diff --git a/senescwheat/model.py b/senescwheat/model.py index 6ca7e44..b38f91a 100755 --- a/senescwheat/model.py +++ b/senescwheat/model.py @@ -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): diff --git a/senescwheat/parameters.py b/senescwheat/parameters.py index b57fde1..6300ed7 100644 --- a/senescwheat/parameters.py +++ b/senescwheat/parameters.py @@ -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 diff --git a/senescwheat/simulation.py b/senescwheat/simulation.py index dbfc274..c8b9927 100755 --- a/senescwheat/simulation.py +++ b/senescwheat/simulation.py @@ -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) diff --git a/test/outputs/desired_roots_outputs.csv b/test/outputs/desired_roots_outputs.csv index f0afeab..9a0f2d6 100644 --- a/test/outputs/desired_roots_outputs.csv +++ b/test/outputs/desired_roots_outputs.csv @@ -1,102 +1,102 @@ t,plant,axis,Nstruct,cytokinins,mstruct,rate_mstruct_death,senesced_mstruct -0,1,MS,0.00053,3.5,0.05,0.0,0.0 -1,1,MS,0.00053,3.5,0.05,0.0,0.0 -2,1,MS,0.00053,3.5,0.05,0.0,0.0 -3,1,MS,0.00053,3.5,0.05,0.0,0.0 -4,1,MS,0.00053,3.5,0.05,0.0,0.0 -5,1,MS,0.00053,3.5,0.05,0.0,0.0 -6,1,MS,0.00053,3.5,0.05,0.0,0.0 -7,1,MS,0.00053,3.5,0.05,0.0,0.0 -8,1,MS,0.00053,3.5,0.05,0.0,0.0 -9,1,MS,0.00053,3.5,0.05,0.0,0.0 -10,1,MS,0.00053,3.5,0.05,0.0,0.0 -11,1,MS,0.00053,3.5,0.05,0.0,0.0 -12,1,MS,0.00053,3.5,0.05,0.0,0.0 -13,1,MS,0.00053,3.5,0.05,0.0,0.0 -14,1,MS,0.00053,3.5,0.05,0.0,0.0 -15,1,MS,0.00053,3.5,0.05,0.0,0.0 -16,1,MS,0.00053,3.5,0.05,0.0,0.0 -17,1,MS,0.00053,3.5,0.05,0.0,0.0 -18,1,MS,0.00053,3.5,0.05,0.0,0.0 -19,1,MS,0.00053,3.5,0.05,0.0,0.0 -20,1,MS,0.00053,3.5,0.05,0.0,0.0 -21,1,MS,0.00053,3.5,0.05,0.0,0.0 -22,1,MS,0.00053,3.5,0.05,0.0,0.0 -23,1,MS,0.00053,3.5,0.05,0.0,0.0 -24,1,MS,0.00053,3.5,0.05,0.0,0.0 -25,1,MS,0.00053,3.5,0.05,0.0,0.0 -26,1,MS,0.00053,3.5,0.05,0.0,0.0 -27,1,MS,0.00053,3.5,0.05,0.0,0.0 -28,1,MS,0.00053,3.5,0.05,0.0,0.0 -29,1,MS,0.00053,3.5,0.05,0.0,0.0 -30,1,MS,0.00053,3.5,0.05,0.0,0.0 -31,1,MS,0.00053,3.5,0.05,0.0,0.0 -32,1,MS,0.00053,3.5,0.05,0.0,0.0 -33,1,MS,0.00053,3.5,0.05,0.0,0.0 -34,1,MS,0.00053,3.5,0.05,0.0,0.0 -35,1,MS,0.00053,3.5,0.05,0.0,0.0 -36,1,MS,0.00053,3.5,0.05,0.0,0.0 -37,1,MS,0.00053,3.5,0.05,0.0,0.0 -38,1,MS,0.00053,3.5,0.05,0.0,0.0 -39,1,MS,0.00053,3.5,0.05,0.0,0.0 -40,1,MS,0.00053,3.5,0.05,0.0,0.0 -41,1,MS,0.00053,3.5,0.05,0.0,0.0 -42,1,MS,0.00053,3.5,0.05,0.0,0.0 -43,1,MS,0.00053,3.5,0.05,0.0,0.0 -44,1,MS,0.00053,3.5,0.05,0.0,0.0 -45,1,MS,0.00053,3.5,0.05,0.0,0.0 -46,1,MS,0.00053,3.5,0.05,0.0,0.0 -47,1,MS,0.00053,3.5,0.05,0.0,0.0 -48,1,MS,0.00053,3.5,0.05,0.0,0.0 -49,1,MS,0.00053,3.5,0.05,0.0,0.0 -50,1,MS,0.00053,3.5,0.05,0.0,0.0 -51,1,MS,0.00053,3.5,0.05,0.0,0.0 -52,1,MS,0.00053,3.5,0.05,0.0,0.0 -53,1,MS,0.00053,3.5,0.05,0.0,0.0 -54,1,MS,0.00053,3.5,0.05,0.0,0.0 -55,1,MS,0.00053,3.5,0.05,0.0,0.0 -56,1,MS,0.00053,3.5,0.05,0.0,0.0 -57,1,MS,0.00053,3.5,0.05,0.0,0.0 -58,1,MS,0.00053,3.5,0.05,0.0,0.0 -59,1,MS,0.00053,3.5,0.05,0.0,0.0 -60,1,MS,0.00053,3.5,0.05,0.0,0.0 -61,1,MS,0.00053,3.5,0.05,0.0,0.0 -62,1,MS,0.00053,3.5,0.05,0.0,0.0 -63,1,MS,0.00053,3.5,0.05,0.0,0.0 -64,1,MS,0.00053,3.5,0.05,0.0,0.0 -65,1,MS,0.00053,3.5,0.05,0.0,0.0 -66,1,MS,0.00053,3.5,0.05,0.0,0.0 -67,1,MS,0.00053,3.5,0.05,0.0,0.0 -68,1,MS,0.00053,3.5,0.05,0.0,0.0 -69,1,MS,0.00053,3.5,0.05,0.0,0.0 -70,1,MS,0.00053,3.5,0.05,0.0,0.0 -71,1,MS,0.00053,3.5,0.05,0.0,0.0 -72,1,MS,0.00053,3.5,0.05,0.0,0.0 -73,1,MS,0.00053,3.5,0.05,0.0,0.0 -74,1,MS,0.00053,3.5,0.05,0.0,0.0 -75,1,MS,0.00053,3.5,0.05,0.0,0.0 -76,1,MS,0.00053,3.5,0.05,0.0,0.0 -77,1,MS,0.00053,3.5,0.05,0.0,0.0 -78,1,MS,0.00053,3.5,0.05,0.0,0.0 -79,1,MS,0.00053,3.5,0.05,0.0,0.0 -80,1,MS,0.00053,3.5,0.05,0.0,0.0 -81,1,MS,0.00053,3.5,0.05,0.0,0.0 -82,1,MS,0.00053,3.5,0.05,0.0,0.0 -83,1,MS,0.00053,3.5,0.05,0.0,0.0 -84,1,MS,0.00053,3.5,0.05,0.0,0.0 -85,1,MS,0.00053,3.5,0.05,0.0,0.0 -86,1,MS,0.00053,3.5,0.05,0.0,0.0 -87,1,MS,0.00053,3.5,0.05,0.0,0.0 -88,1,MS,0.00053,3.5,0.05,0.0,0.0 -89,1,MS,0.00053,3.5,0.05,0.0,0.0 -90,1,MS,0.00053,3.5,0.05,0.0,0.0 -91,1,MS,0.00053,3.5,0.05,0.0,0.0 -92,1,MS,0.00053,3.5,0.05,0.0,0.0 -93,1,MS,0.00053,3.5,0.05,0.0,0.0 -94,1,MS,0.00053,3.5,0.05,0.0,0.0 -95,1,MS,0.00053,3.5,0.05,0.0,0.0 -96,1,MS,0.00053,3.5,0.05,0.0,0.0 -97,1,MS,0.00053,3.5,0.05,0.0,0.0 -98,1,MS,0.00053,3.5,0.05,0.0,0.0 -99,1,MS,0.00053,3.5,0.05,0.0,0.0 -100,1,MS,0.00053,3.5,0.05,0.0,0.0 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