Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Menu
Open sidebar
SimAquaLife
GR3D
Commits
b7a07c60
Commit
b7a07c60
authored
Jul 03, 2020
by
Lambert Patrick
Browse files
Merge branch 'Camille_Bis' into patrick
parents
436afde3
2acc64b3
Changes
5
Hide whitespace changes
Inline
Side-by-side
data/input/atlanticarea/BNaaBasins.xml
View file @
b7a07c60
...
...
@@ -13,6 +13,6 @@
<seaBasinNameLabel>
BASIN_NAME
</seaBasinNameLabel>
<continentPathName>
ID
</continentPathName>
<distanceGridFileName>
data/input/atlanticarea/distanceGridAA.csv
</distanceGridFileName>
<temperatureCatchmentFile>
data/input/atlanticarea/aa_sst_
depuis1800
.csv
</temperatureCatchmentFile>
<temperatureCatchmentFile>
data/input/atlanticarea/aa_sst_
histo
.csv
</temperatureCatchmentFile>
<useRealPDam>
false
</useRealPDam>
</environment.BasinNetworkSWithContinent>
\ No newline at end of file
data/input/atlanticarea/aa_sst_
depuis1800
.csv
→
data/input/atlanticarea/aa_sst_
histo
.csv
View file @
b7a07c60
File moved
data/input/atlanticarea/fishTryRealBV_CC.xml
→
data/input/atlanticarea/fishTryRealBV_CC
_Alosa
.xml
View file @
b7a07c60
...
...
@@ -19,11 +19,11 @@
<excretionRate
class=
"hashtable"
>
<entry>
<string>
P
</string>
<double>
2.17
E-
6
</double>
<double>
5.208
E-
5
</double>
</entry>
<entry>
<string>
N
</string>
<double>
2.471
E-
5
</double>
<double>
5.9304
E-
4
</double>
</entry>
</excretionRate>
<fishFeaturesPreSpawning
class=
"hashtable"
>
...
...
@@ -280,7 +280,7 @@
<exportSeason>
SPRING
</exportSeason>
<fileNameOutput>
effectiveBiomassFluxesBeforeReproduction
</fileNameOutput>
</species.WriteEffectiveAndBiomassFluxes>
<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>
ASYNCHRONOUS
</synchronisationMode>
<reproductionSeason>
SPRING
</reproductionSeason>
...
...
@@ -297,11 +297,17 @@
<initialLength>
2.0
</initialLength>
<sigmaRecruitment>
0.2
</sigmaRecruitment>
<survivalRateAfterReproduction>
0.1
</survivalRateAfterReproduction>
<maxNumberOfSuperIndividualPerReproduction>
5
00.0
</maxNumberOfSuperIndividualPerReproduction>
<maxNumberOfSuperIndividualPerReproduction>
1
00.0
</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>
false
</withDiagnose>
<displayFluxesOnConsole>
false
</displayFluxesOnConsole>
</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<species.WriteEffectiveAndBiomassFluxes>
<synchronisationMode>
ASYNCHRONOUS
</synchronisationMode>
<exportSeason>
SPRING
</exportSeason>
<fileNameOutput>
effectiveBiomassFluxesAfterReproduction
</fileNameOutput>
</species.WriteEffectiveAndBiomassFluxes>
<species.MigrateToSea>
<seaMigrationSeason>
SUMMER
</seaMigrationSeason>
<synchronisationMode>
ASYNCHRONOUS
</synchronisationMode>
...
...
data/input/northeastamerica/fishTryRealBV_CC_Sapidissima.xml
View file @
b7a07c60
...
...
@@ -198,7 +198,7 @@
<parameterSetLine>
0
</parameterSetLine>
<yearOfTheUpdate>
0
</yearOfTheUpdate>
<basinsToUpdateFile>
data/input/reality/basinsToUpdate.csv
</basinsToUpdateFile>
<outputPath>
data/output/
</outputPath>
<outputPath>
data/output/
northeastamerica/
</outputPath>
<minYearToWrite>
1900
</minYearToWrite>
<fileNameFluxes>
nutrientFluxes
</fileNameFluxes>
<lengthAtHatching>
2.8
</lengthAtHatching>
...
...
@@ -297,7 +297,7 @@
<initialLength>
2.8
</initialLength>
<sigmaRecruitment>
0.2
</sigmaRecruitment>
<survivalRateAfterReproduction>
0.1
</survivalRateAfterReproduction>
<maxNumberOfSuperIndividualPerReproduction>
1
5
0.0
<maxNumberOfSuperIndividualPerReproduction>
1
0
0.0
</maxNumberOfSuperIndividualPerReproduction>
<withDiagnose>
false
</withDiagnose>
<displayFluxesOnConsole>
false
</displayFluxesOnConsole>
...
...
@@ -318,7 +318,7 @@
<processesAtEnd>
<species.WriteNutrientImportFluxes>
<synchronisationMode>
ASYNCHRONOUS
</synchronisationMode>
<fileName>
f
luxes
</fileName>
<fileName>
nutrientImportfF
luxes
</fileName>
</species.WriteNutrientImportFluxes>
<species.WriteNutrientExportFluxes>
...
...
src/main/java/species/DiadromousFishGroup.java
View file @
b7a07c60
...
...
@@ -89,10 +89,10 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
private
long
yearOfTheUpdate
;
/**
* list of the basins to be updated
column 1: name of the basin column 2: Pattractive: how the bassin become
*
attractive (0 not attractive, 1 ??? normal weight associated to catchment size) column 3: Paccessible: how the
* bassin become a
cesssibl
e (0 not a
ccessibl
e, 1 ???normal weight
to inter
catchment
distance
)
*
* list of the basins to be updated
*
column 1: name of the basin
*
column 2: Pattractive: how the
bassin become a
ttractiv
e (0 not a
ttractiv
e, 1 ???
normal weight
associated to
catchment
size
)
*
column 3: Paccessible: how the bassin become acesssible (0 not accessible, 1 ???normal weight to inter catchment distance )
* @unit
*/
private
String
basinsToUpdateFile
=
"data/input/reality/basinsToUpdate.csv"
;
...
...
@@ -108,33 +108,38 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
private
transient
String
sep
;
/**
* map <key> basin name <value> Duo <first> pAttractive <second> pAccessible
*
* map
* <key> basin name
* <value> Duo
* <first> pAttractive
* <second> pAccessible
* @unit
*/
private
transient
Map
<
String
,
Duo
<
Double
,
Double
>>
basinsToUpdate
;
/**
* length when fish hatchs (
when the diadromousFish is created after reproduction) no diffrence between gender
* length when fish hatchs (when the diadromousFish is created after reproduction) no diffrence between gender
*
* @unit cm
*/
private
double
lengthAtHatching
=
2
.;
/**
* L infinity of the van Bertalanffy growth curve for female
L = Linf *(1-exp(-K*(t-t0))
*
* L infinity of the van Bertalanffy growth curve for
female
*
L = Linf *(1-exp(-K*(t-t0))
* @unit cm
*/
public
double
linfVonBertForFemale
=
60
.;
/**
* L infinity of the van Bertalanffy growth curve for male L = Linf *(1-exp(-K*(t-t0))
*
* L infinity of the van Bertalanffy growth curve for male
* L = Linf *(1-exp(-K*(t-t0))
*
* @unit cm
*/
public
double
linfVonBertForMale
=
60
.;
/**
* Brody growth coefficient of the von Bertalanffy growth curve for female (calculated from the parameterset file) *
* L = Linf *(1-exp(-K*(t-t0))
...
...
@@ -199,11 +204,9 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
double
aResidenceTime
=
30
;
Map
<
String
,
Double
>
anExcretionRate
=
new
Hashtable
<
String
,
Double
>();
anExcretionRate
.
put
(
"N"
,
24.71
E
-
6
);
// values from Barber et al, Alosa sapidissima in ug/g wet mass/hour :
// convertit en g
anExcretionRate
.
put
(
"P"
,
2.17
E
-
6
);
// values from Barber et al, Alosa sapidissima in ug/g wet mass/hour:
// convertit en g
Map
<
String
,
Double
>
anExcretionRate
=
new
Hashtable
<
String
,
Double
>();
anExcretionRate
.
put
(
"N"
,
24.71
E
-
6
*
24
);
//values from Barber et al, Alosa sapidissima in ug/g wet mass/hour : convertit en g
anExcretionRate
.
put
(
"P"
,
2.17
E
-
6
*
24
);
//values from Barber et al, Alosa sapidissima in ug/g wet mass/hour: convertit en g
/*
* A feature pre spawning
...
...
@@ -508,11 +511,6 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, BasinNet
}
}
/*
* while (scanner.hasNext()) { scanner.next(); // skip basin_id String basin_name = scanner.next(); String
* obs = scanner.next(); scanner.next(); // skip obs_1851_1950, scanner.next(); // skip obs_1951_2010 if
* (obs != null) obs1900.put(basin_name, Integer.valueOf(obs)); }
*/
reader
.
close
();
scanner
.
close
();
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment