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a800_04_60_11_01_for_Chalup_coarse_molecules.py
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a800_04_60_11_01_for_Chalup_coarse_molecules.py
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'''
Created on Jan 23, 2016
Note:
About a803s
Simplify the model
*putting DNA and RNA together
*putting togehter the constant pool
*removing chl N and so on.
Revision note: 193-37
note:
This is a good one. This can be possible for thesis.
@author: Keisuke
'''
from pylab import *
from af001_energy_calculation import *
from Dmax_computation16 import *
global What_is_limiting
What_is_limiting=1 #0: P-limiting 1:N-limiting
if What_is_limiting==0:
#for P limiting data
from Healey85_data_08_Chl_from_Nlimited_added import healey85C
elif What_is_limiting==1:
#for N limiting data
from Chalup90_data_00 import chalup90
DPI = 600
#AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
#Function beging here
#AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
def kkI(data): #this t00function calculate for the same irradiance
print(data.i)
I=data.Lightintensity
if data.i ==0:
plotcolor='#3953A9'
elif data.i ==1:
plotcolor='#EE2C3B'
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
#Parameters
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
if What_is_limiting==0:
#For P-limiting case
Pin=0.002 #(mol/m3) Phosphorus concentration in the incoming medium (Healey 1985)
Nin=0.2 #(mol/m3) Nitrate concentration in the incoming medium (Healey 1985)
Qc=1.03*10**(-12)/12 #(molC/cell) biomass C per cell (196-18)(from Healey 1985)
elif What_is_limiting==1:
#For N-limiting case
Pin=0.025 #(mol/m3) Phosphorus concentration in the incoming medium (Healey 1985)
Nin=0.025 #(mol/m3) Nitrate concentration in the incoming medium (Healey 1985)
Qc=10**(-12)/12 #(molC/cell) biomass C per cell (196-18)(from Healey 1985)
E3=evalue()
E=E3.E
R=1.63*10**(-6)
h=0.0007174 #used in the next equation
ep3=h #diffusivity of glycolipid layer compared to alginate layer (132-23)
Ra=0 #(dimensionless) the ratio of alginate layer to the cell radius
La=R*Ra #(m) thickness of alginate layer (132-23)
Rg=0.1 #ratio of glycolipid layer to the cell radius
Lg=R*Rg #(m) thickness of glycolipid layer
x0=1/h*(1/R-1/(R+Lg))+ep3/h*1/(R+Lg)+(1/(R+Lg+La))*(1-ep3/h) #effect of
r5=1/(x0*R) #diffusivity efficiency of cell membrane
V=4/3*pi*R**3 #Volume of the cell (m3/cell)
C=6
Ddmax=1.6
#Dmax=4
Dstep=0.001
Dd=arange(Dstep,Ddmax+Dstep,Dstep) #(h-1) growth rate
U=arange(0,Ddmax/Dstep,1)
D=Dd/(3600*24)
#Qc=10**(-12)/12 #(molC/cell) biomass C per cell (196-18)(from Healey 1985)
rho=Qc/V #(molC m-3) biomass C per volume in the cell
Do20=2.12*10**(-9) #Diffusion coefficient of O2 in the water (m2/s)
Do2=Do20*r5 #Diffusion coefficient of O2 in the water (m2/s)
Dch0=6.728*10**(-10) #Diffusion coefficient of glucose in the water (m2/s)
Dch=Dch0*r5 #Diffusion coefficient of glucose in the water (m2/s)
Dnh40=1.98*10**(-9) #Diffusion coefficient of ammonium in the water (m2/s)
Dnh4=Dnh40*r5 #Diffusion coefficient of ammonium in the water (m2/s)
Dno30=1.9*10**(-9) #Diffusion coefficient of nitrate in the water (m2/s) (Li 1974 at 25C)
Dno3=Dnh40*r5 #Diffusion coefficient of nitrate in the water (m2/s)
Dh2po40=8.46*10**(-10) #Diffusion coefficient of H2PO4- in water at 25C (m2 s-1) (Li 1974)
Dhpo40=7.34*10**(-10) #Diffusion coefficient of HPO42- in water at 25C (m2 s-1) (Li 1974)
Dp0=(Dh2po40+Dhpo40)/2 #Take the average as at around Ph 7.5 (healey 1985 paper' initial condition) They exist about half and half
Dp=Dp0*r5 #diffusion coefficient of P through membrane
Mchl=893.49 #(g / mol chlorophyll) mollar mass of chlorophyll
#==============================
#New parameters
#==============================
#------------------------------
#Photosynthesis
#------------------------------
Pmax0=7 #(g C /(g Chl h) Maximum production rate per chlorophyll (around 6 by Cullen 1990)
Pmax=Pmax0*Mchl/12/3600/55 #(mol C s-1 mol chl-1) carbon fixing rate (156-10) (156-15) for unit conversion)
Pmax=0.00209835928190267
OT=0.0065661503085636
Pchl=Pmax*(1-exp(-OT*I)) #(C mol s-1 Chl mol-1) Carbohydrate fixation rate per chlorophyll (167-1)(193-25)
m=5*10**(-19) #(mol C s-1 cell-1) maintenance carbonhydrate consumption (idea from 172-7)
m=4.78224745056655E-19
ls=D*Qc #(molC s-1) Biomass synthesis rate (193-25)
#------------------------------
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#Key parameters: parameterization ideas -> Kei 193-28
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
Daverage=0.6*86400
#================================
#Constant parameters
#================================
Ynphoto_chl=3.0056463754677 #((molN cell-1)/(molC chl cell-1)) the stoichiometric ratio for cell photosynthetic enzyme (Rubisco etc.) nitrogen to chlorophyll (193-25)
Ypthylakoid_chl=0.0281633095303638 #((molP cell-1)/(molC chl cell-1)) the shoichiometric ratio for cell phosphorus in thylakoid membrane to chlorophyll (193-26)
Cnproteinsynth=24000 #(s) Constant for protein synthesis nitrogen calculation (193-25)
Cnbiosynth=2.53367759328165E-10 #(molN cell-1 s) Constant for varible part of biosynthesis protein nitrogen (193-37)
Cnrna_variable=6212.592499 #(s) Constant for Variable part of RNA (193-26)
Cndna_variable=1.60e-15 #(molN cell-1 s) Constant for variable part of DNA (193-26)
#================================
#================================
#Y intercept parameters
#================================
Nconst_protein=5.4e-15*1.4 #(molN cell-1) Constant protein pool in nitrogen (193-25)
Nconst_protein=1.18274979779916E-15
Nstore_max=2.91679384515998E-15 #(molN cell-1) Constant protein pool in nitrogen (193-25)
Nconst_dnarna=2.78e-15/5/2.8 #(molN cell-1) Constant part of nitrogen in DNA and RNA (193-26)
Nconst_other=2.78e-16 #(molN cell-1) Other kinds of nitrogen assuming constant (193-33)
Pconst_other=5.44534485638617E-17 #(molP cell-1) Constant part of phosphorus (193-26) * This includes ATP ADP, Phospholipid and DNA RNA
#================================
Molar_mass_DNA_AT_average=307.47 #(g mol-1) Molar mass AT average (from "10 Amino acids and nucleic acids stoichiometry.xlsx")
Molar_mass_DNA_CG_average=307.97 #(g mol-1) Molar mass CG average (from "10 Amino acids and nucleic acids stoichiometry.xlsx")
Molar_mass_RNA_AT_average=316.47 #(g mol-1) Molar mass AT average (from "10 Amino acids and nucleic acids stoichiometry.xlsx")
Molar_mass_RNA_CG_average=323.97 #(g mol-1) Molar mass CG average (from "10 Amino acids and nucleic acids stoichiometry.xlsx")
#================================
#E coli
#================================
CG_Ecoli=0.506 #(dimensionless) from [http://www.ncbi.nlm.nih.gov/genome/167 (accessed 06/18/2016)]
AT_Ecoli=1-CG_Ecoli #(dimensionless)
Molar_mass_DNA_Ecoli=Molar_mass_DNA_AT_average*CG_Ecoli+Molar_mass_DNA_CG_average*AT_Ecoli #(g mol-1) Molar mass of DNA unit
Molar_mass_RNA_Ecoli=Molar_mass_RNA_AT_average*CG_Ecoli+Molar_mass_RNA_CG_average*AT_Ecoli #(g mol-1) Molar mass of RNA unit
RNA_DNA_mass_ratio=20/7.6 #(ug/ug) Bremer and Dennis 1996
RNA_DNA_mass_ratio=17.844/6.5239 #(ug/ug) from values ad D=0 "07 Bremer and Dennis 1996 data plot.xlsx"
RNA_DNA_molar_ratio=RNA_DNA_mass_ratio/Molar_mass_RNA_Ecoli*Molar_mass_DNA_Ecoli #(mol mol-1)
#================================
#Stoichiometric parameters
#================================
YcyanoC_N=2 #(molC molN) C/N molar ratio of cyanophycin
YpgC_P=40 #(molC molP) C/P molar ratio of PG: Phosphatidyl glycerol (assuming C16 fatty acids (since actually mostly C16 (Huflejt et al., 1990)
CG=0.563 #GC% [http://www.ncbi.nlm.nih.gov/genome/13522 (accessed 06/18/2016)]
YnucacidP_N=1/(3.5*(1-CG)+4*CG) #(molP molN-1) P/N molar ratio of RNA (193-26) values (193-28) excel file "08 N to P ratio in DNA and RNA.xlsx"
YdnaC_N=3.5*(1-CG)+2.5*CG #(molC molN-1) C/N molar ratio of dna (based on "10 Amino acids and nucleic acids stoichiometry.xlsx)
YrnaC_N=3.25*(1-CG)+2.5*CG #(molC molN-1) C/N molar ratio of rna (based on "10 Amino acids and nucleic acids stoichiometry.xlsx)
DNAmb=2.1269 #(Mb) Megabase pair of synechococcus DNA in mega (million) base pairs [http://www.ncbi.nlm.nih.gov/genome/13522 (accessed 06/18/2016)]
Avogadro=6.022*10**23 #(molecules mol-1) Avogadro constant
Pdna_const=DNAmb*2*10**6/Avogadro #(molP cell-1) Constant part of DNA in phosphorus
Prna_const=Pdna_const*RNA_DNA_molar_ratio #(molP cell-1) Constant part of RNA in phosphorus
#* Make sure to multiply by 2 as they are base PAIRs"
Ndna_const=Pdna_const/YnucacidP_N #(molN cell-1) Constant part of DNA in nitrogen
Nrna_const=Ndna_const*RNA_DNA_molar_ratio #(molN cell-1) Constatn part of RNA in phosphorus
#print(Ndna_const*Avogadro,Nconst_protein*Avogadro)
#YdnaN_P=1/3.75 #(molP molN-1) P/N molar ratio of DNA (193-26) values (193-28) excel file "08 N to P ratio in DNA and RNA.xlsx"
Ynrnaconst_dnarnaconst=1/2 #(dimensionless) N molar ratio of RNA (constant part) to DNA + RNA (constant part) (193-33) reffering to around p.112 of Biology of Prokyariotes
Yndnaconst_dnarnaconst=1-Ynrnaconst_dnarnaconst #(dimensionless) N molar ratio of DNA (constant part) to DNA + RNA (constant part) (193-33) refering to around p.112 of Biology of Prokyariotes
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
#Calculation
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Chl=((1+E)*ls+m)/Pchl #(molC chl cell-1) Chlrophyll concentration (193-25)
Nphoto=Chl*Ynphoto_chl #(molN cell-1) Photosynthesis related protein nitrogen (193-25)
Nproteinsynth=(Nphoto+Nconst_protein)*D*Cnproteinsynth/(1-D*Cnproteinsynth) #(molN cell-1) protein synthesis related protein in N (193-25)
Nbiosynth=D*Cnbiosynth #(molN cell-1) various part of biosynthesis related protein in N (193-37)
Nprotein=Nphoto+Nconst_protein+Nbiosynth #(molN cell-1) All the proteins in N (193-26)
Nrna_variable=Nprotein*D*Cnrna_variable #(molN cell-1) variable part of nitrogen in RNA (193-26)(193-37)
Ndna_variable=Ndna_const*Dd/1.2*(18.3-7.6)/7.6 #(molN cell-1) variable part of nitrogen in DNA (193-26) Increasing ratio based on Bremmer 1996
Ndna_variable=0*Dd #(molN cell-1) While Bremer and Dennis shows increasing trend, Parrott 1980 shows decreasing trend.
#print(Dd/1.2*(18.3-7.6)/7.6)
#Ndnarna=Nconst_dnarna+Nnucacid_variable
Nchl=Chl*4/55 #(molN cell-1) Chlorophyll nitrogen (actually almost negligiable)
Pthylakoid=Chl*Ypthylakoid_chl #(molP cel-1) Phosphorus in thylakoid membranes: phospholipid, etc. (193-26)
Prna_variable=Nrna_variable*YnucacidP_N #(molP cell-1) variable part of phosphorus in RNA (193-26)
Pdna_variable=Ndna_variable*YnucacidP_N #(molP cell-1) variable part of phosphorus in DNA (193-26)
#=================================
#Constant part
#=================================
# Nconst_dna=Nconst_dnarna*Yndnaconst_dnarnaconst #(molN cell-1) Constant part of DNA in nitorgen (193-33)
# Nconst_rna=Nconst_dnarna*Ynrnaconst_dnarnaconst #(molN cell-1) Constant part of RNA in nitrogen (193-33)
# Pconst_dna=Nconst_dna*YdnaN_P #(molP cell-1) phosphorus in constant part of DNA (193-33)
# Pconst_rna=Nconst_rna*YrnaN_P #(molP cell-1) phosphorus in constant part of RNA (193-33)
#=================================
#=================================
#Total calculation
#=================================
r2s=1
Qn_max=Nprotein+Nrna_variable+Nrna_const+Ndna_variable+Ndna_const+Nchl+Nstore_max #(molN cell-1) nitrogen content in the cell (193-26) #(molN cell-1) total phosphorus content in the cell (193-26)
Qp_max=25/(3.097e16) #(molP cell-1) total phosphorus content in the cell (193-26)
Qn_min=Nprotein+Nrna_variable+Nrna_const+Ndna_variable+Ndna_const+Nchl #(molN cell-1) total nitrogen in the cell without storage
Qp_min=Pconst_other+Pthylakoid+Prna_variable*(1+r2s)+Prna_const*(1+r2s)+Pdna_variable+Pdna_const #(molP cell-1) total phosphorus in the cell without storage
#=================================
#Vector preparation
#=================================
Nstore=zeros(size(Dd))
X=zeros(size(Dd))
Qn_test=zeros(size(Dd))
Qp_test=copy(X)
Qp=copy(X)
Qn=copy(X)
Pstore=copy(X)
#=================================
#Population calculation
#=================================
Xn_max=Nin/Qn_min
Xp_max=Pin/Qp_min
for i in U:
if Xn_max[i]>Xp_max[i]:
X[i]=Xp_max[i]
Qp[i]=Qp_min[i]
Qn_test[i]=Nin/X[i]
Pstore[i]=Prna_variable[i]+Prna_const
if Qn_test[i]<Qn_max[i]:
Qn[i]=Qn_test[i]
Nstore[i]=Qn_test[i]-Nprotein[i]-Nrna_variable[i]-Nrna_const-Ndna_variable[i]-Ndna_const-Nchl[i] #(molN cell-1) Nitrogen storage in the cell
else:
Qn[i]=Qn_max[i]
Nstore[i]=Nstore_max
else:
X[i]=Xn_max[i]
Qn[i]=Qn_min[i]
Qp_test[i]=Pin/X[i]
if Qp_test[i]<Qp_max:
Qp[i]=Qp_test[i]
else:
Qp[i]=Qp_max
Pstore[i]=Qp[i]-Pconst_other-Pthylakoid[i]-Prna_variable[i]-Prna_const-Pdna_variable[i]-Pdna_const #(molP cell-1) Stored phosphorus in the cell
#X=Pin/Qp #(cells m-3) Number density of cells (193-27)
# x=Nin/Qn #(cells m-3) number density of cells (193-27)
#
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#For plotting 1
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
BiomassC=12*X*Qc #(mg C L-1) Biomass concentration
NtoCplot=Qn/Qc*14*10**6/(12*10**3) #(ug N / mg C) biomass N to C ratio (164-20)
PtoCplot=Qp/Qc*30.97*10**6/(12*10**3) #(ug P / mg C) biomass P to C ratio (164-20)
NtoPplot=Qn/Qp*14*10**6/(30.97*10**6) #(ug N /ug P) biomass N to P ratio (164-20)
ChltoC0=Chl/Qc #(mol C chl mol C -1) Chlorophyll to carbon ratio
Mchl=893.49 #(g / mol chlorophyll) mollar mass of chlorophyll
ChltoCplot=ChltoC0/12/1000*Mchl/55*10**6 #(ug chlorophyll a mg C-1) (see 157-36 for conversion)
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#For plotting 2 (calculation of dna, rna, etc)
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
# Ndna=Nconst_dna+Ndna_variable #(molN cell-1) nitorgen in DNA (193-33)
# Nrna=Nconst_rna+Nrna_variable #(molN cell-1) nitrogen in RNA (193-33)
# Pdna=Ndna*YdnaN_P #(molP cell-1) phosphorus in DNA (193-33)
# Prna=Nrna*YrnaN_P #(molP cell-1) phosphorus in RNA (193-33)
#Pconst_other=Pconst-Pconst_dna-Pconst_rna #(molP cell-1) phosphorus in other parts (ex. phospholipid in outer membrane, ATP, ADP, etc. (assuming constant) (193-33)
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#For plotting 3 (unit adjustment)
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
Nunit=1/Qc*14*10**6/(12*10**3) #((ug N / mgC)/(molN cell-1) unit conversion term (164-20)
Punit=1/Qc*30.97*10**6/(12*10**3) #((ug P / mgC)/(molP cell-1) unit conversion term (164-20)
Numbertoarray=ones(size(Dd)) #(dimensionless) Number to array converter
#=======================================
#Calculation of carbon usage (195-16)
#=======================================
CNprotein=4.49 #(molC molN) the ratio of C to N in protein (derived from Brown 1991) calculation in "13 Amino acid composition of different phytoplankton.xlsx"
#-------------------
#C protein
#-------------------
Cphoto=Nphoto*CNprotein #(molC cell-1) carbon in photosystem protein (195-16)
Cbiosynth=Nbiosynth*CNprotein #(molC cell-1) carbon in biosynthesis protein (195-16)
Cconst_protein=Nconst_protein*CNprotein #(molC cell-1) carbon in other protein assumed constant (195-16)
#----------------------
#C chlorophyll
#----------------------
Cchl=Chl #(molC cell-1) carbon in chlorophyll (195-16)
#----------------------
#C DNA RNA
#----------------------
Crna_const=Nrna_const*YrnaC_N #(molC cell-1) carbon in variable part of RNA (195-16)
Crna_variable=Nrna_variable*YrnaC_N #(molC cell-1) carbon in variable part of RNA (195-16)
Cdna_const=Ndna_const*YdnaC_N #(molC cell-1) carbon in constant part of DNA (195-16)
Cdna_variable=Ndna_variable*YdnaC_N #(molC cell-1) carbon in variable part of DNA (195-16)
Cessential=3.57361118517991E-14 #(molC cell-1) essential carbon (lipid membrane, etc.) *8.33e-14/10 is 10%
Cnstore=Nstore*YcyanoC_N #(molC cell-1) carbon in nitrogen storage (cyanophycin)
CthylakoidPG=Pthylakoid*YpgC_P #(molC cell-1) carbon in PG (phosphatidyl glycerol) in thylakoid membranes
#---------------------------------------------------
#C other: Here revised to include Nstore reduction
#---------------------------------------------------
#print(Qc)
Cother_without_Nstore=Qc-Cphoto-Cbiosynth-Cconst_protein-Cchl\
-Crna_const-Crna_variable-Cdna_const-Cdna_variable\
-Cessential-CthylakoidPG
Cother_with_full_Nstore=Qc-Cphoto-Cbiosynth-Cconst_protein-Cchl\
-Crna_const-Crna_variable-Cdna_const-Cdna_variable\
-Cessential-Cnstore-CthylakoidPG
Cother=Cother_with_full_Nstore
Nstore_reduce=logical_and(Cother_without_Nstore>0, Cother_with_full_Nstore<0)
Cnstore[Nstore_reduce]=Cother_without_Nstore[Nstore_reduce]
Nstore0=copy(Nstore)
Nstore[Nstore_reduce]=Cother_without_Nstore[Nstore_reduce]/YcyanoC_N
Cother[Nstore_reduce]=0
Qn[Nstore_reduce]=Qn[Nstore_reduce]+Nstore[Nstore_reduce]-Nstore0[Nstore_reduce]
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#For plotting 1
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
BiomassC=12*X*Qc #(mg C L-1) Biomass concentration
NtoCplot=Qn/Qc #(mol / mol) biomass N to C ratio (164-20)
PtoCplot=Qp/Qc*30.97*10**6/(12*10**3) #(ug P / mg C) biomass P to C ratio (164-20)
NtoPplot=Qn/Qp*14*10**6/(30.97*10**6) #(ug N /ug P) biomass N to P ratio (164-20)
ChltoC0=Chl/Qc #(mol C chl mol C -1) Chlorophyll to carbon ratio
Mchl=893.49 #(g / mol chlorophyll) mollar mass of chlorophyll
ChltoCplot=ChltoC0/12/1000*Mchl/55*10**6 #(ug chlorophyll a mg C-1) (see 157-36 for conversion)
#=======================================
#C for plot in
#=======================================
#*percentorratio=100 #100: percent, 1:ratio
percentorratio=100 #100: percent, 1:ratio
Cphoto_plot=Cphoto/Qc*percentorratio
Cbiosynth_plot=Cbiosynth/Qc*percentorratio
Cconst_protein_plot=Cconst_protein/Qc*percentorratio*Numbertoarray
Cchl_plot=Cchl/Qc*percentorratio
Crna_const_plot=Crna_const/Qc*percentorratio*Numbertoarray
Crna_variable_plot=Crna_variable/Qc*percentorratio
Cdna_const_plot=Cdna_const/Qc*percentorratio*Numbertoarray
Cdna_variable_plot=Cdna_variable/Qc*percentorratio
# Cother_plot=1*percentorratio-Cphoto_plot-Cbiosynth_plot-Cconst_protein_plot-Cchl_plot\
# -Crna_const_plot-Crna_variable_plot-Cdna_const_plot-Cdna_variable_plot
Cother_plot=Cother/Qc*percentorratio
Cessential_plot=Cessential/Qc*percentorratio*Numbertoarray
Cnstore_plot=Cnstore/Qc*percentorratio
CthylakoidPG_plot=CthylakoidPG/Qc*percentorratio
#=======================================
#N for plot ***(Mainly from 193-33)***
#=======================================
Nphoto_plot=Nphoto/Qc #(ug N/ mgC) Photosynthesis related protein nitrogen (193-25)(193-33)
#Nproteinsynth_plot=Nproteinsynth*Nunit #(ug N/ mgC) protein synthesis related protein in N (193-25)(193-33)
Nbiosynth_plot=Nbiosynth/Qc #(ug N/ mgC) biosynthesis related protein in N (193-37)
Nconst_protein_plot=Nconst_protein*Numbertoarray/Qc #(ug N/ mgC) constant protein pool in nitrogen (193-25)(193-33)
# Nrna_plot=Nrna*Nunit #(ug N/ mgC) nitrogen in RNA (193-33)
# Ndna_plot=Ndna*Nunit #(ug N/ mgC) nitrogen in DNA (193-33)
Nchl_plot=Nchl/Qc #(ug N/ mgC) Chlorophyll nitrogen (actually almost negligiable) (193-33)
# Nconst_other_plot=Nconst_other*Nunit*Numbertoarray #(ug N/ mgC) Other kinds of nitrogen assuming constant (193-33)
Nrna_variable_plot=Nrna_variable/Qc #(ug N/ mgC) Nitrogen in Variable part of nucleic acid (193-37)
Ndna_variable_plot=Ndna_variable/Qc #(ug N/ mgC) Nitrogen in Variable part of nucleic acid (193-37)
Ndna_const_plot=Ndna_const*Numbertoarray/Qc #(ug N/ mgC) Nitrogen in constant part of DNA
Nrna_const_plot=Nrna_const*Numbertoarray/Qc #(ug N/ mgC) Nitrogen in constant part of RNA
Nstore_plot=Nstore #(ug N/ mgC) Nitrogen in storage
#=======================================
#P for plot ***(Mainly from 193-33)***
#=======================================
# Pdna_plot=Pdna*Punit #(ug P/ mgC) phosphorus in DNA (193-33)
# Prna_plot=Prna*Punit #(ug P/ mgC) phosphorus in RNA (193-33)
Prna_variable_plot=Prna_variable*Punit #(ug P/mgC) Phosphorus in variable part of RNA (193-37)
Pdna_variable_plot=Pdna_variable*Punit #(ug P/mgC) Phosphorus in variable part of DNA (193-37)
Pthylakoid_plot=Pthylakoid*Punit #(ug P/ mgC) Phosphorus in thylakoid membranes: phospholipid, etc. (193-26)(193-33)
Pconst_other_plot=Pconst_other*Punit*Numbertoarray #(ug P/ mgC) PHosphorus in other parts (ex. phospholipid in outer membrane, ATP, ADP, etc. (assuming constant) (193-33)
#PtoCplot2=Pdna_plot+Prna_plot+Pthylakoid_plot+Pconst_other_plot #For calculation check
Pdna_const_plot=Pdna_const*Punit*Numbertoarray #(ug P/ mgC) Phosphorus in constant part of DNA
Prna_const_plot=Prna_const*Punit*Numbertoarray #(ug P/ mgC) Phosphorus in constant part of RNA
Pstore_plot=Pstore*Punit #(ug P/ mgC) Phosphorus in phosphorus storage
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#Applying chl max
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#Chlmax=NC0*0.16 #(g chl g C-1) making it a functioni of N to C ratio
Chlmax=0.048
#for i in U:
# if Chlmax*1000 < ChltoCplot[i]: # *1000 is unit converstion from (g chl g C-1) to (ug chl mg C-1)
# BiomassC[i]=nan
# PtoCplot[i]=nan
# NtoCplot[i]=nan
# ChltoCplot[i]=nan
#Dd[Chlmax*1000<ChltoCplot]=nan #this line seems to be causing warning
Dd[Cother<0]=nan
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#Plot free parameters #Here units adjusted for paper
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
from decimal import Decimal
def sci(Numb):
Numb='%.2E' % Decimal(Numb)
return Numb
print("m",sci(m/Qc*86400))
print("Pmax",sci(Pmax*86400))
print("Apho",sci(OT))
print("Ynphoto_chl",sci(Ynphoto_chl*CNprotein))
print("Abio",sci(Cnbiosynth/Qc*CNprotein/86400))
print("Cother_protein",sci(Nconst_protein/Qc*CNprotein))
print("Arna",sci(Cnrna_variable/CNprotein/86400*YnucacidP_N))
print("Ythylakoid_chl_P",sci(Ypthylakoid_chl))
print("Pconst_other",sci(Pconst_other/Qc))
print("Nstore_max",sci(Nstore_max/Qc))
print("Cessential",sci(Cessential/Qc))
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
#5.Plot
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
rcParams.update({'font.size': 25,
'lines.markersize':12,
'lines.markeredgewidth':1})
rcParams.update({'xtick.major.pad': 15})
rcParams.update({'xtick.major.pad': 15})
rcParams.update({'font.serif': 'Times New Roman'})
rcParams.update({'figure.autolayout': True})
rcParams['figure.figsize']=8,6.5
rcParams.update({'figure.facecolor':'W'})
rcParams.update({'lines.linewidth':3})
rcParams.update({'patch.edgecolor':'none'})
rcParams.update({'axes.linewidth':1.5})
rcParams.update({'xtick.major.width':1})
rcParams.update({'ytick.major.width':1})
rcParams.update({'mathtext.default': 'regular' })
lowlim=0
highlim=Ddmax+1e-5
step=0.2
AxisFontSize = 30
#==================================
#Plot control * 1=on other=off
#==================================
Plot_NC=1
Plot_Chl=1
Plot_NC_stack=1
Plot_C_stack=1
Plot_C_stack_small=0
#============================================
#What is limiting: output folder controll
#============================================
if What_is_limiting==0:
Whatislimiting="P-limiting"
elif What_is_limiting==1:
Whatislimiting="N-limiting"
#============================================
Xmax=1.8000001
XTICKS=arange(0.0,1.5+0.5,0.5)
if Plot_NC==1:
figure(6)
plot(Dd, NtoCplot, color=plotcolor,label=str(int(round(I,0)))+' $\mu$mol m$^{-2}$ s$^{-1}$')
plot(data.Dnc, data.NC,'o' ,color=plotcolor)
xlabel('$\mu$ (d$^{-1}$)',fontsize=AxisFontSize)
ylabel('mol N mol C$^{-1}$',fontsize=AxisFontSize)
ylim(ymin=0)
if What_is_limiting==0:
ylim(ymax=0.30001)
elif What_is_limiting==1:
ylim(ymax=0.30001)
#ylim([0,801])
#yticks(arange(0,801,100))
xticks(XTICKS)
legend(loc='upper right', borderaxespad=0.6, fontsize=24, ncol=1)
xlim(xmax=Xmax)
savefig("C:\\Users\\Keiin\\OneDrive\\desktop\\figures\\01\\Phytoplankton model\\"+Whatislimiting+"\\Chalup90\\N to C.png",dpi = DPI)
# ylim([0,21])
# yticks(arange(0,21,5))
if Plot_Chl==1:
figure(7)
plot(Dd,ChltoCplot,color=plotcolor,label=str(int(I))+' $\mu$E m$^{-2}$ s$^{-1}$')
# plot(Dh,Dh,color=plotcolor)
plot(data.Dchl, data.Chl,'o' ,color=plotcolor)
xlabel('$\mu$ (d$^{-1}$)',fontsize=AxisFontSize)
ylabel('$\mu$g chlorophyll a mg C$^{-1}$',fontsize=AxisFontSize)
# title('Chlorophyll a concentration')
xticks(XTICKS)
ylim([0,55])
yticks(arange(0,56,10))
xlim(xmax=Xmax)
# legend(loc='upper right', borderaxespad=0.6, fontsize=20, ncol=1)
savefig("C:\\Users\\Keiin\\OneDrive\\desktop\\figures\\01\\Phytoplankton model\\"+Whatislimiting+"\\Chalup90\\Chl to C.png",dpi = DPI)
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
#Stack plot part
#OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
Color_DNA_const='orange'
Color_RNA_const='yellow'
Color_protein_const='blue'
Color_photo='yellow'
Color_RNA_variable='red'
Color_DNA_variable='blue'
Color_protein_biosynthesis='pink'
Color_chl='#66FF66'
#Color_chl='#207446'
Color_other='#006400'
#Color_other='cyan'
Color_other='#008000'
Color_P_const='#CCFFFF'
Color_DNA='black'
Color_RNA='red'
Color_Nstore='purple'
Color_Pstore='#D0CECE'
Color_Cessential='brown'
Color_thylakoid='#FFD966'
Color_Photo='#FFC000' #change
Color_Bio='#66FF66' #change
Color_Other='#0070C0' #change
Color_Nstore='#FFCCCC'
Color_other='#FFFF99'
StackPlotColorsN=(Color_Nstore,Color_protein_const,Color_photo,Color_protein_biosynthesis,Color_DNA,Color_RNA,Color_chl)
StackPlotColorsP=(Color_P_const,Color_thylakoid,Color_DNA,Color_RNA,Color_Pstore)
StackPlotColorsC=(Color_Cessential,Color_Nstore,Color_protein_const,Color_photo,Color_protein_biosynthesis,Color_DNA,Color_RNA,Color_chl,Color_thylakoid,\
Color_other)
StackPlotColorsCsmalls=(Color_DNA,Color_RNA,Color_chl,Color_thylakoid)
StackPlotColorsN=(Color_Other,Color_Photo,Color_Bio,Color_Nstore)
StackPlotColorsC=(Color_Other,Color_Photo,Color_Bio,Color_Nstore,Color_other)
FigurenumberN_C=10
if data.i>-1:
if Plot_NC_stack==1:
figure(FigurenumberN_C+data.i)
stackplot(Dd,Nconst_protein_plot+Ndna_const_plot+Ndna_variable_plot,Nphoto_plot+Nchl_plot,Nbiosynth_plot+Nrna_const_plot+Nrna_variable_plot,Nstore_plot,colors=StackPlotColorsN)
# stackplot(Dd,Nconst_other_plot,Nconst_protein_plot,Nproteinsynth_plot,Nphoto_plot,Ndna_plot,Nrna_plot,Nchl_plot,colors=StackPlotColorsN)
plot(data.Dnc, data.NC,'o' ,color='black')
xlabel('$\mu$ (d$^{-1}$)', fontsize=AxisFontSize) #copied from 73
ylabel('mol N mol C$^{-1}$', fontsize=AxisFontSize) #copied from 73
# ylim([0,25])
# yticks(arange(0,26,5))
xticks(XTICKS)
xlim([lowlim,highlim])
ylim([0,0.3000001])
First_part="C:\\Users\\Keiin\\OneDrive\\desktop\\figures\\01\\Phytoplankton model\\"+Whatislimiting+"\\Chalup90\\N-C broad\\Fig."
Figure_number=str(FigurenumberN_C+data.i)
Last_part=".png"
xlim(xmax=Xmax)
savefig(First_part+Figure_number+Last_part,dpi = DPI)
FigurenumberC=20
if Plot_C_stack==1:
figure(FigurenumberC+data.i)
stackplot(Dd,Cessential_plot+Cconst_protein_plot+Cdna_const_plot+Cdna_variable_plot,\
Cphoto_plot+CthylakoidPG_plot+Cchl_plot,Crna_const_plot+Crna_variable_plot+Cbiosynth_plot,Cnstore_plot,Cother_plot,colors=StackPlotColorsC)
#plot(healey85data.D_PtoC, healey85data.PtoC,'o' ,color="black")
xlabel('$\mu$ (d$^{-1}$)', fontsize=AxisFontSize) #copied from 73
ylabel('C allocation ($\%$)', fontsize=AxisFontSize) #copied from 73
# ylim([0,25])
# yticks(arange(0,26,5))
xticks(XTICKS)
xlim([lowlim,highlim])
First_part="C:\\Users\\Keiin\\OneDrive\\desktop\\figures\\01\\Phytoplankton model\\"+Whatislimiting+"\\Chalup90\\C allocation broad\\Fig."
Figure_number=str(FigurenumberC+data.i)
Last_part=".png"
ylim(ymax=percentorratio+1e-20)
xlim(xmax=Xmax)
title('Light: '+str(int(round(I,0)))+' $\mu$mol m$^{-2}$ s$^{-1}$',y=1.02)
savefig(First_part+Figure_number+Last_part,dpi = DPI)
FigurenumberCsmalls=25
if Plot_C_stack_small==1:
figure(FigurenumberCsmalls+data.i)
# stackplot(Dd,Cconst_protein_plot,Cphoto_plot,Cbiosynth_plot,Cchl_plot,Cdna_const_plot,Cdna_variable_plot,\
# Crna_const_plot,Crna_variable_plot,Cother_plot,colors=StackPlotColorsC)
stackplot(Dd,Cdna_const_plot+Cdna_variable_plot,\
Crna_const_plot+Crna_variable_plot,Cchl_plot,CthylakoidPG_plot,colors=StackPlotColorsCsmalls)
#plot(healey85data.D_PtoC, healey85data.PtoC,'o' ,color="black")
xlabel('$\mu$ (d$^{-1}$)', fontsize=AxisFontSize) #copied from 73
ylabel('C allocation ($\%$)', fontsize=AxisFontSize) #copied from 73
# ylim([0,25])
# yticks(arange(0,26,5))
xticks(arange(lowlim,highlim+step,step))
xlim([lowlim,highlim])
First_part="C:\\Users\\Keiin\\OneDrive\\desktop\\figures\\01\\Phytoplankton model\\"+Whatislimiting+"\\C allocation smalls\\Fig."
Figure_number=str(FigurenumberCsmalls+data.i)
Last_part=".png"
ylim(ymax=10)
savefig(First_part+Figure_number+Last_part,dpi = DPI)
#Adding Mu max values==================================================
Lightintensity=arange(0.1,2500+0.1,0.1)
Dmax0=dmax_comp(Lightintensity,What_is_limiting,m,Pmax,OT,Ynphoto_chl,Cnbiosynth,Nconst_protein,Cnrna_variable,\
Ypthylakoid_chl,Pconst_other,Qp_max,Cessential,Nstore_max)
Dmax=Dmax0.Dmax
ChltoCplot=Dmax0.ChltoCplot
NtoCplot=Dmax0.NtoCplot
if data.i ==1:
if Plot_NC==1:
figure(6)
NunitData = 14*10**6/(12*10**3)
plot(Dmax*86400,NtoCplot/NunitData,':',color='black',zorder=-1,label='$\mu_{max}$')
legend(loc='upper right', borderaxespad=0.6, fontsize=22, labelspacing=0.2, ncol=1)
savefig("C:\\Users\\Keiin\\OneDrive\\desktop\\figures\\01\\Phytoplankton model\\"+Whatislimiting+"\\Chalup90\\N to C.png",dpi = DPI)
if Plot_Chl==1:
figure(7)
plot(Dmax*86400,ChltoCplot,':',color='black',zorder=-1)
savefig("C:\\Users\\Keiin\\OneDrive\\desktop\\figures\\01\\Phytoplankton model\\"+Whatislimiting+"\\Chalup90\\Chl to C.png",dpi = DPI)
#======================================================================
return
#AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
data=chalup90()
for a in data:
kkI(a)
show()