fishRIOBasin_Sapidissima.xml 11 KB
Newer Older
Poulet Camille's avatar
Poulet Camille committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
<list>
	<species.DiadromousFishGroup>
		<name>species A</name>
		<color>
			<red>255</red>
			<green>0</green>
			<blue>0</blue>
			<alpha>255</alpha>
		</color>

		<dMaxDisp>300.0</dMaxDisp>

		<nutrientRoutine>
			<nutrientsOfInterest>
				<string>N</string>
				<string>P</string>
			</nutrientsOfInterest>
			<residenceTime>30.0</residenceTime>
			<excretionRate class="hashtable">
				<entry>
					<string>P</string>
					<double>2.17E-6</double>
				</entry>
				<entry>
					<string>N</string>
					<double>2.471E-5</double>
				</entry>
			</excretionRate>
			<fishFeaturesPreSpawning class="hashtable">
				<entry>
					<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
					<hashtable>
						<entry>
							<string>bLW_Gonad</string>
							<double>3.3838</double>
						</entry>
						<entry>
							<string>aLW_Gonad</string>
							<double>-8.8744</double>
						</entry>
						<entry>
							<string>bLW</string>
							<double>3.2252</double>
						</entry>
						<entry>
							<string>aLW</string>
							<double>0.004095817237891344</double>
						</entry>
					</hashtable>
				</entry>
				<entry>
					<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
					<hashtable>
						<entry>
							<string>bLW_Gonad</string>
							<double>2.6729</double>
						</entry>
						<entry>
							<string>aLW_Gonad</string>
							<double>-5.2425</double>
						</entry>
						<entry>
							<string>bLW</string>
							<double>3.3429</double>
						</entry>
						<entry>
							<string>aLW</string>
							<double>0.002665367811305362</double>
						</entry>
					</hashtable>
				</entry>
			</fishFeaturesPreSpawning>
			<fishFeaturesPostSpawning class="hashtable">
				<entry>
					<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
					<hashtable>
						<entry>
							<string>bLW_Gonad</string>
							<double>3.8331</double>
						</entry>
						<entry>
							<string>aLW_Gonad</string>
							<double>-11.285</double>
						</entry>
						<entry>
							<string>bLW</string>
							<double>2.9973</double>
						</entry>
						<entry>
							<string>aLW</string>
							<double>0.010383887012522573</double>
						</entry>
					</hashtable>
				</entry>
				<entry>
					<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
					<hashtable>
						<entry>
							<string>bLW_Gonad</string>
							<double>2.8545</double>
						</entry>
						<entry>
							<string>aLW_Gonad</string>
							<double>-6.6234</double>
						</entry>
						<entry>
							<string>bLW</string>
							<double>2.9418</double>
						</entry>
						<entry>
							<string>aLW</string>
							<double>0.013199187556948952</double>
						</entry>
					</hashtable>
				</entry>
			</fishFeaturesPostSpawning>
			<juvenileFeatures class="hashtable">
				<entry>
					<string>bLW</string>
					<double>3.0306</double>
				</entry>
				<entry>
					<string>aLW</string>
					<double>0.006986429759979109</double>
				</entry>
			</juvenileFeatures>
			<compoCarcassPreSpawning class="hashtable">
				<entry>
					<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
					<hashtable>
						<entry>
							<string>P</string>
							<double>0.00666</double>
						</entry>
						<entry>
							<string>N</string>
							<double>0.02941</double>
						</entry>
					</hashtable>
				</entry>
				<entry>
					<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
					<hashtable>
						<entry>
							<string>P</string>
							<double>0.006730000000000001</double>
						</entry>
						<entry>
							<string>N</string>
							<double>0.029580000000000002</double>
						</entry>
					</hashtable>
				</entry>
			</compoCarcassPreSpawning>
			<compoGametes class="hashtable">
				<entry>
					<species.DiadromousFish_-Gender>MALE</species.DiadromousFish_-Gender>
					<hashtable>
						<entry>
							<string>P</string>
							<double>0.00724</double>
						</entry>
						<entry>
							<string>N</string>
							<double>0.0325</double>
						</entry>
					</hashtable>
				</entry>
				<entry>
					<species.DiadromousFish_-Gender>FEMALE</species.DiadromousFish_-Gender>
					<hashtable>
						<entry>
							<string>P</string>
							<double>0.0032</double>
						</entry>
						<entry>
							<string>N</string>
							<double>0.03242</double>
						</entry>
					</hashtable>
				</entry>
			</compoGametes>
			<compoJuvenile class="hashtable">
				<entry>
					<string>P</string>
					<double>0.00887</double>
				</entry>
				<entry>
					<string>N</string>
					<double>0.02803</double>
				</entry>
			</compoJuvenile>
		</nutrientRoutine>

		<fileNameInputForInitialObservation>data/input/reality/Obs1900.csv</fileNameInputForInitialObservation>
		<centileForRange>0.95</centileForRange>
		<parameterSetfileName>data/input/reality/parameterSet.csv</parameterSetfileName>
		<parameterSetLine>0</parameterSetLine>
		<yearOfTheUpdate>0</yearOfTheUpdate>
		<basinsToUpdateFile>data/input/reality/basinsToUpdate.csv</basinsToUpdateFile>
		<outputPath>data/output/northeastamerica/</outputPath>
		<minYearToWrite>1900</minYearToWrite>
		<fileNameFluxes>nutrientFluxes</fileNameFluxes>
		<lengthAtHatching>2.8</lengthAtHatching>
		<linfVonBertForFemale>76.0</linfVonBertForFemale>
		<linfVonBertForMale>76.0</linfVonBertForMale>
		<lFirstMaturityForFemale>45.0</lFirstMaturityForFemale>
		<lFirstMaturityForMale>40.0</lFirstMaturityForMale>
		<processes>
			<processesAtBegin>

			</processesAtBegin>

			<processesEachStep>
				<environment.InformTime>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<consoleDisplay>true</consoleDisplay>
				</environment.InformTime>

				<species.PlopProcess>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<temporisation>0</temporisation>
				</species.PlopProcess>

				<species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<nbFishPerSI>100000</nbFishPerSI>
					<initialLength>2.8</initialLength>
					<etaPopulate>40.0</etaPopulate>
					<timesOfPopulate>5</timesOfPopulate>
					<populateSeason>SPRING</populateSeason>
				</species.PopulateBasinNetworkSeveralTimesAccordingToBasinSize>

				<species.Age>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
				</species.Age>

				<species.Grow>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<tempMinGrow>3.0</tempMinGrow>
					<tempMaxGrow>26.0</tempMaxGrow>
					<tempOptGrow>17.0</tempOptGrow>
					<kOptForFemale>0.3236</kOptForFemale>
					<kOptForMale>0.2141</kOptForMale>
					<sigmaDeltaLVonBert>0.2</sigmaDeltaLVonBert>
				</species.Grow>

				<species.MigrateBetweenOffshores>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<migrationSeasonToReachWinteringOffshore>AUTOMN</migrationSeasonToReachWinteringOffshore>
					<migrationSeasonToReachSummeringOffshore>SPRING</migrationSeasonToReachSummeringOffshore>
				</species.MigrateBetweenOffshores>

				<species.MigrateFromOffshoreToInshore>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<migrationSeasonToReachInshore>SPRING</migrationSeasonToReachInshore>
				</species.MigrateFromOffshoreToInshore>

				<species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<alpha0Rep>-2.9</alpha0Rep>
					<alpha1Rep>19.7</alpha1Rep>
					<alpha3Rep>0.0</alpha3Rep>
					<meanBvSurface>17351</meanBvSurface>
					<standardDeviationBvSurface>35594</standardDeviationBvSurface>
					<meanInterDistance>300.0</meanInterDistance>
					<standardDeviationInterDistance>978.0</standardDeviationInterDistance>
					<pHomingForReachEquil>0.97</pHomingForReachEquil>
					<pHomingAfterEquil>0.97</pHomingAfterEquil>
					<NbYearForInstallPop>0</NbYearForInstallPop>
					<riverMigrationSeason>SPRING</riverMigrationSeason>
					<alpha2Rep>0.0</alpha2Rep>
					<meanSpawnersLengthAtRepro>45.0</meanSpawnersLengthAtRepro>
					<standardDeviationOfSpawnersLengthAtRepro>2.0</standardDeviationOfSpawnersLengthAtRepro>
					<weightOfDeathBasin>0.4</weightOfDeathBasin>
				</species.DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin>

				<species.Survive>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<tempMinSurvivalSpawnerInRiv>8</tempMinSurvivalSpawnerInRiv>
					<tempOptSurvivalSpawnerInRiv>17.0</tempOptSurvivalSpawnerInRiv>
					<tempMaxSurvivalSpawnerInRiv>26</tempMaxSurvivalSpawnerInRiv>
					<survivalProbOptSpawnerInRiv>1.0</survivalProbOptSpawnerInRiv>
					<!--<mortalityRateInRiver>0.4</mortalityRateInRiver> -->
					<mortalityRateInSea>0.4</mortalityRateInSea>
					<mortalityRateInOffshore>0.4</mortalityRateInOffshore>
				</species.Survive>

				<species.WriteEffectiveAndBiomassFluxes>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<exportSeason>SPRING</exportSeason>
					<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput>
				</species.WriteEffectiveAndBiomassFluxes>

				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<reproductionSeason>SPRING</reproductionSeason>
					<tempMinRep>10</tempMinRep>
					<tempOptRep>17</tempOptRep>
					<tempMaxRep>30</tempMaxRep>
					<eta>2.4</eta>
					<ratioS95__S50>1.9</ratioS95__S50>
					<a>270000</a>
					<delta__t>0.33</delta__t>
					<survOptRep>0.0017</survOptRep>
					<lambda>4.1E-4</lambda>
					<proportionOfFemaleAtBirth>0.5</proportionOfFemaleAtBirth>
					<initialLength>2.8</initialLength>
					<sigmaRecruitment>0.2</sigmaRecruitment>
					<survivalRateAfterReproduction>0.1</survivalRateAfterReproduction>
					<maxNumberOfSuperIndividualPerReproduction>100.0
					</maxNumberOfSuperIndividualPerReproduction>
					<withDiagnose>false</withDiagnose>
					<displayFluxesOnConsole>false</displayFluxesOnConsole>
				</species.ReproduceAndSurviveAfterReproductionWithDiagnose>

				<species.MigrateFromRiverToInshore>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<migrationSeasonToReachInshore>SPRING</migrationSeasonToReachInshore>
					<displayFluxesOnConsole>true</displayFluxesOnConsole>
					
				</species.MigrateFromRiverToInshore>

				<species.MigrateToOffshore>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<migrationSeasonToReachSummeringOffshore>SPRING</migrationSeasonToReachSummeringOffshore>
				</species.MigrateToOffshore>

				<environment.updateTemperatureInRealBasin>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<offshoreTemperature>12.0</offshoreTemperature>
				</environment.updateTemperatureInRealBasin>
			</processesEachStep>

			<processesAtEnd>
				<species.WriteNutrientImportFluxes>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<fileName>nutrientImportfFluxes</fileName>
				</species.WriteNutrientImportFluxes>

				<species.WriteNutrientExportFluxes>
					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
					<fileName>nutrientExportFluxes</fileName>
				</species.WriteNutrientExportFluxes>

			</processesAtEnd>
		</processes>
		<useCemetery>false</useCemetery>
	</species.DiadromousFishGroup>
</list>