def start(dt=dt):
analitic = Analitic(r=1,
v=-gamma_div_2m,
r_function=r_analitic_function,
v_function=v_analitic_function,
a_function=a_function)
verlet = Verlet(r=1, v=-gamma_div_2m, a_function=a_function, dt=dt)
beeman = Beeman(r=1, v=-gamma_div_2m, a_function=a_function, dt=dt)
gear = Gear5(r=1, v=-gamma_div_2m, a_function=a_function, dt=dt, k=k, m=m)
strr = ""
for index in xrange(1, int(tf / dt) + 1):
t = index * dt
#import ipdb; ipdb.set_trace()
analitic.loop(t)
verlet.loop()
beeman.loop()
gear.loop()
#strr+= (str(verlet[R])) + '\t' + str(analitic[R]) + '\t' + (str(verlet[V])) + '\t' + str(analitic[V]) + '\t' + (str(verlet[A])) + '\t' + str(analitic[A]) + '\n'
plot(analitic.r_history, verlet.r_history, beeman.r_history,
gear.r_history)
with open('output_particle/data.txt', 'w') as outfile:
methods = [verlet, beeman, gear]
outfile.write(
reduce(
lambda accum, elem: accum + str(elem.__class__) + str(
elem.get_error(analitic.r_history)) + " ,", methods, ""))
def __init__(self,
dim=3,
n_a=3,
st=0.01,
sts=100,
algorithm='LeapFrog',
force_fields=['SoftWall', 'MinBarrierMin'],
parameters=[[1, 10], [5, 10, 3, 0.02]]):
self.n_atoms = int(n_a)
self.atoms = [Atom(dim, st) for i in range(self.n_atoms)]
self.time_step = float(st)
self.steps = int(sts)
if algorithm == 'Verlet':
self.algorithm = Verlet()
elif algorithm == 'VelocityVerlet':
self.algorithm = VelocityVerlet()
elif algorithm == 'LeapFrog':
self.algorithm = LeapFrog()
else:
sys.exit('Wrong algorithm name')
self.force_fields = []
for f in range(len(force_fields)):
if force_fields[f] == 'SoftWall':
self.force_fields.append(SoftWall(parameters[f]))
for a in self.atoms:
a.Recalculate(st, True)
elif force_fields[f] == 'MinBarrierMin':
self.force_fields.append(MinBarrierMin(parameters[f]))
for a in self.atoms:
a.Recalculate(st, True)
elif force_fields[f] == 'LenardJones':
self.force_fields.append(LenardJones(parameters[f]))
for a in self.atoms:
for i in range(a.coords_t.dim):
if a.coords_t[i] >= 0:
a.coords_t[i] += a.number
else:
a.coords_t[i] -= a.number
else:
sys.exit('Wrong potential name')
def set_positions(self):
model = LennartJonesModel('H',1,2)
algo = Verlet(model, self)
v = algo.run(10)
for atom in self:
atom.pos = atom.pos + v