def makeplot(): # pragma: no cover
atom1 = np.zeros(3)
rcut = 2.5
potAA = BLJCut(2, 0, rcut=rcut)
potAB = BLJCut(2, 1, rcut=rcut)
potBB = BLJCut(2, 2, rcut=rcut)
eAA = []
eAB = []
eBB = []
v = vec_random_ndim(3)
v /= np.linalg.norm(v)
rlist = np.arange(.85, 3, .01)
for r in rlist:
atom2 = atom1 + r * v
x = np.array(list(atom1) + list(atom2))
eAA.append(potAA.getEnergy(x))
eAB.append(potAB.getEnergy(x))
eBB.append(potBB.getEnergy(x))
import matplotlib.pyplot as plt
plt.plot(rlist, eAA)
plt.plot(rlist, eAB)
plt.plot(rlist, eBB)
plt.show()
def makeplot(): # pragma: no cover
atom1 = np.zeros(3)
rcut = 2.5
potAA = BLJCut(2, 0, rcut=rcut)
potAB = BLJCut(2, 1, rcut=rcut)
potBB = BLJCut(2, 2, rcut=rcut)
eAA = []
eAB = []
eBB = []
v = vec_random_ndim(3)
v /= np.linalg.norm(v)
rlist = np.arange(.85, 3, .01)
for r in rlist:
atom2 = atom1 + r * v
x = np.array(list(atom1) + list(atom2))
eAA.append(potAA.getEnergy(x))
eAB.append(potAB.getEnergy(x))
eBB.append(potBB.getEnergy(x))
import matplotlib.pyplot as plt
plt.plot(rlist, eAA)
plt.plot(rlist, eAB)
plt.plot(rlist, eBB)
plt.show()
def test_rcut2(self):
pot = BLJCut(2, 1, rcut=self.rcut)
atom2 = self.atom1 + self.rcut * 0.7 * self.v
# print np.linalg.norm(atom2 - self.atom1)
x = np.array(list(self.atom1) + list(atom2))
e = pot.getEnergy(x)
self.assertGreater(np.abs(e), 1e-5)
def test_rcut2(self):
pot = BLJCut(2, 1, rcut=self.rcut)
atom2 = self.atom1 + self.rcut * 0.7 * self.v
# print np.linalg.norm(atom2 - self.atom1)
x = np.array(list(self.atom1) + list(atom2))
e = pot.getEnergy(x)
self.assertGreater(np.abs(e), 1e-5)
def test_rcut(self):
pot = BLJCut(2, 1, rcut=self.rcut)
atom2 = self.atom1 + self.rcut * 1.001 * self.v
x = np.array(list(self.atom1) + list(atom2))
e = pot.getEnergy(x)
self.assertLess(e, 1e-20)
def test_rcut(self):
pot = BLJCut(2, 1, rcut=self.rcut)
atom2 = self.atom1 + self.rcut * 1.001 * self.v
x = np.array(list(self.atom1) + list(atom2))
e = pot.getEnergy(x)
self.assertLess(e, 1e-20)