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1160 2992d 09h werner /branches/iland_regen/src/core/ bug-fixes of the new establishment module (carbon)

first part of the YNP water limitation in establishment.		  
1157 2993d 18h werner /branches/iland_regen/ merge of changes in the trunk (up to the version used for the 2016 DICE simulation batch).  
1104 3063d 16h 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 3132d 09h 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 3650d 10h werner /branches/port_qt5_64bit/src/core/ calculate 're' also when snags are empty (to avoid errors when snags are not properly initialized)  
779 4047d 11h werner /branches/port_qt5_64bit/  
771 4177d 16h werner /trunk/src/core/ mini-change: calculate climate fators really only when snag is non-empty (see previous commit)  
770 4177d 16h 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 4540d 16h 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 4587d 08h 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 4630d 12h werner /trunk/src/ Necessary changes for GPL licence (i.e. headers in all source files)  
639 4791d 09h werner / move current content to the "trunk"  
609 4856d 16h werner /src/ implementing CarbonFlow output and book keeping code.  
607 4857d 08h 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 4860d 15h 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 4874d 18h 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 4888d 16h werner /src/core/ added carbon-bookkeeping in the regeneration layer.  
587 4889d 05h werner /src/ added carbon output.
lots of changes necessary to get this done (especially budgeting of biomass pools)		  
574 4891d 17h 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 4902d 09h 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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