def make_polycrystal(grns,uc,n1,n2,n3,two_dim=False):
"""
THIS ROUTINE IS NOT THAT UNIVERSAL.
Each grain has to have neighboring grains within a supercell,
otherwise there will be some unexpecting grain boundries.
In order to do so, the system should be large enough and
the number of grains should be large enough.
"""
#...Calc the minimum bond distance in unit cell and use it as penetration depth
dmin = 1.0e+30
for i in range(uc.num_atoms()-1):
for j in range(i+1,uc.num_atoms()):
dij = uc.get_distance(i,j)
dmin = min(dij,dmin)
print(' Minimum bond distance in the unitcell: ',dmin)
dmin = dmin *DMIN_RATE
penetration_depth = dmin*2
print(' Minimum bond distance allowed in the new system: ',dmin)
sv,nsv= shift_vector(two_dim)
# print(' nsv =',nsv)
# for i in range(nsv):
# print(' i,sv[i]=',i,sv[i])
nsys= NAPSystem(specorder=uc.specorder)
nsys.set_lattice(uc.alc,uc.a1*n1,uc.a2*n2,uc.a3*n3)
hmat = nsys.get_hmat()
hmati = nsys.get_hmat_inv()
nmax = n1*n2*n3 *uc.num_atoms()
sidsl = np.zeros(nmax,dtype=int)
symsl = []
possl = np.zeros((nmax,3))
velsl = np.zeros((nmax,3))
frcsl = np.zeros((nmax,3))
ix0 = -n1/2-1
ix1 = n1/2+2
iy0 = -n2/2-1
iy1 = n2/2+2
iz0 = -n3/2-1
iz1 = n3/2+2
if two_dim:
if n3 != 1:
raise ValueError('n3 should be 1 in case two_dim is ON.')
iz0 = 0
iz1 = 1
print(' x range = ',ix0,ix1)
print(' y range = ',iy0,iy1)
print(' z range = ',iz0,iz1)
inc = 0
for ig in range(len(grns)):
grain= grns[ig]
rmat= grain.rmat # Rotation matrix of the grain
pi= grain.point # Grain center in reduced coordinate
api= np.dot(hmat,pi) # Grain center in Cartessian coordinate
print(' grain-ID = ',ig+1)
for ix in range(ix0,ix1):
# print('ix=',ix)
for iy in range(iy0,iy1):
for iz in range(iz0,iz1):
for m in range(uc.num_atoms()):
sidt = uc.get_atom_attr(m,'sid')
rt= np.zeros((3,))
pm = uc.get_atom_attr(m,'pos')
rt[0]= (pm[0]+ix)/n1
rt[1]= (pm[1]+iy)/n2
rt[2]= (pm[2]+iz)/n3
#...rt to absolute position
art= np.dot(hmat,rt)
#...Rotate
ari= np.dot(rmat,art)
#...Shift origin to the grain center
ari[0]= ari[0]+api[0]
ari[1]= ari[1]+api[1]
ari[2]= ari[2]+api[2]
#...check distance from all the grain points
di= distance(ari,api,two_dim)
isOutside= False
for jg in range(len(grns)):
gj= grns[jg]
for isv in range(nsv):
pj= gj.point
if jg == ig:
if not two_dim and isv == 13:
continue
elif two_dim and isv == 4:
continue
svi= sv[isv]
pj= pj +svi
apj = np.dot(hmat,pj)
dj= distance(ari,apj,two_dim)
if dj +penetration_depth < di: # Allow some penetration here
isOutside= True
break
if isOutside:
break
if isOutside:
break
#...here ri is inside this grain, register it
#...Cartessian coord to reduced coord
ri = np.dot(hmati,ari)
ri[0]= pbc(ri[0])
ri[1]= pbc(ri[1])
ri[2]= pbc(ri[2])
sidsl[inc] = sidt
possl[inc] = ri
velsl[inc,:] = 0.0
frcsl[inc,:] = 0.0
symsl.append(nsys.specorder[sidt-1])
inc += 1
if inc > nmax:
raise ValueError('inc > nmax')
#...Create filled arrays from non-filled ones
poss = np.array(possl[:inc])
vels = np.array(velsl[:inc])
frcs = np.array(frcsl[:inc])
nsys.add_atoms(symsl,poss,vels,frcs)
#...remove too-close atoms at the grain boundaries
print(' Making pair list in order to remove close atoms...')
print(' Number of atoms: ',nsys.num_atoms())
nsys.make_pair_list(RCUT)
nsys.write('POSCAR_orig')
short_pairs = []
# dmin2= dmin**2
# xij= np.zeros((3,))
print(' Making the list of SHORT pairs...')
for ia in range(nsys.num_atoms()):
lst= nsys.get_atom_attr(ia,'lspr')
for j in range(len(lst)):
ja= lst[j]
if ja > ia:
continue
dij = nsys.get_distance(ia,ja)
if dij < dmin:
short_pairs.append((ia,ja,dij))
print(' Number of short pairs: ',len(short_pairs))
#...Remove only relevant atoms, not all the atoms in the short_pairs.
ls_remove = []
ls_not_remove = []
for pair in short_pairs:
ia = pair[0]
ja = pair[1]
if ia not in ls_not_remove and ja not in ls_not_remove:
ls_remove.append(ia)
ls_not_remove.append(ja)
elif ia not in ls_not_remove:
ls_remove.append(ia)
elif ja not in ls_not_remove:
ls_remove.append(ja)
else: # Both atoms are already in not_remove list, which should be avoided.
ls_not_remove.remove(ia)
ls_remove.append(ia)
ls_not_remove.append(ja)
#...Remove double registered IDs
ls_remove = uniq(ls_remove)
print(' Number of to be removed atoms: ',len(ls_remove))
nsys.remove_atoms(*ls_remove)
return nsys
p0= np.zeros((nmeasure,3))
pp= np.zeros(3)
msd= np.zeros((len(infiles),nmeasure,3))
npbc= np.zeros((3,),dtype=int)
hmat= np.zeros((3,3))
for ifile in range(len(infiles)):
file= infiles[ifile]
system= NAPSystem()
system.read_akr(file)
hmat[0]= system.a1 *system.alc
hmat[1]= system.a2 *system.alc
hmat[2]= system.a3 *system.alc
#...human-readable ID to computer-oriented ID
i= id-1
pi= system.get_atom_attr(i,'pos')
if ifile == 0:
pp= pi
else:
#...correct periodic motion
dev= pi -pp
if dev[0] > 0.5:
npbc[0] += -1
elif dev[0] < -0.5:
npbc[0] += 1
if dev[1] > 0.5:
npbc[1] += -1
elif dev[1] < -0.5:
npbc[1] += 1
if dev[2] > 0.5:
npbc[2] += -1
