def make_nacl(latconst=1.0, specorder=None):
if specorder is None:
specorder = ['Na', 'Cl']
if len(specorder) < 2:
specorder = ['Na', 'Cl']
print('Since len(specorder) < 2, specorder is reset to ', specorder)
s = NAPSystem(specorder=specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([0.0, 1.0, 0.0])
a3 = np.array([0.0, 0.0, 1.0])
s.set_lattice(latconst, a1, a2, a3)
poss = [
[0.00, 0.00, 0.00],
[0.50, 0.00, 0.00],
[0.00, 0.50, 0.00],
[0.00, 0.00, 0.50],
[0.50, 0.50, 0.00],
[0.50, 0.00, 0.50],
[0.00, 0.50, 0.50],
[0.50, 0.50, 0.50],
]
symbols = ['Na', 'Cl', 'Cl', 'Cl', 'Na', 'Na', 'Na', 'Cl']
vels = [[0., 0., 0.] for i in range(len(poss))]
frcs = [[0., 0., 0.] for i in range(len(poss))]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_zincblend(latconst=1.0, specorder=None):
"""
Make a cell of diamond structure.
"""
if specorder is None:
specorder = ['Ga', 'N']
if len(specorder) < 2:
specorder = ['Ga', 'N']
print('Since len(specorder) < 2, specorder is reset to ', specorder)
s = NAPSystem(specorder=specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([0.0, 1.0, 0.0])
a3 = np.array([0.0, 0.0, 1.0])
s.set_lattice(latconst, a1, a2, a3)
poss = [[0.00, 0.00, 0.00], [0.50, 0.50, 0.00], [0.50, 0.00, 0.50],
[0.00, 0.50, 0.50], [0.25, 0.25, 0.25], [0.75, 0.75, 0.25],
[0.75, 0.25, 0.75], [0.25, 0.75, 0.75]]
symbols = [
specorder[0] if i < 4 else specorder[1] for i in range(len(poss))
]
vels = [[0., 0., 0.] for i in range(len(poss))]
frcs = [[0., 0., 0.] for i in range(len(poss))]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_wurtzite(latconst=1.0, specorder=None, celltype='conventional'):
"""
Make a cell of wurtzite structure.
- celltype: conventional or primitive
"""
if specorder is None:
specorder = ['Ga', 'N']
if len(specorder) < 2:
specorder = ['Ga', 'N']
print('Since len(specorder) < 2, specorder is reset to ', specorder)
s = NAPSystem(specorder=specorder)
if celltype[0] == 'c':
#...conventional cell
a1 = np.array([1.00, 0.00, 0.00])
a2 = np.array([0.00, np.sqrt(3.0), 0.00])
a3 = np.array([0.00, 0.00, 1.633])
s.set_lattice(latconst, a1, a2, a3)
poss = [
[0.00, 0.00, 0.00],
[0.50, 0.50, 0.00],
[0.50, 0.5 / 3, 0.50],
[0.00, 0.5 / 3 + 0.5, 0.50],
[0.50, 0.5 / 3, 0.125],
[0.00, 0.5 / 3 + 0.5, 0.125],
[0.00, 0.00, 0.625],
[0.50, 0.50, 0.625],
]
symbols = [
specorder[0] if i < 4 else specorder[1] for i in range(len(poss))
]
elif cenlltype[0] == 'p':
#...primitive cell
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([-0.5, np.sqrt(3.0) / 2, 0.0])
a3 = np.array([0.0, 0.0, 1.633])
s.set_lattice(latconst, a1, a2, a3)
poss = [
[0.00, 0.00, 0.00],
[2.0 / 3, 1.0 / 3, 0.125],
[2.0 / 3, 1.0 / 3, 0.50],
[0.00, 0.00, 0.625],
]
symbols = [
specorder[0] if i < 2 else specorder[1] for i in range(len(poss))
]
vels = [[0., 0., 0.] for i in range(len(poss))]
frcs = [[0., 0., 0.] for i in range(len(poss))]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_sc(latconst=1.0):
"""
Make a cell of simple cubic structure.
"""
s = NAPSystem(specorder=_default_specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([0.0, 1.0, 0.0])
a3 = np.array([0.0, 0.0, 1.0])
s.set_lattice(latconst, a1, a2, a3)
symbol = _default_specorder[0]
symbols = [symbol]
poss = [[0.00, 0.00, 0.00]]
vels = [[0., 0., 0.]]
frcs = [[0., 0., 0.]]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_hcp(latconst=1.0):
"""
Make a cell of hcp structure.
"""
s = NAPSystem(specorder=_default_specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([-0.5, np.sqrt(3.0) / 2, 0.0])
a3 = np.array([0.0, 0.0, 1.633])
s.set_lattice(latconst, a1, a2, a3)
poss = [[0.00, 0.00, 0.00], [1.0 / 3, 2.0 / 3, 0.50]]
symbol = _default_specorder[0]
symbols = [symbol for i in range(len(poss))]
vels = [[0., 0., 0.] for i in range(len(poss))]
frcs = [[0., 0., 0.] for i in range(len(poss))]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_bcc110(latconst=1.0):
"""
Make a cell of bcc structure with z along [110].
"""
s = NAPSystem(specorder=_default_specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([0.0, 1.414, 0.0])
a3 = np.array([0.0, 0.0, 1.414])
s.set_lattice(latconst, a1, a2, a3)
symbol = _default_specorder[0]
symbols = [symbol, symbol, symbol, symbol]
poss = [[0.00, 0.00, 0.00], [0.00, 0.50, 0.50], [0.50, 0.50, 0.00],
[0.50, 0.00, 0.50]]
vels = [[0., 0., 0.] for i in range(4)]
frcs = [[0., 0., 0.] for i in range(4)]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_sc(latconst=1.0, specorder=None):
"""
Make a cell of simple cubic structure.
"""
if specorder is None:
raise ValueError('specorder must be given.')
s = NAPSystem(specorder=specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([0.0, 1.0, 0.0])
a3 = np.array([0.0, 0.0, 1.0])
s.set_lattice(latconst, a1, a2, a3)
symbols = [specorder[0]]
poss = [[0.00, 0.00, 0.00]]
vels = [[0., 0., 0.]]
frcs = [[0., 0., 0.]]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_bcc(latconst=1.0, specorder=None):
"""
Make a cell of bcc structure with z along [001].
"""
if specorder is None:
specorder = ['Fe']
s = NAPSystem(specorder=specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([0.0, 1.0, 0.0])
a3 = np.array([0.0, 0.0, 1.0])
s.set_lattice(latconst, a1, a2, a3)
poss = [[0.00, 0.00, 0.00], [0.50, 0.50, 0.50]]
symbol = _default_specorder[0]
symbols = [symbol for i in range(len(poss))]
vels = [[0., 0., 0.] for i in range(len(poss))]
frcs = [[0., 0., 0.] for i in range(len(poss))]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_diamond(latconst=1.0):
"""
Make a cell of diamond structure.
"""
s = NAPSystem(specorder=_default_specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([0.0, 1.0, 0.0])
a3 = np.array([0.0, 0.0, 1.0])
s.set_lattice(latconst, a1, a2, a3)
poss = [[0.00, 0.00, 0.00], [0.50, 0.50, 0.00], [0.50, 0.00, 0.50],
[0.00, 0.50, 0.50], [0.25, 0.25, 0.25], [0.75, 0.75, 0.25],
[0.75, 0.25, 0.75], [0.25, 0.75, 0.75]]
symbol = _default_specorder[0]
symbols = [symbol for i in range(len(poss))]
vels = [[0., 0., 0.] for i in range(len(poss))]
frcs = [[0., 0., 0.] for i in range(len(poss))]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_bcc111(latconst=1.0):
"""
Make a cell of bcc structure with z along [111].
"""
s = NAPSystem(specorder=_default_specorder)
#...lattice
a1 = np.array([1.414, 0.0, 0.0])
a2 = np.array([0.0, 2.449, 0.0])
a3 = np.array([0.0, 0.0, 1.732])
s.set_lattice(latconst, a1, a2, a3)
symbol = _default_specorder[0]
poss = [[0.00, 0.00, 0.00], [0.00, 0.00, 0.50], [0.00, 0.333, 0.167],
[0.00, 0.333, 0.667], [0.00, 0.667, 0.333], [0.00, 0.667, 0.833],
[0.50, 0.167, 0.333], [0.50, 0.167, 0.833], [0.50, 0.50, 0.00],
[0.50, 0.50, 0.50], [0.50, 0.833, 0.167], [0.50, 0.833, 0.667]]
symbols = [symbol for i in range(len(poss))]
vels = [[0., 0., 0.] for i in range(len(poss))]
frcs = [[0., 0., 0.] for i in range(len(poss))]
s.add_atoms(symbols, poss, vels, frcs)
return s
def make_2D_triangle(latconst=3.8, size=(1, 1, 1)):
"""
Make 2D triangle lattice on x-z plane.
Note that it is not x-y plane.
"""
specorder = ['Ar']
s = NAPSystem(specorder=specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([0.0, 10.0, 0.0])
a3 = np.array([0.0, 0.0, np.sqrt(3.0)])
s.set_lattice(latconst, a1, a2, a3)
poss = [[0.00, 0.50, 0.00], [0.50, 0.50, 0.50]]
symbol = _default_specorder[0]
symbols = [symbol for i in range(len(poss))]
vels = [[0., 0., 0.] for i in range(len(poss))]
frcs = [[0., 0., 0.] for i in range(len(poss))]
s.add_atoms(symbols, poss, vels, frcs)
s.repeat(*size)
s.add_vacuum(2. * latconst, 0.0, 10. * latconst * np.sqrt(3))
return s
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
