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 hook2(lattice):
logger = getLogger()
logger.info("Hook2: Show rings in Yaplot format.")
# copied from svg_poly
graph = nx.Graph(lattice.graph) #undirected
cellmat = lattice.repcell.mat
s = ""
s += yp.Layer(2)
s += yp.Color(0)
for i, j in graph.edges():
pi, pj = lattice.reppositions[i], lattice.reppositions[j]
d = pj - pi
d -= np.floor(d + 0.5)
s += yp.Line(pi @ cellmat, (pi + d) @ cellmat)
for ring in cr.CountRings(graph, pos=lattice.reppositions).rings_iter(
lattice.largestring):
deltas = np.zeros((len(ring), 3))
d2 = np.zeros(3)
for k, i in enumerate(ring):
d = lattice.reppositions[i] - lattice.reppositions[ring[0]]
d -= np.floor(d + 0.5)
deltas[k] = d
comofs = np.sum(deltas, axis=0) / len(ring)
deltas -= comofs
com = lattice.reppositions[ring[0]] + comofs
com -= np.floor(com)
# rel to abs
com = np.dot(com, cellmat)
deltas = np.dot(deltas, cellmat)
s += face(com, deltas)
print(s)
logger.info("Hook2: end.")
def drawbox(origin, box, halfshift=True, diag=False):
s = ""
if halfshift:
center = (box[0] + box[1] + box[2]) / 2
ori = origin - center
else:
ori = origin
for v in (np.zeros(3), box[1], box[2], box[1] + box[2]):
s += yp.Line(v + ori, v + ori + box[0])
for v in (np.zeros(3), box[0], box[2], box[0] + box[2]):
s += yp.Line(v + ori, v + ori + box[1])
for v in (np.zeros(3), box[0], box[1], box[0] + box[1]):
s += yp.Line(v + ori, v + ori + box[2])
if diag:
s += yp.Line(ori, ori + box[0] + box[1] + box[2])
return s
def hook1(lattice):
lattice.logger.info("Hook1: Draw the cell in Yaplot format.")
s = yp.Layer(2)
x, y, z = lattice.repcell.mat
for p, q, r in ((x, y, z), (y, z, x), (z, x, y)):
for a in (np.zeros(3), p, q, p + q):
s += yp.Line(a, a + r)
print(s, end="")
lattice.logger.info("Hook1: end.")
def draw_cell(self):
s = yp.Color(2)
ex = np.array([1., 0., 0.])
ey = np.array([0., 1., 0.])
ez = np.array([0., 0., 1.])
x = np.dot(ex, self.cell)
y = np.dot(ey, self.cell)
z = np.dot(ez, self.cell)
zero = np.zeros_like(x)
for vx in (zero, x):
for vy in (zero, y):
s += yp.Line(vx + vy, vx + vy + z)
for vx in (zero, x):
for vz in (zero, z):
s += yp.Line(vx + vz, vx + y + vz)
for vz in (zero, z):
for vy in (zero, y):
s += yp.Line(vy + vz, x + vy + vz)
return s
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 draw_edge(self, i, j):
ci = self.coord[i] # 0..1
cj = self.coord[j]
d = cj - ci
d -= np.floor(d + 0.5)
xi = np.dot(ci, self.cell)
xj = np.dot(ci + d, self.cell)
if self.has_edge(i, j):
return yp.Color(4) + yp.ArrowType(2) + yp.Arrow(xi, xj)
elif self.has_edge(j, i):
return yp.Color(5) + yp.ArrowType(2) + yp.Arrow(xj, xi)
else:
return yp.Color(0) + yp.Line(xi, xj)
def yaplot(self):
maxcir = 16
maxrad = 6
# 16x6=96 color variations
s = ""
for cir in range(maxcir):
for rad in range(maxrad):
angle = cir * 360 / maxcir
hue = ((angle - 60 + 360) / 360) % 1.0
bri = rad / (maxrad - 1)
sat = sin(angle * pi / 180)**2
logging.debug((angle, sat, bri))
r, g, b = colorsys.hsv_to_rgb(hue, sat, bri)
n = cir * maxrad + rad + 3
s += yp.SetPalette(n, int(r * 255), int(g * 255), int(b * 255))
for pair, center, twist in self.iter():
if twist == 0:
# not an appropriate pair
continue
a, b = pair
d = self.relcoord[b] - self.relcoord[a]
d -= np.floor(d + 0.5)
apos = np.dot(self.relcoord[a], self.cell)
bpos = apos + np.dot(d, self.cell)
cosine = twist.real
sine = twist.imag
angle = atan2(sine, cosine) * 180 / pi
if angle < 0:
angle += 360
cir = int(angle * maxcir / 360 + 0.5)
# rad is squared.
rad = int(abs(twist)**2 * maxrad)
if cir > maxcir - 1:
cir -= maxcir
if rad > maxrad - 1:
rad = maxrad - 1
palette = cir * maxrad + rad + 3
# logging.info((abs(twist),rad,cir,palette))
s += yp.Color(palette)
s += yp.Line(apos, bpos)
s += "# angle {0} rad {1} cir {2} rad {3}\n".format(
angle, abs(twist), hue, rad)
return s
def draw_cell(voro_cell, box, kind=0):
layer = kind + 2
if layer > 30:
layer = 30
# draw frame
s = yp.Layer(layer)
s += yp.Color(0)
origin = voro_cell['original']
voro_vertices = voro_cell['vertices']
voro_faces = voro_cell['faces']
g = voro_cell['graph']
for i, j in g.edges():
di = voro_vertices[i] - origin
dj = voro_vertices[j] - origin
s += yp.Line(origin + di * 0.9, origin + dj * 0.9)
# draw faces
s += yp.Color(kind + 10)
for face in voro_faces:
points = []
for point in face['vertices']:
d = voro_vertices[point] - origin
points.append(d * 0.89 + origin)
s += yp.Polygon(points)
return s
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 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)