currentCohort%size_class) + currentCohort%n
@@ -639,7 +643,7 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)
          ! This is the opposite of the demotion weighting... 
          currentCohort => currentPatch%tallest 
          do while (associated(currentCohort))
-            currentCohort%c_area = c_area(currentCohort)
+            call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)
             if(currentCohort%canopy_layer == i_lyr+1)then !look at the cohorts in the canopy layer below... 
                if (ED_val_comp_excln .ge. 0.0_r8 ) then
                   ! normal (stochastic) case, as above.
@@ -720,8 +724,8 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)
                      currentCohort%dbh = currentCohort%dbh - 0.000000000001_r8 
                      copyc%dbh = copyc%dbh + 0.000000000001_r8
 
-                     currentCohort%c_area = c_area(currentCohort)          
-                     copyc%c_area = c_area(copyc)
+                     call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)
+                     call carea_allom(copyc%dbh,copyc%n,currentSite%spread,copyc%pft,copyc%c_area)
 
                      !----------- Insert copy into linked list ------------------------!                         
                      copyc%shorter => currentCohort
@@ -738,8 +742,8 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)
 
                      ! update area AFTER we sum up the losses. the cohort may shrink at this point,
                      ! if the upper canopy spread is smaller. this shold be dealt with by the 'excess area' loop.  
-                     currentCohort%c_area = c_area(currentCohort) 
-                     
+                     call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)
+
                      ! keep track of number and biomass of promoted cohort
                      currentSite%promotion_rate(currentCohort%size_class) = &
                            currentSite%promotion_rate(currentCohort%size_class) + currentCohort%n
@@ -826,7 +830,7 @@ subroutine canopy_spread( currentSite )
        !calculate canopy area in each patch...
        currentCohort => currentPatch%tallest
        do while (associated(currentCohort))
-          currentCohort%c_area = c_area(currentCohort) 
+          call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)
           if(EDPftvarcon_inst%woody(currentCohort%pft) .eq. 1 .and. currentCohort%canopy_layer .eq. 1 ) then
              sitelevel_canopyarea = sitelevel_canopyarea + currentCohort%c_area
           endif
@@ -862,7 +866,6 @@ subroutine canopy_summarization( nsites, sites, bc_in )
     use EDPatchDynamicsMod   , only : set_patchno
     use EDPatchDynamicsMod   , only : set_root_fraction
     use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
-    use EDGrowthFunctionsMod , only : tree_lai, c_area
     use EDtypesMod           , only : area
     use EDPftvarcon            , only : EDPftvarcon_inst
 
@@ -921,9 +924,9 @@ subroutine canopy_summarization( nsites, sites, bc_in )
 
 
              currentCohort%b = currentCohort%balive+currentCohort%bdead+currentCohort%bstore
+             call carea_allom(currentCohort%dbh,currentCohort%n,sites(s)%spread,currentCohort%pft,currentCohort%c_area)
              currentCohort%treelai = tree_lai(currentCohort)
-
-             currentCohort%c_area = c_area(currentCohort)
+
              canopy_leaf_area = canopy_leaf_area + currentCohort%treelai *currentCohort%c_area
 
              if(currentCohort%canopy_layer==1)then
@@ -976,7 +979,6 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)
     !
     ! !USES:
 
-    use EDGrowthFunctionsMod , only : tree_lai, tree_sai, c_area 
     use EDtypesMod           , only : area, dinc_ed, hitemax, n_hite_bins
 
     !
@@ -1026,8 +1028,8 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)
        currentPatch%canopy_layer_lai(:) = 0._r8
        NC = 0
        currentCohort => currentPatch%shortest
-       do while(associated(currentCohort))       
-          currentCohort%c_area = c_area(currentCohort)
+       do while(associated(currentCohort))     
+          call carea_allom(currentCohort%dbh,currentCohort%n,currentSite%spread,currentCohort%pft,currentCohort%c_area)  
           currentPatch%canopy_area = currentPatch%canopy_area + currentCohort%c_area
           NC = NC+1
           currentCohort => currentCohort%taller    
@@ -1594,8 +1596,8 @@ subroutine CanopyLayerArea(currentPatch,layer_index,layer_area)
 
      layer_area = 0.0_r8
      currentCohort => currentPatch%tallest
-     do while (associated(currentCohort))   
-        currentCohort%c_area = c_area(currentCohort) ! Reassess cohort area. 
+     do while (associated(currentCohort))
+        call carea_allom(currentCohort%dbh,currentCohort%n,currentPatch%siteptr%spread,currentCohort%pft,currentCohort%c_area)
         if (currentCohort%canopy_layer .eq. layer_index) then
            layer_area = layer_area + currentCohort%c_area
         end if
@@ -1623,7 +1625,7 @@ function NumPotentialCanopyLayers(currentPatch,include_substory) result(z)
      type(ed_cohort_type),pointer :: currentCohort
 
      integer :: z
-
+     real(r8) :: c_area
      real(r8) :: arealayer
 
      z = 1
@@ -1638,7 +1640,8 @@ function NumPotentialCanopyLayers(currentPatch,include_substory) result(z)
         currentCohort => currentPatch%tallest
         do while (associated(currentCohort))  
            if(currentCohort%canopy_layer == z) then
-              arealayer = arealayer + c_area(currentCohort)
+              call carea_allom(currentCohort%dbh,currentCohort%n,currentPatch%siteptr%spread,currentCohort%pft,c_area)
+              arealayer = arealayer + c_area
            end if
            currentCohort => currentCohort%shorter
         enddo