def geo(filename, ftype, n_spe):
#maybe some old stupid habits....
ab = fx.info(filename, ftype, n_spe)
tot_num = ab.tot_num
cell = ab.cell
data = ab.data
return cell, data, tot_num
def all_NNs(a, N_type, cutoff):
aa = fx.info(a, 'cfg', N_type)
cell = aa.cell
data1 = aa.data
#data1=[x for x in data1 if (x[0]==1.07868200e+02)]
tot_num = int(len(data1))
tmp = np.arange(len(data1))
tmp = tmp.reshape(len(data1), 1)
data = np.concatenate((data1, tmp), axis=1)
pool = multiprocessing.Pool(processes=8)
query_list = [79951, 71056]
NN_list = [
pool.apply_async(get_NN.get_NN, args=(cell, data, i, cutoff)).get()
for i in query_list
]
#print(NN_list[0][0])
#print(NN_list[0][1])
#print(NN_list[0][2])
#print(NN_list[0][3])
#a=id_orientation(NN_list[0][1])
#a=norm_NN_vectors(NN_list[0][3])
b = orthogonal_2nn(NN_list[0][3])
b0 = rotation_M_2NN_ref_001(b) #rotation matrix ref to [100][010][001]
b1 = decompose_R(b0)
print b1
return
def select_surface(file_in,nnn,nb1,nb3,cn):
aa=fx.info(file_in,'cfg',1)
data=aa.data
n_type=aa.atom_type_num
lst=np.argwhere(nnn <= cn)
tot_num=len(lst)
lst=lst.flatten()
data_new=data[lst,:]
aa.data=data_new
aa.tot_num=tot_num
aa.get_cfg_file('surface.cfg')
return
def surface_atoms_filter(a, N_type, N_space, estimate):
aa = fx.info(a, 'cfg', N_type)
cell = aa.cell
data = aa.data
n_type = aa.atom_type_num
tot_num = int(len(data))
data_new = cutoff_surf_atoms(data, estimate)
aa.data = np.asarray(data_new)
aa.tot_num = int(len(aa.data))
aa.atom_type_num = [n_type[1]]
aa.get_cfg_file_one('cutoff.cfg')
xx, yy = np.meshgrid(np.linspace(0.0, 1.0, N_space - 1),
np.linspace(0.0, 1.0, N_space - 1))
M = np.array(
[[x1, x1 + 1.0 / float(N_space), x2, x2 + 1.0 / float(N_space)]
for x1, x2 in zip(np.ravel(xx), np.ravel(yy))])
pool = multiprocessing.Pool(processes=4)
surface_atoms = [
pool.apply_async(get_surf_atoms,
args=(cell, data_new, n_type, M[i])).get()
for i in range(len(M))
]
#surface_atoms = [pool.apply_async(get_surf_atoms, args=(cell,data,n_type,M[i])).get() for i in range(len(M))]
surface_atoms = [x for x in surface_atoms if x is not None]
surface_atoms = np.asarray(surface_atoms)
with open("surf.dat", 'w') as fout:
for i in range(3):
fout.write("%12.8f %12.8f %12.8f\n" %
(cell[i][0], cell[i][1], cell[i][2]))
fout.write("%12d\n" % (len(surface_atoms)))
for i in range(len(surface_atoms)):
fout.write("%12.8f %12.8f %12.8f %12.8f\n" %
(surface_atoms[i][0], surface_atoms[i][1],
surface_atoms[i][2], surface_atoms[i][3]))
#print np.asarray(surface_atoms)
#print(len(surface_atoms))
aa.data = np.asarray(surface_atoms)
aa.tot_num = int(len(aa.data))
aa.atom_type_num = [n_type[1]]
aa.get_cfg_file_one('surface.cfg')
return
def surface_roughness(a,N_type,N_space):
aa=fx.info(a,'cfg',2)
cell=aa.cell
data=aa.data
n_type=aa.atom_type_num
tot_num=int(sum(n_type))
#data=np.delete(data,np.arange(n_type[0]))
surface_atoms=[]
for ii in range(N_space):
xmin=ii/float(N_space)
xmax=(ii+1)/float(N_space)
for jj in range(N_space):
ymin=jj/float(N_space)
ymax=(jj+1)/float(N_space)
l2 = [data[i] for i in range(tot_num) if data[i][1] > xmin and data[i][1] < xmax and data[i][2] > ymin and data[i][2] < ymax and data[i][0]==1.07868200e+02 ]
l2 = sorted(l2,key=lambda x:x[3],reverse=True)
if len(l2)==0: pass
else:
surface_atoms.append(l2[0])
aa.data=np.asarray(surface_atoms)
aa.tot_num=int(len(aa.data))
aa.atom_type_num=[n_type[1]]
aa.get_cfg_file_one('surface.cfg')
return
for i in range(tot_num):
data[i][1] -= dis_x
data[i][2] -= dis_y
data[i][3] -= dis_z
return data
'''
#check if atom coordinates is out of boundary (not finished yet)
def check_boundary(cell,data,tot_num):
for i in range(tot_num):
while
tmp = int(data[i][1]/ cell[0][0])
'''
a = fx.info('CONTCAR', 'vasp', 1)
cutoff = 3.5
pm = expd_prmt(a.cell, cutoff)
tot_num_0 = a.tot_num
b = cell_expd_frac_2sides(a.cell, a.data, a.tot_num, pm)
#op.get_xsf('F',b[0],b[1],b[2],'tmp.xsf')
a.cell = b[0]
a.data = b[1]
a.tot_num = b[2]
a.get_cfg_file('tmp.cfg')
original_lst = [i for i in range(tot_num_0)]
#a.get_RDF_list(original_lst,cutoff)
#a.get_ADF_list(original_lst,cutoff)
#Q=a.get_BOP(original_lst,cutoff,8)
#np.save('saved_values/Q_8.npy',Q)
def surface_statistics(a, N_space):
with open(a, 'r') as fin:
mylines = fin.readlines()
cell = np.zeros((3, 3))
tmp1 = int(mylines[3].split()[0])
data = np.zeros((tmp1, 4))
for i in range(3):
cell[i][0] = float(mylines[i].split()[0])
cell[i][1] = float(mylines[i].split()[1])
cell[i][2] = float(mylines[i].split()[2])
for i in range(tmp1):
for j in range(4):
data[i][j] = float(mylines[4 + i].split()[j])
lowest_h = np.amin(data, axis=0)[3]
h_bar = np.mean(data[:, 3]) - lowest_h
w = np.std(data[:, 3])
print "mean height:", h_bar * cell[2][2]
print "RMS ave of height devieation Rq(std):", w * cell[2][2]
tmp = np.zeros((len(data), 1))
for i in range(len(data)):
tmp[i] = abs(data[i][3] - h_bar)
if tmp[i] < 0.0: tmp[i] += 1.0
print "Arithmetic average of the absolute values", np.mean(
tmp) * cell[2][2]
for i in range(len(data)):
data[i][3] -= lowest_h
if data[i][3] < 0.0: data[i][3] += 1.0
samples = []
M = np.zeros((N_space, N_space))
for ii in range(N_space):
xmin = ii / float(N_space)
xmax = (ii + 1) / float(N_space)
for jj in range(N_space):
ymin = jj / float(N_space)
ymax = (jj + 1) / float(N_space)
flag1 = 0
for i in range(len(data)):
if (data[i][1] > xmin and data[i][1] < xmax
and data[i][2] > ymin and data[i][2] < ymax):
samples.append(np.asarray(data[i]))
M[ii][jj] = float(data[i][3])
flag1 = 1
break
if flag1 == 0:
samples.append(
np.array([
1.07868200e+02, (xmin + xmax) / 2.0,
(ymin + ymax) / 2.0, 0.0
]))
M[ii][jj] = 0.0
samples = np.asarray(samples)
M = np.asarray(M)
#----------generate cfg--------------
aa = fx.info('surface.cfg', 'cfg', 1)
aa.data = np.asarray(samples)
aa.tot_num = int(len(aa.data))
aa.atom_type_num = [aa.tot_num]
aa.get_cfg_file_one('sample.cfg')
#-----done generate cfg--------------
#Fk = fft.fft2(M)/N_space
#Fk = fft.fft2(M)/N_space # Fourier coefficients (divided by n) nu = fft.fftfreq(n,dx) # Natural frequencies
#Fk = fft.fftshift(Fk) # Shift zero freq to center
#freqs = fft.fftfreq(N_space)
#freqs = fft.fftshift(freqs)
##nu = fft.fftshift(nu) # Shift zero freq to center
#psd2D = np.abs( Fk )**2
#X, Y = np.meshgrid(freqs, freqs)
#fig = plt.figure()
#ax = plt.axes(projection='3d')
#ax.contour3D(X, Y, psd2D, 50, cmap='binary')
#fig.savefig('1.png')
return