def calculate_region_rectangle(x, y, corner0, corner1):
# Return boolean array of same shape as x and y.
xy = np.stack((x.ravel(), y.ravel()), axis=1) # Shape (npoints, 2)
rectangle = Rectangle(corner0,
width=corner1[0] - corner0[0],
height=corner1[1] - corner0[1])
region = rectangle.contains_points(xy) # Shape (2*npoints)
region.shape = x.shape # Shape (npoints, 2)
return region
def rotate_xyz(file,nx,nz,Nx=40,Nz=5,name='',opt='',**kwargs):
'''Generates .xyz files corresponding to individual rotation
- file : path to cif file (.xyz files will be put in the same folder )
- Nrot : number of rotation to perform within 0,pi/2
'''
crys = file
if isinstance(file,str):
crys = Crystal.from_cif(file)
if not name : name = file.replace('.cif','')
a1,a2,a3 = np.array(crys.lattice_vectors)
ax1,by2,cz3 = np.array(crys.lattice_parameters[:3])
nxz = int(cz3/ax1)
#int(nx.max()+nxz*nz.max()), int(nx.max()/nxz+nz.max())
xy0 = (0,(Nz-nz.max())*cz3)
print('super cell calculation ...')
crys0 = crys.supercell(Nx,1,Nz)
pattern = np.array([
[a.atomic_number]+list(a.coords_cartesian)+[a.occupancy,wobbles[a.atomic_number]] for a in crys0.atoms])
coords0 = np.array([a.coords_cartesian for a in crys0.atoms])
files = []
Cs = [cs[E] for E in pattern[:,0]]
for i1,i2 in zip(nx,nz):
# i1,i2 = i,Nrot-i; n0 = gcd(i1,i2)
# i1,i2 = i1/n0,i2/n0;#print(i1,i2)
cz = i1*a1+i2*a3; #print(cz)
ax = np.array([cz[1],-cz[0]]); #print(cz)
c,angle = np.linalg.norm(cz),np.arctan(cz[0]/cz[2])
if not i1%i2*nxz:
n0 = i1/gcd(i1,i2*nxz)
if not n0%2 : n0/=2
a = np.linalg.norm([i2*nxz/i1,1])*cz3*n0
else:
a = np.linalg.norm([i2*nxz,i1])*cz3
# a = np.linalg.norm([i2*nxz,i1])*cz3
print(green+'i1=%d,i2=%d,angle=%.2f' %(i1,i2,angle*180/np.pi)+black)
rect=Rectangle(xy0,1.0*a,1.0*c,angle=-angle*180/np.pi,edgecolor='k',linewidth=2,alpha=0.1)
print('finding points ...')
idc = rect.contains_points(coords0[:,[0,2]],radius=0.001)
print('done')
n = (i1,0,i2)
xyz = name+'%d%d%d.xyz' %n
if opt:
path = dsp.dirname(name)
x,z = coords0[:,[0,2]].T;
x0,z0 = (coords0[idc,:])[:,[0,2]].T
X,Z = np.hstack([x,x0]),np.hstack([z,z0])
S = np.array([10]*x.size+[30]*x0.size)
C = Cs+list(np.array(Cs)[idc,:])
dsp.stddisp(scat=[X,Z,S,C],patches=[rect],equal=1,figsize='12',
xyTicks=[ax1,cz3],pOpt='tGeX',xylims=[0,40*ax1,-10*cz3,10*cz3],
opt=opt,name=path+'figures/'+dsp.basename(xyz).replace('xyz','png'))
plt.show()
lat_vec = [a,a2[1],c]#np.array([Nrot*(a3+a1),a2,Nrot*(a3-a1)])#
cc = coords0[idc,:]
cc[:,2]-=xy0[1]
coords = Rot(-angle).dot(cc.T).T
pattern[idc,1:4] = coords
# make_xyz(xyz,pattern[idc,:],np.diag(lat_vec),n,fmt='%.4f',dopt='s')
files+=[xyz] #dsp.basename(xyz)]
return files
