def test_1():
a = Atom("Ne", [-1.0, 0.0, 0.0])
b = Atom("Ne", [1.0, 0.0, 0.0])
am = Molecule([a, b])
# Force vector exterted on the first atom TODO, for optimization
# purposes, this function should not take atom objects but coords.
f = lennard_jones(a, b)
def test_1():
a = Atom("Ne", [-1.0, 0.0, 0.0])
b = Atom("Ne", [1.0, 0.0, 0.0])
am = Molecule([a, b])
# Force vector exterted on the first atom TODO, for optimization
# purposes, this function should not take atom objects but coords.
f = lennard_jones(a, b)
def test_energy():
'''This is made as a test to verify is the potential produced is
correct by using correct units and whatever.
'''
arr = np.array([[0.0, 0.0, 0.0], [0.30e-9, 0.0, 0.0]])
rs = []
ens = []
myens = []
forces = []
myforces = []
eps, sigma = lj.typetolj['Ar']
for i in range(200):
rs.append(arr[1,0])
ens.append(cenergy.lennard_jones(arr, 'Ar', periodic=False))
force = cforces.lennard_jones(arr, 'Ar', periodic=False)[0,0]
forces.append(force*1e-32)
sonr = sigma/arr[1,0]
r = arr[1,0]
#print sonr**12, sonr**6
myen = 4*eps*(sonr)**12 - 4*eps*(sonr)**6
myforce = -24*eps*( 2*(sigma**12/r**13) - (sigma**6/r**7) )
myforces.append(myforce*1e-32)
myens.append(myen)
arr[1,0] += 0.001e-9
print(force, myforce)
import pylab as pl
pl.plot(rs, ens)
pl.plot(rs, myens)
pl.plot(rs, myforces)
#pl.plot(rs, forces)
pl.show()
def test_energy():
'''This is made as a test to verify is the potential produced is
correct by using correct units and whatever.
'''
arr = np.array([[0.0, 0.0, 0.0], [0.30e-9, 0.0, 0.0]])
rs = []
ens = []
myens = []
forces = []
myforces = []
eps, sigma = lj.typetolj['Ar']
for i in range(200):
rs.append(arr[1,0])
ens.append(cenergy.lennard_jones(arr, 'Ar', periodic=False))
force = cforces.lennard_jones(arr, 'Ar', periodic=False)[0,0]
forces.append(force*1e-32)
sonr = sigma/arr[1,0]
r = arr[1,0]
#print sonr**12, sonr**6
myen = 4*eps*(sonr)**12 - 4*eps*(sonr)**6
myforce = -24*eps*( 2*(sigma**12/r**13) - (sigma**6/r**7) )
myforces.append(myforce*1e-32)
myens.append(myen)
arr[1,0] += 0.001e-9
print force, myforce
import pylab as pl
pl.plot(rs, ens)
pl.plot(rs, myens)
pl.plot(rs, myforces)
#pl.plot(rs, forces)
pl.show()
