def test_one_particle(self):
gfrdbase.place_particle(self.w, self.S, [0.0, 0.0, 0.0])
t = self.s.t
for i in range(5):
self.s.step()
self.failIf(t == self.s.t)
def test_one_particle(self):
gfrdbase.place_particle(self.w, self.S, [0.0,0.0,0.0])
t = self.s.t
for i in range(5):
self.s.step()
self.failIf(t == self.s.t)
def singlerun(T):
sigma = 5e-9
r0 = sigma
D = 1e-12
D_tot = D * 2
kf = 100 * sigma * D_tot
m = model.ParticleModel(1e-3)
A = model.Species('A', D, sigma / 2)
m.add_species_type(A)
B = model.Species('B', D, sigma / 2)
m.add_species_type(B)
C = model.Species('C', D, sigma / 2)
m.add_species_type(C)
r1 = model.create_binding_reaction_rule(A, B, C, kf)
m.network_rules.add_reaction_rule(r1)
w = gfrdbase.create_world(m, 3)
nrw = gfrdbase.create_network_rules_wrapper(m)
s = _gfrd._EGFRDSimulator(w, nrw, myrandom.rng)
class check_reactions:
def __init__(self):
self.reactions = []
def __call__(self, ri):
self.reactions.append(ri)
cr = check_reactions()
s.reaction_recorder = cr
pid1 = gfrdbase.place_particle(w, A, [0, 0, 0])[0]
pid2 = gfrdbase.place_particle(
w, B, [float(A['radius']) + float(B['radius']) + 1e-23, 0, 0])[0]
end_time = T
while s.step(end_time):
if len(cr.reactions) != 0:
cr.reactions = []
return 0, s.t
p1 = s.world.get_particle(pid1)[1]
p2 = s.world.get_particle(pid2)[1]
distance = w.distance(p1.position, p2.position)
return distance, s.t
def singlerun(T):
sigma = 5e-9
r0 = sigma
D = 1e-12
D_tot = D * 2
kf = 100 * sigma * D_tot
m = model.ParticleModel(1e-3)
A = model.Species('A', D, sigma/2)
m.add_species_type(A)
B = model.Species('B', D, sigma/2)
m.add_species_type(B)
C = model.Species('C', D, sigma/2)
m.add_species_type(C)
r1 = model.create_binding_reaction_rule(A, B, C, kf)
m.network_rules.add_reaction_rule(r1)
w = gfrdbase.create_world(m, 3)
nrw = gfrdbase.create_network_rules_wrapper(m)
s = _gfrd._EGFRDSimulator(w, nrw, myrandom.rng)
class check_reactions:
def __init__(self):
self.reactions = []
def __call__(self, ri):
self.reactions.append(ri)
cr = check_reactions()
s.reaction_recorder = cr
pid1 = gfrdbase.place_particle(w, A, [0,0,0])[0]
pid2 = gfrdbase.place_particle(w, B, [float(A['radius']) +
float(B['radius'])+1e-23,0,0])[0]
end_time = T
while s.step(end_time):
if len(cr.reactions) != 0:
cr.reactions = []
return 0, s.t
p1 = s.world.get_particle(pid1)[1]
p2 = s.world.get_particle(pid2)[1]
distance = w.distance(p1.position, p2.position)
return distance, s.t
def test_immobile_is_immobile(self):
particleA = gfrdbase.place_particle(self.w, self.A, [0.0,0.0,0.0])
gfrdbase.place_particle(self.w, self.B, [1.5000001e-8,0.0,0.0])
initial_position = particleA[1].position
for i in range(10):
self.s.step()
#print particleA[1].position
new_position = particleA[1].position
dist = self.w.distance(initial_position, new_position)
self.failIf(dist != 0, 'initial pos: %s,\tnew pos: %s' %
(initial_position, new_position))
def singlerun2(T):
#s.set_user_max_shell_size(1e-7)
#s.set_user_max_shell_size(1e-3)
sigma = 5e-9
r0 = sigma
D = 1e-12
D_tot = D * 2
kf = 100 * sigma * D_tot
m = model.ParticleModel(1e-3)
A = model.Species('A', D, sigma / 2)
m.add_species_type(A)
B = model.Species('B', D, sigma / 2)
m.add_species_type(B)
C = model.Species('C', D, sigma / 2)
m.add_species_type(C)
r1 = model.create_binding_reaction_rule(A, B, C, kf)
m.network_rules.add_reaction_rule(r1)
w = gfrdbase.create_world(m, 3)
nrw = gfrdbase.create_network_rules_wrapper(m)
s = EGFRDSimulator(w, myrandom.rng, nrw)
particleA = gfrdbase.place_particle(w, A, [0, 0, 0])
particleB = gfrdbase.place_particle(
w, B, [float(A['radius']) + float(B['radius']) + 1e-23, 0, 0])
end_time = T
while 1:
s.step()
if s.last_reaction:
#print 'reaction'
return 0.0, s.t
next_time = s.get_next_time()
if next_time > end_time:
s.stop(end_time)
break
distance = w.distance(s.get_position(particleA), s.get_position(particleB))
return distance, s.t
def test_immobile_is_immobile(self):
particleA = gfrdbase.place_particle(self.w, self.A, [0.0, 0.0, 0.0])
gfrdbase.place_particle(self.w, self.B, [1.5000001e-8, 0.0, 0.0])
initial_position = particleA[1].position
for i in range(10):
self.s.step()
#print particleA[1].position
new_position = particleA[1].position
dist = self.w.distance(initial_position, new_position)
self.failIf(
dist != 0,
'initial pos: %s,\tnew pos: %s' % (initial_position, new_position))
def singlerun(T, S):
m = model.ParticleModel(1e-3)
A = model.Species('A', 1e-12, 5e-9)
m.add_species_type(A)
w = gfrdbase.create_world(m, 3)
nrw = gfrdbase.create_network_rules_wrapper(m)
# s = EGFRDSimulator(w, myrandom.rng, nrw)
# s.set_user_max_shell_size(S)
s = _gfrd._EGFRDSimulator(w, nrw, myrandom.rng, 1, 1e-5, S)
particleA = gfrdbase.place_particle(w, A, [0, 0, 0])
end_time = T
s.step()
while 1:
next_time = s.t + s.dt
if next_time > end_time:
# s.stop(end_time)
s.step(end_time)
break
s.step()
pos = w.get_particle(iter(w.get_particle_ids(A.id)).next())[1].position
distance = w.distance([0, 0, 0], pos)
return distance, s.t
def singlerun(T, S):
m = model.ParticleModel(1e-3)
A = model.Species('A', 1e-12, 5e-9)
m.add_species_type(A)
w = gfrdbase.create_world(m, 3)
nrw = gfrdbase.create_network_rules_wrapper(m)
# s = EGFRDSimulator(w, myrandom.rng, nrw)
# s.set_user_max_shell_size(S)
s = _gfrd._EGFRDSimulator(w, nrw, myrandom.rng, 1, 1e-5, S)
particleA = gfrdbase.place_particle(w, A, [0, 0, 0])
end_time = T
s.step()
while 1:
next_time = s.t + s.dt
if next_time > end_time:
# s.stop(end_time)
s.step(end_time)
break
s.step()
pos = w.get_particle(iter(w.get_particle_ids(A.id)).next())[1].position
distance = w.distance([0,0,0], pos)
return distance, s.t
def singlerun2(T):
#s.set_user_max_shell_size(1e-7)
#s.set_user_max_shell_size(1e-3)
sigma = 5e-9
r0 = sigma
D = 1e-12
D_tot = D * 2
kf = 100 * sigma * D_tot
m = model.ParticleModel(1e-3)
A = model.Species('A', D, sigma/2)
m.add_species_type(A)
B = model.Species('B', D, sigma/2)
m.add_species_type(B)
C = model.Species('C', D, sigma/2)
m.add_species_type(C)
r1 = model.create_binding_reaction_rule(A, B, C, kf)
m.network_rules.add_reaction_rule(r1)
w = gfrdbase.create_world(m, 3)
nrw = gfrdbase.create_network_rules_wrapper(m)
s = EGFRDSimulator(w, myrandom.rng, nrw)
particleA = gfrdbase.place_particle(w, A, [0,0,0])
particleB = gfrdbase.place_particle(w, B, [float(A['radius']) + float(B['radius'])+1e-23,0,0])
end_time = T
while 1:
s.step()
if s.last_reaction:
#print 'reaction'
return 0.0, s.t
next_time = s.get_next_time()
if next_time > end_time:
s.stop(end_time)
break
distance = w.distance(s.get_position(particleA), s.get_position(particleB))
return distance, s.t
def test_three_particles(self):
gfrdbase.place_particle(self.w, self.S, [0.0, 0.0, 0.0])
gfrdbase.place_particle(self.w, self.S, [5e-6, 5e-6, 5e-6])
gfrdbase.place_particle(self.w, self.S, [1e-7, 1e-7, 1e-7])
t = self.s.t
for i in range(5):
self.s.step()
self.failIf(t == self.s.t)
def test_three_particles(self):
gfrdbase.place_particle(self.w, self.S, [0.0,0.0,0.0])
gfrdbase.place_particle(self.w, self.S, [5e-6,5e-6,5e-6])
gfrdbase.place_particle(self.w, self.S, [1e-7,1e-7,1e-7])
t = self.s.t
for i in range(5):
self.s.step()
self.failIf(t == self.s.t)