我有一个大的函数,用来模拟一个反应系统的时间。我在函数中添加了一个 leap_couner
来计算时间上的步数。
def gillespie_tau_leaping(propensity_calc, popul_num, LHS, stoch_rate, popul_num_all, tao_all, rxn_vector, delta_t, tao, epsi):
t = simulation_timer()
t.start()
while tao < tmax:
propensity = propensity_calc(LHS, popul_num, stoch_rate)
a0 = (sum(propensity))
if a0 == 0.0:
print("Propensity sum is zero end execution")
break
if popul_num.any() < 0:
print("Molecules numbers below zero end execution")
break
lam = (propensity_calc(LHS, popul_num, stoch_rate)*delta_t)
rxn_vector = np.random.poisson(lam)
if tao + delta_t > tmax:
break
tao += delta_t
leap_counter = 0
if delta_t >= 1 / a0:
for j in range(len(rxn_vector)):
state_change_lambda = np.squeeze(np.asarray(state_change_array[j])*rxn_vector[j])
popul_num = popul_num + state_change_lambda
leap_counter += 1 # Not working!
popul_num_all.append(popul_num)
tao_all.append(tao)
leap_counter += 1
else: # else execute the ssa because it's faster
next_t = np.random.exponential(1/a0)
rxn_probability = propensity / a0
num_rxn = np.arange(rxn_probability.size)
if tao + next_t > tmax:
tao = tmax
break
j = stats.rv_discrete(values=(num_rxn, rxn_probability)).rvs()
tao = tao + next_t
popul_num = popul_num + np.squeeze(np.asarray(state_change_array[j]))
popul_num_all.append(popul_num)
tao_all.append(tao)
print("Molecule numbers:\n", popul_num)
print("Time of final simulation:\n", tao)
print("leap counter:\n", leap_counter)
t.stop()
return popul_num_all.append(popul_num), tao_all.append(tao), popul_num
这就是完整的功能,下面是计数器的具体位。
if tao + delta_t > tmax:
break
tao += delta_t
leap_counter = 0
if delta_t >= 1 / a0:
for j in range(len(rxn_vector)):
state_change_lambda = np.squeeze(np.asarray(state_change_array[j])*rxn_vector[j])
popul_num = popul_num + state_change_lambda
leap_counter += 1 # Not working!
popul_num_all.append(popul_num)
tao_all.append(tao)
tao
是当前的时间。delta_t
是增加的价值和 tmax
是最大的模拟时间。如果 tao + delta_t
小于 tmax
那么当前时间就会以 delta_t
.
然后我用 delta_t
来决定我使用哪种闰土法。如果我使用第一种闰土法 if delta_t >= 1/a0
然后,我想计算每次递增的时间(由 delta_t
),并返回增量的数量 leap_counter
只不过我现在的计数器有问题,它只是返回零,我不知道怎么改才能让它正常工作。
干杯
你需要移动这一行
leap_counter = 0
在while循环外。目前它被设置为 0
每次迭代