def rotate_and_save(prototype,alpha,beta,gamma):
rot_arr = calc_rot_array(alpha,beta,gamma)
rotated = copy.deepcopy(prototype)
rotate(rotated,rot_arr)
rotated.write_real_xyz(rotated.filename[:-4] + '_rotated_{0}.{1}.{2}'.format(alpha,beta,gamma)
+ rotated.filename[-4:])
return rotated
def generate_arrays(alpha,beta,gamma,start=0,stop=360,step=15):
a = alpha; b = beta; c = gamma;
arrays = []
array_code = []
print('set rotations /1*{0}/;'.format((stop/step)**3))
for a in range(start,stop,step):
for b in range(start,stop,step):
for c in range(start,stop,step):
rot = calc_rot_array(a,b,c)
arrays.append(rot)
gamsrot = [ [0 for i in range(len(rot[0])+1)] for j in range(len(rot)+1)]
for i in range(1,len(gamsrot)):
for j in range(1,len(gamsrot[i])):
gamsrot[i][j] = rot[i-1][j-1]
for i in range(len(gamsrot)):
gamsrot[i][0] = i
for j in range(len(gamsrot[0])):
gamsrot[0][j] = j
gamsrot[0][0] = '_'
ptable = printTable(gamsrot)
ptable = ptable.replace('_',' ')
array_code.append( ['* Angle = {0}'.format(a), 'table rotation{0}(d1,d2)'.format(a/step+1), ptable+';'] )
print('* Angles = {0},{1},{2}'.format(a,b,c))
print('table rotation{0}(d1,d2)'.format(len(array_code)))
print(ptable+';')
print('parameter RotationMats(rotations,d1,d2);')
i = 1
for a in range(start,stop,step):
for b in range(start,stop,step):
for c in range(start,stop,step):
print("RotationMats('{0}',d1,d2) = rotation{0}(d1,d2);".format(i))
i += 1
return arrays
def create_basic_models():
lattice_param = 1
a = 30
b = 135
c = 45
rot_arr = calc_rot_array(a,b,c,deg=True)
perfect = icosahedron(lattice_param,save=True,filename='icosahedron.perfect.xyz')
convert(perfect,'prototype','icosahedron.perfect.txt')
sm = copy.deepcopy(perfect)
swap_atom(sm,2,3)
sm.write_real_xyz('icosahedron.perfect.swap.xyz')
convert(sm,'polyhedron','icosahedron.perfect.swap.txt')
rm = copy.deepcopy(perfect)
rotate(rm,rot_arr)
rm.write_real_xyz('icosahedron.perfect.rot.xyz')
convert(rm,'polyhedron','icosahedron.perfect.rot.txt')
rm = copy.deepcopy(sm)
rotate(rm,rot_arr)
rm.write_real_xyz('icosahedron.perfect.swap.rot.xyz')
convert(rm,'polyhedron','icosahedron.perfect.swap.rot.txt')
imperfect = copy.deepcopy(perfect)
perturb_atom(imperfect,1,0.1,0)
imperfect.write_real_xyz('icosahedron.imperfect.xyz')
convert(imperfect,'prototype','icosahedron.imperfect.txt')
sim = copy.deepcopy(imperfect)
swap_atom(sim,2,3)
sim.write_real_xyz('icosahedron.imperfect.swap.xyz')
convert(sim,'polyhedron','icosahedron.imperfect.swap.txt')
rim = copy.deepcopy(imperfect)
rotate(rim,rot_arr)
rim.write_real_xyz('icosahedron.imperfect.rot.xyz')
convert(rim,'polyhedron','icosahedron.imperfect.rot.txt')
rim = copy.deepcopy(sim)
rotate(rim,rot_arr)
rim.write_real_xyz('icosahedron.imperfect.swap.rot.xyz')
convert(rim,'polyhedron','icosahedron.imperfect.swap.rot.txt')
def main():
prototype = Model(sys.argv[1])
#polygon = Model(sys.argv[2])
alpha = 15
beta = 45
gamma = 135
# Assume no permutation of the atoms
polygon = rotate_and_save(prototype,alpha,beta,gamma)
# Take the prototype and the polygon and rotate the polygon to the prototype
# for every rotation matrix, and calculate the value of epsilon for that
# rotation. Store the angle,epsilon values in two arrays for later analysis.
start = 0
stop = 360
step = 15
xdata = []
ydata = []
m = (100000,(1,2,3,),)
#m = 5.9520869802
count = 0
for a in xrange(start,stop,step):
for b in xrange(start,stop,step):
for c in xrange(start,stop,step):
rot = calc_rot_array(-a,-b,-c)
rotpolygon = copy.deepcopy(polygon)
rotate(rotpolygon, rot)
epsilon = sum( dist(prototype.atoms[i].coord,rotpolygon.atoms[i].coord) for i in range(prototype.natoms) )
#if(epsilon < min[0]): m = (epsilon, (-a,-b,-c,),)
#if(epsilon == m): print( count, (epsilon, (-a,-b,-c,),) )
#print(round(epsilon,2))
xdata.append(a)
ydata.append(epsilon)
count += 1
print(min)
# Do a fit to abs(sin(...)) based on the data recorded above
xdata = np.array(xdata)
ydata = np.array(ydata)
popt, pcov = curve_fit(sin2, xdata, ydata,p0=[83.5,700,10,0])
a,b,c,d = tuple(popt)
#print(a,b,c,d)
#print(pcov)
for x,y in zip(xdata,ydata):
print("{0}\t{1}".format(x,y))
def create_randomized_model(num,dir=dir):
lattice_param = 1
perfect = icosahedron(lattice_param,save=True,filename='icosahedron.perfect.xyz')
perfect.write(perfect.filename)
return 0
for i in range(num):
print(i)
a = random.uniform(0,360)
b = random.uniform(0,360)
c = random.uniform(0,360)
#a = random.randrange(0,345,15)
#b = random.randrange(0,345,15)
#c = random.randrange(0,345,15)
rot_arr = calc_rot_array(a,b,c,deg=True)
imperfect = copy.deepcopy(perfect)
perturb_atom(imperfect,axis='all')
#swap_atom(imperfect)
imperfect.write_real_xyz(dir+'icosahedron.{0}.random.xyz'.format(i))
convert(imperfect,'polyhedron',dir+'icosahedron.{0}.random.txt'.format(i))
rotate(imperfect,rot_arr)
imperfect.write_real_xyz(dir+'icosahedron.{0}.random.rot.xyz'.format(i))
convert(imperfect,'polyhedron',dir+'icosahedron.{0}.random.rot.txt'.format(i))
