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 Ncyl, coord, cell, waters, fixed
assert re.match("^[0-9]+$", arg) is not None, "Argument must be an integer."
Ncyl = int(arg)
logger.info("Superlattice {0}xFAU".format(Ncyl))
dec = decorate(waters1c, cell1c, pairs1c, Ncyl)
coord='relative'
cell = cellvectors(a=dec.cell[0,0],
b=dec.cell[1,1],
c=dec.cell[2,2])
waters = dec.vertices
fixed = dec.fixedEdges
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"
def argparser(arg):
global sides, rows, bondlen, density, cell, waters, coord
a = [int(x) for x in arg.split(",")]
if len(a) > 0:
sides = a[0]
if len(a) > 1:
rows = a[1]
L = 2.75
bondlen = 3
R = L / 2 / sin(pi / sides)
density = sides * rows / (L**3 * 400 * rows) * 18 / 6.022e23 * 1e24
waters = []
for j in range(rows):
for i in range(sides):
x = R * cos(i * pi * 2 / sides)
y = R * sin(i * pi * 2 / sides)
z = j * L
waters.append([x, y, z])
coord = "absolute"
cell = cellvectors(a=L * 20, b=L * 20, c=L * rows)
15 0.5 0.14668 0.81207
15 0.5 0.85332 0.31207
15 0.0 0.64668 0.81207
15 0.0 0.35332 0.31207
12 0.23619 0.10832 0.46142
12 0.76381 0.89168 0.96142
12 0.23619 0.89168 0.96142
12 0.73619 0.60832 0.46142
12 0.76381 0.10832 0.46142
12 0.26381 0.39168 0.96142
12 0.73619 0.39168 0.96142
12 0.26381 0.60832 0.46142
12 0.5 0.24977 0.2145
12 0.5 0.75023 0.7145
12 0.0 0.74977 0.2145
12 0.0 0.25023 0.7145
"""
bondlen = 3
cell = """
16.277534865206228 114.43420763235943 21.692280574253285
"""
density = 0.33732372106521624
from genice.cell import cellvectors
cell = cellvectors(a=16.277534865206228,
b=114.43420763235943,
c=21.692280574253285)
12 0.0 0.5 0.0
12 0.0 -0.5 0.5
16 0.0 0.0 0.09294
16 0.0 0.0 -0.59294
12 0.15661 -0.15661 0.75
16 0.66667 0.33333 -0.15626
12 0.66667 0.33333 0.1269
12 -0.31322 -0.15661 0.75
12 -0.5 -0.5 0.0
16 -0.33333 -0.66667 0.65626
16 -0.66667 -0.33333 -0.65626
12 -0.33333 -0.66667 -0.6269
"""
bondlen = 3
cell = """
13.698097440028898 0.0 0.0
-6.849048720014445 11.862900366579614 0.0
2.7457556179095828e-15 4.755788235387074e-15 44.84159220146225
"""
density = 0.5578770598708237
from genice.cell import cellvectors
cell = cellvectors(a=13.698097440028898,
b=13.6980974400289,
c=44.84159220146225,
C=119.99999999999999)
# coding: utf-8
#This is not useful for generating the graph
density = 0.92 #default density
bondlen = 3 #bond threshold
cell = """
4.5328691711 7.84813412606925 7.37735062301457
"""
waters = """
0.25 0.333 0.125
0.75 0.833 0.125
0.25 0.667 0.25
0.75 0.167 0.25
0.25 0.667 0.625
0.75 0.167 0.625
0.75 0.833 0.75
0.25 0.333 0.75
"""
coord = "relative"
from genice.cell import cellvectors
cell = cellvectors(a=4.5328691711,
b=7.84813412606925,
c=7.37735062301457)
12 0.24555 -0.5 -0.07155
12 0.0 -0.23102 -0.22147
16 0.0 0.5 0.15428
14 0.26723 0.0 -0.39814
12 0.5 0.24555 0.07155
14 -0.26723 0.0 -0.39814
16 0.5 0.0 -0.15428
12 0.5 0.0 0.40317
16 0.0 0.0 0.0
12 0.0 -0.5 -0.40317
14 0.0 0.26723 0.39814
15 0.5 -0.5 -0.2849
12 0.0 0.23102 -0.22147
12 -0.5 -0.24555 0.07155
15 0.5 0.5 0.2849
12 -0.24555 0.5 -0.07155
"""
bondlen = 3
cell = """
13.206829585688627 13.206829585688627 31.824243573568793
"""
density = 0.6138770078065939
from genice.cell import cellvectors
cell = cellvectors(a=13.206829585688627,
b=13.206829585688627,
c=31.824243573568793)
8.7032 9.5286 3.5978 2.0782 5.7037 1.5336 8.7032 1.8787 5.6619 1.1806 2.8746 3.5978 1.1806 10.5245 1.5336 7.8056 6.6995 5.6619 4.0795 11.1616 3.5978 10.7045 7.3367 1.5336 4.0795 3.5118 5.6619 5.0223 21.4810 1.7001 11.6473 17.6561 5.8284 12.5450 20.4852 3.7643 5.9200 16.6603 1.7001 12.5450 12.8353 5.8284 9.6461 12.1981 3.7643 9.6461 19.8480 1.7001 3.0211 16.0231 5.8284 2.0782 21.0035 3.5978 8.7032 17.1785 1.5336 2.0782 13.3536 5.6619 7.8056 14.3494 3.5978 7.8056 21.9993 1.5336 1.1806 18.1744 5.6619 10.7045 22.6365 3.5978 4.0795 18.8115 1.5336 10.7045 14.9866 5.6619 """ from genice.cell import cellvectors cell = cellvectors(a=13.25, b=22.9496665056, c=6.19244244367)
12 0.5 1.25 -0.20232
15 0.5 1.25 1.01482
14 0.0 -0.25 -0.42811
15 0.0 -0.25 -0.26482
12 0.5 -0.25 0.65095
14 0.0 0.01781 0.20424
14 0.0 0.50227 -0.90152
12 0.0 0.75 0.40095
12 0.0 1.25 0.70232
14 0.0 0.75 0.67811
14 0.5 0.25 0.07189
15 0.5 0.25 0.23518
12 0.0 0.25 0.15095
12 0.5 0.25 0.45232
14 0.73219 1.25 0.95424
12 0.0 0.0 0.0
"""
bondlen = 3
cell = """
12.877303192396422 12.877303192396422 121.54450994600208
"""
density = 0.6465960600253263
from genice.cell import cellvectors
cell = cellvectors(a=12.877303192396422,
b=12.877303192396422,
c=121.54450994600208)
12 -0.5 -0.32746 0.79334
12 0.5 0.32746 0.29334
12 0.0 0.42418 0.30451
14 -0.5 -0.64149 0.68373
15 1.0 0.59186 0.18695
15 0.0 -0.04137 1.17099
12 -0.24833 0.21522 1.05404
16 -0.5 -0.70952 0.92996
12 0.24833 -0.21522 0.55404
12 0.0 0.44768 0.99228
12 -0.24833 -0.21522 0.55404
12 0.5 0.17079 0.31306
12 -0.5 -0.05232 0.99228
"""
bondlen = 3
cell = """
15.106429533183366 98.03113793959956 21.936018274703592
"""
density = 0.41957820843744786
from genice.cell import cellvectors
cell = cellvectors(a=15.106429533183366,
b=98.03113793959956,
c=21.936018274703592)
0.3881 0.0000 0.8186
0.3881 0.3881 0.8186
0.0000 0.6119 0.8186
0.6119 0.0000 0.8186
0.3881 0.3881 0.6815
0.0000 0.6119 0.6815
0.6119 0.0000 0.6815
0.6119 0.6119 0.6815
1.0000 0.3881 0.6815
0.3881 0.0000 0.6815
0.7914 0.5827 0.8877
0.7913 0.2086 0.8877
0.4173 0.2087 0.8877
0.2086 0.4173 0.8877
0.2087 0.7914 0.8877
0.5827 0.7913 0.8877
0.2086 0.4173 0.6123
0.2087 0.7914 0.6123
0.5827 0.7913 0.6123
0.7914 0.5827 0.6123
0.7913 0.2086 0.6123
0.4173 0.2087 0.6123
"""
from genice.cell import cellvectors
cell = cellvectors(a=12.4212113964,
b=12.421211396338748,
c=10.0656455142*2,
C=120.0000000000566)
12 0.0 0.25245 0.4904
15 0.5 0.55839 0.35892
14 1.0 0.85793 0.11745
12 -0.27446 -0.46724 0.6799
12 -0.27446 0.46724 1.1799
14 -0.23774 -0.17574 0.73903
12 0.5 0.00984 0.92661
14 -0.23774 0.17574 1.23903
12 0.27446 0.46724 0.1799
12 0.0 0.49016 0.42661
14 -0.5 -0.29248 0.86608
16 1.0 0.92258 0.49254
12 0.5 0.07394 0.17845
16 0.0 0.07742 0.99254
14 0.0 0.20752 0.86608
14 0.0 0.28704 0.11292
"""
bondlen = 3
cell = """
14.905144573524241 67.5212848021559 21.91947448011618
"""
density = 0.4335854541833566
from genice.cell import cellvectors
cell = cellvectors(a=14.905144573524241,
b=67.5212848021559,
c=21.91947448011618)
12 0.0000 0.7500 0.2500
12 0.2500 0.7500 0.0000
12 0.7500 0.2500 0.0000
12 0.7500 0.0000 0.2500
12 0.5000 0.7500 0.7500
12 0.7500 0.7500 0.5000
16 0.6250 0.1250 0.6250
16 0.1250 0.6250 0.6250
16 0.8750 0.3750 0.3750
16 0.3750 0.8750 0.3750
16 0.3750 0.3750 0.8750
16 0.6250 0.6250 0.1250
16 0.8750 0.8750 0.8750
16 0.1250 0.1250 0.1250
"""
from genice import FrankKasper
from genice.genice import parse_cages
from genice.cell import cellvectors
cell = cellvectors(a=12.747893943706936,
b=12.747893943706936,
c=12.747893943706936)
cagepos, cagetype = parse_cages(cages)
waters = [w for w in FrankKasper.toWater(cagepos, cell)]
coord = "relative"
density = FrankKasper.estimate_density(waters, cell, 2.76)
bondlen = 2.76*1.1
cages = """ 12 0.5000 0.2500 0.2500 12 0.5000 0.5000 0.5000 12 0.2500 0.5000 0.2500 12 0.0000 0.2500 0.7500 12 0.2500 0.0000 0.7500 12 0.0000 0.5000 0.0000 12 0.2500 0.2500 0.5000 12 0.5000 0.0000 0.0000 12 0.7500 0.5000 0.7500 12 0.0000 0.0000 0.5000 12 0.0000 0.7500 0.2500 12 0.2500 0.7500 0.0000 12 0.7500 0.2500 0.0000 12 0.7500 0.0000 0.2500 12 0.5000 0.7500 0.7500 12 0.7500 0.7500 0.5000 16 0.6250 0.1250 0.6250 16 0.1250 0.6250 0.6250 16 0.8750 0.3750 0.3750 16 0.3750 0.8750 0.3750 16 0.3750 0.3750 0.8750 16 0.6250 0.6250 0.1250 16 0.8750 0.8750 0.8750 16 0.1250 0.1250 0.1250 """ from genice.cell import cellvectors cell = cellvectors(a=6.20577, b=6.20577, c=6.20577)
0.6197999999999996 0.8098000000000001 0.05545000000000045
0.6197999999999995 0.8098000000000001 0.5554500000000006
0.05980000000000009 0.36979999999999963 0.30545000000000044
0.05980000000000016 0.3697999999999996 0.8054500000000004
0.05980000000000009 0.8697999999999997 0.30545000000000044
0.05980000000000005 0.8697999999999996 0.8054500000000004
0.5598000000000001 0.36979999999999963 0.30545000000000044
0.5598000000000001 0.3697999999999996 0.8054500000000004
0.5598 0.8697999999999997 0.30545000000000044
0.5597999999999999 0.8697999999999996 0.8054500000000004
0.19019999999999992 0.44454999999999956 0.3802000000000003
0.19019999999999992 0.44454999999999956 0.8802000000000003
0.19019999999999992 0.9445499999999996 0.3802000000000003
0.1901999999999998 0.9445499999999996 0.8802000000000003
0.6901999999999997 0.44454999999999956 0.3802000000000003
0.6901999999999999 0.44454999999999956 0.8802000000000003
0.6901999999999999 0.9445499999999996 0.3802000000000003
0.6901999999999998 0.9445499999999996 0.8802000000000003
"""
coord = "relative"
bondlen = 3
density = 1.3072141048893433
from genice.cell import cellvectors
cell = cellvectors(a=15.070097094562836,
b=15.070097094562836,
c=15.070097094562838,
A=70.1,
B=70.1,
C=70.1)
9 15 11 13 11 14 12 14 12 13 13 15 14 8 8 10 15 10 12 10 8 16 11 19 12 20 15 23 17 16 17 19 17 23 19 21 19 22 20 22 20 21 21 23 22 16 16 18 23 18 20 18 """ from genice.cell import cellvectors cell = cellvectors(a=6.928203230275509, b=6.0, c=14.14213562373095)
16 -0.49949 0.75 -0.42264
12 0.11678 0.25 0.6354
15 0.25 0.75 0.10761
15 0.75 0.25 0.301
12 -0.25 -0.00053 -0.48213
14 0.75 0.25 0.06924
12 0.01029 -0.48246 -0.19046
12 -0.01029 -0.98246 0.19046
15 0.41593 0.25 0.01159
15 -0.25 1.25 -0.10761
16 0.49949 0.25 0.42264
12 0.25 0.25 0.82812
12 0.51029 0.01754 0.19046
12 -0.12215 1.25 -0.33614
12 -0.25 0.75 -0.82812
12 -0.51029 -0.01754 -0.19046
"""
bondlen = 3
cell = """
26.304377127143944 14.227456687621972 34.12719015977335
"""
density = 0.5055099148935727
from genice.cell import cellvectors
cell = cellvectors(a=26.304377127143944,
b=14.227456687621972,
c=34.12719015977335)
12 -0.5 -0.24539 0.2047
15 0.5 0.5 0.0711
12 -0.22799 0.0 -0.11019
15 -0.5 0.5 -0.0711
12 0.5 0.24539 0.2047
16 0.0 0.5 0.15388
12 0.24539 0.5 -0.7047
14 -0.28877 0.0 0.5
12 0.0 0.5 0.5
12 0.24539 -0.5 0.7047
16 0.5 0.0 -0.65388
15 -0.5 0.5 0.5711
12 0.0 0.22799 -0.61019
"""
bondlen = 3
cell = """
13.461566776635882 13.461566776635882 51.46652347023254
"""
density = 0.5832934360403821
from genice.cell import cellvectors
cell = cellvectors(a=13.461566776635882,
b=13.461566776635882,
c=51.46652347023254)
12 0.4534 0.42903 0.14753
12 0.2201 0.14011 -0.07108
14 0.07396 0.3201 -0.24488
12 -0.46584 0.45429 -0.11922
14 0.2445 0.23866 0.20316
12 -0.4534 0.92903 0.35247
16 -0.40992 -0.26928 -0.20675
12 -0.7201 0.85989 0.42892
16 -0.09008 1.26928 0.29325
14 -0.41351 0.89688 0.07663
12 0.10225 0.04853 0.36374
15 0.34771 -0.3184 0.99555
12 0.03416 0.04571 0.11922
14 -0.08649 0.10312 -0.42337
14 0.32485 -0.48232 0.70666
12 -0.0466 0.07097 -0.14753
"""
bondlen = 3
cell = """
25.610527765228145 26.685332528187622 26.68240066618309
"""
density = 0.5245243856482863
from genice.cell import cellvectors
cell = cellvectors(a=25.610527765228145,
b=26.685332528187622,
c=26.68240066618309)
15 0.22864 0.65382 0.25
12 0.92551 0.24446 -0.25
12 0.35308 0.5 0.0
14 0.6333 0.12928 -0.25
15 0.27136 -0.15382 -0.25
16 0.0 0.11825 0.25
12 0.0 -0.5 0.5
16 0.0 -0.11825 0.75
15 0.77136 0.65382 0.25
12 0.14692 0.0 -0.5
16 0.5 0.38175 0.75
12 -0.42551 0.25554 0.25
12 -0.14692 0.0 0.5
12 0.42551 0.25554 0.25
12 -0.42551 -0.25554 0.75
15 0.27136 0.15382 0.25
"""
bondlen = 3
cell = """
49.88351534567095 17.84622037904867 13.527667556276105
"""
density = 0.565900889084785
from genice.cell import cellvectors
cell = cellvectors(a=49.88351534567095,
b=17.84622037904867,
c=13.527667556276105)
11.9564748463 5.28656809283 10.0048601303 1.38333866068 10.0048601303 5.28656809283 8.05324541418 3.33495337675 11.9564748463 3.33495337675 8.05324541418 1.38333866068 10.0048601303 1.38333866068 8.05324541418 5.28656809283 11.9564748463 10.0048601303 11.9564748463 5.28656809283 3.33495337675 1.38333866068 10.0048601303 8.05324541418 8.05324541418 3.33495337675 1.38333866068 3.33495337675 8.05324541418 11.9564748463 10.0048601303 1.38333866068 5.28656809283 8.05324541418 11.9564748463 3.33495337675 1.38333866068 5.28656809283 10.0048601303 11.9564748463 10.0048601303 5.28656809283 5.28656809283 3.33495337675 11.9564748463 10.0048601303 8.05324541418 1.38333866068 3.33495337675 1.38333866068 8.05324541418 8.05324541418 11.9564748463 10.0048601303 1.38333866068 5.28656809283 3.33495337675 11.9564748463 10.0048601303 8.05324541418 5.28656809283 3.33495337675 1.38333866068 10.0048601303 8.05324541418 11.9564748463 3.33495337675 1.38333866068 5.28656809283 """ coord = "absolute" bondlen = 3 density = 0.604398971981 from genice.cell import cellvectors cell = cellvectors(a=13.339813507, b=13.339813507, c=13.339813507)
12 0.0 0.5 0.60564
12 0.5 0.0 0.39436
12 0.0 0.5 0.89436
12 0.5 0.0 0.89436
12 0.0 0.5 0.39436
12 0.5 0.0 0.60564
12 0.5 0.0 0.10564
15 0.13956 0.13956 0.5
15 0.86044 0.86044 0.5
15 0.36044 0.63956 0.0
15 0.63956 0.36044 0.0
14 0.0 0.0 0.04905
14 0.5 0.5 0.54905
14 0.5 0.5 0.45095
14 0.0 0.0 0.95095
"""
bondlen = 3
cell = """
15.612917728598969 15.612917728598969 93.43202863446575
"""
density = 0.24148249589841608
from genice.cell import cellvectors
cell = cellvectors(a=15.612917728598969,
b=15.612917728598969,
c=93.43202863446575)
bondlen = 0.4 #bond threshold cell = """ 1.0 1.0 0.94 """ waters = """ 0.16666 0.16666 0.0 0.16666 0.16666 0.47 0.16666 0.83333 0.0 0.16666 0.83333 0.47 0.83333 0.16666 0.0 0.83333 0.16666 0.47 0.83333 0.83333 0.0 0.83333 0.83333 0.47 0.33333 0.33333 0.235 0.33333 0.33333 0.705 0.33333 0.66666 0.235 0.33333 0.66666 0.705 0.66666 0.33333 0.235 0.66666 0.33333 0.705 0.66666 0.66666 0.235 0.66666 0.66666 0.705 """ coord = "absolute" from genice.cell import cellvectors cell = cellvectors(a=1.0, b=1.0, c=0.94)
12 0.0 0.13639 -0.27339
14 -0.2873 0.0 0.5
16 0.0 -0.31111 0.5
12 0.25 0.25 0.0
12 -0.5 0.36361 -0.27339
12 -0.25 0.25 0.0
14 0.2873 0.0 0.5
12 0.5 0.5 0.0
12 0.0 0.13639 0.27339
16 0.0 0.31111 0.5
12 -0.5 -0.36361 -0.27339
15 0.5 0.91311 0.0
12 0.5 0.36361 0.27339
"""
bondlen = 3
cell = """
13.57394342524781 42.02206158541215 13.401283360817141
"""
density = 0.578713601239932
from genice.cell import cellvectors
cell = cellvectors(a=13.57394342524781,
b=42.02206158541215,
c=13.401283360817141)
12 0.07594 0.86787 -0.44698
14 0.45156 0.83579 -0.29458
15 -0.32306 -0.26031 0.05674
12 1.17531 0.31106 -0.30253
14 0.18931 0.58602 -0.42468
12 -0.31657 -0.5518 0.1732
14 0.81069 0.41398 -0.42468
14 -0.04844 -0.33579 0.29458
12 -0.67531 -0.18894 0.30253
12 -0.42406 -0.36787 0.44698
12 0.81657 -0.0518 -0.1732
12 -0.17531 0.68894 -0.30253
12 0.31657 0.5518 0.1732
12 0.18343 1.0518 -0.1732
14 0.04844 0.33579 0.29458
12 0.67531 0.18894 0.30253
"""
bondlen = 3
cell = """
17.918034918814932 25.85585726509846 19.94194341745186
"""
density = 0.51764847234306
from genice.cell import cellvectors
cell = cellvectors(a=17.918034918814932,
b=25.85585726509846,
c=19.94194341745186)
"""
# P2_1 2_1 2
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)
12 -0.25 0.75 -0.25
15 0.0 1.25 -0.10599
12 0.5 1.0 0.5
15 0.0 1.25 -0.22092
12 -0.27345 0.75 -0.07333
12 0.5 1.25 0.33882
14 0.5 -0.03468 0.16167
16 0.5 0.75 1.03964
14 0.0 0.53468 0.33833
12 0.25 0.25 0.25
12 0.0 0.0 0.0
14 0.5 1.53468 0.16167
15 0.5 1.75 0.27908
"""
bondlen = 3
cell = """
13.381639854230002 13.612318076820417 65.1514368338849
"""
density = 0.5742502288858397
from genice.cell import cellvectors
cell = cellvectors(a=13.381639854230002,
b=13.612318076820417,
c=65.1514368338849)
