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Newton_preg.py
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Newton_preg.py
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import equations
import math
import numpy as np
from Newton import Jac
def newton_preg_rat(func,x,k,cell):
if cell.species != 'rat':
print('species:' + cell.species)
raise Exception('newton_preg_rat only for rat model')
if cell.sex.lower() != 'female':
print('sex: ' + cell.sex)
raise Exception('newton_preg only for pregnant female rat')
fun=equations.conservation_eqs
f=np.matrix(fun(x,k))
TOLpcn = 1
i = 1
iter = 0
if k==0:
maxiter = 300
else:
maxiter = 150
# check
if np.isnan(np.linalg.norm(f)):
raise Exception(cell.segment + ' norm(f) is Nan')
while(np.linalg.norm(f) > 0.0001) and (iter<maxiter+1):
if np.linalg.norm(f)>1e15 or np.isnan(np.linalg.norm(f)):
if cell.segment == 'CCD' or cell.segment == 'OMCD' or cell.segment == 'IMCD':
raise Exception('Newton solver diverged in ' + cell.segment + ' at cell number: ' + str(k))
else:
raise Exception('Newton solver diverged in '+cell.type + ' ' + cell.segment + ' at cell number: ' + str(k))
elif iter == maxiter:
if cell.segment == 'CCD' or cell.segment == 'OMCD' or cell.segment == 'IMCD':
print('Warning!!: Newton solver did not converge in <'+str(iter)+' iterations in ' + cell.segment + ' cell number ' + str(k) + '\n')
else:
print('Warning!!: Newton solver did not converge in <'+str(iter)+' iterations in ' + cell.type + ' ' + cell.segment + ' cell number ' + str(k) + '\n')
print('error size: '+ str(np.linalg.norm(f)) + '\n')
i += 1
J = np.matrix(Jac(fun,x,k))
IJ = J.I
F = np.matrix(fun(x,k))
# PCT
if cell.segment == 'PT':
amp = 1.0
# S3
elif cell.segment == 'S3':
amp = 1.0
# SDL
elif cell.segment == 'SDL':
amp = 1.0
# LDL
elif cell.segment == 'LDL':
if np.linalg.norm(f)>5000:
amp = 0.5
elif iter>75:
amp = 0.95
elif iter>100:
amp = 0.5
else:
amp = 1.0
# LAL
elif cell.segment == 'LAL':
if np.linalg.norm(f)>5000:
amp = 0.5
elif iter>75:
amp = 0.95
else:
amp = 1.0
# mTAL
elif cell.segment == 'mTAL':
if np.linalg.norm(f)>5000:
amp = 0.2
elif np.linalg.norm(f)>2000:
amp = 0.3
elif np.linalg.norm(f)>1000:
amp = 0.5
elif np.linalg.norm(f)>100:
amp = 0.9
else:
amp = 1.0
# cTAL
elif cell.segment == 'cTAL':
if np.linalg.norm(f)>5000:
amp = 0.2
elif np.linalg.norm(f)>2000:
amp = 0.3
elif np.linalg.norm(f)>1000:
amp = 0.5
elif np.linalg.norm(f)>100:
amp = 0.9
else:
amp = 1.0
# DCT
elif cell.segment == 'DCT':
# the options were added for the HTN model
if cell.HT != 'N':
if np.linalg.norm(f)>1e5:
if cell.type == 'jux1':
if k==0:
amp = 1.0
else:
amp = 0.4
elif cell.type == 'jux4':
if k==0:
amp = 1.0
else:
amp = 0.3
elif cell.type == 'jux5':
if k==0:
amp = 1.0
else:
amp = 0.5
elif cell.type == 'jux2':
if k==0:
amp = 1.0
else:
amp = 0.4
elif cell.type == 'jux3':
if k==0:
amp=1.0
else:
if k<160:
amp = 0.5 #1.0 #0.25 #0.45 #0.3
else:
amp = 0.2
else:
amp = 1.0
elif np.linalg.norm(f)>5000:
if cell.type == 'jux4':
if k==0:
amp = 1.0
else:
amp = 0.4 #0.475 #0.5
elif cell.type == 'jux1':
if k==0:
amp = 1.0
elif k>180:
amp = 0.3 #1.0
else:
amp = 0.25 #0.45 #0.3
elif cell.type == 'jux2':
if k==0:
amp = 1.0
else:
amp = 0.3
elif cell.type == 'jux3':
if k==0:
amp = 1.0
else:
if k<160:
amp = 0.75 #0.5 #1.0 #0.225 #0.3 #0.4
else:
amp = 0.25
else:
amp = 1.0
elif np.linalg.norm(f)>1000:
if cell.type == 'jux1':
if k==0:
amp = 1.0
else:
amp = 0.4
elif cell.type == 'jux2':
if k==0:
amp = 1.0
elif k>160:
amp = 0.5
else:
amp = 1.0
elif cell.type == 'jux3':
if k==0:
amp = 1.0
else:
amp = 0.75 #0.4
elif cell.type == 'jux4':
if k==0:
amp = 1.0
else:
amp = 0.5
else:
amp = 1.0
elif np.linalg.norm(f)>250:
if cell.type == 'jux1':
if k==0:
amp = 1.0
else:
amp = 1.0
elif cell.type == 'jux4':
if k==0:
amp = 1.0
else:
amp = 0.7
elif cell.type == 'jux3':
if k==0:
amp = 1.0
else:
amp = 0.7
else:
amp = 1.0
elif np.linalg.norm(f)>50:
if cell.type == 'jux4':
if k==0:
amp = 1.0
else:
amp = 1.0 #0.7 #0.8
elif cell.type == 'jux3':
if k==0:
amp = 1.0
elif k<160:
amp = 0.7
else:
amp = 0.25 #0.5 #1.0
else:
amp = 1.0
elif iter>20:
if cell.type == 'jux4':
if np.linalg.norm(f)>10:
amp = 0.75
else:
amp = 1.0
elif cell.type == 'jux1':
if np.linalg.norm(f)>10:
amp = 0.75
else:
amp = 1.0
else:
amp = 1.0
else:
amp = 1.0
else:
amp = 1.0
# CNT
elif cell.segment == 'CNT':
if np.linalg.norm(f)>1e6:
if k==0:
if cell.inhib == 'HKA-100':
amp = 0.5 #0.75 #1.0
elif cell.inhib == 'HKA-100preg':
amp = 0.5
else:
amp = 0.4
else:
amp = 0.35 #0.55
elif np.linalg.norm(f)>5000:
if cell.preg == 'mid':
if cell.type == 'jux1':
if cell.HT != 'N':
if k==0:
amp = 1.0
else:
amp = 0.3
else:
if cell.inhib == 'ENaC-70':
amp = 1.0
else:
amp = 0.275
elif cell.type == 'jux2':
if cell.HT != 'N':
amp = 0.25
elif cell.inhib == 'HKA-100':
if k==0:
amp = 1.0
else:
amp = 1.0
else:
amp = 0.3
elif cell.type == 'jux3':
if k==0:
amp = 1.0 #0.5
else:
amp = 0.25
elif cell.type == 'jux4':
if k==0:
if cell.preg == 'mid':
if cell.inhib == 'ENaC-100':
amp = 0.5
else:
amp = 1.0
else:
amp = 0.25
else:
amp = 0.25 #0.277
elif cell.type == 'jux5':
if k==0:
if cell.inhib == 'HKA-100preg':
amp = 0.5
elif cell.inhib == 'ENaC-100':
amp = 0.6
else:
amp = 1.0 #0.4
else:
amp = 0.25 #0.5
elif cell.type == 'sup':
if k==0:
if cell.inhib == 'HKA-100':
amp = 0.8 #0.5
else:
amp = 1.0
else:
amp = 1.0
else:
if k==0:
amp = 0.75 #1.0
else:
amp = 0.5
elif cell.preg == 'late':
if cell.type == 'jux1':
if k==0:
if cell.inhib == 'ENaC-100':
amp = 1.0
else:
amp = 0.45
else:
amp = 0.45
elif cell.type == 'jux2':
amp = 0.4
elif cell.type == 'jux3':
amp = 0.4
elif cell.type == 'jux4':
amp = 0.5
else:
amp = 0.65
elif np.linalg.norm(f)>2000:
if cell.preg == 'mid':
if cell.inhib == 'HKA-100':
amp = 1.0
elif cell.inhib == 'HKA-100preg':
amp = 1.0
else:
amp = 0.85
elif cell.preg == 'late':
amp = 0.85
elif np.linalg.norm(f)>1000:
if cell.preg == 'mid':
if k==0:
if cell.inhib == 'HKA-100':
amp = 1.0
elif cell.inhib == 'HKA-100preg':
amp = 1.0
else:
amp = 0.5
else:
amp = 0.9 #1.0 #0.8
elif cell.preg == 'late':
amp = 0.9
elif np.linalg.norm(f)>150:
if cell.preg == 'mid':
amp = 1.0
elif cell.preg == 'late':
amp = 0.95
elif iter>100:
amp = 0.55
elif iter > 30:
if np.linalg.norm(f)>15:
if cell.type == 'jux4':
amp = 1.0
else:
amp = 0.85
elif np.linalg.norm(f)>5:
if cell.type == 'jux4':
amp = 0.75
else:
amp = 0.5
else:
if cell.type == 'jux4':
amp = 0.5
else:
amp = 0.76
elif iter>10:
if np.linalg.norm(f)<1:
amp = 0.5
else:
amp = 1.0
else:
amp = 1.0
# CCD
elif cell.segment == 'CCD':
if np.linalg.norm(f)>1e6:
amp = 0.3
elif cell.preg == 'mid':
if np.linalg.norm(f)>5000:
if k==0:
if cell.HT == 'Y':
amp = 1.0
else:
amp = 0.5
else:
amp = 0.75
elif np.linalg.norm(f)>1000:
amp = 0.75
elif iter > 50:
if np.linalg.norm(f)>1:
amp = 0.8
else:
amp = 0.95
else:
amp = 1.0
elif cell.preg == 'late':
if np.linalg.norm(f)>5000:
if k==0:
amp = 0.35
else:
amp = 0.55
elif np.linalg.norm(f)>2000:
if k==0:
amp = 0.5
else:
amp = 0.75
elif np.linalg.norm(f)>1000:
if k==0:
amp = 0.75
else:
amp = 0.95
elif iter > 100:
amp = 1.0
elif iter > 125:
if np.linalg.norm(f)>1:
amp = 0.8
else:
amp = 0.75
else:
amp = 1.0
# OMCD
elif cell.segment == 'OMCD':
if np.linalg.norm(f)>1e6:
if cell.inhib == 'HKA-100preg':
amp = 0.65 #0.25 #0.8 #1.0 #0.4 #0.55 #1.0
elif cell.inhib == 'ENaC-100':
amp = 0.6 #1.0
elif cell.preg == 'late':
if k == 0:
amp = 0.75
else:
amp = 0.4
else:
amp = 0.4
elif np.linalg.norm(f)>5000:
if k==0:
if cell.inhib == 'HKA-100preg':
amp = 0.25 #1.0 #0.8 #0.75 #0.55 #0.3 #1.0
elif cell.inhib == 'ENaC-100':
if cell.preg == 'mid':
amp = 0.8
else:
amp = 1.0
elif cell.type == 'late':
amp = 0.8
else:
amp = 0.75
else:
amp = 1.0
elif np.linalg.norm(f)>1000:
if k==0:
if cell.inhib == 'HKA-100preg':
amp = 1.0
else:
amp = 0.75
else:
amp = 1.0
elif np.linalg.norm(f)>100:
amp = 1.0
elif iter>50:
amp = 0.9
elif iter>100:
amp = 0.8
else:
amp = 1.0
# IMCD
elif cell.segment == 'IMCD':
if np.linalg.norm(f)>5000:
if k==0:
amp = 0.25
else:
amp = 0.5
elif np.linalg.norm(f)>1000:
amp = 1.0 #0.5
elif iter>100:
if np.linalg.norm(f)>10:
amp = 1.0
elif np.linalg.norm(f)>1:
amp = 0.8
else:
amp = 0.5
elif iter>75:
if np.linalg.norm(f)>10:
amp = 1.0
elif np.linalg.norm(f)>5:
amp = 0.85
elif np.linalg.norm(f)>1:
amp = 0.62
else:
amp = 0.5
elif iter>50:
if np.linalg.norm(f)>10:
amp = 0.8
elif np.linalg.norm(f)>1:
amp = 0.75
else:
amp = 1.0
else:
amp = 1.0
else:
print('What is this segment?', cell.segment)
raise Exception('cell.segment is not characterized')
delta = amp*np.array(F*IJ.T)[0]
xold = x
x -= delta
f = np.matrix(fun(x,k))
# extra check
if np.isnan(np.linalg.norm(f)) or np.linalg.norm(f)>1e14:
amp = amp/2
delta = amp*np.array(F*IJ.T)[0]
x = xold - delta
f = np.matrix(fun(x,k))
iter+=1
#print(iter, np.linalg.norm(f))
TOLpcn = np.max(delta/x)
#print(f)
#input('pausing...')
return x