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steepest_descent.py
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steepest_descent.py
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#!/usr/bin/python
import numpy as np
from energy import get_energy
from force import get_forces, move_vertices
from transition import T1_transition
from plot import plot_network
def steepest_descent(vertices, edges, polys, parameters, folder):
epsilon = 10**-6
delta_t = parameters['delta_t']
lx = parameters['lx']
ly = parameters['ly']
L = np.array([lx,ly])
t = 0.
energylist = []
forces = 10**6
while np.sum(forces**2)**(0.5) > epsilon:
# get energy for network
energy = get_energy(vertices, polys, edges, parameters)
energylist.append(energy)
# get forces for network
forces = get_forces(vertices, polys, edges, parameters)
print np.sum(forces**2)**(0.5)
# move vertices
vertices = move_vertices(vertices, forces, parameters)
# check for T1 transitions
cells, edges = T1_transition(vertices, polys, edges, parameters)
# plot_network(vertices, polys, L, "%s/%.2f.jpg" % (folder,t))
t += delta_t
return
# def steepest_descent(network, vertices, cells, edges, delta_t, epsilon, folder):
# # keep track of time steps
# time = []
# t = 0
# # keep track of energy
# energy = []
# # for T1 transition
# min_dist = 0.2
# L = network.L
# # while forces are greater than epsilon
# forces = epsilon**0.5
# count = 0
# # generate random angle vectors
# for cell in cells:
# cell.theta = rand_angle()
# os.mkdir("noise/hex/%s" % folder)
# # f = open("energy/energy.txt", "w+")
# while count < 50:
# # while np.sum(forces**2)**(0.5) > epsilon:
# # plot_network(vertices, cells, L, "motility/%d.jpg" % count)
# # if count % 200 == 0:
# # for cell in cells:
# # cell.theta = rand_angle()
# # # write cell vertices for MSD
# os.chdir("noise/hex/%s" % folder)
# np.savetxt("%d.txt" % count, vertices)
# os.chdir("..")
# os.chdir("..")
# os.chdir("..")
# # get energy for network
# energy = network.get_energy(vertices, cells, edges)
# # get forces for network
# forces = network.get_forces(vertices, cells, edges)
# # move vertices with forces
# vertices = network.move_vertices(forces, vertices)
# ka = network.parameters['ka']
# A0 = 1.
# print t, energy / (24.*ka*(A0**2)), np.sum(forces**2)**(0.5)
# # norm_energy = np.array(energy / (24.*ka*(A0**2)))
# # f.write("%f\n" % norm_energy)
# # new time step
# t += delta_t
# # # check for T1 transitions
# cells, edges = T1_transition(network, vertices, cells, edges, min_dist)
# count += 1
# # f.close()
# return vertices