def d(T, d_max, s):
return d_max * exp(-s * T)
if __name__ == "__main__":
seed(76567)
d_max = 10000
s = 1e-4
E, E_tot_0, E_tot_5, last_bend = 0, 0, 0, 0
E_list_0, bend_list_0 = zeros(1), zeros(1)
E_list_5, bend_list_5 = zeros(1), zeros(1)
protein_0 = Protein(15, 1e-15)
protein_5 = Protein(15, 500)
protein_5.potentials = protein_0.potentials
it = 0
while (protein_0.valid_bends < 5000):
it += 1
print(protein_0.valid_bends, it)
if protein_0.bend_protein():
E_list_0 = append(E_list_0, E)
E_tot_0 += E * (protein_0.valid_bends - last_bend)
last_bend = protein_0.valid_bends
E = protein_0.u
E_list_0 = append(E_list_0, E)
bend_list_0 = append(bend_list_0, [last_bend, last_bend])
from Protein_class import Protein
path.__delitem__(0)
from numpy import linspace, flip, zeros, append, savez, array
from numpy.random import seed
if __name__ == "__main__":
seed(669311)
bends_per_T = 600
num_T = 51
T_min, T_max = 0.0000000000001, 1500
n_monomers = 30
T_list = flip(linspace(T_min, T_max, num_T), 0)
protein = Protein(n_monomers, 0)
E_list = zeros(1)
L_list = array([n_monomers])
bend_list = zeros(1)
E, L, last_bend = 0, n_monomers, 0
for T_ind in range(num_T):
print(T_list[T_ind])
protein.T = T_list[T_ind]
E_tot, L_tot = 0, 0
while (protein.valid_bends < bends_per_T * (T_ind + 1)):
if protein.bend_protein():
E_list = append(E_list, E)
L_list = append(L_list, L)
bend_list = append(bend_list, protein.valid_bends)
s = 5 * 1e-4
num_T = 151
length = 30
T_list = linspace(0.00001, 1500, num_T)
E, E_tot, L_tot, L, last_bend = 0, 0, 0, length, 0
E_list, L_list = zeros(num_T), zeros(num_T)
seed_list = [
1337, 1, 10352, 9234, 999922, 999999999, 235359, 863286248, 124872,
4652742
]
for k in range(len(seed_list)):
seed(seed_list[k])
protein = Protein(length, 0)
U_mat = protein.potentials
print("\n{}\n".format(k))
for i in range(num_T):
print(T_list[i], d(T_list[i], d_max, s))
protein = Protein(length, T_list[i])
protein.potentials = U_mat
E, E_tot, L_tot, L, last_bend = 0, 0, 0, length, 0
while (protein.valid_bends < d(T_list[i], d_max, s)):
if protein.bend_protein():
L_tot += L * (protein.valid_bends - last_bend)
E, E_tot, L_tot, L, last_bend = 0, 0, 0, length, 0
E_list, L_list = zeros(num_T), zeros(num_T)
old_seed_list = [
1337, 1, 10352, 9234, 999922, 999999999, 235359, 863286248, 124872,
4652742
]
seed_list = [
186072, 895242, 418811, 153930, 446805, 511978, 537066, 436767, 457513,
739423
]
for k in range(len(seed_list)):
print("\n{}\n".format(k))
seed(seed_list[k])
for i in range(num_T):
print(T_list[i], d(T_list[i], d_max, s))
protein = Protein(length, T_list[i])
E, E_tot, L_tot, L, last_bend = 0, 0, 0, length, 0
while (protein.valid_bends < d(T_list[i], d_max, s)):
if protein.bend_protein():
L_tot += L * (protein.valid_bends - last_bend)
E_tot += E * (protein.valid_bends - last_bend)
last_bend = protein.valid_bends
L = protein.L
E = protein.u
E_tot += E * (protein.valid_bends - last_bend)
L_tot += L * (protein.valid_bends - last_bend)
E_list[i] += E_tot / protein.valid_bends
L_list[i] += L_tot / protein.valid_bends
for i in range(num_T):
E_list[i] = E_list[i] / len(seed_list)
L_list[i] = L_list[i] / len(seed_list)
from numpy import savez, empty, load, copy
from numpy.random import seed
if __name__=="__main__":
seed(6443578)
T = 510
n_monomers = 30
max_bends = 1e6
npzfile = load(abs_path + r'/Data_files/Oppgave_4_1_{}_pot.npz'.format(str(n_monomers)))
potentials = copy(npzfile['potentials'])
npzfile.close()
protein = Protein(n_monomers, T)
lowest_E = 0
lowest_L = 0
protein_lowest_E = empty(n_monomers)
protein.potentials = potentials
print (potentials-protein.potentials)
E, L, last_bend_or_change_T = 0, n_monomers, 0
while (protein.valid_bends < max_bends):
if (protein.valid_bends%1000==0):
print (protein.valid_bends)
if protein.bend_protein():
if (protein.u < lowest_E):
lowest_E = protein.u
from sys import path
from os.path import dirname
abs_path = dirname(dirname(__file__))
path.insert(0, abs_path + r'/Protein_class')
from Protein_class import Protein
path.__delitem__(0)
from numpy.random import seed
if __name__ == "__main__":
seed(27643)
protein = Protein(10, 300)
protein.plot_protein()
protein.bend_protein()
protein.plot_protein()
while (protein.valid_bends < 2):
protein.bend_protein()
protein.plot_protein()
start = time()
while (len(seed_list) < 128):
new_seed = randint(10, int(4294967290 / 2)) * 2 - randint(0, 2)
valid_seed = True
for old_seed in seed_list:
if old_seed == new_seed:
valid_seed = False
if valid_seed:
print("\n{}\n".format(len(seed_list) + 1))
seed((new_seed))
seed_list = append(seed_list, new_seed)
protein0 = Protein(length, 0)
for i in range(41):
print(T_list[i], d(T_list[i], d_max, s))
protein = Protein(length, T_list[i])
protein.potentials = protein0.potentials
E, E_tot, L_tot, L, last_bend = 0, 0, 0, length, 0
while (protein.valid_bends < d(T_list[i], d_max, s)):
if protein.bend_protein():
L_tot += L * (protein.valid_bends - last_bend)
E_tot += E * (protein.valid_bends - last_bend)
last_bend = protein.valid_bends
L = protein.L