def make_waters(xs):
# All waters will be rigid objects with the same geometry:
w = Rigid(read_xyz("spc.xyz"))
# print xs
# print read_xyz ("spc.xyz")
# But at different locations and orientation:
ss = [w.pinv(x) for x in xs]
return [Rigid(w(s)) for s in ss]
def make_waters (xs):
# All waters will be rigid objects with the same geometry:
w = Rigid (read_xyz ("spc.xyz"))
# print xs
# print read_xyz ("spc.xyz")
# But at different locations and orientation:
ss = [w.pinv (x) for x in xs]
return [Rigid (w (s)) for s in ss]
def make_uranyl (x, flexible=6):
"""
Return the "best" linear approximation to the uranyl geometry as a
Fixed() func.
"""
from pts.zmat import ZMat
# Make uranyl linear:
zmt = ZMat ([(None, None, None),
(1, None, None),
(1, 2, None)], base=1)
# Bond length and the bond angle for uranyl, use the same Z-matrix
# for uranyl:
s = zmt.pinv (x)
# Set the bond lengths equal and 180 degrees angle. Note that if
# you plug these internal variables into z-matrix you will not get
# zmt(s) ~ x even when s was derived from x. That is because of
# the default orientation z-matrix chooses:
s_bond = 1.79 # A or sum (s[:2]) / 2
s = [s_bond, s_bond, pi]
# Uranyl may or may not be fixed, but to adjust orientation,
# rotate a rigid object:
Y = Rigid (zmt (s))
y = Y (Y.pinv (x))
if flexible == 0:
return Fixed (y) # 0 dof
elif flexible == 2:
# liear uranyl with flexible bonds:
def f (x):
ra, rb = x
return array ([[0., 0., 0.],
[0., 0., ra],
[0., 0., -rb]])
return Affine (f, array ([0., 0.])) # 2 dof
elif flexible == 6:
# return Move (relate (x, zmt (s)), zmt)
return ManyBody (Fixed (x[0:1]), Cartesian (x[1:3]), dof=[0, 6])
else:
assert False
def make_uranyl(x, flexible=6):
"""
Return the "best" linear approximation to the uranyl geometry as a
Fixed() func.
"""
from pts.zmat import ZMat
# Make uranyl linear:
zmt = ZMat([(None, None, None), (1, None, None), (1, 2, None)], base=1)
# Bond length and the bond angle for uranyl, use the same Z-matrix
# for uranyl:
s = zmt.pinv(x)
# Set the bond lengths equal and 180 degrees angle. Note that if
# you plug these internal variables into z-matrix you will not get
# zmt(s) ~ x even when s was derived from x. That is because of
# the default orientation z-matrix chooses:
s_bond = 1.79 # A or sum (s[:2]) / 2
s = [s_bond, s_bond, pi]
# Uranyl may or may not be fixed, but to adjust orientation,
# rotate a rigid object:
Y = Rigid(zmt(s))
y = Y(Y.pinv(x))
if flexible == 0:
return Fixed(y) # 0 dof
elif flexible == 2:
# liear uranyl with flexible bonds:
def f(x):
ra, rb = x
return array([[0., 0., 0.], [0., 0., ra], [0., 0., -rb]])
return Affine(f, array([0., 0.])) # 2 dof
elif flexible == 6:
# return Move (relate (x, zmt (s)), zmt)
return ManyBody(Fixed(x[0:1]), Cartesian(x[1:3]), dof=[0, 6])
else:
assert False
waters = [X] * 5
atoms = read ("uo22+,5h2o.xyz")
xa = atoms.get_positions ()
# Bond length and the bond angle for uranyl, use the same Z-matrix for
# uranyl:
s = zmt.pinv (xa[:3])
# Average bond length and 180 degrees angle:
s_bond = sum (s[:2]) / 2
s = [s_bond, s_bond, pi]
# Uranyl will be fixed, but to adjust orientation, rotate a rigid
# object:
Y = Rigid (zmt (s))
uranyl = Fixed (Y (Y.pinv (xa[:3])))
trafo = ManyBody (uranyl, *waters)
# Here initial positions and orientation of 5 rigid waters are
# computed to approximate the geometry from the xyz-file. Uranyl is
# fixed:
s = trafo.pinv (xa)
calc = ParaGauss (cmdline=command, input="uranyl+water.scm")
clean ()
with QFunc (atoms, calc) as f:
f = Memoize (f, DirStore (salt="uranyl+water, qm"))
f = Memoize(f, DirStore(salt="h2o, qm"))
e = compose(f, zmt)
print s, e(s)
s, info = minimize(e, s, algo=1, ftol=1.0e-2, xtol=1.0e-2)
print s, e(s), info["converged"]
#
# Internal coordinates:
#
# In: 0.97843364 0.97826543 1.87152024
# Out: 0.98477091 0.98477695 1.88111918
#
# Rigid water with optimized internal coordinates:
#
X = Rigid(zmt(s))
# Five optimized rigid waters, actual location and orientation to be
# specified ...
waters = [X] * 5
atoms = read("uo22+,5h2o.xyz")
xa = atoms.get_positions()
# Bond length and the bond angle for uranyl, use the same Z-matrix for
# uranyl:
s = zmt.pinv(xa[:3])
# Average bond length and 180 degrees angle:
s_bond = sum(s[:2]) / 2
s = [s_bond, s_bond, pi]