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1217 2871d 21h werner / clean up repository - make 1.0 trunk again!  
1202 2922d 19h werner /branches/iland_regen/src/ searching/fixing issues with carbon cycle: NEP as provided by carbonflow output (NPP-Rh-Mgmt) is different from NEP as derived by the delta of the carbon stocks.
As usual, very hard to track down these issues, but:
* bark beetle module: foliage loss from BB-trees now correctly routed to soil
* order of modules in model: switched disturbances and carbon cylcle (in order to correctly track all carbon changes due to disturbances)
* fixed a problem with the calculation of NPP: after disturbances stand level NPP was set to 0 (since statistics were recalculated after disturbaces, but NPP values are not available then). Introduced: StandStatistics::clearOnlyTrees()
* flow from branches to the atmosphere (decay of branches) now tracked correctly (changes the NEP calulation).
 
1177 3048d 18h werner /branches/iland_regen/src/ updating the sapling growth (calculation of stem numbers)  
1163 3088d 00h werner /branches/iland_regen/src/ removed the "sapling.h" everywhere.
open:
* establishment: use better random order of species (e.g. by providing N random lists in speciesSet)
 
1158 3089d 20h werner /branches/iland_regen/src/ further performance improvements in regeneration/sapling module.
In total (sim 80 yrs WBT 2km2, from bare ground), iLand is +- 35% faster:
* seed dispersal (not today)
* optimized use of LRI-correction
* better linearization in sapling growth (height growth potential)
 
1157 3090d 03h werner /branches/iland_regen/ merge of changes in the trunk (up to the version used for the 2016 DICE simulation batch).  
1104 3160d 01h werner /branches/iland_regen/ Branch dedicated to playing around with establishment/regeneration.
Goals are:
(i) speed up
(ii) introduction of new features for Yellowstone
 
1102 3160d 14h werner /branches/port_qt5_64bit/src/ fixed couple of clang warnings.

some debugging/profiling work w.r.t. establishment/regen.
 
936 3677d 19h werner /branches/port_qt5_64bit/src/ searching for bugs in the bookkeeping of increments, volumes.
very cumbersome....
 
863 3936d 20h werner /branches/port_qt5_64bit/ renaming of the FOME to AMIE.
unfortunately, some partial merge of changes in Qt4-branch.
 
855 3964d 20h werner /branches/port_qt5_64bit/src/ fixed bug in landscape output
added (not already included) mode for dynamicstand output to aggregate to ru level (without species level)
now newly recruited trees are also included in the stand statistics (ru-level).
 
837 3971d 22h werner /branches/port_qt5_64bit/src/ * added total carbon to stand output
* created a new output "landscape" for stand aggregates on landscape level (per species)
* improved error handling ModelController
* improved ilandc: now model settings can be changed via command line (and javascript function can be called)
* finalized "background external seeds"
 
824 3977d 01h werner /branches/port_qt5_64bit/src/ fixed *big* regeneration bug. The map with the height of saplings on a resource unit was used in the establishment subroutine although it was *invalid*. Now the establishment and the regeneration are (again?) in one function and use the same valid map.
this removed the strange stripes in the regeneration pattern (there should have been crashes, but weren't). Consequently, the performance debug output was modified.
added better formatting to debugtimer.cpp for large times (in hours, minutes, seconds).
 
779 4143d 20h werner /branches/port_qt5_64bit/  
697 4683d 17h werner /trunk/ Doxygen documentation revisited.
After re-establishing doxygen documentation (last update: 2009) a lot of smaller/medium documentation fixes.
Documentation is something that could definitely be always improved ;)
 
671 4726d 21h werner /trunk/src/ Necessary changes for GPL licence (i.e. headers in all source files)  
639 4887d 18h werner / move current content to the "trunk"  
615 4946d 22h werner /src/ removed windows specific _isnan() calls  
588 4985d 01h werner /src/core/ added carbon-bookkeeping in the regeneration layer.  
587 4985d 15h werner /src/ added carbon output.
lots of changes necessary to get this done (especially budgeting of biomass pools)
 

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