def compute_and_save_steady_states(n, v0=5):
for k in [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]:
if not os.path.isfile(
'C:/Users/Bill/Documents/Python/hemo/hemo/data/networks100/G_%i_%i.gpickle'
% (n, k)):
continue
G = nx.read_gpickle(
'C:/Users/Bill/Documents/Python/hemo/hemo/data/networks100/G_%i_%i.gpickle'
% (n, k))
sims.create_source(G)
importlib.reload(system)
def obj(y):
return system.dydt(y, 1)
y0 = np.zeros(2 * len(G.edges()))
if k == 1:
start = time.time()
print('Solver output for n=%i, k=%i:' % (n, k))
y = scipy.optimize.newton_krylov(obj, y0, verbose=True)
end = time.time()
print('Solved in %.01f seconds' % (end - start))
else:
y = scipy.optimize.newton_krylov(obj, y0, verbose=False)
np.save(
'C:/Users/Bill/Documents/Python/hemo/hemo/data/networks100/steady_states_v0_%.0f/%i_%i'
% (n, k, v0), y)
def solve_for_steady_state(G):
start = time.time()
sims.create_source(G)
importlib.reload(system)
def obj(y):
return system.dydt(y, 1)
y0 = np.zeros(2 * len(G.edges()))
y = scipy.optimize.root(obj, y0, method='krylov')
end = time.time()
print('Solved in %.0f seconds.' % (end - start))
return y['x']
def run_sim(n, k=0, symmetric=False):
if symmetric:
G = nx.read_gpickle(
'C:/Users/Bill/Documents/Python/hemo/hemo/data/networks/G_%i_symm.gpickle'
% n)
else:
G = nx.read_gpickle(
'C:/Users/Bill/Documents/Python/hemo/hemo/data/networks/G_%i_%i.gpickle'
% (n, k))
sims.create_source(G)
importlib.reload(system)
times = np.linspace(0, 450, 450 + 1)
y0 = np.zeros(2 * len(G.edges()))
soln = scipy.integrate.odeint(system.dydt, y0, times)
#wt = get_Wt(G, times, soln)
return times, soln
def run_example_sim(n):
G = create_network_multiple_sources_and_sinks(n)
sims.create_source(G)
importlib.reload(system)
times = np.linspace(0, 3600, 3600 + 1)
y0 = np.zeros(2 * len(G.edges()))
soln = scipy.integrate.odeint(system.dydt, y0, times)
wt = get_Wt(G, times, soln)
plt.figure(1)
plt.plot(times / 60, wt)
plt.xlabel('time (min)')
plt.ylabel('w(t)')
plt.show()
plt.figure(2)
radii = [G[src][sink]['radius'] for src, sink in G.edges()]
plt.hist(radii)
plt.show()
def get_wt(G, y):
wt = 0
n_edges = len(G.edges())
for src, sink in G.edges():
wt += 30 * G[src][sink]['volume'] * y[n_edges + G[src][sink]['idx']]
return wt
radius, steady_state = [], []
for k in [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]:
for n in [4, 5, 6, 7, 8, 9, 10]:
G = nx.read_gpickle(
'C:/Users/Bill/Documents/Python/hemo/hemo/data/networks/G_%i_%i.gpickle'
% (n, k))
sims.create_source(G)
importlib.reload(system)
def obj(y):
return system.dydt(y, 1)
y0 = np.zeros(2 * len(G.edges()))
y = scipy.optimize.root(obj, y0, method='krylov')
radius.append(
np.mean(
[10**4 * G[src][sink]['radius'] for src, sink in G.edges()]))
steady_state.append(get_wt(G, y['x']))
for k in [0, 1, 2, 3]:
n = 11
G = nx.read_gpickle(