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)
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"
--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)
