def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''2. Solvng System'''
start1 = timer()
# '''calculate dt'''
# Vn_conv = vn_conv_max(set, sol, coef)
# Vb_conv = vb_conv_max(set, sol, coef)
# print 'V_max', V_conv
# dt_conv_n = set['h']/(2*Vn_conv)
# dt_conv_b = set['h']/(2*Vb_conv)
# dt_diff_n = (set['h'])**2/(2*coef['D_n'])
# dt_diff_b = (set['h'])**2/(2*coef['D_b'])
# dt_diff_c = (set['h'])**2/(2*coef['D_c'])
# # set['dt'] = 0.001
# set['dt'] = min(dt_diff_n, dt_diff_b, dt_diff_c , dt_conv_n, dt_conv_b)
# set['t'] += set['dt']
# sol['time'].append(set['t'])
# print 'dt', set['dt']
sol['age'] += set['dt']
if set['Dimension'] == '1D':
sol = system_1d(coef, set, sol) #2.3
elif set['Dimension'] == '2D':
sol = system_2d(coef, set, sol) #2.3
start2 = timer()
print 'Solve system time', start2 - start1
return sol
def boolean_1_iter(coef, set, sol, check = 'out'): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
start1 = timer()
# Solving X1,X2,X3,X4 continuously
sol = c_f_T(coef, set, sol) #2.3
start2 = timer()
# Movement of X4
sol = hybrid_tech_c(coef, set, sol) #2.2
start3 = timer()
'''
if len(sol['matrix_tip']) == 0:
sol['stop_iter'] = 100000
print 'all is absorbed'
check == 'in'
else:
start1 = timer()
# Solving X1,X2,X3,X4 continuously
sol = c_f_T(coef, set, sol) #2.3
start2 = timer()
# Movement of X4
sol = hybrid_tech(coef, set, sol) #2.2
start3 = timer()
'''
if not check == 'in':
print 'Hybrid for X4 time', start2-start1
print 'Solve X1,X2,X3 time', start3-start2
return sol
def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
sol['time'] = [0]
else:
'''2. Solvng System'''
start1 = timer()
'''calculate dt'''
V_conv = v_conv_max(set, sol, coef)
print 'V_max', V_conv
dt_conv = set['h']/(2*V_conv)
dt_diff = (set['h'])**2/(2*coef['D_n'])
# set['dt'] = 0.001
set['dt'] = min(dt_diff,dt_conv)
set['t'] += set['dt']
sol['time'].append(set['t'])
print 'dt', set['dt']
'''Solve system'''
sol = system_1d(coef, set, sol) #2.3
start2 = timer()
print 'Solve system time', start2-start1
return sol
def boolean_1_iter(coef, set, sol, check='out'): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
start1 = timer()
# Solving X1,X2,X3,X4 continuously
sol = c_f_T(coef, set, sol) #2.3
start2 = timer()
# Movement of X4
sol = hybrid_tech_c(coef, set, sol) #2.2
start3 = timer()
'''
if len(sol['matrix_tip']) == 0:
sol['stop_iter'] = 100000
print 'all is absorbed'
check == 'in'
else:
start1 = timer()
# Solving X1,X2,X3,X4 continuously
sol = c_f_T(coef, set, sol) #2.3
start2 = timer()
# Movement of X4
sol = hybrid_tech(coef, set, sol) #2.2
start3 = timer()
'''
if not check == 'in':
print 'Hybrid for X4 time', start2 - start1
print 'Solve X1,X2,X3 time', start3 - start2
return sol
def boolean_1_iter(coef, set, sol, check='out'): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
if len(sol['sp_stop']) == len(sol['matrix_tip']):
sol['stop_iter'] = 100000 #sp_stop harus dicek di setiap movement and branching. karena sudah tidak bergerak lagi yang ada di list ini.
print 'all looping itself or anastomosis'
check = 'in'
else:
'''2. Branching and Movement'''
start1 = timer()
if set['layout'] == '2D':
sol = hybrid_tech_c(coef, set, sol) #2.2
if set['layout'] == '3D':
sol = hybrid_tech_c_3d(coef, set, sol)
start2 = timer()
'''1. Anastomosis & Tip Cell'''
#sol = check_anastomosis(sol)
start3 = timer()
'''Solving c,f,T'''
if set['layout'] == '2D':
sol = c_f_T(coef, set, sol) #2.3
if set['layout'] == '3D':
sol = c_f_T_3d(coef, set, sol)
start4 = timer()
if not check == 'in':
print 'Check Anastomosis Time', start3 - start2
print 'Hybrid for n time', start2 - start1
print 'Solve c,f,T time', start4 - start3
return sol
def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''2. Solvng System'''
start1 = timer()
# sol['age'] += set['dt']
'''calculate dt'''
V_1 = v_1_max(set, sol)
V_2 = v_2_max(set, sol, coef)
dt_1 = set['h']/V_1
dt_2 = set['h']/V_2
dt_3 = (set['h'])**2/(2*coef['D_n'])
set['dt'] = min(dt_1,dt_2,dt_3)
set['t'] += set['dt']
print 'dt', set['dt']
'''Solve system'''
if set['Dimension'] == '1D':
sol = system_1d(coef, set, sol) #2.3
elif set['Dimension'] == '2D':
sol = system_2d(coef, set, sol) #2.3
start2 = timer()
print 'Solve system time', start2-start1
return sol
def boolean_1_iter(coef, set, sol, check = 'out'):
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol)
else:
if len(sol['sp_stop']) == len(sol['matrix_tip']):
sol['stop_iter'] = 100000 #sp_stop harus dicek di setiap movement and branching. karena sudah tidak bergerak lagi yang ada di list ini.
print 'all looping itself or anastomosis'
check = 'in'
else:
'''2. Branching and Movement'''
start1 = timer()
if set['layout'] == '2D':
sol, n_o = hybrid_tech_c(coef, set, sol)
if set['layout'] == '3D':
sol = hybrid_tech_c_3d(coef, set, sol)
start2 = timer()
'''1. Anastomosis & Tip Cell'''
#sol = check_anastomosis(sol)
start3 = timer()
'''Solving c,f,T'''
if set['layout'] == '2D':
sol = c_f_T(coef, set, sol)
# sol = system_2d(coef, set, sol, n_o) #2.3
if set['layout'] == '3D':
sol = c_f_T_3d(coef, set, sol)
start4 = timer()
if not check == 'in':
print 'Check Anastomosis Time', start3-start2
print 'Hybrid for n time', start2-start1
print 'Solve c,f,T time', start4-start3
return sol
def continuous_iter(coef, set, sol):
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''Solving X1,X2,X3,X4'''
start1 = timer()
sol = c_f_T(coef, set, sol) #2.3
start2 = timer()
print 'Solve X1,X2,X3,X4 time', start2-start1
return sol
def continuous_iter(coef, set, sol):
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''Solving X1,X2,X3,X4'''
start1 = timer()
sol = c_f_T(coef, set, sol) #2.3
start2 = timer()
print 'Solve X1,X2,X3,X4 time', start2 - start1
return sol
def continuous_iter(coef, set, sol):
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''Solving c,b,n'''
n_o = 0
if set['layout'] == '2D':
start1 = timer()
sol = c_f_T(coef, set, sol, n_o) #2.3
start2 = timer()
print 'Solve c,f,T time', start2 - start1
return sol
def continuous_iter(coef, set, sol):
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''Solving c,b,n'''
n_o = 0
if set['layout'] == '2D':
start1 = timer()
sol = c_f_T(coef, set, sol, n_o) #2.3
start2 = timer()
print 'Solve c,f,T time', start2-start1
return sol
def con_(coef, set, sol, check = 'out'):
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol)
else:
'''Solving n'''
sol = continuous_n_(coef, set, sol)
'''Solving c,f,T'''
if set['layout'] == '2D':
sol = c_f_T(coef, set, sol)
if set['layout'] == '3D':
sol = c_f_T_3d(coef, set, sol)
return sol
def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''Solving c,f,T'''
start1 = timer()
sol = system_3d(coef, set, sol) #2.3
start2 = timer()
'''2. Branching and Movement'''
sol = hybrid_tech(coef, set, sol) #2.2
start3 = timer()
print 'Solve c,f,T time', start2-start1
print 'Hybrid for n time', start3-start2
return sol
def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
start1 = timer()
'''Solving c'''
sol = system_2d(coef, set, sol) #2.3
start2 = timer()
'''2. Branching and Movement'''
sol = hybrid_tech(coef, set, sol) #2.2
start3 = timer()
print 'Hybrid for n time', start2 - start1
print 'Solving c time', start3 - start2
return sol
def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''2. Branching and Movement'''
start1 = timer()
sol, n_o = hybrid_tech(coef, set, sol) #2.2
start2 = timer()
'''Solving c,f,T'''
sol = c_f_T(coef, set, sol, n_o) #2.3
start3 = timer()
print 'Hybrid for n time', start2 - start1
print 'Solve c,f,T time', start3 - start2
return sol
def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
sol['time'] = [0]
else:
start1 = timer()
set['t'] += set['dt']
sol['time'].append(set['t'])
print 'time', set['t']
'''Solve system'''
sol = system_1d(coef, set, sol) #2.3
start2 = timer()
print 'Solve system time', start2-start1
return sol
def boolean_1_iter(coef, set, sol, check = 'out'):
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol)
sol = init_m(coef,set,sol)
else:
if len(sol['sp_stop']) == len(sol['matrix_tip']):
sol['stop_iter'] = 100000 #sp_stop harus dicek di setiap movement and branching. karena sudah tidak bergerak lagi yang ada di list ini.
print 'all looping itself or anastomosis'
check = 'in'
else:
'''2. Branching and Movement'''
start1 = timer()
sol = hybrid_tech_c(coef, set, sol)
start2 = timer()
'''1. Anastomosis & Tip Cell'''
sol = check_anastomosis(sol)
start3 = timer()
if not coef['Mic'] == 0 or not coef['Kappa'] == 0:
#print set['tm'], set['t']
if set['t'] >= set['tm']:
#print sol['kk']
if sol['kk'] == 1:
#sol = init_m(coef,set,sol)
sol['kk']+= 1
else:
sol['kk'] = 10
#print 'enter here'
sol = hybrid_tech_m(coef, set, sol)
start4 = timer()
'''Solving c,f,T'''
sol = c_f_T(coef, set, sol)
start5 = timer()
if not check == 'in':
print 'Check Anastomosis Time', start3-start2
print 'Hybrid for n time', start2-start1
if not coef['Mic'] == 0 or not coef['Kappa'] == 0:
if sol['kk'] > 2:
print 'Hybrid for m time', start4-start3
print 'Solve c,f,T time', start5-start4
else:
print 'Solve c,f,T time', start5-start3
else:
print 'Solve c,f,T time', start5-start3
return sol
def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''2. Solvng System'''
start1 = timer()
'''calculate dt'''
V_1 = v_1_max(set, sol)
dt_1 = set['h'] / V_1
dt_3 = (set['h'])**2 / (2 * coef['D_n'])
set['dt'] = 0.001 #min(dt_1,dt_3)
set['t'] += set['dt']
print 'dt', set['dt']
'''Solve system'''
sol = system_1d(coef, set, sol) #2.3
start2 = timer()
print 'Solve system time', start2 - start1
return sol
def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
else:
'''2. Solvng System'''
start1 = timer()
'''calculate dt'''
V_1 = v_1_max(set, sol)
dt_1 = set['h']/V_1
dt_3 = (set['h'])**2/(2*coef['D_n'])
set['dt'] = 0.001#min(dt_1,dt_3)
set['t'] += set['dt']
print 'dt', set['dt']
'''Solve system'''
sol = system_1d(coef, set, sol) #2.3
start2 = timer()
print 'Solve system time', start2-start1
return sol
def boolean_1_iter(coef, set, sol): #2
if set['k'] == 0:
'''Initial Profile'''
sol = initial_prof(coef, set, sol) #2.1
sol['time'] = [0]
else:
start1 = timer()
# '''calculate dt'''
# V_conv = v_conv_max(set, sol, coef)
# print 'V_max', V_conv
# dt_conv = set['h']/(2*V_conv)
# dt_diff = (set['h'])**2/(2*coef['D_n'])
# # set['dt'] = 0.001
# set['dt'] = min(dt_diff,dt_conv)
set['t'] += set['dt']
sol['time'].append(set['t'])
print 'time', set['t']
'''Solve system'''
sol = system_1d(coef, set, sol) #2.3
start2 = timer()
print 'Solve system time', start2 - start1
return sol
'''Import all files. We run all the files through run_main_code.py'''
from coef_setting import declare_coef #Ref.1
from initial_conditions import initial_prof #Ref.2
import main_code as main #Ref.4
import picture_2d as pic #Ref.5
'''Import additional functions to support calculation and graphics'''
import numpy
from timeit import default_timer as timer
import time
import matplotlib.pyplot as plt
plt.ion() #to plot interactively
'''declare coefficients & initial settings'''
coef, set, sol = declare_coef() #Ref.1
'''Initialize functions for k=0 (first iteration), t=0 (initial time)'''
sol = initial_prof(coef, set, sol) #Ref.2
pic.pic_2d(coef, set,
sol) #to generate the picture of initial condition #Ref.5
print '''All Coefficients:'''
print coef
print '''All Set'''
print set
'''PRINTING RESULT AS CONTROL'''
print 'at Time', set['t']
print 'Total Tips:', len(sol['matrix_tip'])
print 'Total Stop Tips:', len(sol['sp_stop'])
print 'Tip Stop:', sol['sp_stop']
print 'Tip Cell Pos:', sol['tip_cell']
print 'Max Value of c, f', sol['c'].max(), ',', sol['f'].max()
print 'Min Value of c, f', sol['c'].min(), ',', sol['f'].min()
'''Main part of the Hybrid calculation'''
