def anim(x,y,z):
f = mlab.gcf()
plt = mlab.points3d(x,y,z, colormap="copper", scale_factor=.25)
while(True):
# TODO: Paralelize
md.evolve(25)
x,y,z = md.get_positions()
stats = md.system_stats()
print('Temp',stats[-1])
plt.mlab_source.set(x=x, y=y, z=z)
f.scene.render()
yield
# GIVE TIME OF EVOLUTION IN PS AND NUMBER OF POINTS
time=10
snapshots = int(round(time/(100*dt)))
steps_to_be_done = int(round(time/dt))
steps_per_snapshot = steps_to_be_done/snapshots
# SIMULATION
md.init_simulation(nx=nx,
ny=ny,
nz=nz,
a=0.37317,
R=R,
T0=T0,
m=m,
f=f,
L=L,
epsilon=epsilon,
dt=dt)
x,y,z,px,py,pz = md.set_particles()
Ek = np.zeros(snapshots+1)
V = np.zeros(snapshots+1)
Vs = np.zeros(snapshots+1)
T = np.zeros(snapshots+1)
P = np.zeros(snapshots+1)
t = np.arange(float(snapshots+1))
L= 2.3
dt = 1e-03
# GIVE TIME OF EVOLUTION IN PS AND NUMBER OF POINTS
time=15
snapshots=int(round(time/dt))
steps_to_be_done = int(round(time/dt))
steps_per_snapshot = steps_to_be_done/snapshots
md.init_simulation(nx=nx,
ny=ny,
nz=nz,
a=0.37317,
R=R,
T0=T0,
m=m,
f=f,
L=L,
epsilon=epsilon,
dt=dt)
md.set_particles()
Ts = np.logspace(0.,4.,num=10,endpoint=False)
for T in Ts:
print(T)
md.change_T(T)
md.termalize()
md.simulate(1.,100,10)
T0= 100.0
m= 39.948
epsilon=1.0
f= 10000.0
L= 2.3
dt= 2e-03
kb=8.31*1e-3
print('# starting test of MolecDyn')
md.init_simulation(nx=5,
ny=5,
nz=5,
a=0.38,
R=0.38,
T0=100.,
m=39.948,
f=10000.0,
L=2.3,
epsilon=1.,
dt=2e-03)
x,y,z,px,py,pz = md.set_particles()
p = np.linspace(0.,20.,num=200)
C = math.sqrt(kb*T0/m)
plt.hist(np.sqrt(px**2+py**2+pz**2)/m,label='|p|',normed=True)
#plt.plot(p/m,4*pi*(m/(2*pi*kb*T0))**(3/2)*(p/m)**2*np.exp(-(p/m)**2/(2*m*kb*T0)))
plt.axvline(math.sqrt(2*kb*T0/m),color='red')
plt.title("velocity histogram")
import mayavi
from mayavi import mlab
import MolecDyn as md # home-made module for molecular dynamics
nx=8
ny=8
nz=8
a=0.38
md.init_simulation(nx=nx,
ny=ny,
nz=nz,
a=0.38,
R=0.38,
T0=110,
m=39.948,
f=10000.0,
L=1.23*(nx-1)*a,
epsilon=1.,
dt=1e-03)
x,y,z,px,py,pz = md.set_particles()
#mlab.figure(1, fgcolor=(1, 1, 1), bgcolor=(0, 0, 0))
#mlab.mesh(x,y,z,transparent=True)
#mlab.points3d(0,0,0)
#r = 2.3
#pi = np.pi
