def main():
#print(rotate([[2,0,0],[0,1,0],[0,0,1]], 90, 'y'))
#print(calc_rot_array_from_hkl(19,-24,28))
modelfile = sys.argv[1]
m = Model(modelfile)
rot_arr = calc_rot_array_from_hkl(41,60,-6)
rot(m,rot_arr)
m.write_real_xyz('temp.real.xyz')
return
# Below is a (the?) rotation matrix of Pei's t1 that gives some planes. Oriented for a specific plane ~.
#rot_arr = [ -0.977103, -0.123352, -0.173361, -0.130450, 0.990997, 0.030118, 0.168085, 0.052043, -0.984398 ]
#rot(m,rot_arr)
# Angles in radians
# Note that these are semi difficult to figure out from the vesta rotation matrix,
# partly because there are negative angles, so you may need to do 2pi - angle you found.
#t1 = np.pi*2 - 0.0371505
#t2 = 0.162790
#t3 = 0
#rot_arr = calc_rot_array(m,t1,t2,t3)
#rot(m,rot_arr)
kx = -0.76094085
ky = 0.028182994
kz = -0.648208872
t2 = np.arctan(-ky/kx)
t3 = 0.0
t1 = np.arctan( (kx*np.cos(t2)-ky*cos(t2))/kz )
t1 = 0.0
print(t1,t2,t3)
rot_arr = calc_rot_array(t1,t2,t3)
rot(m,rot_arr)
def main():
# NOTE: Cutoff can either be a single integer or it
# can be a dictionary where the keys are two-tuples
# of atomic numbers (e.g. (40,13)=3.5 for Zr,Al).
modelfile = sys.argv[1]
submodelfile = sys.argv[2]
rotatedsubmodelfile = sys.argv[3]
m = Model(modelfile)
try:
cut = 3.5 # float(sys.argv[2])
cutoff = {}
for z1 in m.atomtypes:
for z2 in m.atomtypes:
cutoff[(z1, z2)] = cut
cutoff[(z2, z1)] = cut
except:
print("You didn't input a cutoff so you much define it in the code.")
voronoi_3d(m, cutoff)
subm = Model(submodelfile)
rotsubm = Model(rotatedsubmodelfile)
for atom in subm.atoms:
if atom in m.atoms:
rotsubm.atoms[atom.id].vp = m.atoms[m.atoms.index(atom)].vp
else:
print("Couldn't find atom {0} in full model!".format(atom))
icofrac(rotsubm)
# rotsubm.write_real_xyz()
rotsubm.write_real_xyz(rotatedsubmodelfile[:-4] + ".icofrac.real.xyz")
def dodecahedron(b,save=False,filename=None):
# http://en.wikipedia.org/wiki/Dodecahedron#Regular_dodecahedron
# b is the nearest-neighbor interatomic bond distance
p = 1.61803398875 # golden ratio
b = b * 0.5 * p
coords = [[0,0,0]]
coords.append([p,0,1./p])
coords.append([-p,0,1./p])
coords.append([-p,0,-1./p])
coords.append([p,0,-1./p])
coords.append([1./p, p, 0])
coords.append([1./p, -p, 0])
coords.append([-1./p, -p, 0])
coords.append([-1./p, p, 0])
coords.append([0, 1./p, p])
coords.append([0, 1./p, -p])
coords.append([0, -1./p, -p])
coords.append([0, -1./p, p])
coords.append([1,1,1])
coords.append([1,-1,1])
coords.append([-1,-1,1])
coords.append([-1,1,1])
coords.append([-1,1,-1])
coords.append([1,1,-1])
coords.append([1,-1,-1])
coords.append([-1,-1,-1])
coords = [ [b*x for x in c] for c in coords]
m = 0
for coord in coords:
for x in coord:
if(abs(x) > m): m = abs(x)
atoms = [Atom(i,14,c[0],c[1],c[2]) for i,c in enumerate(coords)]
model = Model(comment='dodecahedron', xsize=m, ysize=m, zsize=m, atoms=atoms)
if(save):
model.write_real_xyz(model.filename)
if(filename == None):
filename = 'dodecahedron.xyz'
else:
model.filename = filename
#f = open(filename,'w')
#f.write(str(len(coords))+'\n')
#f.write('{0} {0} {0} comment\n'.format(m))
#for c in coords:
# f.write('Si ' + ' '.join([str(x) for x in c]) + '\n')
#f.close()
return model
def dump_to_modelfiles(dump,masses,base_modelname):
flag = None
for line in open(dump):
if('ITEM: TIMESTEP' in line):
if(flag):
# Save the model
comment = 'timestep {0}'.format(timestep)
lx = bounds[0]
ly = bounds[1]
lz = bounds[2]
m = Model(comment,lx,ly,lz, atoms)
m.atoms = sorted(m.atoms, key=operator.itemgetter('id'))
filename = base_modelname + '_' + str(timestep) + '.xyz'
m.write_real_xyz(filename)
flag = 'TIMESTEP'
continue
elif('ITEM: NUMBER OF ATOMS' in line):
flag = 'NUMBER OF ATOMS'
continue
elif('ITEM: BOX BOUNDS pp pp pp' in line):
flag = 'BOX BOUNDS'
bounds = []
continue
elif('ITEM: ATOMS id type xs ys zs' in line):
flag = 'ATOMS'
atoms = []
continue
if(flag == 'TIMESTEP'):
timestep = int(line.strip())
elif(flag == 'NUMBER OF ATOMS'):
natoms = int(line.strip())
elif(flag == 'BOX BOUNDS'):
bounds.append( [float(x) for x in line.strip().split()] )
bounds[-1] = sum([abs(x) for x in bounds[-1]])
elif(flag == 'ATOMS'):
line = line.strip().split()
id = int(line[0])
znum = masses[ int(line[1]) ]
x,y,z = frac_to_cart(float(line[2]), float(line[3]), float(line[4]), bounds[0],bounds[1],bounds[2])
atoms.append( Atom(id,znum,x,y,z) )
# Save the last model
comment = 'timestep {0}'.format(timestep)
lx = bounds[0]
ly = bounds[1]
lz = bounds[2]
m = Model(comment,lx,ly,lz, atoms)
m.atoms = sorted(m.atoms, key=operator.itemgetter('id'))
filename = base_modelname + '_' + str(timestep) + '.xyz'
m.write_real_xyz(filename)
def icosahedron(b,save=False,filename=None):
# http://en.wikipedia.org/wiki/Regular_icosahedron
# b is the nearest-neighbor interatomic bond distance
b = b * sqrt(2)* 1.113516364 / 1.84375
coords = [atom.coord for atom in dodecahedron(b).atoms]
vertices = range(1,21)
faces = [
[15, 2, 12, 16, 9],
[11, 19, 10, 4, 18],
[6, 7, 14, 15, 12],
[10, 18, 17, 5, 8],
[9, 16, 13, 8, 5],
[7, 6, 20, 19, 11],
[5, 1, 13, 4, 18],
[4, 19, 6, 14, 1],
[1, 9, 13, 12, 14],
[2, 3, 20, 7, 15],
[2, 16, 8, 17, 3],
[3, 20, 11, 10, 17]]
face_coords = [(0,0,0)]
for f in faces:
center = (sum(coords[i][0] for i in f)/5., sum(coords[i][1] for i in f)/5., sum(coords[i][2] for i in f)/5.)
face_coords.append(center)
m = 0
for coord in face_coords:
for x in coord:
if(abs(x) > m): m = abs(x)
atoms = [Atom(i,14,c[0],c[1],c[2]) for i,c in enumerate(face_coords)]
model = Model(comment='icosahedron', xsize=m, ysize=m, zsize=m, atoms=atoms)
if(save):
model.write_real_xyz(model.filename)
if(filename == None):
filename = 'icosahedron.xyz'
else:
model.filename = filename
#f = open(filename,'w')
#f.write(str(len(face_coords))+'\n')
#f.write('{0} {0} {0} comment\n'.format(m))
#for c in face_coords:
# f.write('Si ' + ' '.join([str(x) for x in c]) + '\n')
#f.close()
return model
