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1160 2997d 08h werner /branches/iland_regen/src/core/ bug-fixes of the new establishment module (carbon)

first part of the YNP water limitation in establishment.		  
/branches/iland_regen/src/core/establishment.cpp
/branches/iland_regen/src/core/establishment.h
/branches/iland_regen/src/core/saplings.cpp
/branches/iland_regen/src/core/saplings.h
/branches/iland_regen/src/core/snag.cpp
/branches/iland_regen/src/core/species.cpp
/branches/iland_regen/src/core/species.h
/branches/iland_regen/src/core/speciesset.cpp
1157 2998d 18h werner /branches/iland_regen/ merge of changes in the trunk (up to the version used for the 2016 DICE simulation batch).  
/branches/iland_regen/src/output/waterout.cpp
/branches/iland_regen/src/output/waterout.h
/branches/iland_regen
/branches/iland_regen/src/abe/actsalvage.cpp
/branches/iland_regen/src/abe/actsalvage.h
/branches/iland_regen/src/abe/fmstand.cpp
/branches/iland_regen/src/abe/fmstand.h
/branches/iland_regen/src/abe/fmtreelist.cpp
/branches/iland_regen/src/abe/fmunit.cpp
/branches/iland_regen/src/abe/fmunit.h
/branches/iland_regen/src/abe/forestmanagementengine.cpp
/branches/iland_regen/src/abe/forestmanagementengine.h
/branches/iland_regen/src/abe/output/abestandout.cpp
/branches/iland_regen/src/abe/output/abestandremovalout.cpp
/branches/iland_regen/src/abe/scheduler.cpp
/branches/iland_regen/src/abe/scheduler.h
/branches/iland_regen/src/core/climate.h
/branches/iland_regen/src/core/grasscover.h
/branches/iland_regen/src/core/grid.h
/branches/iland_regen/src/core/model.cpp
/branches/iland_regen/src/core/model.h
/branches/iland_regen/src/core/modelcontroller.cpp
/branches/iland_regen/src/core/production3pg.cpp
/branches/iland_regen/src/core/resourceunit.cpp
/branches/iland_regen/src/core/resourceunit.h
/branches/iland_regen/src/core/resourceunitspecies.cpp
/branches/iland_regen/src/core/sapling.cpp
/branches/iland_regen/src/core/snag.cpp
/branches/iland_regen/src/core/snag.h
/branches/iland_regen/src/core/soil.cpp
/branches/iland_regen/src/core/species.cpp
/branches/iland_regen/src/core/speciesset.cpp
/branches/iland_regen/src/core/standloader.cpp
/branches/iland_regen/src/core/standstatistics.cpp
/branches/iland_regen/src/core/standstatistics.h
/branches/iland_regen/src/core/threadrunner.cpp
/branches/iland_regen/src/core/threadrunner.h
/branches/iland_regen/src/core/tree.cpp
/branches/iland_regen/src/core/tree.h
/branches/iland_regen/src/core/watercycle.cpp
/branches/iland_regen/src/core/watercycle.h
/branches/iland_regen/src/iland/iland.pro
/branches/iland_regen/src/iland/mainwindow.cpp
/branches/iland_regen/src/iland/tests.cpp
/branches/iland_regen/src/iland/version.cpp
/branches/iland_regen/src/ilandc/consoleshell.cpp
/branches/iland_regen/src/ilandc/ilandc.pro
/branches/iland_regen/src/output/carbonflowout.cpp
/branches/iland_regen/src/output/carbonflowout.h
/branches/iland_regen/src/output/carbonout.cpp
/branches/iland_regen/src/output/carbonout.h
/branches/iland_regen/src/output/dynamicstandout.cpp
/branches/iland_regen/src/output/landscapeout.cpp
/branches/iland_regen/src/output/managementout.cpp
/branches/iland_regen/src/output/outputmanager.cpp
/branches/iland_regen/src/output/snapshot.cpp
/branches/iland_regen/src/output/standout.cpp
/branches/iland_regen/src/plugins/barkbeetle/barkbeetle.pro
/branches/iland_regen/src/plugins/barkbeetle/barkbeetlemodule.cpp
/branches/iland_regen/src/plugins/barkbeetle/barkbeetlemodule.h
/branches/iland_regen/src/plugins/barkbeetle/barkbeetleout.cpp
/branches/iland_regen/src/plugins/barkbeetle/barkbeetlescript.cpp
/branches/iland_regen/src/plugins/barkbeetle/barkbeetlescript.h
/branches/iland_regen/src/plugins/fire/fire.pro
/branches/iland_regen/src/plugins/fire/firemodule.cpp
/branches/iland_regen/src/plugins/wind/wind.pro
/branches/iland_regen/src/plugins/wind/windmodule.cpp
/branches/iland_regen/src/plugins/wind/windmodule.h
/branches/iland_regen/src/plugins/wind/windscript.cpp
/branches/iland_regen/src/plugins/wind/windscript.h
/branches/iland_regen/src/tools/colors.cpp
/branches/iland_regen/src/tools/expressionwrapper.cpp
/branches/iland_regen/src/tools/gisgrid.cpp
/branches/iland_regen/src/tools/gisgrid.h
/branches/iland_regen/src/tools/globalsettings.cpp
/branches/iland_regen/src/tools/globalsettings.h
/branches/iland_regen/src/tools/scriptglobal.cpp
/branches/iland_regen/src/tools/scriptglobal.h
1104 3068d 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		  
/branches/iland_regen
1088 3137d 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).		  
/branches/port_qt5_64bit/src/abe/actsalvage.cpp
/branches/port_qt5_64bit/src/abe/actsalvage.h
/branches/port_qt5_64bit/src/abe/fmstand.cpp
/branches/port_qt5_64bit/src/abe/fomewrapper.cpp
/branches/port_qt5_64bit/src/abe/forestmanagementengine.cpp
/branches/port_qt5_64bit/src/core/grid.h
/branches/port_qt5_64bit/src/core/layeredgrid.h
/branches/port_qt5_64bit/src/core/snag.cpp
/branches/port_qt5_64bit/src/core/tree.cpp
/branches/port_qt5_64bit/src/plugins/barkbeetle/barkbeetlescript.cpp
/branches/port_qt5_64bit/src/plugins/barkbeetle/barkbeetlescript.h
/branches/port_qt5_64bit/src/plugins/wind/windscript.cpp
/branches/port_qt5_64bit/src/tools/spatialanalysis.cpp
925 3655d 10h werner /branches/port_qt5_64bit/src/core/ calculate 're' also when snags are empty (to avoid errors when snags are not properly initialized)  
/branches/port_qt5_64bit/src/core/snag.cpp
779 4052d 11h werner /branches/port_qt5_64bit/  
/branches/port_qt5_64bit
771 4182d 15h werner /trunk/src/core/ mini-change: calculate climate fators really only when snag is non-empty (see previous commit)  
/trunk/src/core/snag.cpp
770 4182d 15h 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)		  
/trunk/src/core/snag.cpp
/trunk/src/iland/version.cpp
713 4545d 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).  
/trunk/src/core/snag.cpp
/trunk/src/core/snag.h
/trunk/src/core/tree.cpp
/trunk/src/core/tree.h
/trunk/src/iland/tests.cpp
/trunk/src/plugins/wind/windmodule.cpp
697 4592d 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 ;)		  
/trunk/doc
/trunk/doc/iland_doxyfile.doxy
/trunk/src/core/environment.cpp
/trunk/src/core/grid.h
/trunk/src/core/layeredgrid.h
/trunk/src/core/management.cpp
/trunk/src/core/model.cpp
/trunk/src/core/modelcontroller.cpp
/trunk/src/core/phenology.cpp
/trunk/src/core/production3pg.cpp
/trunk/src/core/resourceunit.cpp
/trunk/src/core/resourceunitspecies.cpp
/trunk/src/core/sapling.cpp
/trunk/src/core/seeddispersal.cpp
/trunk/src/core/snag.cpp
/trunk/src/core/soil.cpp
/trunk/src/core/species.cpp
/trunk/src/core/speciesresponse.cpp
/trunk/src/core/speciesset.cpp
/trunk/src/core/stamp.h
/trunk/src/core/stampcontainer.h
/trunk/src/core/standloader.cpp
/trunk/src/core/standstatistics.cpp
/trunk/src/core/tree.cpp
/trunk/src/core/watercycle.cpp
/trunk/src/core/watercycle.h
/trunk/src/iland/maindoc.cpp
/trunk/src/plugins/fire/firemodule.cpp
/trunk/src/plugins/fire/firemodule.h
/trunk/src/plugins/fire/firescript.cpp
/trunk/src/tools/csvfile.cpp
/trunk/src/tools/dem.h
/trunk/src/tools/expressionwrapper.cpp
/trunk/src/tools/gisgrid.cpp
/trunk/src/tools/mapgrid.cpp
/trunk/src/tools/scriptglobal.cpp
/trunk/src/tools/sqlhelper.cpp
671 4635d 12h werner /trunk/src/ Necessary changes for GPL licence (i.e. headers in all source files)  
/trunk/src/core/climate.cpp
/trunk/src/core/climate.h
/trunk/src/core/environment.cpp
/trunk/src/core/environment.h
/trunk/src/core/establishment.cpp
/trunk/src/core/establishment.h
/trunk/src/core/exception.h
/trunk/src/core/global.h
/trunk/src/core/grid.h
/trunk/src/core/layeredgrid.h
/trunk/src/core/management.cpp
/trunk/src/core/management.h
/trunk/src/core/model.cpp
/trunk/src/core/model.h
/trunk/src/core/modelcontroller.cpp
/trunk/src/core/modelcontroller.h
/trunk/src/core/modelsettings.cpp
/trunk/src/core/modelsettings.h
/trunk/src/core/phenology.cpp
/trunk/src/core/phenology.h
/trunk/src/core/plugin_interface.h
/trunk/src/core/production3pg.cpp
/trunk/src/core/production3pg.h
/trunk/src/core/resourceunit.cpp
/trunk/src/core/resourceunit.h
/trunk/src/core/sapling.cpp
/trunk/src/core/sapling.h
/trunk/src/core/seeddispersal.cpp
/trunk/src/core/seeddispersal.h
/trunk/src/core/snag.cpp
/trunk/src/core/snag.h
/trunk/src/core/soil.cpp
/trunk/src/core/soil.h
/trunk/src/core/species.cpp
/trunk/src/core/species.h
/trunk/src/core/speciesresponse.cpp
/trunk/src/core/speciesresponse.h
/trunk/src/core/speciesset.cpp
/trunk/src/core/speciesset.h
/trunk/src/core/stamp.cpp
/trunk/src/core/stamp.h
/trunk/src/core/stampcontainer.cpp
/trunk/src/core/stampcontainer.h
/trunk/src/core/standloader.cpp
/trunk/src/core/standloader.h
/trunk/src/core/standstatistics.cpp
/trunk/src/core/standstatistics.h
/trunk/src/core/threadrunner.cpp
/trunk/src/core/threadrunner.h
/trunk/src/core/timeevents.cpp
/trunk/src/core/timeevents.h
/trunk/src/core/tree.cpp
/trunk/src/core/tree.h
/trunk/src/core/watercycle.cpp
/trunk/src/core/watercycle.h
/trunk/src/iland/aboutdialog.cpp
/trunk/src/iland/aboutdialog.h
/trunk/src/iland/aboutdialog.ui
/trunk/src/iland/mainwindow.cpp
/trunk/src/iland/mainwindow.h
/trunk/src/iland/paintarea.cpp
/trunk/src/iland/paintarea.h
/trunk/src/iland/stable.h
/trunk/src/iland/tests.cpp
/trunk/src/iland/tests.h
/trunk/src/iland/version.h
/trunk/src/output/carbonflowout.cpp
/trunk/src/output/carbonflowout.h
/trunk/src/output/carbonout.cpp
/trunk/src/output/carbonout.h
/trunk/src/output/dynamicstandout.cpp
/trunk/src/output/dynamicstandout.h
/trunk/src/output/managementout.cpp
/trunk/src/output/managementout.h
/trunk/src/output/output.cpp
/trunk/src/output/output.h
/trunk/src/output/outputmanager.cpp
/trunk/src/output/outputmanager.h
/trunk/src/output/productionout.cpp
/trunk/src/output/productionout.h
/trunk/src/output/saplingout.cpp
/trunk/src/output/saplingout.h
/trunk/src/output/standdeadout.cpp
/trunk/src/output/standdeadout.h
/trunk/src/output/standout.cpp
/trunk/src/output/standout.h
/trunk/src/output/treeout.cpp
/trunk/src/output/treeout.h
/trunk/src/plugins/fire/firemodule.cpp
/trunk/src/plugins/fire/firemodule.h
/trunk/src/plugins/fire/fireout.cpp
/trunk/src/plugins/fire/fireout.h
/trunk/src/plugins/fire/fireplugin.cpp
/trunk/src/plugins/fire/fireplugin.h
/trunk/src/tools/climateconverter.cpp
/trunk/src/tools/climateconverter.h
/trunk/src/tools/csvfile.cpp
/trunk/src/tools/csvfile.h
/trunk/src/tools/dem.cpp
/trunk/src/tools/dem.h
/trunk/src/tools/expression.cpp
/trunk/src/tools/expression.h
/trunk/src/tools/expressionwrapper.cpp
/trunk/src/tools/expressionwrapper.h
/trunk/src/tools/floatingaverage.cpp
/trunk/src/tools/floatingaverage.h
/trunk/src/tools/gisgrid.cpp
/trunk/src/tools/gisgrid.h
/trunk/src/tools/globalsettings.cpp
/trunk/src/tools/globalsettings.h
/trunk/src/tools/helper.cpp
/trunk/src/tools/helper.h
/trunk/src/tools/mapgrid.cpp
/trunk/src/tools/mapgrid.h
/trunk/src/tools/modules.cpp
/trunk/src/tools/modules.h
/trunk/src/tools/random.cpp
/trunk/src/tools/random.h
/trunk/src/tools/scriptglobal.cpp
/trunk/src/tools/scriptglobal.h
/trunk/src/tools/settingmetadata.cpp
/trunk/src/tools/settingmetadata.h
/trunk/src/tools/sqlhelper.cpp
/trunk/src/tools/sqlhelper.h
/trunk/src/tools/ticktack.cpp
/trunk/src/tools/ticktack.h
/trunk/src/tools/xmlhelper.cpp
/trunk/src/tools/xmlhelper.h
639 4796d 09h werner / move current content to the "trunk"  
/trunk/executable
/trunk/src
/executable
/src
609 4861d 16h werner /src/ implementing CarbonFlow output and book keeping code.  
/src/core/model.cpp
/src/core/resourceunit.cpp
/src/core/snag.cpp
/src/core/snag.h
/src/core/soil.cpp
/src/core/soil.h
/src/output/carbonflowout.cpp
607 4862d 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		  
/src/core/grid.h
/src/core/management.cpp
/src/core/management.h
/src/core/snag.cpp
/src/core/snag.h
605 4865d 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.		  
/src/output/carbonflowout.cpp
/src/output/carbonflowout.h
/src/core/resourceunit.cpp
/src/core/resourceunitspecies.cpp
/src/core/snag.cpp
/src/core/speciesresponse.cpp
/src/core/watercycle.cpp
/src/iland/iland.pro
/src/output/outputmanager.cpp
/src/tools/globalsettings.cpp
595 4879d 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.		  
/src/core/sapling.cpp
/src/core/snag.cpp
/src/core/snag.h
/src/core/species.cpp
/src/core/species.h
/src/core/tree.cpp
588 4893d 16h werner /src/core/ added carbon-bookkeeping in the regeneration layer.  
/src/core/sapling.cpp
/src/core/sapling.h
/src/core/snag.cpp
/src/core/snag.h
/src/core/standstatistics.cpp
/src/core/tree.cpp
587 4894d 05h werner /src/ added carbon output.
lots of changes necessary to get this done (especially budgeting of biomass pools)		  
/src/output/carbonout.cpp
/src/output/carbonout.h
/src/core/model.cpp
/src/core/snag.cpp
/src/core/snag.h
/src/core/standstatistics.cpp
/src/core/standstatistics.h
/src/iland/iland.pro
/src/output/outputmanager.cpp
574 4896d 16h 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		  
/src/core/grid.h
/src/core/model.cpp
/src/core/model.h
/src/core/resourceunit.cpp
/src/core/resourceunit.h
/src/core/snag.cpp
/src/output/dynamicstandout.cpp
/src/output/managementout.cpp
/src/output/productionout.cpp
/src/output/saplingout.cpp
/src/output/standdeadout.cpp
/src/output/standout.cpp
/src/tools/expressionwrapper.cpp
/src/tools/globalsettings.h
564 4907d 08h 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.		  
/src/core/management.cpp
/src/core/management.h
/src/core/resourceunitspecies.cpp
/src/core/sapling.cpp
/src/core/sapling.h
/src/core/snag.cpp
/src/core/tree.cpp
/src/core/tree.h
/src/tools/mapgrid.cpp
/src/tools/mapgrid.h

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