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)
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
sys.exit()
Dmin = float(args["<dmin>"])
Dmax = float(args["<dmax>"])
N = int(args["<N>"])
Drange = np.linspace(Dmin, Dmax, N).round(2)
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"
[email protected] 02/10/15 """ import numpy as np from numpy.linalg import norm 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."
if args["water"]:
mol = gen_water(shift=shift, shiftPt=posPt, theta=theta, phi=phi)
print mol
if args["--save"]:
mol.save(args["--save"]) # "water.xyz"
elif args["Pt"]:
cluster = args["<cluster>"]
mol = gen_Pt(cluster=cluster, shift=shift)
print mol
if args["--save"]:
mol.save(args["--save"]) # "Pt.xyz"
elif args["carbon"]:
a = 1.42
Nh, Nv = int(args["<Nh>"]), int(args["<Nv>"])
mol = gen_carbon(Nh, Nv, shift=shift)
if args["--addH"]:
b = float(args["--Ha"])
mol += add_hydrogens(mol.coords, a, b)
print mol
if args["--save"]:
mol.save(args["--save"])
else: # single atom
name = args["--atom"]
coords = [0, 0, 0]
xyz = Atoms(name, coords)
print xyz
if args["--save"]:
xyz.save(args["--save"])
sys.exit()
Dmin = float(args["<dmin>"])
Dmax = float(args["<dmax>"])
N = int(args["<N>"])
Drange = np.linspace(Dmin, Dmax, N).round(2)
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"
args = docopt(__doc__)
#print args
try:
pos = args["<pos>"]
except int(pos) not in range(1, 7):
print "Allowed position numbers are 1...6, see README."
sys.exit()
maindir = os.path.expanduser("~/DPDcoeffs/TA_WaterBlob")
blobdir = os.path.expanduser("~/DPDcoeffs/Files/Waterblobs")
blobnum = args["--blobnum"] # blob number used, default is 0
blobfile = os.path.join(blobdir, "waterblob_" + blobnum + ".xyz")
outdir = maindir + "/Pos_" + pos
blob = Atoms().read(blobfile)
blob.shift_com()
triflic = Atoms().read(os.path.expanduser("~/DPDcoeffs/Files/triflic.xyz"))
if args["--counterpoise"]:
triflic.names = [i + "(fragment=1)" for i in triflic.names]
blob.names = [i + "(fragment=2)" for i in blob.names]
outdir = maindir + "/Pos_" + pos + "_CP"
if not os.path.exists(outdir):
os.mkdir(outdir)
Dmin = float(args["<dmin>"])
Dmax = float(args["<dmax>"])
delta = float(args["<delta>"])
Drange = np.arange(Dmin, Dmax, delta).round(2)
--seed <seed> Random seed [default: 123]
--all Wiggle all atoms randomly
--bymol Wiggle each water molecule separately
[email protected], 14/08/15
"""
from docopt import docopt
import numpy as np
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)
--sigma <s> Gaussian sigma [default: 0.1]
--seed <seed> Random seed [default: 123]
--all Wiggle all atoms randomly
--bymol Wiggle each water molecule separately
[email protected], 14/08/15
"""
from docopt import docopt
import numpy as np
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)
args = docopt(__doc__)
#print args
try:
pos = args["<pos>"]
except int(pos) not in range(1, 7):
print "Allowed position numbers are 1...6, see README."
sys.exit()
maindir = os.path.expanduser("~/DPDcoeffs/TA_WaterBlob")
blobdir = os.path.expanduser("~/DPDcoeffs/Files/Waterblobs")
blobnum = args["--blobnum"] # blob number used, default is 0
blobfile = os.path.join(blobdir, "waterblob_" + blobnum + ".xyz")
outdir = maindir + "/Pos_" + pos
blob = Atoms().read(blobfile)
blob.shift_com()
triflic = Atoms().read(os.path.expanduser("~/DPDcoeffs/Files/triflic.xyz"))
if args["--counterpoise"]:
triflic.names = [i + "(fragment=1)" for i in triflic.names]
blob.names = [i + "(fragment=2)" for i in blob.names]
outdir = maindir + "/Pos_" + pos + "_CP"
if not os.path.exists(outdir):
os.mkdir(outdir)
Dmin = float(args["<dmin>"])
Dmax = float(args["<dmax>"])
delta = float(args["<delta>"])
Drange = np.arange(Dmin, Dmax, delta).round(2)