def main(argv):
format = None
zmat = None
while argv[0].startswith("--"):
if argv[0] == '--format':
format = argv[1]
argv = argv[2:]
elif argv[0] == '--zmatrix':
__, zmat, v_name, __, __, __, __ = read_zmt_from_file(argv[1])
argv = argv[2:]
elif argv[0] == '--help':
print __doc__
return
geo1 = read(argv[0], format=format)
geos = [read(arg, format=format) for arg in argv[1:]]
if zmat == None:
fun = Cartesian()
else:
fun = ZMat(zmat)
symbols = geo1.get_chemical_symbols()
assert len(geos) > 0
for geo in geos:
assert geo.get_chemical_symbols() == symbols
compare(geo1.get_positions(), geo.get_positions(), symbols, fun)
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
def get_transformation(zmi, len_carts, zmt_format):
# extract data from (several) zmatrices
if zmt_format == "gx":
datas = [read_zmt_from_gx(zm) for zm in zmi]
elif zmt_format == "gauss":
datas = [read_zmt_from_gauss(zm) for zm in zmi]
else:
datas = [read_zmt_from_file(zm) for zm in zmi]
names, zmat, var_nums, mult, d_nums, size_sys, size_nums, size_carts, mask1 = restructure(
datas)
# decide if global positioning is needed
# it is needed if there are more than one option, first one checks for
# if there are cartesian coordinates
with_globs = (len_carts > size_sys) or len(zmat) > 1
# gx mask, only valid if gx's zmat is for complete system
if with_globs:
mask1 = None
else:
mask1 = mask1[0]
# first only the zmatrix functions, allow multiple use of variables
funcs = []
quats = []
# build function for every zmatrix
for i, zm, va_nm, mul in zip(range(len(var_nums)), zmat, var_nums, mult):
fun = ZMat(zm)
# some variables are used several times
if mul > 0:
fun = With_equals(fun, va_nm)
# global positioning needed
if with_globs:
fun = With_globals(fun)
quats.append(True)
# attention, this changes number of internal coordinates
# belonging to this specific zmatrix
size_nums[i] = size_nums[i] + 6
else:
quats.append(False)
funcs.append(fun)
# if not all variables are used up, the rest are in Cartesians
if len_carts > size_sys:
funcs.append(Cartesian())
# there is also some need to specify their sizes
size_nums.append(len_carts - size_sys)
size_carts.append(len_carts - size_sys)
quats.append(False)
d_nums.append([])
# how many atoms per single function
# needed for Mergefuncs.pinv
size_carts = [s / 3. for s in size_carts]
# now merge the functions to one:
if len(size_nums) > 1:
func = Mergefuncs(funcs, size_nums, size_carts)
else:
# no need to merge a single function
func = funcs[0]
return func, d_nums, quats, size_nums, mask1
except:
pass
command = "salloc -n16 mpirun ~/darcs/ttfs-mac/runqm"
calc = ParaGauss (cmdline=command, input="water.scm")
atoms = read ("h2o.xyz")
x = atoms.get_positions ()
#
# Z-matrix for water:
#
zmt = ZMat ([(None, None, None),
(1, None, None),
(1, 2, None)], base=1)
#
# Initial values of internal coordinates:
#
s = zmt.pinv (x)
assert max (abs (s - zmt.pinv (zmt (s)))) < 1.0e-10
clean ()
with QFunc (atoms, calc) as f:
f = Memoize (f, DirStore (salt="h2o, qm"))
e = compose (f, zmt)
print s, e (s)
Function for generating starting values. Use a mask to reduce the
complete vector.
"""
vec_red = []
for i, m in enumerate(mask):
if m:
vec_red.append(vec[i])
return asarray(vec_red)
if testfun == "zmat":
"""
Zmatrix description with a starting values for nice symmetry
behaviour. Lenth to be equal in C2V symmetry fullfil this at start
to an accuracy of < 1e-15 Angstrom.
"""
func = ZMat([(), (0,), (0, 1), (1, 2, 0)])
min1 = [var1, var1, var3, var1, var3, var4]
min2 = [var1, var1, var3, var1, var3, 2 * pi -var4]
middle = [var1, var1, var3, var1, var3, var8]
elif testfun == "zmate":
"""
Zmatrix and startingvalues as in zmat2. But in this case there are
added some variables for global orientation, set to zero on every
position at start.
"""
func1 = ZMat([(), (0,), (0, 1), (1, 2, 0)])
func = With_globals(func1)
min1 = [var1, var1, var3, var1, var3, var4, 0. ,0. ,0. ,0. ,0. ,0. ]
except:
pass
command = "salloc -n16 mpirun ~/darcs/ttfs-mac/runqm"
calc = ParaGauss(cmdline=command, input="water.scm")
atoms = read("h2o.xyz")
x = atoms.get_positions()
#
# Z-matrix for water:
#
zmt = ZMat([(None, None, None), (1, None, None), (1, 2, None)], base=1)
#
# Initial values of internal coordinates:
#
s = zmt.pinv(x)
assert max(abs(s - zmt.pinv(zmt(s)))) < 1.0e-10
clean()
with QFunc(atoms, calc) as f:
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)