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Use same rate of roots senescence for both pre and post flowering.
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@mngauthier
mngauthier committed Mar 19, 2020
1 parent 417b7b8 commit 915360d
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Showing 4 changed files with 108 additions and 116 deletions.
16 changes: 5 additions & 11 deletions senescwheat/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -211,35 +211,29 @@ def calculate_remobilisation_proteins(cls, organ, element_index, proteins, relat
return remob_proteins, delta_amino_acids, delta_Nresidual

@classmethod
def calculate_roots_senescence(cls, mstruct, Nstruct, postflowering_stages):
def calculate_roots_senescence(cls, mstruct, Nstruct):
"""Root senescence
:param float mstruct: structural mass (g)
:param float Nstruct: structural N (g)
:param bool postflowering_stages: Option : True to run a simulation with postflo parameter
:return: Rate of mstruct loss by root senescence (g mstruct s-1), rate of Nstruct loss by root senescence (g Nstruct s-1)
:rtype: tuple [float, float]
"""
if postflowering_stages:
rate_senescence = parameters.SENESCENCE_ROOTS_POSTFLOWERING
else:
rate_senescence = parameters.SENESCENCE_ROOTS_PREFLOWERING
return mstruct * rate_senescence, Nstruct * rate_senescence
return mstruct * parameters.SENESCENCE_ROOTS, Nstruct * parameters.SENESCENCE_ROOTS

@classmethod
def calculate_relative_delta_mstruct_roots(cls, rate_mstruct_death, root_mstruct, delta_t):
def calculate_relative_delta_mstruct_roots(cls, rate_mstruct_death, root_mstruct, delta_teq):
"""Relative delta of root structural dry matter (g) over delta_t
:param float rate_mstruct_death: Rate of mstruct loss by root senescence (g mstruct s-1)
:param float root_mstruct: actual mstruct of roots (g)
:param float delta_t: value of the timestep (s)
:param float delta_teq: Temperature-consensated time = time duration at a reference temperature (s)
:return: relative_delta_mstruct (dimensionless)
:rtype: float
"""
return (rate_mstruct_death * delta_t) / root_mstruct
return (rate_mstruct_death * delta_teq) / root_mstruct

@classmethod
def calculate_delta_mstruct_root(cls, rate_mstruct_death, rate_Nstruct_death, delta_teq):
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4 changes: 1 addition & 3 deletions senescwheat/parameters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,7 @@

N_MOLAR_MASS = 14 #: Molar mass of nitrogen (g mol-1)

SENESCENCE_ROOTS_POSTFLOWERING = 3.5E-7 * CONVERSION_FACTOR_20_TO_12 #: Rate of root turnover at 12°C (s-1). Value at 20°C coming from Johnson and Thornley (1985), see also Asseng et al. (1997).
SENESCENCE_ROOTS_PREFLOWERING = 0
# TODO: should be ontogenic for vegetative stages, 0 in Asseng 1997, but not null in Johnson and Thornley
SENESCENCE_ROOTS = 3.5E-7 * CONVERSION_FACTOR_20_TO_12 #: Rate of root turnover at 12°C (s-1). Value at 20°C coming from Johnson and Thornley (1985), see also Asseng et al. (1997).

FRACTION_N_MAX = {'blade': 0.5, 'stem': 0.425} # Threshold of ([proteins]/[proteins]max) below which tissue death is triggered

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2 changes: 1 addition & 1 deletion senescwheat/simulation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ def run(self, forced_max_protein_elements=None, opt_full_remob=False, postflower
delta_teq = all_axes_inputs[roots_inputs_id]['delta_teq_roots']

# loss of mstruct and Nstruct
rate_mstruct_death, rate_Nstruct_death = model.SenescenceModel.calculate_roots_senescence(roots_inputs_dict['mstruct'], roots_inputs_dict['Nstruct'], postflowering_stages)
rate_mstruct_death, rate_Nstruct_death = model.SenescenceModel.calculate_roots_senescence(roots_inputs_dict['mstruct'], roots_inputs_dict['Nstruct'])
relative_delta_mstruct = model.SenescenceModel.calculate_relative_delta_mstruct_roots(rate_mstruct_death, roots_inputs_dict['mstruct'], delta_teq)
delta_mstruct, delta_Nstruct = model.SenescenceModel.calculate_delta_mstruct_root(rate_mstruct_death, rate_Nstruct_death, delta_teq)
# loss of cytokinins (losses of nitrates, amino acids and sucrose are neglected)
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202 changes: 101 additions & 101 deletions test/outputs/desired_roots_outputs.csv
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Original file line number Diff line number Diff line change
@@ -1,102 +1,102 @@
t,plant,axis,Nstruct,cytokinins,mstruct,rate_mstruct_death,senesced_mstruct
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92,1,MS,0.00052969949,3.4980155,0.04997165,7.875e-09,2.835e-05
93,1,MS,0.00052969949,3.4980155,0.04997165,7.875e-09,2.835e-05
94,1,MS,0.00052969949,3.4980155,0.04997165,7.875e-09,2.835e-05
95,1,MS,0.00052969949,3.4980155,0.04997165,7.875e-09,2.835e-05
96,1,MS,0.00052969949,3.4980155,0.04997165,7.875e-09,2.835e-05
97,1,MS,0.00052969949,3.4980155,0.04997165,7.875e-09,2.835e-05
98,1,MS,0.00052969949,3.4980155,0.04997165,7.875e-09,2.835e-05
99,1,MS,0.00052969949,3.4980155,0.04997165,7.875e-09,2.835e-05
100,1,MS,0.00052969949,3.4980155,0.04997165,7.875e-09,2.835e-05

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