def discretize_cython_check():
import discretize # this imports lognormal_translated.py
import discretize_cy
import discretize_py # this imports lognormal.py
k0 = np.array([1e-7, 0.8, 0.15], dtype=DTYPE)
length, _, _, _, mu, sigma, _, n, _, _, _ = importing(k0)
args = [mu, sigma]
breakage = discretize_py.breakage_discretize(length, n, k0, *args)
selection = discretize_py.selection_discretize(length, n, k0, breakage,
*args)
python_break = discretize_py.breakage_discretize(length, n, k0, *args)
python_selec = discretize_py.selection_discretize(length, n, k0,
python_break, *args)
cython_break = discretize_cy.breakage_discretize(length, n, k0, *args)
cython_selec = discretize_cy.selection_discretize(length, n, k0,
cython_break, *args)
assert np.allclose(breakage, python_break,
cython_break), 'breakages not match'
assert np.allclose(selection, python_selec,
cython_selec), 'selections not match'
print('No error')
def phi(method='python', it=1000):
import discretize_parallel
import phi
import phi_cy
import phi_cy_parallel
k0 = np.array([1.5e-07, 4.8e-01, 3.9e-01], dtype=DTYPE)
length, volume, number, Y0, mu, sigma, t, n, N, p, Q = importing(k0)
number0 = number[:, 0]
args = [mu, sigma]
Z0 = np.zeros(n * (p + 1))
Z0[0:n] = number0.copy()
dbs = discretize_parallel.discretize(length, n, p, k0, 1e-8, *args)
if method == 'python':
total = 0
for i in range(it):
tic = time.time()
res = phi.phi_breakage(Z0, dbs, n, p, 1e-8)
toc = time.time()
total += toc - tic
aver_time = total / it * 1e3
print('constructing phi takes %5.2f ms.' % aver_time)
elif method == 'cython':
it *= 10
total = 0
for i in range(it):
tic = time.time()
res = phi_cy.phi_breakage(Z0, dbs, n, p, 1e-8)
toc = time.time()
total += toc - tic
aver_time = total / it * 1e3
print('constructing phi takes %5.2f ms.' % aver_time)
elif method == 'parallel':
it *= 10
total = 0
for i in range(it):
tic = time.time()
res = phi_cy_parallel.phi_breakage(Z0, dbs, n, p, 1e-8)
toc = time.time()
total += toc - tic
aver_time = total / it * 1e3
print('constructing phi takes %5.2f ms.' % aver_time)
def ode(method='python', it=100000):
import discretize
import ode
import ode_cy
import ode_cy_parallel
k0 = np.array([1e-7, 0.8, 0.15], dtype=DTYPE)
length, volume, number, Y0, mu, sigma, t, n, N, p, Q = importing(k0)
number0 = number[:, 0]
args = [mu, sigma]
brk_mat, slc_vec = discretize.discretize(length, n, p, k0, 1e-8,
*args)[0:2]
if method == 'python':
total = 0
for i in range(it):
tic = time.time()
res = ode.breakage(number0, brk_mat, slc_vec)
toc = time.time()
total += toc - tic
aver_time = total / it * 1e6
print('constructing ode takes %5.2f \u03BCs.' % aver_time)
elif method == 'cython':
total = 0
it *= 50
for i in range(it):
tic = time.time()
res = ode_cy.breakage(number0, brk_mat, slc_vec)
toc = time.time()
total += toc - tic
aver_time = total / it * 1e6
print('constructing ode takes %5.2f \u03BCs.' % aver_time)
elif method == 'parallel':
total = 0
for i in range(it):
tic = time.time()
res = ode_cy_parallel.breakage(number0, brk_mat, slc_vec)
toc = time.time()
total += toc - tic
aver_time = total / it * 1e6
print('constructing ode takes %5.2f \u03BCs.' % aver_time)
def phi_parallel_check():
import discretize_parallel
import phi_cy
import phi_cy_parallel
k0 = np.array([1.5e-07, 4.8e-01, 3.9e-01], dtype=DTYPE)
length, volume, number, Y0, mu, sigma, t, n, N, p, Q = importing(k0)
number0 = number[:, 0]
args = [mu, sigma]
Z0 = np.zeros(n * (p + 1))
Z0[0:n] = number0.copy()
dbs = discretize_parallel.discretize(length, n, p, k0, 1e-8, *args)
dzdt_serial = phi_cy.phi_breakage(Z0, dbs, n, p, 1e-8)
dzdt_parallel = phi_cy_parallel.phi_breakage(Z0, dbs, n, p, 1e-8)
assert np.allclose(dzdt_serial, dzdt_parallel), 'Error in phi'
print('No error')
def ode_check():
import discretize
import ode
import ode_cy
import ode_cy_parallel
k0 = np.array([1e-7, 0.8, 0.15], dtype=DTYPE)
length, volume, number, Y0, mu, sigma, t, n, N, p, Q = importing(k0)
number0 = number[:, 0]
args = [mu, sigma]
brk_mat, slc_vec = discretize.discretize(length, n, p, k0, 1e-8,
*args)[0:2]
dndt_py = ode.breakage(number0, brk_mat, slc_vec)
dndt_cy = ode_cy.breakage(number0, brk_mat, slc_vec)
dndt_parallel = ode_cy_parallel.breakage(number0, brk_mat, slc_vec)
assert np.allclose(dndt_py, dndt_cy, dndt_parallel), 'Error in ode'
print('No error')
def discretize_parallel_check():
import discretize
import discretize_parallel
k0 = np.array([1.5e-07, 4.8e-01, 3.9e-01], dtype=DTYPE)
length, _, _, _, mu, sigma, _, n, _, _, _ = importing(k0)
args = [mu, sigma]
serial_break = discretize.breakage_discretize(length, n, k0, *args)
serial_selec = discretize.selection_discretize(length, n, k0, serial_break,
*args)
parallel_break = discretize_parallel.breakage_discretize(
length, n, k0, *args)
parallel_selec = discretize_parallel.selection_discretize(
length, n, k0, parallel_break, *args)
assert np.allclose(serial_break, parallel_break), 'breakages not match'
assert np.allclose(serial_selec, parallel_selec), 'selections not match'
print('No error')
def plot(params=np.array([5e-04, 5e-01, 3e-01, 3.0, 100])):
from data_import import importing
from solve_ode import solve_jac
import pbm
k0 = np.asarray(params)
length, volume, number, Y0, mu, sigma, t, n, N, p, Q = importing(k0)
args = [length, mu, sigma, 2]
tic = time.time()
Y, Jac = solve_jac(pbm.phi, number, t, k0, n, p, N, False, 1e-8, *args)
toc = time.time() - tic
print('solving ODE took %5.2f seconds' % toc)
f = 0
r = number - Y
for i in range(N):
f += r[:, i] @ Q @ r[:, i] / 2
plotvolume(Y, volume, t, length)
print('SSE is ', f)
return r
print(
"{0:5d}|{1:10.4e}|{2:11.3e}|{3:10.2e}|{4:8.1e}| Not cal"
.format(it, f, hn, gn, mu))
else:
print(
"{0:5d}|{1:10.4e}|{2:11.3e}|{3:10.2e}|{4:8.1e}|{5:8.1e}"
.format(it, f, hn, gn, mu, rho))
info = [it, ter]
output = [k, Y, info]
return output
except OverflowError as oerr:
print(oerr.args)
return
except AssertionError as aerr:
print(aerr.args)
return
if __name__ == '__main__':
import pbm
from data_import import importing
k0 = np.array([8e-7, 0.5, 0.4])
length, volume, number, Y0, mu, sigma, t, n, N, p, Q = importing(k0)
args = [length, mu, sigma]
res = lm_ode(pbm.phi, number, t, k0, Q, [1e-3, 1e-8, 1e-8, 1000], *args)
def discretize(method='python', it=1):
import discretize
import discretize_py
import discretize_cy
import discretize_parallel
k0 = np.array([1.5e-07, 4.8e-01, 3.9e-01], dtype=DTYPE)
length, _, _, _, mu, sigma, _, n, _, _, _ = importing(k0)
args = [mu, sigma]
if method == 'python':
total = 0
for i in range(it):
tic = time.time()
bmat = discretize_py.breakage_discretize(length, n, k0, *args)
toc = time.time()
total += toc - tic
aver_time = total / it
print('discretization of breakage takes %6.3f s.' % aver_time)
total = 0
for i in range(it):
tic = time.time()
res = discretize_py.selection_discretize(length, n, k0, bmat,
*args)
toc = time.time()
total += toc - tic
aver_time = total / it
print('discretization of selection takes %6.3f s.' % aver_time)
elif method == 'cython':
total = 0
for i in range(it):
tic = time.time()
bmat = discretize_cy.breakage_discretize(length, n, k0, *args)
toc = time.time()
total += toc - tic
aver_time = total / it
print('discretization of breakage takes %6.3f s.' % aver_time)
total = 0
for i in range(it):
tic = time.time()
res = discretize_cy.selection_discretize(length, n, k0, bmat,
*args)
toc = time.time()
total += toc - tic
aver_time = total / it
print('discretization of selection takes %6.3f s.' % aver_time)
elif method == 'serial':
it *= 10
total = 0
for i in range(it):
tic = time.time()
bmat = discretize.breakage_discretize(length, n, k0, *args)
toc = time.time()
total += toc - tic
aver_time = total / it
print('discretization of breakage takes %6.3f s.' % aver_time)
total = 0
for i in range(it):
tic = time.time()
res = discretize.selection_discretize(length, n, k0, bmat, *args)
toc = time.time()
total += toc - tic
aver_time = total / it
print('discretization of selection takes %6.3f s.' % aver_time)
elif method == 'parallel':
it *= 10
total = 0
for i in range(it):
tic = time.time()
bmat = discretize_parallel.breakage_discretize(
length, n, k0, *args)
toc = time.time()
total += toc - tic
aver_time = total / it
print('discretization of breakage takes %6.3f s.' % aver_time)
total = 0
for i in range(it):
tic = time.time()
res = discretize_parallel.selection_discretize(
length, n, k0, bmat, *args)
toc = time.time()
total += toc - tic
aver_time = total / it
print('discretization of selection takes %6.3f s.' % aver_time)