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run_modvege.py
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run_modvege.py
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#!/usr/bin env python3
# Mod Vege main code, had to rewrite most of the functions as the Java code was a complete mess
# This code runs a single geographical "Cell" (as the Java code was trying to do on a grid)
# This function *should* be self sustaining, nothing else needed.
import numpy as np
#Import the model function
from modvege import *
# Import ModVege read input files library:
# params.csv
# weather.csv
from lib_read_input_files import *
# ONLY FOR DEV
from lib_read_output_files import *
# Define the name of the input params file
input_params_csv='params.csv'
# Define the name of the input environment file
input_weather_csv='weather.csv'
def run_modvege(input_params_csv, input_weather_csv):
"""
Pre-Process the inputs to run Mod Vege model as a function
:param input_params_csv: Filename of the csv input parameters
:param input_weather_csv: Filename of the csv input weather file
"""
# Read Parameter files into array
params = read_params(input_params_csv)
# Read weather file into array
# arr[0][0] = DOY[0] = 1
# arr[0][1] = Temperature[0] = -0.84125
# arr[0][2] = PARi[0] = 2.22092475
# arr[0][3] = PP[0] = 0.119
# arr[0][4] = PET[0] = 0.602689848
# arr[0][5] = ETA[0] = 0.301344 # RS simulated
# arr[0][6] = LAI[0] = 0.864162 # RS simulated
# arr[0][7] = gcut_height[0] = 0.0 [default is 0.05 if cut]
# arr[0][8] = grazing_animal_count[0] = 0 [default is 1 for test ]
# arr[0][9] = grazing_avg_animal_weight[0] = 0 [ default is 400 for cow ]
weather = read_weather(input_weather_csv)
# ONLY FOR DEV
out = read_out(out_csv)
startdoy = 1
enddoy = 365
# Initialize the run and return arrays
gv_b, dv_b, gr_b, dr_b, h_b, i_b, gro, abc, sumT, gva, gra, dva, dra, sea, ftm, env, pgr, atr = modvege(params, weather, startdoy, enddoy)
# Print the output
#print(output)
################################################ ###################
# Definition of columns in out_cut.csv Eq. from output run
################################################ ###################
# 0 day
# 1 Mean biomass (kg DM/ha) gv_b+gr_b+dv_b+dr_b
# 2 Mean green vegetative biomass (kg DM/ha) gv_b
# 3 Mean green reproductive biomass (kg DM/ha) gr_b
# 4 Mean dry vegetative biomass (kg DM/ha) dv_b
# 5 Mean dry reproductive biomass (kg DM/ha) dr_b
# 6 Harvested Biomass (kg DM/ha) h_b
# 7 Ingested Biomass (kg DM/ha) i_b
# 8 Mean GRO biomass (kg DM/ha) gro
# 9 Mean available biomass for cut (kg DM/ha) abc
#PLOT
out_doy = [out[i][0] for i in range(len(out)-1) ]
out_gvb = [out[i][2] for i in range(len(out)-1) ]
out_grb = [out[i][3] for i in range(len(out)-1) ]
out_dvb = [out[i][4] for i in range(len(out)-1) ]
out_drb = [out[i][5] for i in range(len(out)-1) ]
out_hb = [out[i][6] for i in range(len(out)-1) ]
out_ib = [out[i][7] for i in range(len(out)-1) ]
out_gro = [out[i][8] for i in range(len(out)-1) ]
out_abc = [out[i][9] for i in range(len(out)-1) ]
import numpy as np
import matplotlib.pyplot as plt
plt.figure(figsize=(15,7))
plt.subplot(331)
plt.plot(out_doy,gv_b,'g-',label="gv_b")
plt.plot(out_doy,out_gvb,'b-',label="out_gvb")
plt.title('Green Vegetative biomass (kg DM/ha)')
plt.legend()
plt.grid()
plt.subplot(332)
plt.plot(out_doy,gr_b,'g-',label="gr_b")
plt.plot(out_doy,out_grb,'b-',label="out_grb")
plt.title('Green Reproductive biomass (kg DM/ha)')
plt.legend()
plt.grid()
plt.subplot(333)
plt.plot(out_doy,sumT,'g-',label="sumT")
plt.plot(out_doy,gva,'b-',label="gv_age")
plt.plot(out_doy,gra,'y-',label="gr_age")
plt.plot(out_doy,dva,'c-',label="dv_age")
plt.plot(out_doy,dra,'r-',label="dr_age")
plt.title('Sum of Temperature (Celsius)')
plt.legend()
plt.grid()
plt.subplot(334)
plt.plot(out_doy,dv_b,'g-',label="dv_b")
plt.plot(out_doy,out_dvb,'b-',label="out_dvb")
plt.title('Dead Vegetative biomass (kg DM/ha)')
plt.legend()
plt.grid()
plt.subplot(335)
plt.plot(out_doy,dr_b,'g-',label="dr_b")
plt.plot(out_doy,out_drb,'b-',label="out_drb")
plt.title('Dead Reproductive biomass (kg DM/ha)')
plt.legend()
plt.grid()
plt.subplot(336)
plt.plot(out_doy,pgr,'m-',label="Pot. Growth")
plt.plot(out_doy,gro,'g-',label="gro")
plt.plot(out_doy,out_gro,'b-',label="out_gro")
plt.title('GRO biomass (kg DM/ha)')
plt.legend()
plt.grid()
plt.subplot(337)
plt.plot(out_doy,abc,'g-',label="abc")
plt.plot(out_doy,out_abc,'b-',label="out_abc")
plt.title('Mean available biomass for cut (kg DM/ha)')
plt.legend()
plt.grid()
# Harvested Biomass Plot
plt.subplot(338)
plt.plot(out_doy,h_b,'g-',label="h_b")
plt.plot(out_doy,out_hb,'b-',label="out_hb")
plt.title('Harvested biomass (kg DM/ha)')
plt.legend()
plt.grid()
plt.subplot(339)
plt.plot(out_doy,atr,'c-',label="a2r")
plt.plot(out_doy,sea,'g-',label="Season")
plt.plot(out_doy,ftm,'r-',label="Temperature")
plt.plot(out_doy,env,'y-',label="Environmental")
plt.title('ENV and other Factors')
plt.legend()
plt.grid()
plt.tight_layout()
plt.show()
# run the main function
run_modvege(input_params_csv, input_weather_csv)