def toWater(coord, cell):
logger = logging.getLogger()
dmin = shortest_distance(coord, cell)
pairs = [
v for v in pl.pairlist_crude(coord, dmin * 1.4, cell, distance=False)
]
for vtet, dtet in tetrahedra(pairs, dmin * 1.4, coord, cell):
p = dtet[0] + (dtet[1] + dtet[2] + dtet[3]) / 4
p -= np.floor(p)
yield p
def prepare_random_graph(self, fixed):
if self.pairs is None:
self.logger.info(" Pairs are not given explicitly.")
self.logger.info(
" Start estimating the bonds according to the pair distances."
)
# make bonded pairs according to the pair distance.
# make before replicating them.
grid = pl.determine_grid(self.cell.mat, self.bondlen)
assert np.product(
grid
) > 0, "Too thin unit cell. Consider use of --rep option if the cell was made by cif2ice."
self.pairs = [
v for v in pl.pairlist_fine(self.waters,
self.bondlen,
self.cell.mat,
grid,
distance=False)
]
# Check using a simpler algorithm.
if self.logger.level <= logging.DEBUG:
pairs2 = [
v for v in pl.pairlist_crude(self.waters,
self.bondlen,
self.cell.mat,
distance=False)
]
self.logger.debug("pairs: {0}".format(len(self.pairs)))
self.logger.debug("pairs2: {0}".format(len(pairs2)))
for pair in self.pairs:
i, j = pair
assert (i, j) in pairs2 or (j, i) in pairs2
for pair in pairs2:
i, j = pair
assert (i, j) in self.pairs or (j, i) in self.pairs
graph = dg.IceGraph()
for i, j in fixed:
graph.add_edge(i, j, fixed=True)
# Fixed pairs are default.
for pair in self.pairs:
i, j = pair
if graph.has_edge(i, j) or graph.has_edge(j, i):
pass
else:
if random.randint(0, 1) == 0:
graph.add_edge(i, j, fixed=False)
else:
graph.add_edge(j, i, fixed=False)
return graph
def main():
mode = "python" #output python module for GenIce
if sys.argv[1] == "-y":
mode = "yaplot"
sys.argv.pop(1)
Ncyl = int(sys.argv[1])
#read O positions
cell, atoms = LoadAR3R(sys.stdin)
#build the network
dmin = shortest_distance(atoms, cell)
pairs = [
v for v in pl.pairlist_crude(atoms, dmin * 1.1, cell, distance=False)
]
#decorate
dec = decorate(atoms, cell, pairs, Ncyl, mode)
print(dec)
def generate_ice(lattice_type, density=-1, seed=1000, rep=(1, 1, 1), stage=3):
logger = logging.getLogger()
logger.info("Ice type: {0}".format(lattice_type))
lat = safe_import("lattice", lattice_type)
#Show the document of the module
try:
for line in lat.__doc__.splitlines():
logger.info("!!! {0}".format(line))
except:
pass
lat.waters = load_numbers(lat.waters)
logger.debug("Waters: {0}".format(len(lat.waters)))
lat.waters = lat.waters.reshape((lat.waters.size // 3, 3))
#prepare cell transformation matrix
if lat.celltype == "rect":
if type(lat.cell) is str:
lat.cell = np.fromstring(lat.cell, sep=" ")
elif type(lat.cell) is list:
lat.cell = np.array(lat.cell)
lat.cell = np.diag(lat.cell)
elif lat.celltype == "monoclinic":
if type(lat.cell) is str:
lat.cell = np.fromstring(lat.cell, sep=" ")
elif type(lat.cell) is list:
lat.cell = np.array(lat.cell)
beta = lat.cell[3] * math.pi / 180.
lat.cell = np.array(
((lat.cell[0] * 1.0, lat.cell[1] * 0.0,
lat.cell[2] * math.cos(beta)),
(lat.cell[0] * 0.0, lat.cell[1] * 1.0,
lat.cell[2] * 0.0), (lat.cell[0] * 0.0, lat.cell[1] * 0.0,
lat.cell[2] * math.sin(beta))))
lat.cell = lat.cell.transpose(
) #all the vector calculations are done in transposed manner.
elif lat.celltype == "triclinic":
"""
Put the vectors like following:
cell = "ax 0 0 bx by 0 cx cy cz"
when you define a unit cell in Lattice/
"""
if type(lat.cell) is str:
lat.cell = np.fromstring(lat.cell, sep=" ")
logger.debug(lat.cell)
elif type(lat.cell) is list:
lat.cell = np.array(lat.cell)
lat.cell = np.reshape(lat.cell, (3, 3))
#assert lat.cell[0,1] == 0 and lat.cell[0,2] == 0 and lat.cell[1,2] == 0
else:
logger.error("unknown cell type: {0}".format(lat.celltype))
sys.exit(1)
#express molecular positions in the coordinate relative to the cell
if lat.coord == "absolute":
lat.waters = np.dot(
lat.waters,
np.linalg.inv(lat.cell),
)
lat.waters = np.array(lat.waters)
random.seed(seed)
np.random.seed(seed)
#Prearranged network topology information (if available)
pairs = None
bondlen = None
try:
if type(lat.pairs) is str:
lines = lat.pairs.split("\n")
pairs = set()
for line in lines:
columns = line.split()
if len(columns) == 2:
i, j = [int(x) for x in columns]
pairs.add(frozenset([i, j]))
elif type(lat.pairs) is list:
pairs = set()
for pair in pairs:
pairs.add(frozenset(pair))
except AttributeError:
logger.info("Graph is not defined.")
#Bond length threshold
try:
bondlen = lat.bondlen
except AttributeError:
logger.info("Bond length is not defined.")
#set density
if density < 0:
density = lat.density
#scale the cell according to the (specified) density
mass = 18 #water
NB = 6.022e23
nmol = lat.waters.shape[0] #nmol in a unit cell
volume = np.linalg.det(lat.cell) #volume of a unit cell in nm**3
d = mass * nmol / (NB * volume * 1e-21)
ratio = (d / density)**(1.0 / 3.0)
lat.cell *= ratio
if bondlen is not None:
bondlen *= ratio
if True:
logger.info("Start placing the bonds.")
if pairs is None:
logger.info(" Pairs are not given explicitly.")
logger.info(
" Start estimating the bonds according to the pair distances."
)
#make bonded pairs according to the pair distance.
#make before replicating them.
grid = pl.determine_grid(lat.cell, bondlen)
pairs = pl.pairlist_fine(lat.waters,
bondlen,
lat.cell,
grid,
distance=False)
if logger.level <= logging.DEBUG:
pairs2 = pl.pairlist_crude(lat.waters,
bondlen,
lat.cell,
distance=False)
logger.debug("pairs: {0}".format(len(pairs)))
logger.debug("pairs2: {0}".format(len(pairs2)))
for pair in pairs:
i, j = pair
assert (i, j) in pairs2 or (j, i) in pairs2
for pair in pairs2:
i, j = pair
assert (i, j) in pairs or (j, i) in pairs
logger.info(" End estimating the bonds.")
shuffled_pairs = []
for pair in pairs:
i, j = pair
if random.randint(0, 1) == 0:
i, j = j, i
shuffled_pairs.append((i, j))
graph = dg.IceGraph()
graph.register_pairs(shuffled_pairs)
logger.info("End placing the bonds.")
#replicate water molecules to make a repeated cell
reppositions = replicate(lat.waters, rep)
#scale the cell
for d in range(3):
lat.cell[:, d] *= rep[d]
result = {
"positions": reppositions,
"cell": lat.cell,
"celltype": lat.celltype,
"bondlen": bondlen
}
if stage == 0:
return result
#return reppositions, None, None, lat.cell, lat.celltype, bondlen
#replicate the graph
#This also shuffles the bond directions
graph = replicate_graph(graph, lat.waters, rep)
result["graph"] = graph
if stage == 1:
return result
#Test
undir = graph.to_undirected()
for node in range(undir.number_of_nodes()):
if node not in undir:
logger.debug("z=0 at {0}".format(node))
else:
z = len(undir.neighbors(node))
if z != 4:
logger.debug("z={0} at {1}".format(z, node))
if graph.number_of_edges() != len(reppositions) * 2:
logger.info(
"Inconsistent number of HBs {0} for number of molecules {1}.".
format(graph.number_of_edges(), len(reppositions)))
return result
#make them obey the ice rule
logger.info("Start making the bonds obey the ice rules.")
graph.purge_ice_defects()
logger.info("End making the bonds obey the ice rules.")
if stage == 2:
result["graph"] = graph
return result
#Rearrange HBs to purge the total dipole moment.
logger.info("Start depolarization.")
double_net_test = True
try:
if lat.double_network:
double_net_test = (rep[0] % 2 == 0) and (rep[1] % 2
== 0) and (rep[2] % 2
== 0)
except:
pass #just ignore.
if not double_net_test:
logger.error(
"In making the ice structure having the double network (e.g. ices 6 and 7), all the repetition numbers (--rep) must be even."
)
sys.exit(1)
spacegraph = dg.SpaceIceGraph(graph, coord=reppositions)
draw = dg.YaplotDraw(reppositions, lat.cell, data=spacegraph)
yapresult = dg.depolarize(spacegraph, lat.cell, draw=draw)
logger.info("End depolarization.")
#determine the orientations of the water molecules based on edge directions.
rotmatrices = orientations(reppositions, spacegraph, lat.cell)
result["rotmatrices"] = rotmatrices
result["graph"] = spacegraph
result["yaplot"] = yapresult
if stage == 3:
return result