def make_triangular_plate(atoms_per_side=10):
"""construct a single triangular plate
"""
theta = 60. * np.pi / 180.
v1 = np.array([1,0,0])
v2 = np.array([0.5, np.sin(theta), 0])
aps = atoms_per_side
plate = RigidFragment()
for i in xrange(aps-1):
for j in xrange(aps-1):
if i + j >= aps-1:
break
xnew = v1*i + v2*j
if (i == 0 and j == 0 or
i == 0 and j == aps-2 or
i == aps-2 and j == 0):
atomtype = OTHER_TYPE
elif i == 0:
atomtype = EDGE1_TYPE
elif j == 0:
atomtype = EDGE2_TYPE
elif i + j == aps-2:
atomtype = EDGE3_TYPE
else:
atomtype = OTHER_TYPE
plate.add_atom(atomtype, xnew, 1)
# draw(coords)
plate.finalize_setup()
return plate
def make_otp():
"""this constructs a single OTP molecule"""
otp = RigidFragment()
otp.add_atom("O", np.array([0.0, -2.0 / 3 * np.sin(7.0 * pi / 24.0), 0.0]), 1.0)
otp.add_atom("O", np.array([cos(7.0 * pi / 24.0), 1.0 / 3.0 * sin(7.0 * pi / 24.0), 0.0]), 1.0)
otp.add_atom("O", np.array([-cos(7.0 * pi / 24.0), 1.0 / 3.0 * sin(7.0 * pi / 24), 0.0]), 1.0)
otp.finalize_setup()
return otp
def water():
water = RigidFragment()
rho = 0.9572
theta = 104.52/180.0*pi
water.add_atom("O", np.array([0., 0., 0.]), 16.)
water.add_atom("H", rho*np.array([0.0, sin(0.5*theta), cos(0.5*theta)]), 1.)
water.add_atom("H", rho*np.array([0.0, -sin(0.5*theta), cos(0.5*theta)]), 1.)
water.finalize_setup()
return water
def make_otp():
"""this constructs a single OTP molecule"""
otp = RigidFragment()
otp.add_atom("O", np.array([0.0, -2. / 3 * np.sin(7. * pi / 24.), 0.0]),
1.)
otp.add_atom(
"O", np.array([cos(7. * pi / 24.), 1. / 3. * sin(7. * pi / 24.), 0.0]),
1.)
otp.add_atom(
"O", np.array([-cos(7. * pi / 24.), 1. / 3. * sin(7. * pi / 24), 0.0]),
1.)
otp.finalize_setup()
return otp
def water():
water = RigidFragment()
rho = 0.9572
theta = 104.52 / 180.0 * pi
water.add_atom("O", np.array([0., 0., 0.]), 16.)
water.add_atom("H",
rho *
np.array([0.0, sin(0.5 * theta),
cos(0.5 * theta)]), 1.)
water.add_atom("H",
rho * np.array([0.0, -sin(0.5 * theta),
cos(0.5 * theta)]), 1.)
water.finalize_setup()
return water
def create_base():
base = RigidFragment()
base.add_atom("O", np.array([-0.4, 0., 0.]), 1.)
base.add_atom("H", np.array([0.4, 0., 0.]), 1.)
base.finalize_setup(shift_com=False)
print("inversion:\n", base.inversion)
print("symmetry:\n", base.symmetries)
base.inversion=None
return base
def create_pap():
pap = RigidFragment()
rho = 0.3572
theta = 104.52/180.0*pi
pap.add_atom("O", np.array([0., 0., 0.]), 1.)
pap.add_atom("H", np.array([-0.038490, 0.1204928, 0.3794728]), 1.)
pap.add_atom("C", np.array([-0.038490, -0.1204928, -0.3794728]), 1.)
pap.finalize_setup(shift_com=False)
print "inversion:\n", pap.inversion
print "symmetry:\n", pap.symmetries
pap.inversion=None
#print pap.S
#pap.S = 0.3*np.identity(3)
return pap
def create_base():
base = RigidFragment()
base.add_atom("O", np.array([-0.4, 0., 0.]), 1.)
base.add_atom("H", np.array([0.4, 0., 0.]), 1.)
base.finalize_setup(shift_com=False)
print "inversion:\n", base.inversion
print "symmetry:\n", base.symmetries
base.inversion=None
return base
def make_otp(self):
"""this constructs a single OTP molecule"""
otp = RigidFragment()
otp.add_atom("O", np.array([0.0, -2./3 * np.sin( 7.*pi/24.), 0.0]), 1.)
otp.add_atom("O", np.array([cos( 7.*pi/24.), 1./3. * sin( 7.* pi/24.), 0.0]), 1.)
otp.add_atom("O", np.array([-cos( 7.* pi/24.), 1./3. * sin( 7.*pi/24), 0.0]), 1.)
otp.finalize_setup()
print "otp"
print otp.atom_positions
return otp
def make_triangular_plate(atoms_per_side=8):
"""construct a single triangular plate
"""
theta = 60. * np.pi / 180.
v1 = np.array([1,0,0])
v2 = np.array([0.5, np.sin(theta), 0])
aps = atoms_per_side
plate = RigidFragment()
for i in range(aps-1):
for j in range(aps-1):
if i + j >= aps-1:
break
xnew = v1*i + v2*j
if (i == 0 and j == 0 or
i == 0 and j == aps-2 or
i == aps-2 and j == 0):
atomtype = OTHER_TYPE
elif i == 0:
atomtype = EDGE1_TYPE
elif j == 0:
atomtype = EDGE2_TYPE
elif i + j == aps-2:
atomtype = EDGE3_TYPE
else:
atomtype = OTHER_TYPE
plate.add_atom(atomtype, xnew, 1)
# draw(coords)
plate.finalize_setup()
return plate
def create_pap():
pap = RigidFragment()
rho = 0.3572
theta = 104.52 / 180.0 * pi
pap.add_atom("O", np.array([0., 0., 0.]), 1.)
pap.add_atom("H", np.array([-0.038490, 0.1204928, 0.3794728]), 1.)
pap.add_atom("C", np.array([-0.038490, -0.1204928, -0.3794728]), 1.)
pap.finalize_setup(shift_com=False)
print "inversion:\n", pap.inversion
print "symmetry:\n", pap.symmetries
pap.inversion = None
#print pap.S
#pap.S = 0.3*np.identity(3)
return pap