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New structure with new libraries for InitialPop, Production and Dispersal #364

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New structure with new libraries for InitialPop, Production and Dispersal #364

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80245f0
[PL] new structure with separation in InitialPop, Production and Disp…
mcwimm Nov 7, 2024
277e3b6
[PL] create PopManager Sub-lib
mcwimm Nov 8, 2024
9fad795
[PL] add doc + remove prints
mcwimm Nov 8, 2024
abfa4d9
[PL] add doc + remove prints
mcwimm Nov 8, 2024
96b8a62
[PL] remove unused inheritance
mcwimm Nov 8, 2024
47a69bf
[PL] add weighted dispersal
mcwimm Nov 8, 2024
388e574
[PL] error message + format + doc
mcwimm Nov 12, 2024
2924a9f
[PL] add production time
mcwimm Nov 12, 2024
b8879aa
[PL] add SizeDependent production
mcwimm Nov 12, 2024
648295f
[PL] typos+doc
mcwimm Nov 12, 2024
4a3f517
[PL] add dispersal around parent plants
mcwimm Nov 19, 2024
44549fd
[PL] fix to call production only when neccessary
mcwimm Dec 5, 2024
4b53237
[PL] allow multiple production rates
mcwimm Dec 5, 2024
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9 changes: 9 additions & 0 deletions Benchmarks/BenchmarkList.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -134,6 +134,15 @@
<FromFile>
<test> FromFile_CI.xml </test>
</FromFile>
<Random_v310>
<test> Random_v310_CI.xml </test>
</Random_v310>
<FromFile_v310>
<test> FromFile_v310_CI.xml </test>
</FromFile_v310>
<Weighted>
<test> Weighted_CI.xml </test>
</Weighted>
</Population>
</ModuleBenchmarks>
</Benchmarks>
12 changes: 5 additions & 7 deletions Benchmarks/ModuleBenchmarks/PlantModules/Bettina/Default/ReferenceTree.xml
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Expand Up @@ -8,14 +8,12 @@
<type> Default </type>
</belowground>
</resources>
<plant_dynamics>
<type> Bettina </type>
<mortality>NoGrowth</mortality>
</plant_dynamics>
<population>
<group>
<name> Initial </name>
<species> Avicennia </species>
<vegetation_model_type> Bettina </vegetation_model_type>
<mortality> NoGrowth </mortality>
<distribution>
<type> Random </type>
<domain>
Expand All @@ -32,16 +30,16 @@
<time_loop>
<type> Simple </type>
<t_start> 0 </t_start>
<t_end> 5e9 </t_end>
<delta_t> 1e6 </delta_t>
<t_end> 3600*24*365.25*50 </t_end>
<delta_t> 3600*24*365.25/12 </delta_t>
</time_loop>
<visualization>
<type> NONE </type>
</visualization>
<output>
<type> OneFile </type>
<allow_previous_output>True</allow_previous_output>
<output_dir>Benchmarks/TestOutputs/</output_dir>
<output_dir>Benchmarks/h_008/</output_dir>
<geometry_output> r_stem </geometry_output>
<geometry_output> h_stem </geometry_output>
<geometry_output> r_crown </geometry_output>
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67 changes: 67 additions & 0 deletions Benchmarks/ModuleBenchmarks/Population/Distance2Parent/Distance2Parent.xml
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@@ -0,0 +1,67 @@
<MangaProject>
<random_seed>643879</random_seed>
<resources>
<aboveground>
<type> AsymmetricZOI </type>
<domain>
<x_1> 0 </x_1>
<y_1> 0 </y_1>
<x_2> 22 </x_2>
<y_2> 22 </y_2>
<x_resolution> 22 </x_resolution>
<y_resolution> 22 </y_resolution>
<allow_interpolation>True</allow_interpolation>
</domain>
</aboveground>
<belowground>
<type> Default </type>
</belowground>
</resources>
<population>
<group>
<name> Initial </name>
<species> Avicennia </species>
<vegetation_model_type> Bettina </vegetation_model_type>
<mortality>NoGrowth</mortality>
<domain>
<x_1> 0 </x_1>
<y_1> 0 </y_1>
<x_2> 22 </x_2>
<y_2> 22 </y_2>
</domain>
<initial_population>
<type>FromFile</type>
<filename>Benchmarks/ModuleBenchmarks/PlantModules/Bettina/ag_initial_population.csv</filename>
</initial_population>
<production>
<type>FixedRate</type>
<n_individuals>50</n_individuals>
<per_individual>True</per_individual>
</production>
<dispersal>
<type> Distance2Parent </type>
<distribution>normal</distribution>
<loc>0</loc>
<scale>0.5</scale>
</dispersal>
</group>
</population>
<time_loop>
<type> Simple </type>
<t_start> 0 </t_start>
<t_end> 1e6 </t_end>
<delta_t> 1e6 </delta_t>
<terminal_print>year</terminal_print>
</time_loop>
<visualization>
<type> NONE </type>
</visualization>
<output>
<type> OneFile </type>
<allow_previous_output>True</allow_previous_output>
<output_dir>Benchmarks/ModuleBenchmarks/Population/Distance2Parent/ReferenceFiles/Distance2Parent</output_dir>
<geometry_output> r_stem </geometry_output>
<growth_output> age </growth_output>
</output>
</MangaProject>

64 changes: 64 additions & 0 deletions Benchmarks/ModuleBenchmarks/Population/Distance2Parent/Distance2Parent_CI.xml
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@@ -0,0 +1,64 @@
<MangaProject>
<random_seed>643879</random_seed>
<resources>
<aboveground>
<type> AsymmetricZOI </type>
<domain>
<x_1> 0 </x_1>
<y_1> 0 </y_1>
<x_2> 22 </x_2>
<y_2> 22 </y_2>
<x_resolution> 22 </x_resolution>
<y_resolution> 22 </y_resolution>
<allow_interpolation>True</allow_interpolation>
</domain>
</aboveground>
<belowground>
<type> Default </type>
</belowground>
</resources>
<population>
<group>
<name> Initial </name>
<species> Avicennia </species>
<vegetation_model_type> Bettina </vegetation_model_type>
<mortality>NoGrowth</mortality>
<domain>
<x_1> 0 </x_1>
<y_1> 0 </y_1>
<x_2> 22 </x_2>
<y_2> 22 </y_2>
</domain>
<initial_population>
<type>FromFile</type>
<filename>Benchmarks/ModuleBenchmarks/PlantModules/Bettina/ag_initial_population.csv</filename>
</initial_population>
<production>
<type>SizeDependent</type>
<formula>0.3 + 0.01*200*x</formula>
<x_geometry>r_stem</x_geometry>
<log>True</log>
</production>
<dispersal>
<type> Uniform </type>
</dispersal>
</group>
</population>
<time_loop>
<type> Simple </type>
<t_start> 0 </t_start>
<t_end> 2e6 </t_end>
<delta_t> 1e6 </delta_t>
</time_loop>
<visualization>
<type> NONE </type>
</visualization>
<output>
<type> OneTimestepOneFile </type>
<output_times> [2e6] </output_times>
<allow_previous_output>True</allow_previous_output>
<output_dir>Benchmarks/TestOutputs</output_dir>
<geometry_output> r_stem </geometry_output>
</output>
</MangaProject>

6 changes: 0 additions & 6 deletions Benchmarks/ModuleBenchmarks/Population/FromFile/FromFile.xml
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Expand Up @@ -33,12 +33,6 @@
<x_2> 22 </x_2>
<y_2> 22 </y_2>
</domain>
<domain>
<x_1> 0 </x_1>
<y_1> 0 </y_1>
<x_2> 22 </x_2>
<y_2> 22 </y_2>
</domain>
<n_recruitment_per_step> 1 </n_recruitment_per_step>
<filename> Benchmarks/ModuleBenchmarks/PlantModules/Bettina/bg_initial_population.csv </filename>
</distribution>
Expand Down
6 changes: 3 additions & 3 deletions ...oduleBenchmarks/Population/FromFile/ReferenceFiles/FromFile/Population_t_0002000000.0.csv
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@@ -1,5 +1,5 @@
plant time x y r_stem h_stem r_crown r_root growth ag_resources bg_resources salinity
Initial_000000001 2000000.0 10 11 0.11226882491685122 5.977097608516402 2.4256390926996296 1.5016725831215985 0.0007462647022652545 0.46210668145556993 0.2732500105651177 0.034999938348613036
Initial_000000002 2000000.0 12 11 0.0246864169126034 3.041566919035289 0.8104585711844785 0.499570285378578 3.209584726357741e-05 0.01102111782194493 0.03122780435210427 0.03499983745979359
Initial_000000003 2000000.0 1.6967331035870423 18.91765402226748 0.005 0.06052472383550822 0.20249829303163297 0.20000000000002865 1.3776831284455835e-05 0.0031415926535897933 0.006962769762615453 0.03499932159840235
Initial_000000001 2000000.0 10 11 0.11236431015237831 5.978509962312709 2.4256427106014393 1.5001837135192426 0.001126115647705317 0.46210735503662836 0.3598015366421273 0.03499990694530467
Initial_000000002 2000000.0 12 11 0.0246864169126034 3.0413387766289546 0.8102321788275856 0.499570285378578 2.9136118164666447e-05 0.011018036960656763 0.04135509806905843 0.03499985243912011
Initial_000000003 2000000.0 1.6967331035870423 18.91765402226748 0.005 0.06016376383550822 0.20241261060741864 0.2 1.330433574935593e-05 0.0031415926535897933 0.010513695559025208 0.03499934486512595
Initial_000000004 2000000.0 9.359615267691863 2.844752946084658 0.005 0.05 0.2 0.2 NaN NaN NaN NaN
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