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1088 3229d 21h 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 3747d 21h werner /branches/port_qt5_64bit/src/core/ calculate 're' also when snags are empty (to avoid errors when snags are not properly initialized)  
779 4144d 22h werner /branches/port_qt5_64bit/  
771 4275d 03h werner /trunk/src/core/ mini-change: calculate climate fators really only when snag is non-empty (see previous commit)  
770 4275d 03h 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 4638d 03h 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 4684d 19h 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 4727d 23h werner /trunk/src/ Necessary changes for GPL licence (i.e. headers in all source files)  
639 4888d 21h werner / move current content to the "trunk"  
609 4954d 04h werner /src/ implementing CarbonFlow output and book keeping code.  
607 4954d 20h 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 4958d 02h 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 4972d 05h 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 4986d 03h werner /src/core/ added carbon-bookkeeping in the regeneration layer.  
587 4986d 17h werner /src/ added carbon output.
lots of changes necessary to get this done (especially budgeting of biomass pools)		  
574 4989d 04h 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 4999d 20h 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.		  
562 5003d 00h werner /src/ calculate ET0 (reference evapotranspiration) that is used for snag decay 're'. Another version of penman monteith is used for calculation.
See the excel - based "re_decomp.xlsx" for details		  
557 5006d 20h werner /src/ added initialization of snags and some new resource unit variables.
Example: model.initialization node:
<snags>
<swdC>12000</swdC>
<swdCN>120</swdCN>
<swdCount>50</swdCount>
<otherC>4000</otherC>
<otherCN>30</otherCN>
<swdDecompRate>0.05</swdDecompRate>
<woodDecompRate>0.05</woodDecompRate>
<swdHalfLife>30</swdHalfLife>
</snags>		  
553 5008d 00h werner /src/core/ another variant to calculate 're', following Adair et al 2008. Based on monthly sums of precipitation and PET. PET is calculated during the water cycle, monthly precipitation is summed in the climate object itself.  

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