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"