def gen_water(shift=np.zeros(3), shiftPt=np.zeros(3), theta=0.0, phi=0.0):
"""Init water molecule, already optimised using 6-311G**"""
coords = np.zeros((3,3))
coords[1, 1] += 0.757009
coords[2, 1] += -0.757009
coords[1:3, 2] += 0.593565
names = ["O", "H", "H"]
mol = Atoms(names, coords)
mol.rotate(theta, phi)
mol.shift(np.dot(Pt_basis(), shiftPt))
mol.shift(shift)
return mol
def save_configs(TA, blob, Drange, theta, phi, outdir, blobnum="0"):
for d in Drange:
xyzname = "run_blob_" + blobnum + "_d" + str(d) + ".xyz"
xyzpath = os.path.join(outdir, xyzname)
dist = np.array([[d, 0, 0]])
dist = Atoms(["A"], dist)
dist.rotate(theta, phi)
dist = dist.coords[0].round(2)
blob.shift(dist)
TA_blob = triflic + blob
blob.shift(-dist) # STUPID TRICK
TA_blob.save(xyzpath)
def save_configs(TA, blob, Drange, theta, phi, outdir, blobnum="0"):
for d in Drange:
xyzname = "run_blob_" + blobnum + "_d" + str(d) + ".xyz"
xyzpath = os.path.join(outdir, xyzname)
dist = np.array([[d, 0, 0]])
dist = Atoms(["A"], dist)
dist.rotate(theta, phi)
dist = dist.coords[0].round(2)
blob.shift(dist)
TA_blob = triflic + blob
blob.shift(-dist) # STUPID TRICK
TA_blob.save(xyzpath)
s = -A.coords[n-1]
A.shift(s)
if args["--align"]:
n1, n2 = [int(i) for i in args["--align"].split()]
if n1 != n2:
A.align(n1, n2)
if args["--flip"]:
n1, n2 = [int(i) for i in args["--flip"].split()]
if n1 == n2:
print "Please choose two different atoms."
else:
A.flip(n1, n2)
if args["--rotate"]:
theta, phi = [radians(float(i)) for i in args["--rotate"].split()]
A.rotate(theta, phi)
if args["--shift"]:
s = [float(i) for i in args["--shift"].split()]
A.shift(s)
if args["--save"]:
fname = args["--save"]
A.save(fname)
else:
print A
args = docopt(__doc__)
#print args
np.random.seed(int(args["--seed"]))
sigma = float(args["--sigma"])
A = Atoms().read(args["<infile>"])
if args["--all"]:
noise = np.random.randn(len(A), 3)*sigma
A.coords += noise
if args["--bymol"]:
Nmols = len(A)/3
for i in range(Nmols):
mol = Atoms(names=A.names[3*i:3*(i+1)], coords=A.coords[3*i:3*(i+1), :])
tempshift = mol.coords[0]
#mol.shift(-tempshift) # put oxygen at [0,0,0]
theta = np.random.randn()*sigma
phi = np.random.randn()*sigma
mol.rotate(theta, phi)
#mol.shift(tempshift)
mol.shift(np.random.randn(3, 3)*sigma)
A.coords[3*i:3*(i+1), :] = np.copy(mol.coords)
if args["--save"]:
A.save(args["--save"])
else:
print A
from xyzlib import Atoms
args = docopt(__doc__)
#print args
np.random.seed(int(args["--seed"]))
sigma = float(args["--sigma"])
A = Atoms().read(args["<infile>"])
if args["--all"]:
noise = np.random.randn(len(A), 3) * sigma
A.coords += noise
if args["--bymol"]:
Nmols = len(A) / 3
for i in range(Nmols):
mol = Atoms(names=A.names[3 * i:3 * (i + 1)],
coords=A.coords[3 * i:3 * (i + 1), :])
tempshift = mol.coords[0]
#mol.shift(-tempshift) # put oxygen at [0,0,0]
theta = np.random.randn() * sigma
phi = np.random.randn() * sigma
mol.rotate(theta, phi)
#mol.shift(tempshift)
mol.shift(np.random.randn(3, 3) * sigma)
A.coords[3 * i:3 * (i + 1), :] = np.copy(mol.coords)
if args["--save"]:
A.save(args["--save"])
else:
print A
