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Rev Age Author Path Log message Diff
1222 3156d 23h werner / public SVN  
1221 3156d 23h werner /branches/ public SVN  
1220 3156d 23h werner /branches/version1.0/ Version 1.0  
1218 3157d 01h werner / clean up repository - make 1.0 trunk again!  
1217 3157d 01h werner / clean up repository - make 1.0 trunk again!  
1182 3302d 23h werner /branches/iland_regen/src/ Torus also effective for seed distribution
new output "SaplingDetails" (super high detail level of individual cohorts)
version information also in ilandc [move version.cpp to core]

[due to a sync problem with the SVN server, some revisions where lost: here they are:]
compiling ilandc

some code clean up - removed old code (sapling.cpp) for sapling trees and establishment.
 
1180 3324d 22h werner /branches/iland_regen/src/ major rewrite of the seed distribution module:
* dispersal kernels fixed (using seeds per area, and not per radius)
* seed production now depends on leaf area of species (on source pixels)
* distribution for all source pixels (skipped the shortcut via continuously covered forest)
* probability of establishment calculated as function of available seedlings (sum of all incoming seedlings)
still testing ;)
more automation functions (e.g. to call OS commands, additional JS event handlers)
 
1177 3333d 23h werner /branches/iland_regen/src/ updating the sapling growth (calculation of stem numbers)  
1172 3358d 06h werner /branches/iland_regen/src/ fixed nasty bug in fire module that caused crashes in release mode (but interestingly not in debug mode).
Reason: The ILAND_GUI #define is *not* visible when building the modules (fire, wind, barkbeetle); a conditional define in species.h has the effect that the structure (i.e. the memory address of some of the member properties) are different (specifically, the "mSeedDispersal" property). From the fire module, accessing the property resolved to a wrong memory address -> crash. Fix: moved the color-property (that is affected by the ILAND_GUI #define) to the end of the object....
 
1167 3366d 07h werner /branches/iland_regen/ merged serotiny from trunk  
1165 3367d 21h werner /branches/iland_regen/src/ implementation of sprouting  
1162 3373d 05h werner /branches/iland_regen/src/ removed the old "mSaplings" from resource unit/model.
Open Issues:
* ActPlanting [init/remove of saplings]
* MapGrid: retrieve list of saplings
* testing of standloader
 
1160 3373d 22h werner /branches/iland_regen/src/core/ bug-fixes of the new establishment module (carbon)

first part of the YNP water limitation in establishment.
 
1104 3445d 05h werner /branches/iland_regen/ Branch dedicated to playing around with establishment/regeneration.
Goals are:
(i) speed up
(ii) introduction of new features for Yellowstone
 
1063 3561d 00h werner /branches/port_qt5_64bit/src/ implementing a first version of the browsing submodule.

many small improvements for ABE.
 
989 3801d 02h werner /branches/port_qt5_64bit/src/ removed the QT GUI library dependency for the console variant of iLand. For this some #ifdef were required.  
837 4257d 03h 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"
 
780 4416d 02h werner /branches/port_qt5_64bit/src/ Steps to build iLand with Qt 5 and with MSVC compiler and 64 bit.
http://iland.boku.ac.at/blogpost44

removed also a couple of warnings that were thrown by the MSVC compiler.
 
779 4429d 01h werner /branches/port_qt5_64bit/  
707 4960d 02h werner /trunk/src/ rework of the random numbers in iland.
Now, many (200000) random numbers are precalculated using a given algorithm (there are three or four choices), then the drandom() etc functions read from this array. After some rotations, the numbers are renewed. The point is: this is now reentrant, so the per-thread storage of MTRand objects is obsolete.
 
705 4960d 22h werner /trunk/src/ series of performance tests / modifications.
Using "valgrind" on the linux virtual machine, some performance
measurements were made.
Some candidates for optimization were tested. (1) the applyLIP()
function (about 30% of total run time in runYear()): here several
inlining options were tested; testing the value of the stamp before
using it (in order to omit the other steps) prooved to be slower than
unsing all stamp values.
(2) the random number generator; here the random number generation is
about 5% of the total run time; the commit contains two/three other
variants.
 
671 5012d 01h werner /trunk/src/ Necessary changes for GPL licence (i.e. headers in all source files)  
667 5047d 10h werner /trunk/src/ finetuning of fire module (new species parameters, xml file parameters, ...)  
639 5172d 23h werner / move current content to the "trunk"  
595 5256d 07h 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.
 
535 5328d 01h werner /src/core/ modified calculation of the Species::soilwaterResponse() following a discussion during paper preparation.
# Supplement
- Eq. S7: ja, sollte glaub ich schon tatsaechlich so ausschauen, wie im Supplement, da sollten wir ev. den Code nachziehen. Wie ist denn deine Einschaetzung, gibts dadurch grosse Aenderungen, und wenn ja in welche Richtung? Und wir sollten wegen der Konsistenz aufpassen. Wenn ich mich recht erinnere ist es ja jetzt so, das wir die Wasserkapazitaet bis zur Psi_sat rechnen (i.e. es wird mehr Wasser gespeichert als wenn wir unsere WHC nur bis Psi_fc definieren wuerden; i.e. mein default setting fuer model.settings.waterUseSoilSaturation=TRUE). Das passt aber schon so weit ich das sehe, i.e. zwischen Psi_sat und Psi_fc sollte die response dann einfach 1 sein.
---> Ich hab das im Code nachgezogen. Der Effekt ist IMHO minimal und wirkt sich dadurch aus, dass bei sehr guter wasserversorgung die soilwaterresponse ein klein wenig besser wird (dritte stelle nach dem komma)
 
534 5328d 02h werner /src/ large(r) update of the soil model. Now, the 'kyl' and 'kyr' parameters (i.e. decomposition rates for the litter/wood-soil pool) are now species parameters and calculated dynamically from the litter inputs.  
528 5331d 19h werner /src/ more enabling of C/N cycling in iLand. little GUI-feature: click on a RU in resource-unit visualization now properly shows RU-related debug outputs.  
511 5360d 06h werner /src/ again, the reineke  
508 5361d 08h werner /src/ fixed calculation of number of saplings (Reineke)  
493 5380d 05h werner /src/ some GUI improvements: paint trees according to a predefined tree color, added also a general info-statusbar-message that shows the runyear/maxrunyear.

use this SQL to add necessary columns:

-- script to add "displayColor" and to fix the spelling error of "reineke"
-- 2010-10-16

alter table species rename to species_copy;

CREATE TABLE "species" ("shortName" CHAR(4),"name" TEXT,"active" INTEGER, "displayColor" TEXT, "LIPFile" TEXT,"specificLeafArea" REAL,"turnoverLeaf" REAL,"turnoverRoot" REAL,"HDlow" TEXT,"HDhigh" TEXT,"woodDensity" REAL,"formFactor" REAL,"bmWoody_a" REAL,"bmWoody_b" REAL,"bmFoliage_a" REAL,"bmFoliage_b" REAL,"bmRoot_a" REAL,"bmRoot_b" REAL,"bmBranch_a" REAL,"bmBranch_b" REAL,"probIntrinsic" REAL,"probStress" REAL,"maximumAge" REAL,"maximumHeight" REAL,"aging" TEXT,
"respVpdExponent" real,"respTempMin" real,"respTempMax" real,"respNitrogenClass" real,"phenologyClass" integer,"isConiferous" INTEGER,"isEvergreen" INTEGER,"maxCanopyConductance" INTEGER,"psiMin" INTEGER,"lightResponseClass" real,"finerootFoliageRatio" real, maturityYears integer, seedYearInterval integer, nonSeedYearFraction real, fecundity_m2 real, seedKernel_as1 real, seedKernel_as2 real, seedKernel_ks0 real,
estMinTemp real, estChillRequirement integer, estGDDMin integer, estGDDMax integer, estGDDBaseTemp real, estBudBirstGDD integer, estFrostFreeDays integer, estFrostTolerance double, sapHeightGrowthPotential text, sapMaxStressYears integer, sapStressThreshold real, sapHDSapling real, sapReinekesR real, sapReferenceRatio real);

insert into species (shortName, name, active, LIPFile, specificLeafArea, turnoverLeaf, turnoverRoot, HDlow, HDhigh, woodDensity, formFactor, bmWoody_a, bmWoody_b, bmFoliage_a, bmFoliage_b, bmRoot_a, bmRoot_b, bmBranch_a, bmBranch_b, probIntrinsic, probStress, maximumAge, maximumHeight, aging, respVpdExponent,
respTempMin, respTempMax, respNitrogenClass, phenologyClass, isConiferous, isEvergreen, maxCanopyConductance, psiMin, lightResponseClass, finerootFoliageRatio, maturityYears, seedYearInterval, nonSeedYearFraction, fecundity_m2, seedKernel_as1, seedKernel_as2, seedKernel_ks0,
estMinTemp, estChillRequirement, estGDDMin, estGDDMax, estGDDBaseTemp, estBudBirstGDD, estFrostFreeDays, estFrostTolerance, sapHeightGrowthPotential, sapMaxStressYears, sapStressThreshold, sapHDSapling, sapReinekesR, sapReferenceRatio
)
select shortName, name, active, LIPFile, specificLeafArea, turnoverLeaf, turnoverRoot, HDlow, HDhigh, woodDensity, formFactor, bmWoody_a, bmWoody_b, bmFoliage_a, bmFoliage_b, bmRoot_a, bmRoot_b, bmBranch_a, bmBranch_b, probIntrinsic, probStress, maximumAge, maximumHeight, aging, respVpdExponent,
respTempMin, respTempMax, respNitrogenClass, phenologyClass, isConiferous, isEvergreen, maxCanopyConductance, psiMin, lightResponseClass, finerootFoliageRatio, maturityYears, seedYearInterval, nonSeedYearFraction, fecundity_m2, seedKernel_as1, seedKernel_as2, seedKernel_ks0,
estMinTemp, estChillRequirement, estGDDMin, estGDDMax, estGDDBaseTemp, estBudBirstGDD, estFrostFreeDays, estFrostTolerance, sapHeightGrowthPotential, sapMaxStressYears, sapStressThreshold, sapHDSapling, sapReineckesR, sapReferenceRatio
FROM species_copy;

update species set displayColor = '3E9C49'; -- a simple green
 
483 5383d 04h werner /src/core/ recruitment: recruit the number of individuals provided by the Reineke equation.
(correct spelling error: reinecke -> reineke)
 
475 5384d 04h werner /src/ * Snag dynamics
debug output "SnagDynamics"
life cycle of Snag objects
include Snag Dynamics in newYear / year end routines

* threadrunner.cpp: parallel execution of species related tasks, e.g. the seed dispersal. In the current form, the ThreadRunner is much nicer:
ThreadRunner runner(mActiveSpecies);
runner.run(func_ptr);
 
470 5388d 08h werner /src/core/ add light response function to sapling growth (rest: constness of lightresponse function calls)  
467 5389d 07h werner /src/core/ added species-parameter "sapReferenceFactor" (for calculation of f_env,yr for sapling growth).  
460 5389d 23h werner /src/ changed label in regeneration debug output,
added minimum height of 4m as requirement for seed production.
 
453 5439d 18h werner /src/ sapling growth now in a basic working state. started to implement recruitment. One bug with the "maximum-establishment-height-grid" known.
added also visualization of regeneration layer. Once I have time, I should restructure the drawing/visualization code as it gets quirky (and a paper-concept is available...)
 
450 5440d 05h werner /src/core/ implementing sapling growth...  
449 5440d 06h werner /src/ start of implementation of sapling growth.
setup of the temporal height-map for saplings.
 
446 5489d 07h werner /src/ put Establishment parameters into database (total of 8 params).
new version 0.3 -- yeah!
just for the records the SQL for regeneration and Establishment:

-- add columns for regeneration
alter table species add maturityYears integer;
alter table species add seedYearInterval integer;
alter table species add nonSeedYearFraction real;
alter table species add fecundity_m2 real;
alter table species add seedKernel_as1 real;
alter table species add seedKernel_as2 real;
alter table species add seedKernel_ks0 real;

-- default values regeneration
update species
set maturityYears=30,seedYearInterval=5, nonSeedYearFraction=0.25, fecundity_m2=100, seedKernel_as1=100, seedKernel_as2=0, seedKernel_ks0=0;


-- add columns for establishment
/* --> corresponding c++-struct:
struct EstablishmentParameters
{
double min_temp; //degC
int chill_requirement; // days of chilling requirement
int GDD_min, GDD_max; // GDD thresholds
double GDD_baseTemperature; // for GDD-calc: GDD=sum(T - baseTemp)
int bud_birst; // GDDs needed until bud burst
int frost_free; // minimum number of annual frost-free days required
double frost_tolerance; //factor in growing season frost tolerance calculation
EstablishmentParameters(): min_temp(-37), chill_requirement(56), GDD_min(177), GDD_max(3261), GDD_baseTemperature(3.4),
bud_birst(255), frost_free(65), frost_tolerance(0.5) {}
}; */

alter table species add estMinTemp real;
alter table species add estChillRequirement integer;
alter table species add estGDDMin integer;
alter table species add estGDDMax integer;
alter table species add estGDDBaseTemp real;
alter table species add estBudBirstGDD integer;
alter table species add estFrostFreeDays integer;
alter table species add estFrostTolerance double;


-- default values establishment
update species
set estMinTemp=-37, estChillRequirement=56, estGDDMin=177, estGDDMaX=3261, estGDDBaseTemp=3.4,
estBudBirstGDD=255, estFrostFreeDays=65, estFrostTolerance=0.5;