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54 changes: 54 additions & 0 deletions
54
...enchmarks/BelowgroundCompetition/FixedSalinity_SimpleKiwi/FixedSalinity_CI_SimpleKiwi.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| <MangaProject> | ||
| <random_seed>643879</random_seed> | ||
| <tree_dynamics> | ||
| <aboveground_competition> | ||
| <type> SimpleTest </type> | ||
| </aboveground_competition> | ||
| <belowground_competition> | ||
| <type> FixedSalinity </type> | ||
| <min_x>0</min_x> | ||
| <max_x>22</max_x> | ||
| <salinity>0.025 0.035</salinity> | ||
| </belowground_competition> | ||
| <tree_growth_and_death> | ||
| <type> SimpleKiwi </type> | ||
| <mortality>NoGrowth</mortality> | ||
| </tree_growth_and_death> | ||
| </tree_dynamics> | ||
| <initial_population> | ||
| <group> | ||
| <name> Initial </name> | ||
| <species> Avicennia </species> | ||
| <distribution> | ||
| <type> GroupFromFile </type> | ||
| <n_recruitment_per_step> 0 </n_recruitment_per_step> | ||
| <filename> Benchmarks/ModuleBenchmarks/BelowgroundCompetition/bg_initial_population.csv </filename> | ||
| </distribution> | ||
| </group> | ||
| </initial_population> | ||
| <tree_time_loop> | ||
| <type> Simple </type> | ||
| <t_start> 0 </t_start> | ||
| <t_end> 2e6 </t_end> | ||
| <delta_t> 1e6 </delta_t> | ||
| </tree_time_loop> | ||
| <visualization> | ||
| <type> NONE </type> | ||
| </visualization> | ||
| <tree_output> | ||
| <type> OneTimestepOneFile </type> | ||
| <output_each_nth_timestep>1</output_each_nth_timestep> | ||
| <output_times> [2e6] </output_times> | ||
| <allow_previous_output>True</allow_previous_output> | ||
| <output_dir>Benchmarks/TestOutputs/</output_dir> | ||
| <geometry_output> r_stem </geometry_output> | ||
| <geometry_output> h_stem </geometry_output> | ||
| <geometry_output> r_crown </geometry_output> | ||
| <geometry_output> r_root </geometry_output> | ||
| <growth_output> growth </growth_output> | ||
| <growth_output> ag_resources </growth_output> | ||
| <growth_output> bg_resources </growth_output> | ||
| <growth_output> salinity </growth_output> | ||
| </tree_output> | ||
| </MangaProject> | ||
|
|
54 changes: 54 additions & 0 deletions
54
...leBenchmarks/BelowgroundCompetition/FixedSalinity_SimpleKiwi/FixedSalinity_SimpleKiwi.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| <MangaProject> | ||
| <random_seed>643879</random_seed> | ||
| <tree_dynamics> | ||
| <aboveground_competition> | ||
| <type> SimpleTest </type> | ||
| </aboveground_competition> | ||
| <belowground_competition> | ||
| <type> FixedSalinity </type> | ||
| <min_x>0</min_x> | ||
| <max_x>22</max_x> | ||
| <salinity>0.025 0.035</salinity> | ||
| </belowground_competition> | ||
| <tree_growth_and_death> | ||
| <type> SimpleKiwi </type> | ||
| <mortality>NoGrowth</mortality> | ||
| </tree_growth_and_death> | ||
| </tree_dynamics> | ||
| <initial_population> | ||
| <group> | ||
| <name> Initial </name> | ||
| <species> Avicennia </species> | ||
| <distribution> | ||
| <type> GroupFromFile </type> | ||
| <n_recruitment_per_step> 0 </n_recruitment_per_step> | ||
| <filename> Benchmarks/ModuleBenchmarks/BelowgroundCompetition/bg_initial_population.csv </filename> | ||
| </distribution> | ||
| </group> | ||
| </initial_population> | ||
| <tree_time_loop> | ||
| <type> Simple </type> | ||
| <t_start> 0 </t_start> | ||
| <t_end> 5e8 </t_end> | ||
| <delta_t> 1e6 </delta_t> | ||
| </tree_time_loop> | ||
| <visualization> | ||
| <type> NONE </type> | ||
| </visualization> | ||
| <tree_output> | ||
| <type> OneTimestepOneFile </type> | ||
| <output_each_nth_timestep>1</output_each_nth_timestep> | ||
| <output_times> [2e6, 5e8] </output_times> | ||
| <allow_previous_output>True</allow_previous_output> | ||
| <output_dir>Benchmarks/TestOutputs/</output_dir> | ||
| <geometry_output> r_stem </geometry_output> | ||
| <geometry_output> h_stem </geometry_output> | ||
| <geometry_output> r_crown </geometry_output> | ||
| <geometry_output> r_root </geometry_output> | ||
| <growth_output> growth </growth_output> | ||
| <growth_output> ag_resources </growth_output> | ||
| <growth_output> bg_resources </growth_output> | ||
| <growth_output> salinity </growth_output> | ||
| </tree_output> | ||
| </MangaProject> | ||
|
|
3 changes: 3 additions & 0 deletions
3
...inity_SimpleKiwi/ReferenceFiles/FixedSalinity_CI_SimpleKiwi/Population_t_0002000000.0.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| tree time x y r_stem h_stem r_crown r_root growth ag_resources bg_resources salinity | ||
| Initial_000000001 2000000.0 10.0 11.0 0.11229440560518016 5.977561731480918 2.4256391000200423 1.50192197878664 0.0008710058585645146 0.4621066828213375 0.29981559104675876 0.029545393832009166 | ||
| Initial_000000002 2000000.0 12.0 11.0 0.024948025976859627 3.049684133519979 0.8080020670065645 0.5034729834247506 0.00014009166686133466 0.05127608005572926 0.03402039286060873 0.030454343318122044 |
3 changes: 3 additions & 0 deletions
3
...Salinity_SimpleKiwi/ReferenceFiles/FixedSalinity_SimpleKiwi/Population_t_0002000000.0.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| tree time x y r_stem h_stem r_crown r_root growth ag_resources bg_resources salinity | ||
| Initial_000000001 2000000.0 10.0 11.0 0.11229440560518016 5.977561731480918 2.4256391000200423 1.50192197878664 0.0008710058585645146 0.4621066828213375 0.29981559104675876 0.029545393832009166 | ||
| Initial_000000002 2000000.0 12.0 11.0 0.024948025976859627 3.049684133519979 0.8080020670065645 0.5034729834247506 0.00014009166686133466 0.05127608005572926 0.03402039286060873 0.030454343318122044 |
3 changes: 3 additions & 0 deletions
3
...Salinity_SimpleKiwi/ReferenceFiles/FixedSalinity_SimpleKiwi/Population_t_0500000000.0.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| tree time x y r_stem h_stem r_crown r_root growth ag_resources bg_resources salinity | ||
| Initial_000000001 500000000.0 10.0 11.0 0.15516244253493314 6.680402181826311 2.616580364882978 1.9634956251799625 0.0013322122445752224 0.5373455684952401 0.5112984352099733 0.02954534075413815 | ||
| Initial_000000002 500000000.0 12.0 11.0 0.08161571767788994 4.773955873206462 1.6580731731063618 1.2493401394273054 0.0007440762311415338 0.2154989894465626 0.20655450071752982 0.030454327253667212 |
72 changes: 72 additions & 0 deletions
72
...ModuleBenchmarks/BelowgroundCompetition/NetworkOGSLargeScale3D/NetworkOGSLargeScale3D.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| <MangaProject> | ||
| <random_seed>643879</random_seed> | ||
| <tree_dynamics> | ||
| <aboveground_competition> | ||
| <type> SimpleTest </type> | ||
| </aboveground_competition> | ||
| <belowground_competition> | ||
| <type>NetworkOGSLargeScale3D</type> | ||
| <f_radius> 0.25 </f_radius> | ||
| <min_x>0</min_x> | ||
| <max_x>22</max_x> | ||
| <salinity>0.025 0.035</salinity> | ||
| <ogs_project_folder>Benchmarks/ModuleBenchmarks/BelowgroundCompetition/NetworkOGSLargeScale3D/</ogs_project_folder> | ||
| <ogs_project_file>ogs_benchmark.prj</ogs_project_file> | ||
| <source_mesh>ogs_benchmark_source.vtu</source_mesh> | ||
| <bulk_mesh>ogs_benchmark_domain.vtu</bulk_mesh> | ||
| <delta_t_ogs>1000000</delta_t_ogs> | ||
| <abiotic_drivers> | ||
| <left_salinity>0.025</left_salinity> | ||
| <right_salinity>0.035</right_salinity> | ||
| </abiotic_drivers> | ||
| <python_script>python_script.py</python_script> | ||
| </belowground_competition> | ||
| <tree_growth_and_death> | ||
| <type> NetworkBettina </type> | ||
| <mortality>NoGrowth</mortality> | ||
| <f_growth> 0.25 </f_growth> | ||
| <variant> V2_adapted </variant> | ||
| </tree_growth_and_death> | ||
| </tree_dynamics> | ||
| <initial_population> | ||
| <group> | ||
| <name> Initial </name> | ||
| <species> Avicennia </species> | ||
| <distribution> | ||
| <type> GroupFromFile </type> | ||
| <n_recruitment_per_step> 0 </n_recruitment_per_step> | ||
| <filename> Benchmarks/ModuleBenchmarks/BelowgroundCompetition/bg_initial_population.csv </filename> | ||
| </distribution> | ||
| </group> | ||
| </initial_population> | ||
| <tree_time_loop> | ||
| <type> Simple </type> | ||
| <t_start> 0 </t_start> | ||
| <t_end> 5e8 </t_end> | ||
| <delta_t> 1e6 </delta_t> | ||
| </tree_time_loop> | ||
| <visualization> | ||
| <type> NONE </type> | ||
| </visualization> | ||
| <tree_output> | ||
| <type> OneTimestepOneFile </type> | ||
| <output_each_nth_timestep>1</output_each_nth_timestep> | ||
| <output_times> [2e6, 5e8] </output_times> | ||
| <allow_previous_output>True</allow_previous_output> | ||
| <output_dir>Benchmarks/TestOutputs/</output_dir> | ||
| <geometry_output> r_stem </geometry_output> | ||
| <geometry_output> h_stem </geometry_output> | ||
| <geometry_output> r_crown </geometry_output> | ||
| <geometry_output> r_root </geometry_output> | ||
| <growth_output> growth </growth_output> | ||
| <growth_output> ag_resources </growth_output> | ||
| <growth_output> bg_resources </growth_output> | ||
| <growth_output> salinity </growth_output> | ||
| <network_output> rgf </network_output> | ||
| <network_output> partner </network_output> | ||
| <network_output> potential_partner </network_output> | ||
| <network_output> water_available </network_output> | ||
| <network_output> water_absorbed </network_output> | ||
| <network_output> water_exchanged </network_output> | ||
| </tree_output> | ||
| </MangaProject> |
72 changes: 72 additions & 0 deletions
72
...uleBenchmarks/BelowgroundCompetition/NetworkOGSLargeScale3D/NetworkOGSLargeScale3D_Cl.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| <MangaProject> | ||
| <random_seed>643879</random_seed> | ||
| <tree_dynamics> | ||
| <aboveground_competition> | ||
| <type> SimpleTest </type> | ||
| </aboveground_competition> | ||
| <belowground_competition> | ||
| <type>NetworkOGSLargeScale3D</type> | ||
| <f_radius> 0.25 </f_radius> | ||
| <min_x>0</min_x> | ||
| <max_x>22</max_x> | ||
| <salinity>0.025 0.035</salinity> | ||
| <ogs_project_folder>Benchmarks/ModuleBenchmarks/BelowgroundCompetition/NetworkOGSLargeScale3D/</ogs_project_folder> | ||
| <ogs_project_file>ogs_benchmark.prj</ogs_project_file> | ||
| <source_mesh>ogs_benchmark_source.vtu</source_mesh> | ||
| <bulk_mesh>ogs_benchmark_domain.vtu</bulk_mesh> | ||
| <delta_t_ogs>1000000</delta_t_ogs> | ||
| <abiotic_drivers> | ||
| <left_salinity>0.025</left_salinity> | ||
| <right_salinity>0.035</right_salinity> | ||
| </abiotic_drivers> | ||
| <python_script>python_script.py</python_script> | ||
| </belowground_competition> | ||
| <tree_growth_and_death> | ||
| <type> NetworkBettina </type> | ||
| <mortality>NoGrowth</mortality> | ||
| <f_growth> 0.25 </f_growth> | ||
| <variant> V2_adapted </variant> | ||
| </tree_growth_and_death> | ||
| </tree_dynamics> | ||
| <initial_population> | ||
| <group> | ||
| <name> Initial </name> | ||
| <species> Avicennia </species> | ||
| <distribution> | ||
| <type> GroupFromFile </type> | ||
| <n_recruitment_per_step> 0 </n_recruitment_per_step> | ||
| <filename> Benchmarks/ModuleBenchmarks/BelowgroundCompetition/bg_initial_population.csv </filename> | ||
| </distribution> | ||
| </group> | ||
| </initial_population> | ||
| <tree_time_loop> | ||
| <type> Simple </type> | ||
| <t_start> 0 </t_start> | ||
| <t_end> 2e6 </t_end> | ||
| <delta_t> 1e6 </delta_t> | ||
| </tree_time_loop> | ||
| <visualization> | ||
| <type> NONE </type> | ||
| </visualization> | ||
| <tree_output> | ||
| <type> OneTimestepOneFile </type> | ||
| <output_each_nth_timestep>1</output_each_nth_timestep> | ||
| <output_times> [2e6] </output_times> | ||
| <allow_previous_output>True</allow_previous_output> | ||
| <output_dir>Benchmarks/TestOutputs/</output_dir> | ||
| <geometry_output> r_stem </geometry_output> | ||
| <geometry_output> h_stem </geometry_output> | ||
| <geometry_output> r_crown </geometry_output> | ||
| <geometry_output> r_root </geometry_output> | ||
| <growth_output> growth </growth_output> | ||
| <growth_output> ag_resources </growth_output> | ||
| <growth_output> bg_resources </growth_output> | ||
| <growth_output> salinity </growth_output> | ||
| <network_output> rgf </network_output> | ||
| <network_output> partner </network_output> | ||
| <network_output> potential_partner </network_output> | ||
| <network_output> water_available </network_output> | ||
| <network_output> water_absorbed </network_output> | ||
| <network_output> water_exchanged </network_output> | ||
| </tree_output> | ||
| </MangaProject> |
3 changes: 3 additions & 0 deletions
3
...etworkOGSLargeScale3D/ReferenceFiles/NetworkOGSLargeScale3D/Population_t_0002000000.0.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| tree time x y r_stem h_stem r_crown r_root growth ag_resources bg_resources salinity rgf partner potential_partner water_available water_absorbed water_exchanged | ||
| Initial_000000001 2000000.0 10.0 11.0 0.11228932083361548 5.9774694928873435 2.4256390966921075 1.5018723846777773 0.000836062281152594 0.4621066824001683 0.2923778659836746 0.031074126738792122 -1 [] [] 0.443594258202854 0.443594258202854 0.0 | ||
| Initial_000000002 2000000.0 12.0 11.0 0.024945157806094673 3.0495688392853544 0.8080020633166772 0.5034289813005122 0.0001378625940889872 0.05127607993828124 0.033545949735452496 0.03130854695888863 -1 [] [] 0.05082133682537293 0.05082133682537293 0.0 |
3 changes: 3 additions & 0 deletions
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...etworkOGSLargeScale3D/ReferenceFiles/NetworkOGSLargeScale3D/Population_t_0500000000.0.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| tree time x y r_stem h_stem r_crown r_root growth ag_resources bg_resources salinity rgf partner potential_partner water_available water_absorbed water_exchanged | ||
| Initial_000000001 500000000.0 10.0 11.0 0.15240783270323774 6.614953569936499 2.5006671803614444 1.948948544280503 0.0011728048167336008 0.4908587662020714 0.46421019571301575 0.03448258609054536 -1 ['Initial2'] [] 0.7977535739243723 0.7978545576196617 -0.00010098369528934023 | ||
| Initial_000000002 500000000.0 12.0 11.0 0.07882835993364216 4.632609493991861 1.5429343847501742 1.2318637074152523 0.0006353770913070857 0.18664035771597587 0.17839281655574565 0.03738710369407493 -1 ['Initial1'] [] 0.3459497344155479 0.34584875072025867 0.00010098369528934023 |
3 changes: 3 additions & 0 deletions
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...orkOGSLargeScale3D/ReferenceFiles/NetworkOGSLargeScale3D_Cl/Population_t_0002000000.0.csv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| tree time x y r_stem h_stem r_crown r_root growth ag_resources bg_resources salinity rgf partner potential_partner water_available water_absorbed water_exchanged | ||
| Initial_000000001 2000000.0 10.0 11.0 0.11228932083361548 5.9774694928873435 2.4256390966921075 1.5018723846777773 0.000836062281152594 0.4621066824001683 0.2923778659836746 0.031074126738792122 -1 [] [] 0.443594258202854 0.443594258202854 0.0 | ||
| Initial_000000002 2000000.0 12.0 11.0 0.024945157806094673 3.0495688392853544 0.8080020633166772 0.5034289813005122 0.0001378625940889872 0.05127607993828124 0.033545949735452496 0.03130854695888863 -1 [] [] 0.05082133682537293 0.05082133682537293 0.0 |
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