mvs = MVarSet({
BibInfo( # Bibliographical Information
name="",
longName="",
version="",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="24/3/2016",
doi="",
# further_references=BibInfo(doi=""),
# modApproach: process based,
# partitioningScheme: fixed,
# claimedDynamicPart: "no",
# spaceScale: global,
# # unit: "1°",
# timeResolution: monthly,
# # unit: month^{-1},
# bibtex: "@article{Luo2012TE,
# address = {Berkeley},
# author = {Yiqi Luo and Ensheng Weng and Yuanhe Yang},
# booktitle = {Encyclopedia of Theoretical Ecology},
# editor = {Alan Hastings and Louis Gross},
# pages = {219-229},
# publisher = {University of California Press},
# title = {Ecosystem Ecology},
# year = {2012}
# }",
#
# abstract: "Ecosystem ecology is a subdiscipline of ecology that focuses on exchange of energy and materials between organisms and the environment. The materials that are commonly studied in ecosystem ecology include water, carbon, nitrogen, phosphorus, and other elements that organisms use as nutrients. The source of energy for most ecosystems is solar radiation. In this entry, material cy-cling and energy exchange are generally described before the carbon cycle is used as an example to illustrate our quantitative and theoretical understanding of ecosystem ecology.",
sym_dict=sym_dict),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((C_f, C_w, C_r)),
np1
})
# C_root: , #"g*m^{-2}"
# C_wood: #"g*m^{-2}"
#})
#
#ntimes = NumericSimulationTimes(np.arange(, , ))
mvs=MVarSet({
BibInfo(# Bibliographical Information
name="CABLE",
longName="CSIRO Atmosphere Biosphere Land Exchange",
version="1",
# basedOn = "CASA'" # Fung et al. (2005) -> Need to look it up
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="14/3/2016",
doi="10.5194/bg-7-2261-2010",
sym_dict=sym_dict
),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((C_leaf, C_root, C_wood)),
# np1
})
(0.5 * N_ava)))) / (1 + (Omega *
(3 - L - W - N_ava)))
a_L = epsilon_L / (1 + (Omega * (3 - L - W - N_ava))) #, "a_L = 1-a_S-a_R"
x = StateVariableTuple((C_S, C_R, C_L))
u = NPP
b = (a_S, a_R, a_L)
Input = InputTuple(u * ImmutableMatrix(b))
A = CompartmentalMatrix([[-gamma_S, 0, 0], [0, -gamma_R, 0], [0, 0, -gamma_L]])
t = TimeSymbol("t")
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="CEVSA2 ",
longName="",
version="2",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="",
doi="10.1016/j.ecocom.2010.04.002",
sym_dict=sym_dict),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((C_S, C_R, C_L)),
})
[0, -gamma_S - R_gS - R_mS, 0],
[0, 0, -gamma_R - R_gR - R_mR]])
#
t = TimeSymbol("t")
# parameter_sets:
# - "Original dataset of the publication":
# values: {k_n: 0.5, omega: 0.8, epsilon_L: 0.35, epsilon_S: 0.1, epsilon_R: 0.55}
# desc: Eastern US and Germany, cold broadleaf deciduous
# doi: 10.1111/j.1365-2486.2004.00890.x
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="CTEM",
longName="Canadian Terrestrial Ecosystem Model",
version="1",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="21/1/2016",
doi="10.1111/j.1365-2486.2004.00890.x",
sym_dict=sym_dict),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(b),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(u),
VegetationCarbonStateVariableTuple((C_L, C_S, C_R)),
})
xk_opt_litter * xk_temp * xk_water *
xk_n_limit(t), # casa_cnp.F90: Line 880, 1030
xk_opt_litter * xk_temp * xk_water * xk_n_limit(t) *
exp(-3 * f_lign_leaf), # casa_cnp.F90: Line 880, 1031-1032
xk_opt_litter * xk_temp * xk_water *
xk_n_limit(t), # casa_cnp.F90: Line 880, 1033
xk_opt_soil * xk_temp * xk_water *
(1 - 0.75 * (silt + clay)), # casa_cnp.F90: Line 884, 1035-1036
xk_opt_soil * xk_temp * xk_water, # casa_cnp.F90: Line 884, 1037
xk_opt_soil * xk_temp * xk_water, # casa_cnp.F90: Line 884, 1038
])
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="cable",
entryAuthor="Markus Müller",
# entryAuthorOrcid="",
# entryCreationDate="22/3/2016",
# doi="10.5194/bg-10-2255-2013",
# further_references=BibInfo(doi="10.5194/bg-10-2255-2013"),
sym_dict=sym_dict,
),
# A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
# VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
# VegetationCarbonInputPartitioningTuple(b),
# VegetationCarbonStateVariableTuple((C_il, C_is, C_ir)),
})
W_s: 100,
W_r: 100,
W_C: 45,
W_N: 30
})
ntimes = NumericSimulationTimes(np.arange(0, 150, 25))
#ntimes = NumericSimulationTimes(np.arange(0, 1, 0.001)) #Fixme: There were 2 in the yaml file, not sure which one works best
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="",
longName="",
version="1",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="29/7/2015",
doi="10.1093/oxfordjournals.aob.a088273",
sym_dict=sym_dict),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(b),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(u),
VegetationCarbonStateVariableTuple((W_N, W_C, W_p, W_s, W_r)),
np1,
nsv1,
ntimes
})
b = (a_il, a_is, a_ir)
Input = InputTuple(u * ImmutableMatrix(b))
A = CompartmentalMatrix(diag(-1 / tau_il, -1 / tau_is, -1 / tau_ir))
t = TimeSymbol("t")
#model_run_data:
# parameter_sets:
# - "Tropical evergreen trees":
# values: {a_il: 0.25,a_is: 0.5,a_ir: 0.25}
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="IBIS",
longName="Integrated Biosphere Simulator",
version="1",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="26/1/2016",
doi="10.1029/96GB02692 ",
#further_references=BibInfo(doi=""),
sym_dict=sym_dict),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((C_il, C_is, C_ir)),
})
# # time_unit=day
#)
#nsv1 = NumericStartValueDict({
# F: , #"Mg/ha"
# W: , #"Mg/ha"
# R: #"Mg/ha"
#})
#
#ntimes = NumericSimulationTimes(np.arange(, , ))
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="G'DAY",
longName="Generic Decomposition and Yield",
version="1",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="27/1/2016",
doi="10.2307/1942099",
sym_dict=sym_dict),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((F, W, R)),
# np1
})
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="TECO",
longName="Terrestrial Ecosystem Model",
version="",
entryAuthor="Carlos A. Sierra",
entryAuthorOrcid="0000-0003-0009-4169",
entryCreationDate="12/4/2018",
doi="",
sym_dict=sym_dict
# bibtex= "@incollection{Luo2012TE,
# Address = {Berkeley},
# Author = {Yiqi Luo and Ensheng Weng and Yuanhe Yang},
# Booktitle = {Encyclopedia of Theoretical Ecology},
# Date-Added = {2015-05-05 15:20:40 +0000},
# Date-Modified = {2015-05-05 15:20:40 +0000},
# Editor = {Alan Hastings and Louis Gross},
# Pages = {219-229},
# Publisher = {University of California Press},
# Title = {Ecosystem Ecology},
# Year = {2012}}
# abstract = {"Ecosystem ecology is a subdiscipline of ecology that focuses on exchange of energy and materials between organisms and the environment. The materials that are commonly studied in ecosystem ecology include water, carbon, nitrogen, phosphorus, and other elements that organisms use as nutrients. The source of energy for most ecosystems is solar radiation. In this entry, material cy-cling and energy exchange are generally described before the carbon cycle is used as an example to illustrate our quantitative and theoretical understanding of ecosystem ecology."}",
),
B, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((C_foliage, C_roots, C_wood)),
np1,
nsv1,
ntimes
})
# doi: 10.2307/1313568
# - "Tropical evergreen rain forest":
# values: {alpha_f: 0.25, alpha_r: 0.25, alpha_w: 0.5, tau_f: 1.5, tau_r: 2, tau_w: 25}
# doi: 10.2307/1313568
#specialVars = {
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="CASA",
longName="Carnegie-Ames-Stanford approach",
version="1",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="17/7/2015",
doi="10.1029/93GB02725",
further_references=BibInfo(doi="10.2307/1313568"),
# Also from PDF in Reflex experiment
sym_dict=sym_dict),
#
# the following variables constitute the compartmental system:
#
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((C_f, C_w, C_r)),
np1
})
Phi_0: 2500, #"MJ*m*^{-2}*year^{-1}"
omega: 5, #"m*^2*kg^{-1}"
gamma_r: 2, #"kg^{-1}"
gamma_f: 0.5
}, #"kg^{-1}"
func_dict=frozendict({}))
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="",
longName="",
version="1",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="29/7/2015",
doi="10.1093/treephys/12.2.119",
sym_dict=sym_dict),
#
# the following variables constitute the compartmental system:
#
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((F, R, W)),
np1
})
A = CompartmentalMatrix(diag(-gamma_f, -gamma_r, -gamma_w))
t = TimeSymbol("t")
# Parameter sets not working because some of the symbols have 2 values.
#model_run_data:
# parameter_sets:
# - "Original dataset of the publication":
# values: {R_c: 0.25*NPP,Q_10: 2,Q_010: 1.94,n_crit: 0.034,I_0: 1.164,k: 0.5,R_0: 27,T_a: 3.8,epsilon_0: (1.05,1.25),sigma: 7.6,a_f: (0.16,0.19),a_r: (0.42,0.58),a_w: (0.23,0.42)}
# doi: 10.1016/S0304-3800(00)00345-8
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="",
longName="",
version="",
# basedOn="G'DAY"
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="16/3/2016",
doi="10.1016/S0304-3800(00)00345-8",
),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((C_f, C_r, C_w)),
})
#nsv1 = NumericStartValueDict({
# C_f: , #"g*m^{-2}"
# C_r: , #"g*m^{-2}"
# C_w: , #"g*m^{-2}"
# N_f: #"g*m^{-2}"
#})
#
#ntimes = NumericSimulationTimes(np.arange(, , ))
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="",
# basedOn="G'DAY",
longName="",
version="",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="15/3/2016",
doi="10.1007/s12080-011-0135-z",
sym_dict=sym_dict),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((C_f, C_r, C_w, N_f)),
# np1
})
b = 1
Input = InputTuple(b*ImmutableMatrix(u))
#"f_v = u + A*x"
A = CompartmentalMatrix(
[[-(1/Y_leaf),0,0],
[0, -(1/Y_stem), 0],
[0, 0, -(1/Y_roots)]]
)
t = TimeSymbol("t")
mvs = MVarSet({
BibInfo(# Bibliographical Information
name="ISAM",
longName="Integrated Science Assessment Model",
version="",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="3/5/2018",
doi="10.1111/j.1365-2486.2004.00890.x",
sym_dict=sym_dict
),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(b),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(u),
VegetationCarbonStateVariableTuple((C_leaf, C_stem, C_roots)),
})
f_GERM * gamma_GERM * (1 / Max(p, k_GERM)), 0, 0, 0, 0
],
[(A_S * (1 - C_RES_S)),
-(f_GERM * gamma_GERM *
(1 / Max(p, k_GERM))) - (1 / tau_S), 0, 0, 0, 0],
[(A_L * (1 - C_RES_L)), 0, -(1 / tau_L), 0, 0, 0],
[(A_R * (1 - C_RES_R)), 0, 0, -(1 / tau_R), 0, 0],
[(A_WL * (1 - C_RES_WL)), 0, 0, 0, -(1 / tau_WL), 0],
[(A_WR * (1 - C_RES_WR)), 0, 0, 0, 0, -1 / tau_WR]])
t = TimeSymbol("t") # "day"
mvs = MVarSet({
BibInfo( # Bibliographical Information
name="JeDi-DGVM",
longName="The Jena Diversity-Dynamic Global Vegetation Model",
version="1",
entryAuthor="Verónika Ceballos-Núñez",
entryAuthorOrcid="0000-0002-0046-1160",
entryCreationDate="",
doi="10.5194/bg-10-4137-2013",
sym_dict=sym_dict),
A, # the overall compartmental matrix
Input, # the overall input
t, # time for the complete system
x, # state vector of the complete system
VegetationCarbonInputScalar(u),
# vegetation carbon partitioning.
VegetationCarbonInputPartitioningTuple(b),
VegetationCarbonStateVariableTuple((C_A, C_S, C_L, C_R, C_WL, C_WR)),
})