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 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 setUp(self):
natoms = 50
rcut = 1.6
ntypeA = int(natoms * 0.8)
self.x0 = _x0.copy()
boxl = 7.
boxvec = np.array([boxl] * 3)
self.pot = BLJCut(natoms, ntypeA, rcut=rcut, boxvec=boxvec)
self.pot_fortran = LJpshift(natoms, ntypeA, boxl=boxl, rcut=rcut)
self.e0 = 6971.685336750815
def setUp(self):
natoms = 50
rcut = 1.6
ntypeA = int(natoms * 0.8)
self.x0 = _x0.copy()
self.pot = BLJCut(natoms, ntypeA, rcut=rcut)
self.e0 = 1412.0144910476681
self.pot_fortran = LJpshift(natoms, ntypeA, rcut=rcut)
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 setUp(self):
np.random.seed(1)
current_dir = os.path.dirname(__file__)
xyz = read_xyz(open(current_dir + "/_blj13_min.xyz", "r"))
self.xmin = xyz.coords.reshape(-1).copy()
ntypeA, self.Emin, rcut, epsAA, sigAA, epsBB, sigBB, epsAB, sigAB = list(map(float, xyz.title.split()[1::2]))
ntypeA = int(ntypeA)
self.rcut = rcut
natoms = self.xmin.size // 3
self.pot = BLJCut(natoms, ntypeA, rcut=rcut, sigAA=sigAA, epsAA=epsAA,
epsBB=epsBB, sigBB=sigBB, epsAB=epsAB, sigAB=sigAB)
self.xrandom = np.random.uniform(-1, 1, self.xmin.size) * 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)