def test2():
v = Vector()
v.p0 = np.ones(3)
assert_true(np.allclose(v, -np.ones(3)))
assert_true(np.allclose(v.p0, np.ones(3)))
assert_true(np.allclose(v.p, np.zeros(3)))
v = Vector(p=[1., 1., 1.], p0=[1., 1., 1.])
assert_true(np.allclose(v, np.zeros(3)))
assert_true(np.allclose(v.p0, np.ones(3)))
assert_true(np.allclose(v.p, np.ones(3)))
v.p0 = np.zeros(3)
assert_true(np.allclose(v, np.ones(3)))
assert_true(np.allclose(v.p0, np.zeros(3)))
assert_true(np.allclose(v.p, np.ones(3)))
v.x = 5.0
assert_equal(v.x, 5.0)
assert_equal(v.x, v.p.x)
v.y = -5.0
assert_equal(v.y, -5.0)
assert_equal(v.y, v.p.y)
v.z = 0.0
assert_equal(v.z, 0.0)
assert_equal(v.z, v.p.z)
v.p0 = np.array([0.5, -10.0, 2.5])
assert_equal(v.p0.x, 0.5)
assert_equal(v.p0.y, -10.0)
assert_equal(v.p0.z, 2.5)
def test2():
v = Vector()
v.p0 = np.ones(3)
assert_true(np.allclose(v, -np.ones(3)))
assert_true(np.allclose(v.p0, np.ones(3)))
assert_true(np.allclose(v.p, np.zeros(3)))
v = Vector(p=[1., 1., 1.], p0=[1., 1., 1.])
assert_true(np.allclose(v, np.zeros(3)))
assert_true(np.allclose(v.p0, np.ones(3)))
assert_true(np.allclose(v.p, np.ones(3)))
v.p0 = np.zeros(3)
assert_true(np.allclose(v, np.ones(3)))
assert_true(np.allclose(v.p0, np.zeros(3)))
assert_true(np.allclose(v.p, np.ones(3)))
v.x = 5.0
assert_equal(v.x, 5.0)
assert_equal(v.x, v.p.x)
v.y = -5.0
assert_equal(v.y, -5.0)
assert_equal(v.y, v.p.y)
v.z = 0.0
assert_equal(v.z, 0.0)
assert_equal(v.z, v.p.z)
v.p0 = np.array([0.5, -10.0, 2.5])
assert_equal(v.p0.x, 0.5)
assert_equal(v.p0.y, -10.0)
assert_equal(v.p0.z, 2.5)
def generate_bundle_coords(self):
"""Generate coordinates of bundle tubes."""
self.r1 = Vector()
self.r2 = Vector()
self.bundle_coords = []
self.r1.x = self.dt + 2 * self.vdw_radius
if self.bundle_packing in ('cubic', 'ccp'):
self.r2.y = self.r1.x
else:
self.r2.x = self.r1.x * np.cos(2 * np.pi / 3)
self.r2.y = self.r1.x * np.sin(2 * np.pi / 3)
if self.bundle_packing is None:
self._bundle_packing = 'hcp'
if self.bundle_geometry == 'hexagon':
nrows = max(self.nx, self.ny, 3)
if nrows % 2 != 1:
nrows += 1
ntubes_per_end_rows = int((nrows + 1) / 2)
row = 0
ntubes_per_row = nrows
while ntubes_per_row >= ntubes_per_end_rows:
if row == 0:
for n in range(ntubes_per_row):
dr = n * self.r1
self.bundle_coords.append(dr)
else:
for nx in range(ntubes_per_row):
for ny in (-row, row):
dr = Vector()
dr.x = abs(ny * self.r2.x)
dr.y = ny * self.r2.y
dr = nx * self.r1 + dr
self.bundle_coords.append(dr)
row += 1
ntubes_per_row = nrows - row
elif self.bundle_geometry == 'rectangle':
Lx = 10 * self.Lx
for nx in range(self.nx):
for ny in range(self.ny):
dr = nx * self.r1 + ny * self.r2
while dr.x < 0:
dr.x += Lx
self.bundle_coords.append(dr)
elif self.bundle_geometry == 'square':
pass
elif self.bundle_geometry == 'triangle':
pass
else:
for nx in range(self.nx):
for ny in range(self.ny):
dr = nx * self.r1 + ny * self.r2
self.bundle_coords.append(dr)
def generate_bundle_coords(self):
"""Generate coordinates of bundle tubes."""
self.r1 = Vector()
self.r2 = Vector()
self.bundle_coords = []
self.r1.x = self.dt + 2 * self.vdw_radius
if self.bundle_packing in ('cubic', 'ccp'):
self.r2.y = self.r1.x
else:
self.r2.x = self.r1.x * np.cos(2 * np.pi / 3)
self.r2.y = self.r1.x * np.sin(2 * np.pi / 3)
if self.bundle_packing is None:
self._bundle_packing = 'hcp'
if self.bundle_geometry == 'hexagon':
nrows = max(self.nx, self.ny, 3)
if nrows % 2 != 1:
nrows += 1
ntubes_per_end_rows = int((nrows + 1) / 2)
row = 0
ntubes_per_row = nrows
while ntubes_per_row >= ntubes_per_end_rows:
if row == 0:
for n in range(ntubes_per_row):
dr = n * self.r1
self.bundle_coords.append(dr)
else:
for nx in range(ntubes_per_row):
for ny in (-row, row):
dr = Vector()
dr.x = abs(ny * self.r2.x)
dr.y = ny * self.r2.y
dr = nx * self.r1 + dr
self.bundle_coords.append(dr)
row += 1
ntubes_per_row = nrows - row
elif self.bundle_geometry == 'rectangle':
Lx = 10 * self.Lx
for nx in range(self.nx):
for ny in range(self.ny):
dr = nx * self.r1 + ny * self.r2
while dr.x < 0:
dr.x += Lx
self.bundle_coords.append(dr)
elif self.bundle_geometry == 'square':
pass
elif self.bundle_geometry == 'triangle':
pass
else:
for nx in range(self.nx):
for ny in range(self.ny):
dr = nx * self.r1 + ny * self.r2
self.bundle_coords.append(dr)