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"
output = header + str(blob12) + "\n\n"
gjfname = "run_blobs_d" + str(d) + ".gjf"
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)
print "Blob position:", pos, "\nDistances: ", Drange
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"
output = header + str(blob12) + "\n\n"
gjfname = "run_blobs_d" + str(d) + ".gjf"
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)
print "Blob position:", pos, "\nDistances: ", Drange
