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1160 3093d 16h werner /branches/iland_regen/src/core/ bug-fixes of the new establishment module (carbon)

first part of the YNP water limitation in establishment.		  
1157 3095d 02h werner /branches/iland_regen/ merge of changes in the trunk (up to the version used for the 2016 DICE simulation batch).  
1104 3164d 23h werner /branches/iland_regen/ Branch dedicated to playing around with establishment/regeneration.
Goals are:
(i) speed up
(ii) introduction of new features for Yellowstone		  
1088 3233d 17h werner /branches/port_qt5_64bit/src/ salavage management bark beetle damages
some fixes w.r.t. the correct extent of grids.
added "year" as stand varaible (abe).		  
925 3751d 18h werner /branches/port_qt5_64bit/src/core/ calculate 're' also when snags are empty (to avoid errors when snags are not properly initialized)  
779 4148d 19h werner /branches/port_qt5_64bit/  
771 4278d 23h werner /trunk/src/core/ mini-change: calculate climate fators really only when snag is non-empty (see previous commit)  
770 4278d 23h werner /trunk/src/ fixed a bug with deadwood decay: (see analysis/extseeds/analyse_total_carbon20130113.docx). For a RU without vegetation (trees/saplings) the water cycle was not calculated -> therefore no values for evapotranspiration were available -> the climate factors for the deadwood decay were only driven by temperature (not by humidity) -> only a very slow decay until a RU got populated. Ouch.
now the water cycle is calculated for every resource unit with non-empty snags (either flux or state non-zero)		  
713 4642d 00h werner /trunk/src/ implemented a way to split the biomass of a dead tree into several pathways (i.e. to soil, to snags, to atmosphere/removal).  
697 4688d 16h 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 4731d 20h werner /trunk/src/ Necessary changes for GPL licence (i.e. headers in all source files)  
639 4892d 17h werner / move current content to the "trunk"  
609 4958d 00h werner /src/ implementing CarbonFlow output and book keeping code.  
607 4958d 16h werner /src/core/ smaller fixes:
* error when exporting ESRI files
* a new JS function "slashSnags()" for managing standing dead trees
* handling of newly burnt tree when removing carbon due to a fire event		  
605 4961d 23h werner /src/ added the "rid" (i.e. a unique id per resource unit) in various debug outputs.
added the "shell" of a new carbonflow output.		  
595 4976d 01h werner /src/core/ changed behavior of coarse roots: if biomass exceeds value from allometric relation, the excell biomass is pushed to the soil (avoid piling up of coarse root carbon in the soil)
inlined some biomass functions in species.h.		  
588 4990d 00h werner /src/core/ added carbon-bookkeeping in the regeneration layer.  
587 4990d 13h werner /src/ added carbon output.
lots of changes necessary to get this done (especially budgeting of biomass pools)		  
574 4993d 00h werner /src/ * modified outputs to write only rows for valid resource units
* dropped setting "woodDecompRate" (snag.cpp)
* calculate the "stockableArea" of a resource unit based on the stand grid
* use the stockableArea for calculation of LAI		  
564 5003d 16h werner /src/ Improvements of the Management API and functionality.
new functionality:
* killSaplings() -> use a "MapGrid" and remove small trees specifically
* properties defining biomass remove fractions during management

Now the tree list of the management object is cleaned up after a management, i.e. successive managements without reloading the tree list are possible.		  

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