def testCreateInitialState(self):
sg_ratio = 0.75
monomer_draw = [0.48772, 0.15174, 0.7886]
initial_monomers = create_initial_monomers(sg_ratio, monomer_draw)
initial_events = create_initial_events(initial_monomers, DEF_RXN_RATES)
initial_state = create_initial_state(initial_events, initial_monomers)
self.assertTrue(len(initial_state) == 3)
self.assertTrue(str(initial_monomers[0]) == str(initial_state[0][MONOMER]))
def testCreate3Monomers(self):
initial_monomers = create_initial_monomers(0.75, [0.48772, 0.15174, 0.7886])
self.assertTrue(len(initial_monomers) == 3)
self.assertTrue(initial_monomers[0].type == S)
self.assertTrue(initial_monomers[1].type == S)
self.assertTrue(initial_monomers[2].type == G)
self.assertTrue(initial_monomers[1] < initial_monomers[2])
self.assertFalse(initial_monomers[0] == initial_monomers[1])
def testFindScaling(self):
test_scaling = False
if test_scaling:
# To test scaling: replicate batch runs with different numbers of monomers
# Here, we are testing with equal amount of S and G (no C)
times = []
sg_ratio = 1
pct_s = sg_ratio / (1 + sg_ratio)
test_vals = np.linspace(50, 150, num=3, dtype='int32')
num_repeats = 5
for num_monos in test_vals:
print(f"Starting batch simulation with {num_monos} monomers")
times.append([])
for i in range(num_repeats):
random_seed = 8 + i
np.random.seed(random_seed)
print(f" Starting repeat", i)
# Generate the initial monomers and events (oxidation)
monomer_draw = np.random.rand(num_monos)
initial_monomers = create_initial_monomers(
pct_s, monomer_draw)
initial_events = create_initial_events(
initial_monomers, DEF_RXN_RATES)
# Set the state and add the option to join initial monomers
initial_state = create_initial_state(
initial_events, initial_monomers)
# Start timing the actual KMC part
# noinspection PyUnboundLocalVariable
start = time.time()
run_kmc(DEF_RXN_RATES,
initial_state,
initial_events,
sg_ratio=sg_ratio,
random_seed=random_seed)
end = time.time()
times[-1].append(end - start)
print(
f'Average time to complete simulation with {num_monos:5n} monomers: '
f'{np.sum(times[-1]) / num_repeats:7.2f} seconds')
# Now we want to fit the times that we just calculated to a generic power law expression $t = aN^b$ to find the
# scaling of our algorithm.
meas_t = [np.mean(one_time) for one_time in times]
# sdev_t = [np.sqrt(np.var(one_time)) for one_time in times]
meas_n = test_vals
sim_t = lambda p, n: p[0] * np.power(n, p[1])
loss = lambda p: np.linalg.norm(sim_t(p, meas_n) - meas_t)
results = optimize.minimize(loss,
np.asarray([1e-5, 2.5]),
bounds=[[0, 1], [0, 10]],
options={'disp': True})
opt_p = results.x
scaling_formula = f'$t = {opt_p[0]:3.1e}N^{{ {opt_p[1]:4.2f} }}$'
print(f'Scaling: {scaling_formula}')
def testMissingRequiredSGRatio(self):
# set up variable to allow running run_kmc without specifying sg_ratio
initial_sg_ratio = 0.75
num_initial_monos = 3
monomer_draw = np.around(np.random.rand(num_initial_monos), MAX_NUM_DECIMAL)
# these are tested separately
initial_monomers = create_initial_monomers(initial_sg_ratio, monomer_draw)
initial_events = create_initial_events(initial_monomers, DEF_RXN_RATES)
initial_state = create_initial_state(initial_events, initial_monomers)
events = {initial_events[i] for i in range(num_initial_monos)}
events.add(Event(GROW, [], rate=1e4))
try:
run_kmc(DEF_RXN_RATES, initial_state, sorted(events), n_max=20, t_max=1, random_seed=10)
self.assertFalse("Should not arrive here; An error should have be raised")
except InvalidDataError as e:
self.assertTrue("A numeric sg_ratio" in e.args[0])
def generate_lignin(num_monomers: int = 1) -> Chem.Mol:
"""Generates lignin molecule.
parameters
----------
num_monomers : int
Number of monomers in lignin molecule.
"""
# Set the percentage of S
sg_ratio = 0
pct_s = sg_ratio / (1 + sg_ratio)
# Set the initial and maximum number of monomers to be modeled.
ini_num_monos = 1
max_num_monos = num_monomers
# Maximum time to simulate, in seconds
t_max = 1 # seconds
mono_add_rate = 1e4 # monomers/second
# Use a random number and the given sg_ratio to determine the monolignol types to be initially modeled
monomer_draw = np.random.rand(ini_num_monos)
initial_monomers = create_initial_monomers(pct_s, monomer_draw)
# Initially allow only oxidation events. After they are used to determine the initial state, add
# GROW to the events, which allows additional monomers to be added to the reaction at the
# specified rate and with the specified ratio
initial_events = create_initial_events(initial_monomers, rxn_rates)
initial_state = create_initial_state(initial_events, initial_monomers)
initial_events.append(Event(GROW, [], rate=mono_add_rate))
# simulate lignin creation
result = run_kmc(rxn_rates,
initial_state,
initial_events,
n_max=max_num_monos,
t_max=t_max,
sg_ratio=sg_ratio)
# using RDKit
nodes = result[MONO_LIST]
adj = result[ADJ_MATRIX]
block = generate_mol(adj, nodes)
mol = MolFromMolBlock(block)
mol = Chem.AddHs(mol)
return mol
def create_sample_kmc_result(max_time=1., num_initial_monos=3, max_monos=10, sg_ratio=0.75, seed=10):
# The set lists are to minimize randomness in testing (adding while debugging source of randomness in some tests;
# leaving because it doesn't hurt a thing; also leaving option to make a monomer_draw of arbitrary length
# using a seed, but rounding those numbers because the machine precision differences in floats was the bug
np.random.seed(seed)
if num_initial_monos == 3:
monomer_draw = MONO_DRAW_3
elif num_initial_monos == 20:
monomer_draw = [0.77132064, 0.02075195, 0.63364823, 0.74880388, 0.49850701, 0.22479665, 0.19806286,
0.76053071, 0.16911084, 0.08833981, 0.68535982, 0.95339335, 0.00394827, 0.51219226,
0.81262096, 0.61252607, 0.72175532, 0.29187607, 0.91777412, 0.71457578]
else:
monomer_draw = np.around(np.random.rand(num_initial_monos), MAX_NUM_DECIMAL)
# these are tested separately elsewhere
initial_monomers = create_initial_monomers(sg_ratio, monomer_draw)
initial_events = create_initial_events(initial_monomers, DEF_RXN_RATES)
initial_state = OrderedDict(create_initial_state(initial_events, initial_monomers))
initial_events.append(Event(GROW, [], rate=1e4))
result = run_kmc(DEF_RXN_RATES, initial_state, initial_events, n_max=max_monos, t_max=max_time,
random_seed=10, sg_ratio=sg_ratio)
return result
# Set the percentage of S
sg_ratio = 1
pct_s = sg_ratio / (1 + sg_ratio)
# Set the initial and maximum number of monomers to be modeled.
ini_num_monos = 2
max_num_monos = 10
# Maximum time to simulate, in seconds
t_max = 1 # seconds
mono_add_rate = 1e4 # monomers/second
# Use a random number and the given sg_ratio to determine the monolignol types to be initially modeled
monomer_draw = np.random.rand(ini_num_monos)
initial_monomers = create_initial_monomers(pct_s, monomer_draw)
# Initially allow only oxidation events. After they are used to determine the initial state, add
# GROW to the events, which allows additional monomers to be added to the reaction at the
# specified rate and with the specified ratio
initial_events = create_initial_events(initial_monomers, rxn_rates)
initial_state = create_initial_state(initial_events, initial_monomers)
initial_events.append(Event(GROW, [], rate=mono_add_rate))
result = run_kmc(rxn_rates,
initial_state,
initial_events,
n_max=max_num_monos,
t_max=t_max,
sg_ratio=sg_ratio)
