def argparser(arg):
global pairs, fixed, waters, coord, density, cell, cagetype, cagepos
logger = getLogger()
# Ref. C2
atoms = """
O1 0.0000 0.0000 0.1937
Ne1 0.0000 0.0000 0.7066
"""
# Ref. C2
# space group: I4_1md No. 109 http://img.chem.ucl.ac.uk/sgp/large/109az1.htm
symops = """
x, y, z
-x, -y, z
-y, 1/2+x, 1/4+z
y, 1/2-x, 1/4+z
-x, y, z
x, -y, z
y, 1/2+x, 1/4+z
-y, 1/2-x, 1/4+z
x+1/2, y+1/2, z+1/2
-x+1/2, -y+1/2, z+1/2
-y+1/2, 1/2+x+1/2, 1/4+z+1/2
y+1/2, 1/2-x+1/2, 1/4+z+1/2
-x+1/2, y+1/2, z+1/2
x+1/2, -y+1/2, z+1/2
y+1/2, 1/2+x+1/2, 1/4+z+1/2
-y+1/2, 1/2-x+1/2, 1/4+z+1/2
""".replace(',', ' ')
# Ref. C2
a = 4.409 / 10.0 #nm
c = 6.251 / 10.0 #nm
from genice.cell import cellvectors
cell = cellvectors(a, a, c)
# helper routines to make from CIF-like data
from genice import CIF
atomd = CIF.atomdic(atoms)
atoms = CIF.fullatoms(atomd, CIF.symmetry_operators(symops))
cagetype = []
cagepos = []
for name, pos in pick_atoms(atoms, ("Ne1", ), repeat=(2, 2, 2)):
cagetype.append(name)
cagepos.append(pos)
waters, pairs = CIF.waters_and_pairs(cell,
atomd,
CIF.symmetry_operators(symops),
rep=(2, 2, 2))
density = 18 * len(waters) / 6.022e23 / (np.linalg.det(cell) * 1e-21)
coord = "relative"
def argparser(arg):
global pairs, fixed, waters, coord, density, cell, cagetype, cagepos
logger = getLogger()
# Ref. Ih
atoms="""
O1 0.0000 0.6699 0.0488
O2 0.0000 0.3377 -0.0557
Ne1 0.0000 0.0013 0.7539
"""
# Ref. Ih
# space group: Cmc2_1
symops="""
x, y, z
-x, y, z
x, -y, 1/2+z
-x, -y, 1/2+z
x+1/2, y+1/2, z
-x+1/2, y+1/2, z
x+1/2, -y+1/2, 1/2+z
-x+1/2, -y+1/2, 1/2+z
""".replace(',', ' ')
# Ref. Ih
a=4.568 / 10.0 #nm
b=7.980 / 10.0 #nm
c=6.894 / 10.0 #nm
from genice.cell import cellvectors
cell = cellvectors(a,b,c)
# helper routines to make from CIF-like data
from genice import CIF
atomd = CIF.atomdic(atoms)
atoms = CIF.fullatoms(atomd, CIF.symmetry_operators(symops))
cagetype = []
cagepos = []
for name, pos in pick_atoms(atoms, ("Ne1",), repeat=(2,1,1)):
cagetype.append(name)
cagepos.append(pos)
waters, pairs = CIF.waters_and_pairs(cell, atomd, CIF.symmetry_operators(symops), rep=(2,1,1))
density = 18*len(waters)/6.022e23 / (np.linalg.det(cell)*1e-21)
coord = "relative"
def argparser(arg):
global pairs, fixed, waters, coord, density, cell
logger = getLogger()
# Ref. 2atom
atoms="""
O1 0.2716 0.0259 -0.1471
O2 0.4798 0.7571 0.3389
D1 0.7284 0.4038 0.4034
D2 0.1491 0.0412 -0.2023
D3 0.7420 0.1978 0.3708
D4 0.4232 0.1954 -0.0164
"""
# Ref. 2cell
# space group: R-3
symops="""
x, y, z
z, x, y
y, z, x
-x, -y, -z
-z, -x, -y
-y, -z, -x
""".replace(',', ' ')
# Ref. 2cell
a=7.78 / 10.0 #nm
A=113.1
from genice.cell import cellvectors
cell = cellvectors(a,a,a,A,A,A)
# helper routines to make from CIF-like data
from genice import CIF
atomd = CIF.atomdic(atoms)
sops = CIF.symmetry_operators(symops)
waters, fixed = CIF.waters_and_pairs(cell, atomd, sops)
# set pairs in this way for hydrogen-ordered ices.
pairs = fixed
import numpy as np
density = 18*len(waters)/6.022e23 / (np.linalg.det(cell)*1e-21)
coord = "relative"
def argparser(arg):
global pairs, fixed, waters, coord, density, cell, cagetype, cagepos
logger = getLogger()
# Ref. 2atom
atoms="""
O1 0.2342 0.4721 0.8019
O2 0.7648 0.5306 0.2941
Ne1 -0.0647 0.7868 0.7669
"""
# Ref.
# space group: P3_2
symops="""
x, y, z
-y,x-y,z+2/3
-x+y,-x,z+1/3
""".replace(',', ' ')
# Ref. 2cell
a=6.177 / 10.0 #nm
c=6.054 / 10.0 #nm
C=120.0
from genice.cell import cellvectors
cell = cellvectors(a,a,c,C=C)
# helper routines to make from CIF-like data
from genice import CIF
atomd = CIF.atomdic(atoms)
atoms = CIF.fullatoms(atomd, CIF.symmetry_operators(symops))
cagetype = []
cagepos = []
for atomname, pos in atoms:
if atomname == "Ne1":
cagetype.append(atomname)
cagepos.append(pos)
waters, pairs = CIF.waters_and_pairs(cell, atomd, CIF.symmetry_operators(symops))
density = 18*len(waters)/6.022e23 / (np.linalg.det(cell)*1e-21)
coord = "relative"
symops = """
x y z
1/2+x 1/2-y -z
1/2-x 1/2+y -z
-x -y z
"""
# in nm
a, b, c = 0.7176, 0.4428, 0.5040
from genice.cell import cellvectors
cell = cellvectors(a, b, c)
# helper routines to make from CIF-like data
from genice import CIF
atomd = CIF.atomdic(atoms)
sops = CIF.symmetry_operators(symops)
# the unit cell is too small to handle; multiply (2,2,2)
waters, fixed = CIF.waters_and_pairs(cell, atomd, sops, rep=(2, 2, 2))
# set pairs in this way for hydrogen-ordered ices.
pairs = fixed
import numpy as np
density = 18 * len(waters) / 6.022e23 / (np.linalg.det(cell) * 1e-21)
coord = "relative"
def argparser(arg):
global pairs, fixed, waters, coord, density, cell, cagepos, cagetype
logger = getLogger()
# Ref. C1
atoms="""
O1 0.2228 0.1966 0.0454
O2 0.5236 0.8974 0.1466
H1 0.8184 0.5344 0.3198
H2 0.2244 0.2188 0.2045
H3 0.4384 0.8815 0.1496
H4 0.5729 -0.0253 0.2297
Ne1 0.0000 0.0000 0.7361
"""
# Ref. C1
# space group: R-3 No. 148
# in a rhombus cell
symops="""
x, y, z
-y, x-y, z
-x+y, -x, z
-x, -y, -z
y, -x+y, -z
x-y, x, -z
x+2/3, y+1/3, z+1/3
-y+2/3, x-y+1/3, z+1/3
-x+y+2/3, -x+1/3, z+1/3
-x+2/3, -y+1/3, -z+1/3
y+2/3, -x+y+1/3, -z+1/3
x-y+2/3, x+1/3, -z+1/3
x+1/3, y+2/3, z+2/3
-y+1/3, x-y+2/3, z+2/3
-x+y+1/3, -x+2/3, z+2/3
-x+1/3, -y+2/3, -z+2/3
y+1/3, -x+y+2/3, -z+2/3
x-y+1/3, x+2/3, -z+2/3
""".replace(',', ' ')
# Ref. C1
a=12.673 / 10.0 #nm
c= 6.017 / 10.0 #nm
C= 120
from genice.cell import cellvectors
cell = cellvectors(a,a,c,C=C)
# helper routines to make from CIF-like data
from genice import CIF
atomd = CIF.atomdic(atoms)
atoms = CIF.fullatoms(atomd, CIF.symmetry_operators(symops))
cagetype = []
cagepos = []
for name, pos in pick_atoms(atoms, ("Ne1",)):
cagetype.append(name)
cagepos.append(pos)
sops = CIF.symmetry_operators(symops)
waters, fixed = CIF.waters_and_pairs(cell, atomd, sops)
# set pairs in this way for hydrogen-ordered ices.
pairs = fixed
density = 18*len(waters)/6.022e23 / (np.linalg.det(cell)*1e-21)
coord = "relative"