def hook6(lattice):
global nwateratoms
lattice.logger.info("Hook6: Output water molecules in Yaplot format.")
lattice.logger.info(" Total number of atoms: {0}".format(
len(lattice.atoms)))
# prepare the reverse dict
waters = defaultdict(dict)
for atom in lattice.atoms:
resno, resname, atomname, position, order = atom
if "O" in atomname:
waters[order]["O"] = position
elif "H" in atomname:
if "H0" not in waters[order]:
waters[order]["H0"] = position
else:
waters[order]["H1"] = position
s = ""
s += yp.Color(3)
for order, water in waters.items():
O = water["O"]
H0 = water["H0"]
H1 = water["H1"]
s += yp.Layer(4)
s += yp.Color(3)
s += yp.Size(0.03)
s += yp.Circle(O)
s += yp.Line(O, H0)
s += yp.Line(O, H1)
s += yp.Size(lattice.yaplot_size_H)
s += yp.Circle(H0)
s += yp.Circle(H1)
s += yp.Color(2)
s += yp.Layer(1)
s += yp.Text(O, "{0}".format(order))
s += yp.Layer(3)
s += yp.Color(4)
s += yp.ArrowType(1)
s += yp.Size(0.03)
for i, j in lattice.spacegraph.edges(data=False):
if i in waters and j in waters: # edge may connect to the dopant
O = waters[j]["O"]
H0 = waters[i]["H0"]
H1 = waters[i]["H1"]
d0 = H0 - O
d1 = H1 - O
rr0 = np.dot(d0, d0)
rr1 = np.dot(d1, d1)
if rr0 < rr1 and rr0 < 0.245**2:
s += yp.Arrow(H0, O)
if rr1 < rr0 and rr1 < 0.245**2:
s += yp.Arrow(H1, O)
print(s, end="")
nwateratoms = len(lattice.atoms)
lattice.logger.info("Hook6: end.")
def to_yaplot(cellmat, rpos, anions, cations, G, cation="N", anion="F"):
"""
cellmat: セル行列(後置記法)
rpos: 分子のセル内相対位置
anions: アニオン番号
cations: カチオン番号
G: 水素結合ネットワーク
"""
# 水分子の原子位置
water = tip4picesites()
s = ""
for mol in G:
if mol not in anions and mol not in cations:
# genuine water molecule.
rO = rpos[mol]
H1, H2 = G[mol]
rH1 = rpos[H1] - rO
rH1 -= np.floor(rH1 + 0.5)
rH2 = rpos[H2] - rO
rH2 -= np.floor(rH2 + 0.5)
# 実座標 (angstrom)
pO = rO @ cellmat
pH1 = rH1 @ cellmat
pH2 = rH2 @ cellmat
ey = pH1 - pH2
ez = pH1 + pH2
ex = np.cross(ey, ez)
# 分子内座標方向の単位ベクトル
ex /= np.linalg.norm(ex)
ey /= np.linalg.norm(ey)
ez /= np.linalg.norm(ez)
# 回転行列
R = np.array([ex, ey, ez])
# 水分子の原子位置
intra = water @ R + pO
s += draw_water(intra)
s += yp.Layer(3)
s += yp.Size(0.5)
s += yp.Color(6)
for mol in G:
if mol in anions:
pos = rpos[mol] @ cellmat
s += yp.Circle(pos)
s += yp.Size(0.3)
s += yp.Color(7)
for mol in G:
if mol in cations:
pos = rpos[mol] @ cellmat
s += yp.Circle(pos)
s += yp.NewPage()
return s
def hook7(lattice):
global nwateratoms
lattice.logger.info("Hook7: Output water molecules in Yaplot format.")
lattice.logger.info(" Total number of atoms: {0}".format(
len(lattice.atoms)))
gatoms = lattice.atoms[nwateratoms:]
palettes = dict()
s = ""
s += yp.Layer(4)
s += yp.ArrowType(1)
H = []
O = ""
for atom in gatoms:
resno, resname, atomname, position, order = atom
if atomname in palettes:
pal = palettes[atomname]
else:
pal = 4 + len(palettes)
palettes[atomname] = pal
s += yp.Color(pal)
s += yp.Size(0.04)
s += yp.Circle(position)
s = '#' + "\n#".join(lattice.doc) + "\n" + s
print(s)
lattice.logger.info("Hook7: end.")
def draw_water(water, povray=False):
s = ""
if povray:
s += pov.Sphere(water[0], r="RH", material="MATH")
s += pov.Sphere(water[1], r="RH", material="MATH")
s += pov.Sphere(water[2], r="RO", material="MATO")
s += pov.Cylinder(water[0], water[2], r="ROH", material="MATOH")
s += pov.Cylinder(water[1], water[2], r="ROH", material="MATOH")
else:
s += yp.Layer(1)
s += yp.Color(5)
s += yp.Size(0.2)
s += yp.Circle(water[0])
s += yp.Circle(water[1])
s += yp.Color(4)
s += yp.Size(0.4)
s += yp.Circle(water[2])
s += yp.Color(2)
d0 = water[0] - water[2]
L0 = np.linalg.norm(d0)
s += yp.Line(water[2] + d0 / L0 * 0.4, water[0] - d0 / L0 * 0.2)
d1 = water[1] - water[2]
L1 = np.linalg.norm(d1)
s += yp.Line(water[2] + d1 / L1 * 0.4, water[1] - d1 / L1 * 0.2)
# draw a tetrahedron
y = water[1] - water[0]
z = (water[1] + water[0]) / 2 - water[2]
x = np.cross(y, z)
x /= np.linalg.norm(x)
y /= np.linalg.norm(y)
z /= np.linalg.norm(z)
com = (water[1] + water[0] + water[2] * 16) / 18
R = 2.76 / 2
a = y * (2 / 3)**0.5 + z * (1 / 3)**0.5
b = -y * (2 / 3)**0.5 + z * (1 / 3)**0.5
c = x * (2 / 3)**0.5 - z * (1 / 3)**0.5
d = -x * (2 / 3)**0.5 - z * (1 / 3)**0.5
s += yp.Layer(2)
for e, f in it.combinations((a, b, c, d), 2):
s += yp.Line(com + e * R, com + f * R)
return s
def main():
import sys
groname, twiname = sys.argv[1:3]
with open(twiname) as twifile:
with open(groname) as grofile:
while True:
if groname[-4:] == ".pdb":
gr = pdb.PDB(grofile, "O", "H", resname="WAT")
else:
# assume it is gromacs
gr = gro.Gromacs(grofile, "Ow", "Hw", "Mw")
btw = btwc.load_BTWC(twifile)
if btw is None or gr is None:
break
celli = np.linalg.inv(gr.cell)
# relative coord
rs = np.array([np.dot(x, celli) for x in gr.solutes])
ro = np.array([np.dot(x, celli) for x in gr.waters])
print(len(rs))
print(len(ro))
grid = pl.determine_grid(gr.cell, 0.245)
shell1 = np.vstack(
pl.pairs_fine_hetero(rs,
ro,
0.4,
gr.cell,
grid,
distance=False))
# some solute atoms are isolated from water.
shell1s = set(shell1[:, 0])
shell1w = set(shell1[:, 1])
#show all bonds in yaplot
s = ""
for i in range(-10, 0):
s += yap.SetPalette(i + 10 + 3, 255 * (-i) // 10, 0, 0)
for i in range(11):
s += yap.SetPalette(i + 10 + 3, 0, 0, 255 * i // 10)
for b in btw:
i, j = b[0]
if i in shell1w or j in shell1w:
s += yap.Layer(1)
else:
s += yap.Layer(2)
r = abs(b[2])
sine = b[2].imag
s += yap.Size(r)
s += yap.Color(int(sine * 10) + 10 + 3)
s += yap.Circle(b[1])
print(s)
def hook2(lattice):
global nwateratoms
if lattice.yaplot_size_H > 0:
return
lattice.logger.info(
"Hook2: Output CoM of water molecules in Yaplot format.")
# prepare the reverse dict
waters = defaultdict(dict)
pos = lattice.reppositions @ lattice.repcell.mat
s = ""
for p in pos:
s += yp.Layer(4)
s += yp.Color(3)
s += yp.Size(0.03)
s += yp.Circle(p)
print(s, end="")
lattice.logger.info("Hook2: end.")
return True
def main():
basicConfig(level=INFO, format="%(levelname)s %(message)s")
logger = getLogger()
every = 1
maxval = 1.0
adjdens = False
while sys.argv[1][0] == "-":
if sys.argv[1] == "-e":
sys.argv.pop(1)
every = int(sys.argv[2])
sys.argv.pop(1)
elif sys.argv[1] == "-v":
maxval = float(sys.argv[2])
sys.argv.pop(1)
sys.argv.pop(1)
elif sys.argv[1] == "-a":
adjdens = True
sys.argv.pop(1)
else:
usage()
gcell, gatoms = LoadGRO(open(sys.argv[1])) # in AA, in AA
ucell, uatoms = LoadGRO(open(sys.argv[2])) # in AA
dens0 = gatoms.shape[0] / np.linalg.det(gcell)
dens1 = uatoms.shape[0] / np.linalg.det(ucell)
ratio = (dens1 / dens0)**(1. / 3.)
if adjdens:
logger.info(f"Scaling ratio: {ratio}")
ucell *= ratio
uatoms *= ratio
gcelli = np.linalg.inv(gcell)
ucelli = np.linalg.inv(ucell)
mode = ""
if len(sys.argv) > 3:
mode = sys.argv[3]
s = ""
s += yp.Color(2)
s += yp.Layer(1)
origin = np.zeros(3)
s += drawbox(origin, gcell, halfshift=False)
#in absolute coord
# unitatoms = np.dot(unitatoms, ucell)
#s += unitatoms)
#s = ""
nline = 0
matched = set()
palette = dict()
while True:
line = sys.stdin.readline()
if len(line) == 0:
break
nline += 1
#parse the line
cols = line.split()
if len(cols) < 13:
break
# 2018-4-9 New output format of matcher.c
msd = float(cols[0])
gcenter = gatoms[int(cols[1])].copy() #atom at the matching center
gcenter -= np.floor(gcenter @ gcelli) @ gcell
ucenter = int(cols[2])
rotmat = np.array([float(x) for x in cols[3:12]]).reshape((3, 3))
N = int(cols[12])
if len(cols) < 13 + N:
break
irot = np.linalg.inv(rotmat)
members = [int(x) for x in cols[13:N + 13]]
#draw matched box
# roll the unit cell to center (abs)
rel = uatoms - uatoms[ucenter]
rel -= np.floor(rel @ ucelli + 0.5) @ ucell
# rel to abs
Slid = rel
# rotate box
Rotucell = ucell @ rotmat
#
Boxslide = -uatoms[ucenter] @ rotmat + gcenter
# rotate atoms in the unit cell
Slidunit = (Slid @ rotmat) + gcenter
#s += yp.Color(3)
if mode == "R":
color = direction2color(rotmat[0] + rotmat[1] + rotmat[2])
elif mode == "T":
color = direction2color(rotmat[2])
else:
color = (0, 3, 0) #green
if color not in palette:
palette[color] = len(palette) + 6
s += yp.SetPalette(palette[color], color[0] * 255 // 3,
color[1] * 255 // 3, color[2] * 255 // 3)
if msd < maxval:
matched |= set(members)
if every != 0 and nline % every == 0 and msd < maxval:
s += yp.Color(palette[color])
# matched box
s += yp.Layer(4)
s += drawbox(gcenter, Rotucell, halfshift=True, diag=(mode == "R"))
# s += yp.Layer(2)
# # unit cell
# s += drawbox(Boxslide,Rotucell,halfshift=True)
s += yp.Layer(2)
#s += drawbox2(Boxslide,Rotucell)
s += yp.Layer(5)
s += yp.Size(0.3)
s += yp.Color(5)
s += drawatoms(Slidunit)
for i in range(len(Slidunit)):
g = gatoms[members[i]]
d = Slidunit[i] - gatoms[members[i]]
d -= np.floor(d @ gcelli + 0.5) @ gcell
s += yp.Line(g, g + d)
# 変位ベクトルはどうやってもうまくいかないので、やめる。
s += yp.Size(0.3)
s += yp.Color(4)
s += yp.Layer(3)
s += drawatoms(gatoms, members=matched)
print(s) # end of frame
def depolarize(spaceicegraph, cell, draw=None):
"""
Find a farthest atom (apsis) from the given atom, and
make the shortest paths between them.
It works much better than depolarize()
"""
logger = logging.getLogger()
#logger.debug(" isZ4: {0}".format(spaceicegraph.isZ4()))
#logger.debug(" defects: {0}".format(spaceicegraph.bernal_fowler_defects()))
spaceicegraph.vector_check()
s = "" # for yaplot
# TSL
# defect-defect chains
defects = []
for node in spaceicegraph.nodes():
if spaceicegraph.degree(node) != 4:
assert spaceicegraph.degree(node) < 4
defects.append(node)
logger.info(" Non Z4: {0}".format(defects))
if len(defects) > 0:
reject_count = 10
while reject_count > 0:
net_polar = spaceicegraph.net_polarization()
if np.dot(net_polar, net_polar) < 0.05**2:
break # without problem
while True:
orig = defects[random.randint(0, len(defects) - 1)]
if spaceicegraph.out_degree(orig) == 2:
break
while True:
dest = defects[random.randint(0, len(defects) - 1)]
if spaceicegraph.in_degree(dest) == 2:
break
path = shortest_path(spaceicegraph, orig, [
dest,
])
if path is None:
continue
logger.debug(" Dipole moment = {0}".format(
spaceicegraph.dipole_moment(path)))
new_net_polar = net_polar - spaceicegraph.dipole_moment(path) * 2
if np.linalg.norm(new_net_polar) < np.linalg.norm(net_polar):
if draw is not None:
s += yp.Size(0.03)
s += draw.draw_cell()
s += draw.draw_path(path)
s += yp.NewPage()
spaceicegraph.invert_path(path)
net_polar = new_net_polar
logger.info(
" Net polarization: [{0:.2f} {1:.2f} {2:.2f}]".format(
*net_polar))
reject_count = 10
else:
logger.debug(" Reject inversion")
reject_count -= 1
while True:
net_polar = spaceicegraph.net_polarization()
logger.info(
" Net polarization: [{0:.2f} {1:.2f} {2:.2f}]".format(*net_polar))
if np.dot(net_polar, net_polar) < 0.2**2:
break # without problem
if -1 <= net_polar[0] <= 1 and -1 <= net_polar[
1] <= 1 and -1 <= net_polar[2] <= 1:
logger.info(" Gave up eliminating the polarization. (2)")
break
if net_polar[0] > 1.0:
logger.debug("Depolarize +X")
axis = np.array([+1.0, 0.0, 0.0])
elif net_polar[0] < -1.0:
logger.debug("Depolarize -X")
axis = np.array([-1.0, 0.0, 0.0])
elif net_polar[1] > 1.0:
logger.debug("Depolarize +Y")
axis = np.array([0.0, +1.0, 0.0])
elif net_polar[1] < -1.0:
logger.debug("Depolarize -Y")
axis = np.array([0.0, -1.0, 0.0])
elif net_polar[2] > 1.0:
logger.debug("Depolarize +Z")
axis = np.array([0.0, 0.0, +1.0])
elif net_polar[2] < -1.0:
logger.debug("Depolarize -Z")
axis = np.array([0.0, 0.0, -1.0])
cycle = traversing_cycle(spaceicegraph, cell, axis, draw)
if cycle is not None:
edges = [(cycle[i], cycle[i + 1]) for i in range(len(cycle) - 1)]
if len(edges) != len(set(edges)):
logger.debug("The cycle is entangled.")
else:
if draw is not None:
s += yp.Size(0.03)
s += draw.draw_cell()
s += draw.draw_path(cycle)
s += yp.NewPage()
spaceicegraph.invert_path(cycle)
spaceicegraph.vector_check()
#logger.debug("isZ4: {0}".format(spaceicegraph.isZ4()))
#logger.debug("defects: {0}".format(spaceicegraph.bernal_fowler_defects()))
return s
def main():
gro = open(sys.argv[1])
box, atoms = LoadGRO(gro)
ratoms = atoms/box
cellmat = np.diag(box)
page1 = ""
page2 = ""
page3 = ""
page4 = ""
page1 += yp.Size(0.05)
grid = None
while True:
line = sys.stdin.readline() #expect *.smatch result of slide-matcher2
if len(line) == 0:
break
cols = line.split()
if len(cols)<7:
break # broken line; maybe end of the file.
i,j = [int(x) for x in cols[:2]]
rad, dx,dy,dz, rmsd = [float(x) for x in cols[2:]]
if grid is None:
grid = pairlist.determine_grid(cellmat, rad)
lastrad = rad
p,q,r = pairlist.pairs_fine(ratoms, rad, cellmat, grid, distance=True, raw=True)
g = nx.Graph()
for k,pq in enumerate(zip(p,q)):
p,q = pq
g.add_edge(p,q,length=r[k])
else:
assert lastrad == rad
d = np.array([dx,dy,dz])
if rmsd < 0.09: # 0.09 for hyper ice T
# page 1: displacement vectors
page1 += yp.Line(atoms[i], atoms[i]+d)
page1 += yp.Circle(atoms[j])
# pages 2: displacement vectors (centered)
page2 += yp.Size(0.05)
page2 += yp.Line(np.zeros(3), d)
page2 += yp.Circle(d)
page2 += yp.Text(d, "{0} {1}".format(i,j))
# page 3..: matching
s = ""
s += yp.Size(0.05)
s += yp.Layer(1)
s += yp.Color(3)
for ni in g[i]:
s += yp.Circle(atoms[ni])
s += yp.Layer(2)
s += yp.Color(4)
for nj in g[j]:
s += yp.Circle(atoms[nj]-atoms[j]+atoms[i])
page3 += s
s = ""
s += yp.Size(0.05)
s += yp.Layer(1)
s += yp.Color(3)
for ni in g[i]:
s += yp.Circle(atoms[ni]-atoms[i])
s += yp.Layer(2)
s += yp.Color(4)
for nj in g[j]:
s += yp.Circle(atoms[nj]-atoms[j])
page4 += s
page4 += yp.NewPage()
print(page1)
print(page2)
print(page3)
print(page4)