Fixing yld 0.17 to 0.6

tests/core/data/all_config.toml

@@ -23,223 +23,222 @@ save_initial_state = true
 a_hd = 116.0
 ca_ratio = 390.43
 f_g = 0.02
+gpp_topslice = 0.1
 h_max = 25.33
 lai = 1.8
 m = 2
 n = 5
 name = 'shrub'
+p_foliage_for_reproductive_tissue = 0.05
 par_ext = 0.5
 resp_f = 0.1
 resp_r = 0.913
+resp_rt = 0.05
 resp_s = 0.044
 rho_s = 200.0
 sla = 14.0
 tau_f = 4.0
 tau_r = 1.04
-yld = 0.17
-zeta = 0.17
-resp_rt = 0.05
 tau_rt = 1
-gpp_topslice = 0.1
-p_foliage_for_reproductive_tissue = 0.05
+yld = 0.6
+zeta = 0.17
 
 [[plants.pft_definition]]
 a_hd = 116.0
 ca_ratio = 390.43
 f_g = 0.02
+gpp_topslice = 0.1
 h_max = 15.33
 lai = 1.8
 m = 2
 n = 5
 name = 'broadleaf'
+p_foliage_for_reproductive_tissue = 0.05
 par_ext = 0.5
 resp_f = 0.1
 resp_r = 0.913
+resp_rt = 0.05
 resp_s = 0.044
 rho_s = 200.0
 sla = 14.0
 tau_f = 4.0
 tau_r = 1.04
-yld = 0.17
-zeta = 0.17
-resp_rt = 0.05
 tau_rt = 1
-gpp_topslice = 0.1
-p_foliage_for_reproductive_tissue = 0.05
+yld = 0.6
+zeta = 0.17
 
 [[animal.functional_groups]]
-name = "carnivorous_bird"
-taxa = "bird"
+adult_mass = 1.0
+birth_mass = 0.1
+development_status = "adult"
+development_type = "direct"
 diet = "carnivore"
+excretion_type = "uricotelic"
 metabolic_type = "endothermic"
+migration_type = "none"
+name = "carnivorous_bird"
+offspring_functional_group = "carnivorous_bird"
 reproductive_environment = "terrestrial"
 reproductive_type = "iteroparous"
-development_type = "direct"
-development_status = "adult"
-offspring_functional_group = "carnivorous_bird"
-excretion_type = "uricotelic"
-migration_type = "none"
+taxa = "bird"
 vertical_occupancy = "ground_canopy"
-birth_mass = 0.1
-adult_mass = 1.0
 
 [[animal.functional_groups]]
-name = "herbivorous_bird"
-taxa = "bird"
+adult_mass = 0.5
+birth_mass = 0.05
+development_status = "adult"
+development_type = "direct"
 diet = "herbivore"
+excretion_type = "uricotelic"
 metabolic_type = "endothermic"
+migration_type = "none"
+name = "herbivorous_bird"
+offspring_functional_group = "herbivorous_bird"
 reproductive_environment = "terrestrial"
 reproductive_type = "iteroparous"
-development_type = "direct"
-development_status = "adult"
-offspring_functional_group = "herbivorous_bird"
-excretion_type = "uricotelic"
-migration_type = "none"
+taxa = "bird"
 vertical_occupancy = "ground_canopy"
-birth_mass = 0.05
-adult_mass = 0.5
 
 [[animal.functional_groups]]
-name = "carnivorous_mammal"
-taxa = "mammal"
+adult_mass = 40.0
+birth_mass = 4.0
+development_status = "adult"
+development_type = "direct"
 diet = "carnivore"
+excretion_type = "ureotelic"
 metabolic_type = "endothermic"
+migration_type = "none"
+name = "carnivorous_mammal"
+offspring_functional_group = "carnivorous_mammal"
 reproductive_environment = "terrestrial"
 reproductive_type = "iteroparous"
-development_type = "direct"
-development_status = "adult"
-offspring_functional_group = "carnivorous_mammal"
-excretion_type = "ureotelic"
-migration_type = "none"
+taxa = "mammal"
 vertical_occupancy = "ground"
-birth_mass = 4.0
-adult_mass = 40.0
 
 [[animal.functional_groups]]
-name = "herbivorous_mammal"
-taxa = "mammal"
+adult_mass = 10.0
+birth_mass = 1.0
+development_status = "adult"
+development_type = "direct"
 diet = "herbivore"
+excretion_type = "ureotelic"
 metabolic_type = "endothermic"
+migration_type = "none"
+name = "herbivorous_mammal"
+offspring_functional_group = "herbivorous_mammal"
 reproductive_environment = "terrestrial"
 reproductive_type = "iteroparous"
-development_type = "direct"
-development_status = "adult"
-offspring_functional_group = "herbivorous_mammal"
-excretion_type = "ureotelic"
-migration_type = "none"
+taxa = "mammal"
 vertical_occupancy = "ground"
-birth_mass = 1.0
-adult_mass = 10.0
 
 [[animal.functional_groups]]
-name = "carnivorous_insect"
-taxa = "insect"
+adult_mass = 0.01
+birth_mass = 0.001
+development_status = "adult"
+development_type = "direct"
 diet = "carnivore"
+excretion_type = "uricotelic"
 metabolic_type = "ectothermic"
+migration_type = "none"
+name = "carnivorous_insect"
+offspring_functional_group = "carnivorous_insect"
 reproductive_environment = "terrestrial"
 reproductive_type = "iteroparous"
-development_type = "direct"
-development_status = "adult"
-offspring_functional_group = "carnivorous_insect"
-excretion_type = "uricotelic"
-migration_type = "none"
+taxa = "insect"
 vertical_occupancy = "soil_ground_canopy"
-birth_mass = 0.001
-adult_mass = 0.01
 
 [[animal.functional_groups]]
-name = "herbivorous_insect"
-taxa = "insect"
+adult_mass = 0.005
+birth_mass = 0.0005
+development_status = "adult"
+development_type = "direct"
 diet = "herbivore"
+excretion_type = "uricotelic"
 metabolic_type = "ectothermic"
+migration_type = "none"
+name = "herbivorous_insect"
+offspring_functional_group = "herbivorous_insect"
 reproductive_environment = "terrestrial"
 reproductive_type = "semelparous"
-development_type = "direct"
-development_status = "adult"
-offspring_functional_group = "herbivorous_insect"
-excretion_type = "uricotelic"
-migration_type = "none"
+taxa = "insect"
 vertical_occupancy = "soil_ground_canopy"
-birth_mass = 0.0005
-adult_mass = 0.005
 
 [[animal.functional_groups]]
-name = "butterfly"
-taxa = "insect"
+adult_mass = 0.005
+birth_mass = 0.0005
+development_status = "adult"
+development_type = "indirect"
 diet = "herbivore"
+excretion_type = "uricotelic"
 metabolic_type = "ectothermic"
+migration_type = "none"
+name = "butterfly"
+offspring_functional_group = "caterpillar"
 reproductive_environment = "terrestrial"
 reproductive_type = "semelparous"
-development_type = "indirect"
-development_status = "adult"
-offspring_functional_group = "caterpillar"
-excretion_type = "uricotelic"
-migration_type = "none"
+taxa = "insect"
 vertical_occupancy = "ground_canopy"
-birth_mass = 0.0005
-adult_mass = 0.005
 
 [[animal.functional_groups]]
-name = "caterpillar"
-taxa = "insect"
+adult_mass = 0.005
+birth_mass = 0.0005
+development_status = "larval"
+development_type = "indirect"
 diet = "herbivore"
+excretion_type = "uricotelic"
 metabolic_type = "ectothermic"
+migration_type = "none"
+name = "caterpillar"
+offspring_functional_group = "butterfly"
 reproductive_environment = "terrestrial"
 reproductive_type = "nonreproductive"
-development_type = "indirect"
-development_status = "larval"
-offspring_functional_group = "butterfly"
-excretion_type = "uricotelic"
-migration_type = "none"
+taxa = "insect"
 vertical_occupancy = "canopy"
-birth_mass = 0.0005
-adult_mass = 0.005
 
 [[animal.functional_groups]]
-name = "frog"
-taxa = "amphibian"
+adult_mass = 0.5
+birth_mass = 0.005
+development_status = "adult"
+development_type = "direct"
 diet = "carnivore"
+excretion_type = "ureotelic"
 metabolic_type = "ectothermic"
+migration_type = "none"
+name = "frog"
+offspring_functional_group = "frog"
 reproductive_environment = "aquatic"
 reproductive_type = "iteroparous"
-development_type = "direct"
-development_status = "adult"
-offspring_functional_group = "frog"
-excretion_type = "ureotelic"
-migration_type = "none"
+taxa = "amphibian"
 vertical_occupancy = "ground"
-birth_mass = 0.005
-adult_mass = 0.5
 
 [[animal.functional_groups]]
-name = "swallow"
-taxa = "bird"
+adult_mass = 0.2
+birth_mass = 0.005
+development_status = "adult"
+development_type = "direct"
 diet = "carnivore"
+excretion_type = "uricotelic"
 metabolic_type = "endothermic"
+migration_type = "seasonal"
+name = "swallow"
+offspring_functional_group = "swallow"
 reproductive_environment = "terrestrial"
 reproductive_type = "iteroparous"
-development_type = "direct"
-development_status = "adult"
-offspring_functional_group = "swallow"
-excretion_type = "uricotelic"
-migration_type = "seasonal"
+taxa = "bird"
 vertical_occupancy = "canopy"
-birth_mass = 0.005
-adult_mass = 0.2
 
 [[animal.functional_groups]]
-name = "earthworm"
-taxa = "insect"
+adult_mass = 0.005
+birth_mass = 0.0005
+development_status = "adult"
+development_type = "direct"
 diet = "herbivore"
+excretion_type = "uricotelic"
 metabolic_type = "ectothermic"
+migration_type = "none"
+name = "earthworm"
+offspring_functional_group = "earthworm"
 reproductive_environment = "terrestrial"
 reproductive_type = "iteroparous"
-development_type = "direct"
-development_status = "adult"
-offspring_functional_group = "earthworm"
-excretion_type = "uricotelic"
-migration_type = "none"
+taxa = "insect"
 vertical_occupancy = "soil"
-birth_mass = 0.0005
-adult_mass = 0.005
-

tests/models/animals/conftest.py

@@ -125,7 +125,7 @@ def animal_fixture_config():
         sla = 14.0
         tau_f = 4.0
         tau_r = 1.04
-        yld = 0.17
+        yld = 0.6
         zeta = 0.17
         resp_rt = 0.05
         tau_rt = 1
@@ -149,7 +149,7 @@ def animal_fixture_config():
         sla = 14.0
         tau_f = 4.0
         tau_r = 1.04
-        yld = 0.17
+        yld = 0.6
         zeta = 0.17
         resp_rt = 0.05
         tau_rt = 1

tests/models/plants/data/pfts.csv

@@ -1,3 +1,3 @@
 name,a_hd,ca_ratio,h_max,lai,par_ext,resp_f,resp_r,resp_s,rho_s,sla,tau_f,tau_r,yld,zeta,f_g,m,n,tau_rt,resp_rt,gpp_topslice,p_foliage_for_reproductive_tissue
-test1,116.0,390.43,25.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5,1,0.05,0.1,0.05
-test2,116.0,390.43,15.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5,1,0.05,0.1,0.05
+test1,116.0,390.43,25.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.6,0.17,0.02,2,5,1,0.05,0.1,0.05
+test2,116.0,390.43,15.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.6,0.17,0.02,2,5,1,0.05,0.1,0.05

virtual_ecosystem/example_data/data/plant_pfts.csv

@@ -1,3 +1,3 @@
 name,a_hd,ca_ratio,h_max,lai,par_ext,resp_f,resp_r,resp_s,rho_s,sla,tau_f,tau_r,yld,zeta,f_g,m,n,tau_rt,resp_rt,gpp_topslice,p_foliage_for_reproductive_tissue
-broadleaf,116.0,390.43,25.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5,1,0.05,0.1,0.05
-shrub,116.0,390.43,15.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.17,0.17,0.02,2,5,1,0.05,0.1,0.05
+broadleaf,116.0,390.43,25.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.6,0.17,0.02,2,5,1,0.05,0.1,0.05
+shrub,116.0,390.43,15.33,1.8,0.5,0.1,0.913,0.044,200.0,14.0,4.0,1.04,0.6,0.17,0.02,2,5,1,0.05,0.1,0.05