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
for c in combinations(blobnums, 2):
combdirname = "Blobs_" + str(c[0]) + "_" + str(c[1])
combdir = os.path.join(maindir, combdirname)
if not os.path.isdir(combdir): # create list of subdirs by combination
os.makedirs(combdir)
print "Created new directory", combdirname
blob1 = Atoms().read(blobdir + "/waterblob_" + str(c[0]) + ".xyz")
blob2 = Atoms().read(blobdir + "/waterblob_" + str(c[1]) + ".xyz")
blob1.shift_com()
blob2.shift_com()
for d in Drange: # in each combdir, create xyz and gjf files for each blob dist
xyzname = "waterblobs_d" + str(d) + ".xyz"
xyzpath = os.path.join(combdir, xyzname)
if not os.path.exists(xyzpath):
blob2.shift([0, 0, d])
blob12 = blob1 + blob2
blob2.shift([0, 0, -d]) # BAD SOLUTION, FIX THIS
blob12.save(xyzpath)
# header = gen_g09_header(params=g09params) #FIX THIS
header = "%nproc=16\n#T B3LYP/6-31G* Test\n\nSome silly text\n\n"
output = header + str(blob12) + "\n\n"
gjfname = "run_blobs_d" + str(d) + ".gjf"
gjfpath = os.path.join(combdir, gjfname)
open(gjfpath, "w").write(output)
print "g09 input file written into", gjfpath
from numpy.matlib import repmat
from scipy.linalg import expm
from math import sqrt, acos, radians
from xyzlib import Atoms
from docopt import docopt
if __name__ == "__main__":
args = docopt(__doc__,version=1.0)
# print args
A = Atoms().read(args["<file>"])
if args["--centre"]:
n = int(args["--centre"])
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()]
print "Range of distances: ", Drange
for c in combinations(blobnums, 2):
combdirname = "Blobs_" + str(c[0]) + "_" + str(c[1])
combdir = os.path.join(maindir, combdirname)
if not os.path.isdir(combdir): # create list of subdirs by combination
os.makedirs(combdir)
print "Created new directory", combdirname
blob1 = Atoms().read(blobdir + "/waterblob_" + str(c[0]) + ".xyz")
blob2 = Atoms().read(blobdir + "/waterblob_" + str(c[1]) + ".xyz")
blob1.shift_com()
blob2.shift_com()
for d in Drange: # in each combdir, create xyz and gjf files for each blob dist
xyzname = "waterblobs_d" + str(d) + ".xyz"
xyzpath = os.path.join(combdir, xyzname)
if not os.path.exists(xyzpath):
blob2.shift([0, 0, d])
blob12 = blob1 + blob2
blob2.shift([0, 0, -d]) # BAD SOLUTION, FIX THIS
blob12.save(xyzpath)
# header = gen_g09_header(params=g09params) #FIX THIS
header = "%nproc=16\n#T B3LYP/6-31G* Test\n\nSome silly text\n\n"
output = header + str(blob12) + "\n\n"
gjfname = "run_blobs_d" + str(d) + ".gjf"
gjfpath = os.path.join(combdir, gjfname)
open(gjfpath, "w").write(output)
print "g09 input file written into", gjfpath
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
