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)
positions=[(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)]
for p in positions:
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
return s
def main(args):
files = args['FILES']
files.sort(key=get_key, reverse=True)
nskip = int(args['--skip'])
del files[:nskip]
prefix = args['--prefix']
out4fp = args['--out4fp']
nsum = 0
volsum = 0.0
asum= bsum= csum= 0.0
alpsum= betsum= gmmsum= 0.0
for i,fi in enumerate(files):
try:
nsys = NAPSystem(fname=fi)
volsum += nsys.volume()
a,b,c,alpha,beta,gamma = nsys2lat(nsys)
asum += a
bsum += b
csum += c
alpsum += alpha
betsum += beta
gmmsum += gamma
nsum += 1
except Exception as e:
print('Failed {0:s} '.format(fi))
pass
if nsum < 1:
raise ValueError('Something went wrong! nsum<1')
vol = volsum /nsum
a = asum/nsum
b = bsum/nsum
c = csum/nsum
alpha = alpsum/nsum
beta = betsum/nsum
gamma = gmmsum/nsum
if out4fp:
with open(prefix+'.vol','w') as f:
f.write('# Volume\n')
f.write(' 1 1.0\n')
f.write('{0:15.3f}\n'.format(vol))
with open(prefix+'.lat','w') as f:
f.write('# Lattice parameters\n')
f.write(' 6 1.0\n')
f.write(' {0:10.3f} {1:10.3f} {2:10.3f}'.format(a,b,c)
+' {0:10.3f} {1:10.3f} {2:10.3f}\n'.format(alpha,beta,gamma))
else:
with open(prefix+'.vol','w') as f:
f.write('{0:15.3f}\n'.format(vol))
with open(prefix+'.lat','w') as f:
f.write(' {0:10.3f} {1:10.3f} {2:10.3f}'.format(a,b,c)
+' {0:10.3f} {1:10.3f} {2:10.3f}\n'.format(alpha,beta,gamma))
print(' Wrote {0:s}.vol {0:s}.lat'.format(prefix))
def main(args):
infname = args['FILE']
aSys = NAPSystem(fname=infname)
natm = len(aSys.atoms)
outfname = infname + ".voro"
f = open(outfname, 'w')
alc = aSys.alc
ax = aSys.a1[0]
ay = aSys.a2[1]
az = aSys.a3[2]
for ia in range(natm):
pos = aSys.atoms[ia].pos
f.write(' {0:4d}'.format(ia + 1))
f.write(' {0:10.3f}'.format(alc * ax * pos[0]))
f.write(' {0:10.3f}'.format(alc * ay * pos[1]))
f.write(' {0:10.3f}'.format(alc * az * pos[2]))
f.write('\n')
f.close()
print('Use voro++ as follows:')
cmd= 'voro++ -p -c " %i %q %v %s %A"' \
+' 0.0 {0:5.1f}'.format(alc*ax) \
+' 0.0 {0:5.1f}'.format(alc*ay) \
+' 0.0 {0:5.1f}'.format(alc*az) \
+' {0:s}'.format(outfname)
print('$ ' + cmd)
os.system(cmd)
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)
p=[0.00, 0.00, 0.00]
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
return s
def make_bcc(latconst=1.0,specorder=_default_specorder):
"""
Make a cell of bcc structure with z along [001].
"""
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)
positions=[(0.00, 0.00, 0.00),
(0.50, 0.50, 0.50)]
for p in positions:
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(specorder[0])
s.add_atom(atom)
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)
positions=[(0.00, 0.00, 0.00),
(1.0/3, 2.0/3, 0.50)]
for p in positions:
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
return s
def get_list_high_energy(gsmpls,threshold):
emin = 1e+30
highsmpls = []
ergs = []
for i,s in enumerate(gsmpls):
smpldir = s[0]
erg = s[1]
#atoms = read(smpldir+'/POSCAR',format='vasp')
atoms = NAPSystem(fname=smpldir+"/pos",format='pmd')
natm = atoms.num_atoms()
erg /= natm
ergs.append(erg)
emin = min(erg,emin)
for i,s in enumerate(gsmpls):
smpldir = s[0]
erg = ergs[i]
if erg-emin > threshold:
highsmpls.append(smpldir)
return highsmpls
def get_list_high_energy(gsmpls,threshold):
emin = 1e+30
highsmpls = []
ergs = []
for i,s in enumerate(gsmpls):
smpldir = s[0]
erg = s[1]
#atoms = read(smpldir+'/POSCAR',format='vasp')
atoms = NAPSystem(fname=smpldir+"/pos",ffmt='pmd')
natm = atoms.num_atoms()
erg /= natm
ergs.append(erg)
emin = min(erg,emin)
for i,s in enumerate(gsmpls):
smpldir = s[0]
erg = ergs[i]
if erg-emin > threshold:
highsmpls.append(smpldir)
return highsmpls
def xdatcar2poscars(fname='XDATCAR', nskip=1):
f = open(fname, 'r')
isys = 0
while True:
#....."Direct configuration= #"
try:
line = f.readline()
#...Check configuration
if not "Direct configuration=" in line:
alc, a1, a2, a3, species, num_atoms = read_header(f)
# print(species)
# print(num_atoms)
natm = 0
for n in num_atoms:
natm += n
continue
elif len(line.split()) == 0:
break
except:
break
#...Skip reading this configuration if requested
if not isys % nskip == 0:
for i in range(natm):
f.readline()
isys += 1
continue
#...Following lines: atom positions
#...Make a NAPSystem from these information and write to POSCAR_#####
nsys = NAPSystem(specorder=species)
nsys.set_lattice(alc, a1, a2, a3)
inc = 0
for inum, ni in enumerate(num_atoms):
for j in range(ni):
inc += 1
ai = Atom()
ai.set_id(inc)
ai.set_symbol(species[inum])
data = f.readline().split()
# print(data)
if not is_number(data[0]):
raise ValueError('Wrong format?')
x1, x2, x3 = [float(x) for x in data[0:3]]
ai.set_pos(x1, x2, x3)
ai.set_vel(0.0, 0.0, 0.0)
nsys.add_atom(ai)
foutname = 'POSCAR_{0:05d}'.format(isys)
print(' >>> ' + foutname)
nsys.write_POSCAR(fname=foutname)
isys += 1
f.close()
return None
def make_honeycomb(latconst=1.0):
"""
Make a cell of 2D honeycomb structure.
"""
s= NAPSystem(specorder=_default_specorder)
#...lattice
a1= np.array([ 1.0, 0.0, 0.0 ])
a2= np.array([ 0.0, 1.5, 0.0 ])
a3= np.array([ 0.0, 0.0, np.sqrt(3.0) ])
s.set_lattice(latconst,a1,a2,a3)
positions=[(0.00, 0.50, 0.00),
(0.50, 0.50, 1./6),
(0.50, 0.50, 0.50),
(0.00, 0.50, 0.5 +1.0/6)]
for p in positions:
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
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_nacl(latconst=1.0):
specorder = ['Na', 'Cl']
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)
positions = [
(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),
]
species = ['Na', 'Cl', 'Cl', 'Cl', 'Na', 'Na', 'Na', 'Cl']
for i, p in enumerate(positions):
atom = Atom()
atom.set_pos(p[0], p[1], p[2])
atom.set_symbol(species[i])
s.add_atom(atom)
return s
def structure2aSys(structure,idoffset=1):
"""
Converts Structure object of pymatgen to NAPSystem object in nap.
Args:
structure (Structure): pymatgen Structure object to be converted
to NAPSystem object..
Returns:
aSys (NAPSystem):
"""
lattice= structure.lattice
alc= 1.0
a1= np.array(lattice.matrix[0])
a2= np.array(lattice.matrix[1])
a3= np.array(lattice.matrix[2])
#... rescale a? vectors
a1= a1/alc
a2= a2/alc
a3= a3/alc
aSys= NAPSystem()
aSys.set_lattice(alc,a1,a2,a3)
for ia in range(structure.num_sites):
ai= Atom()
si= structure[ia]
crd= si.frac_coords
ai.set_pos(crd[0],crd[1],crd[2])
sid= structure.symbol_set.index(si.species_string)+idoffset
ai.set_sid(sid)
ai.set_id(ia+1)
aSys.add_atom(ai)
return aSys
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_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 from_ase(atoms, specorder=None):
"""
Convert ASE Atoms object to NAPSystem object.
"""
spcorder = []
if specorder is not None:
spcorder = specorder
symbols = atoms.get_chemical_symbols()
spos = atoms.get_scaled_positions()
vels = atoms.get_velocities()
cell = atoms.get_cell()
celli = np.linalg.inv(cell)
if spos is None:
raise ValueError('ASE atoms object has no atom in it.')
#...Initialize and remake self.specorder
for s in symbols:
if s not in spcorder:
spcorder.append(s)
nsys = NAPSystem(specorder=spcorder)
# nsys = cls(specorder=spcorder)
nsys.alc = 1.0
nsys.a1[:] = atoms.cell[0]
nsys.a2[:] = atoms.cell[1]
nsys.a3[:] = atoms.cell[2]
#...First, initialize arrays
natm = len(atoms)
sids = [0 for i in range(natm)]
poss = np.array(spos)
if vels is None:
vels = np.zeros((natm, 3))
else:
vels = np.array(vels)
frcs = np.zeros((natm, 3))
#...Create arrays to be installed into nsys.atoms
sids = [nsys.specorder.index(si) + 1 for si in symbols]
nsys.atoms.sid = sids
nsys.atoms[['x', 'y', 'z']] = poss
for i in range(len(vels)):
vels[i] = np.dot(celli, vels[i])
nsys.atoms[['vx', 'vy', 'vz']] = vels
nsys.atoms[['fx', 'fy', 'fz']] = frcs
return nsys
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_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)
positions = [(0.00, 0.50, 0.00), (0.50, 0.50, 0.50)]
for p in positions:
atom = Atom()
atom.set_pos(p[0], p[1], p[2])
atom.set_symbol(specorder[0])
s.add_atom(atom)
s.repeat(*size)
s.add_vacuum(2. * latconst, 0.0, 10. * latconst * np.sqrt(3))
return s
def make_nacl(latconst=1.0):
specorder = ['Na','Cl']
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)
positions=[(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),]
species = ['Na','Cl','Cl','Cl','Na','Na','Na','Cl']
for i,p in enumerate(positions):
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(species[i])
s.add_atom(atom)
return s
def xdatcar2poscars(fname='XDATCAR',nskip=1):
f= open(fname,'r')
isys = 0
while True:
#....."Direct configuration= #"
try:
line = f.readline()
#...Check configuration
if not "Direct configuration=" in line:
alc,a1,a2,a3,species,num_atoms = read_header(f)
# print(species)
# print(num_atoms)
natm = 0
for n in num_atoms:
natm += n
continue
elif len(line.split()) == 0:
break
except:
break
#...Skip reading this configuration if requested
if not isys%nskip == 0:
for i in range(natm):
f.readline()
isys += 1
continue
#...Following lines: atom positions
#...Make a NAPSystem from these information and write to POSCAR_#####
nsys = NAPSystem(specorder=species)
nsys.set_lattice(alc,a1,a2,a3)
inc = 0
for inum,ni in enumerate(num_atoms):
for j in range(ni):
inc += 1
ai = Atom()
ai.set_id(inc)
ai.set_symbol(species[inum])
data= f.readline().split()
# print(data)
if not is_number(data[0]):
raise ValueError('Wrong format?')
x1,x2,x3 = [ float(x) for x in data[0:3] ]
ai.set_pos(x1,x2,x3)
ai.set_vel(0.0,0.0,0.0)
nsys.add_atom(ai)
foutname = 'POSCAR_{0:05d}'.format(isys)
print(' >>> '+foutname)
nsys.write_POSCAR(fname=foutname)
isys += 1
f.close()
return None
def prepare(infname='POSCAR', dlt1max=0.01, dlt2max=0.06):
#...original system
nsys0 = NAPSystem(fname=infname)
#orig_atoms = read(infname,format='vasp')
orig_atoms = nsys0.to_ase_atoms()
#...get deformations
fmats = get_deformations(dlt1max, dlt2max)
#...deform original system and save to _prefix_##/POSCAR
for i, fmat in enumerate(fmats):
atoms = orig_atoms.copy()
#nsys = copy.deepcopy(nsys0)
dname = _prefix + "{0:02d}".format(i)
os.system('mkdir -p {}'.format(dname))
print(dname)
cell0 = atoms.get_cell()
emat = 0.5 * (np.dot(fmat.T, fmat) - np.identity(3)) + np.identity(3)
cell = np.dot(emat, cell0)
#print(i,emat,cell)
# cell = np.dot(cell0,fmat.T)
atoms.set_cell(cell, scale_atoms=True)
atoms.write(dname + '/POSCAR',
format='vasp',
vasp5=True,
direct=True,
sort=False)
print('prepare done')
print('')
print('After performing VASP or pmd calculations in these directories, ' +
'run the following command:')
print(' $ python elasticity.py analyze str.ref')
print('or')
print(' $ python elasticity.py analyze strs.pmd')
print('')
def rdf_average(infiles,nr,specorder,dr=0.1,rmax=3.0,pairwise=False):
nspcs = len(specorder)
agr= np.zeros((nspcs+1,nspcs+1,nr),dtype=float)
nsum= 0
for infname in infiles:
if not os.path.exists(infname):
print("[Error] File, {0}, does not exist !!!".format(infname))
sys.exit()
nsys= NAPSystem(fname=infname,specorder=specorder)
print(' File =',infname)
rd,gr= rdf(nsys,nspcs,dr,rmax,pairwise=pairwise)
agr += gr
nsum += 1
agr /= nsum
return rd,agr
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)
positions=[(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)]
for p in positions:
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
return s
def read_sample(dirname):
"""
Read system, energy, forces and stress information of given DIRNAME.
"""
#...The directory must have erg.ref, frc.ref, strs.ref, and pos files.
files = ('pos', 'erg.ref', 'frc.ref', 'strs.ref')
for f in files:
if not os.path.exists(dirname + '/' + f):
raise RuntimeError('The file ' + f + ' does not exist in ' +
dirname)
#...Read pos first
nsys = NAPSystem(fname=dirname + '/pos', ffmt='pmd')
erg = read_erg(fname=dirname + '/erg.ref')
frcs = read_frc(fname=dirname + '/frc.ref')
strs = read_strs(fname=dirname + '/strs.ref')
return nsys, erg, frcs, strs
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)
positions=[(0.00, 0.50, 0.00),
(0.50, 0.50, 0.50)]
for p in positions:
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(specorder[0])
s.add_atom(atom)
s.repeat(*size)
s.add_vacuum(2.*latconst, 0.0, 10.*latconst*np.sqrt(3))
return s
def write_input(self, atoms, properties=None, system_changes=None):
"""Write input parameters to in.pmd file."""
FileIOCalculator.write_input(self, atoms, properties, system_changes)
if self.label == 'pmd':
infname = 'in.pmd'
# write_pmd(atoms,fname='pmdini',specorder=self.specorder)
nsys = NAPSystem.from_ase_atoms(atoms, specorder=self.specorder)
nsys.write_pmd(fname='pmdini')
with open(infname, 'w') as f:
fmvs, ifmvs = get_fmvs(atoms)
for i in range(len(fmvs)):
for ii in range(3):
if fmvs[i][ii] > 0.1 and not self.dimension[ii]:
fmvs[i][ii] = 0.0
f.write(get_input_txt(self.parameters, fmvs))
def make_dimer(distance, latconst, spcs):
if distance > latconst / 2:
raise ValueError('Lattice size is too small for given distance.')
s = NAPSystem(specorder=spcs)
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)
pos = [(0.0, 0.0, 0.0), (distance / latconst, 0.0, 0.0)]
#...Atom 1
atom = Atom()
p = pos[0]
atom.set_pos(p[0], p[1], p[2])
atom.set_symbol(spcs[0])
s.add_atom(atom)
#...Atom 2
atom = Atom()
p = pos[1]
atom.set_pos(p[0], p[1], p[2])
atom.set_symbol(spcs[1])
s.add_atom(atom)
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)
p = [0.00, 0.00, 0.00]
atom = Atom()
atom.set_pos(p[0], p[1], p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
return s
def adf_average(infiles,
dang=1.0,
rcut=3.0,
triplets=[],
no_average=False,
specorder=None):
na = int(180.0 / dang) + 1
aadf = np.zeros((len(triplets), na), dtype=float)
nsum = 0
for infname in infiles:
if not os.path.exists(infname):
print("[Error] File, {0}, does not exist !!!".format(infname))
sys.exit()
nsys = NAPSystem(fname=infname, specorder=specorder)
print(' File = ', infname)
angd, df, n = adf(nsys, dang, rcut, triplets)
aadf += df
nsum += n
if not no_average:
aadf /= nsum
return angd, aadf
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)
positions = [(0.00, 0.00, 0.00), (1.0 / 3, 2.0 / 3, 0.50)]
for p in positions:
atom = Atom()
atom.set_pos(p[0], p[1], p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
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_bcc(latconst=1.0, specorder=_default_specorder):
"""
Make a cell of bcc structure with z along [001].
"""
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)
positions = [(0.00, 0.00, 0.00), (0.50, 0.50, 0.50)]
for p in positions:
atom = Atom()
atom.set_pos(p[0], p[1], p[2])
atom.set_symbol(specorder[0])
s.add_atom(atom)
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_honeycomb(latconst=1.0):
"""
Make a cell of 2D honeycomb structure.
"""
s = NAPSystem(specorder=_default_specorder)
#...lattice
a1 = np.array([1.0, 0.0, 0.0])
a2 = np.array([0.0, 1.5, 0.0])
a3 = np.array([0.0, 0.0, np.sqrt(3.0)])
s.set_lattice(latconst, a1, a2, a3)
positions = [(0.00, 0.50, 0.00), (0.50, 0.50, 1. / 6), (0.50, 0.50, 0.50),
(0.00, 0.50, 0.5 + 1.0 / 6)]
for p in positions:
atom = Atom()
atom.set_pos(p[0], p[1], p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
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_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)
positions = [(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)]
for p in positions:
atom = Atom()
atom.set_pos(p[0], p[1], p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
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_dimer(distance,latconst,spcs):
if distance > latconst/2:
raise ValueError('Lattice size is too small for given distance.')
s = NAPSystem(specorder=spcs)
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)
pos=[(0.0, 0.0, 0.0),
(distance/latconst, 0.0, 0.0)]
#...Atom 1
atom = Atom()
p = pos[0]
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(spcs[0])
s.add_atom(atom)
#...Atom 2
atom = Atom()
p = pos[1]
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(spcs[1])
s.add_atom(atom)
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
files = args['FILES']
sid = int(args['--sid'])
width = float(args['-w'])
sgm = float(args['--sigma'])
if sgm < 0.0:
sgm = abs(sgm)*width
specorder = args['--specorder'].split(',')
if 'None' in specorder and not files[0].find('POSCAR') > -1:
raise ValueError('ERROR: specorder must be specified, unless files are POSCAR format.')
if sid == 0:
raise ValueError('ERROR: sid should be specified and should not be 0.')
files.sort(key=get_key,reverse=True)
nsys0 = NAPSystem(fname=files[0],specorder=specorder)
a,b,c = nsys0.get_lattice_angles()
if abs(a-np.pi/2) > 180.0/np.pi or abs(b-np.pi/2) > 180.0/np.pi \
or abs(c-np.pi/2) > 180.0/np.pi:
raise ValueError('ERROR: Currently only available for orthogonal lattice, a,b,c=',a,b,c)
ndivs = get_num_division(nsys0,width)
if np.dot(ndivs,ndivs) > 10000000:
raise ValueError('ERROR: ndivs too large.',ndivs)
else:
print(' # of divisions = {0:d} {1:d} {2:d}'.format(*ndivs))
pdist = np.zeros(ndivs,dtype=float)
for f in files:
print(' Reading {0:s}...'.format(f))
nsys = NAPSystem(fname=f,specorder=specorder)
pdist += get_prob_dist(ndivs,nsys,sid,sgm)
def convert(fname,specorder,index):
"""
Convert data in fname to fitpot format.
"""
ry2ev = 13.605698066
au2ang = 0.529177249
ryau2evang = ry2ev/au2ang
if not os.path.exists(fname):
raise RuntimeError(fname+' not found.')
#atoms= read('POSCAR',index=0,format='vasp')
try:
natm,nspcs,spcs,cell,pos,elems,erg,frcs,pos_unit,strs \
= read_espresso_out(fname)
except IOError as e:
print('IOError({0:s}): {1:s}'.format(e.errno,e.strerror))
raise
erg = erg *Ry_to_eV
psys = NAPSystem(specorder=specorder)
psys.set_hmat(cell)
hi = unitvec_to_hi(cell[0,:],cell[1,:],cell[2,:])
# converting force here, not when reading the file
frcs[:,:] *= ryau2evang
for ia in range(natm):
ai = Atom()
pi = pos[ia,:]
if pos_unit != "crystal":
sx,sy,sz = cartesian_to_scaled(hi,pi[0],pi[1],pi[2])
else:
sx,sy,sz = pi[:]
ai.set_pos(sx,sy,sz)
ai.set_frc(frcs[ia,0],frcs[ia,1],frcs[ia,2])
ai.set_symbol(elems[ia])
psys.add_atom(ai)
psys.assign_pbc()
if os.path.exists('POSCAR'):
print(' cp original POSCAR to POSCAR.orig')
os.system('cp POSCAR POSCAR.orig')
psys.write_POSCAR()
psys.write_pmd(fname='pos')
write_ergref(fname='erg.ref',erg=erg)
write_frcref(fname='frc.ref',frcs=frcs)
#...write stress
with open('strs.ref','w') as f:
for s in strs:
f.write(' {0:8.2f}'.format(s))
f.write('\n')
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])
system= NAPSystem(specorder=uc.specorder)
system.set_lattice(uc.alc,uc.a1*n1,uc.a2*n2,uc.a3*n3)
hmat= np.zeros((3,3))
hmat[0]= system.a1 *system.alc
hmat[1]= system.a2 *system.alc
hmat[2]= system.a3 *system.alc
hmati= np.linalg.inv(hmat)
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)
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(len(uc.atoms)):
rt= np.zeros((3,))
rt[0]= (uc.atoms[m].pos[0]+ix)/n1
rt[1]= (uc.atoms[m].pos[1]+iy)/n2
rt[2]= (uc.atoms[m].pos[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
atom= Atom()
#...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])
atom.set_pos(ri[0],ri[1],ri[2])
atom.set_symbol(uc.atoms[m].symbol)
system.add_atom(atom)
#...remove too-close atoms at the grain boundaries
print(' Making pair list in order to remove close atoms...')
print(' Number of atoms: ',system.num_atoms())
system.make_pair_list(RCUT)
system.write('POSCAR_orig')
short_pairs = []
# dmin2= dmin**2
# xij= np.zeros((3,))
print(' Making the list of SHORT pairs...')
for ia in range(system.num_atoms()):
# ai= system.atoms[ia]
# pi= ai.pos
nlst= system.nlspr[ia]
lst= system.lspr[ia]
for j in range(nlst):
ja= lst[j]
if ja > ia:
continue
dij = system.get_distance(ia,ja)
if dij < dmin:
short_pairs.append((ia,ja,dij))
# aj= system.atoms[ja]
# pj= aj.pos
# xij[0]= pj[0]-pi[0] -anint(pj[0]-pi[0])
# xij[1]= pj[1]-pi[1] -anint(pj[1]-pi[1])
# xij[2]= pj[2]-pi[2] -anint(pj[2]-pi[2])
# xij= np.dot(hmat,xij)
# d2= xij[0]**2 +xij[1]**2 +xij[2]**2
# if d2 < dmin2:
# if not ia in ls_remove:
# ls_remove.append(ia)
# elif not ja in ls_remove:
# ls_remove.append(ja)
# print('ia,len(ls_remove)=',ia,len(ls_remove))
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))
# print(' Number of to be removed atoms: ',len(ls_remove))
#...one of two will survive
# print(' One of two too-close atoms will survive...')
# count= [ ls_remove.count(ls_remove[i]) for i in range(len(ls_remove))]
# for i in range(0,len(ls_remove),2):
# if count[i] > count[i+1]:
# ls_remove[i+1]= -1
# elif count[i] < count[i+1]:
# ls_remove[i]= -1
# else:
# n= int(random()*2.0) # 0 or 1
# ls_remove[i+n]= -1
ls_remove.sort()
# for ia in range(len(ls_remove)-1,-1,-1):
# n= ls_remove[ia]
# if ia != len(ls_remove)-1:
# if n == nprev: continue
# system.atoms.pop(n)
# nprev= n
for i in reversed(range(len(ls_remove))):
ia = ls_remove[i]
system.atoms.pop(ia)
return system
pi[1]= random()
if two_dim:
pi[2]= 0.0
ai[0]= 0.0
ai[1]= 0.0
ai[2]= random()*np.pi*2 -np.pi
else:
pi[2]= random()
ai[0]= random()*np.pi*2 -np.pi
ai[1]= random()*np.pi/2 -np.pi/2
ai[2]= random()*np.pi*2 -np.pi
print(' point,angle =',pi,ai)
gi= Grain(pi,ai)
grains.append(gi)
uc= makestruct(latconst)
uc.write('POSCAR_uc')
gsys = NAPSystem(specorder=['H'])
gsys.set_lattice(uc.alc, uc.a1*nx, uc.a2*ny, uc.a3*nz)
for g in grains:
pi = g.point
a = Atom()
a.set_pos(pi[0],pi[1],pi[2])
a.set_symbol('H')
gsys.add_atom(a)
gsys.write('POSCAR_gpoints')
system= make_polycrystal(grains,uc,nx,ny,nz,two_dim)
system.write(ofname)
print(' Elapsed time = {0:12.2f}'.format(time.time()-t0))
print(' Wrote a file: {0:s}'.format(ofname))
def reduce_cij(atoms0,cij0,eps=1.e-4):
"""
Reduce number of independent Cij according to the crystal system of original cell.
It is not Cij=Cji.
"""
cij = cij0
symdata = spglib.get_symmetry_dataset(atoms0)
napsys = NAPSystem(ase_atoms=atoms0)
sgnum = symdata['number']
print('Spacegroup number = ',sgnum,' ==> ',end='')
a,b,c = napsys.get_lattice_lengths()
alpha,beta,gamma = napsys.get_lattice_angles()
aeqb = abs(a-b) < eps*min(a,b)
beqc = abs(b-c) < eps*min(b,c)
ceqa = abs(c-a) < eps*min(c,a)
aleqpi2 = abs(alpha-np.pi/2) < eps*np.pi/2
bteqpi2 = abs(beta -np.pi/2) < eps*np.pi/2
gmeqpi2 = abs(gamma-np.pi/2) < eps*np.pi/2
if 0 < sgnum <= 2: # Triclinic
print('Triclinic')
pass
elif sgnum <= 15: # Monoclinic
print('Monoclinic')
pass
elif sgnum <= 74: # Orthorhombic
print('Orthorhombic')
pass
elif sgnum <= 142: # Tetragonal
print('Tetragonal')
pass
elif sgnum <= 194: # Hexagonal
print('Hexagonal')
print('Number of independent C_ij elements are reduced to 6.')
print('C_66 should be 1/2(C_11-C_12) but this is not enforced now.')
if not aleqpi2:
c22 = (cij[1,1] +cij[2,2])/2
c13 = (cij[0,1] +cij[0,2])/2
c55 = (cij[4,4] +cij[5,5])/2
cij[1,1] = cij[2,2] = c22
cij[0,1] = cij[0,2] = c13
cij[4,4] = cij[5,5] = c55
elif not bteqpi2:
c11 = (cij[0,0] +cij[2,2])/2
c12 = (cij[0,1] +cij[1,2])/2
c44 = (cij[3,3] +cij[5,5])/2
cij[0,0] = cij[2,2] = c11
cij[0,1] = cij[1,2] = c12
cij[3,3] = cij[5,5] = c44
elif not gmeqpi2:
c11 = (cij[0,0] +cij[1,1])/2
c12 = (cij[0,2] +cij[1,2])/2
c44 = (cij[3,3] +cij[4,4])/2
cij[0,0] = cij[1,1] = c11
cij[0,2] = cij[1,2] = c12
cij[3,3] = cij[4,4] = c44
elif sgnum <= 230: # Cubic
print('Cubic')
print('Number of independent C_ij elements are reduced to 3.')
c11 = (cij[0,0] +cij[1,1] +cij[2,2])/3
c12 = (cij[0,1] +cij[0,2] +cij[1,2])/3
c44 = (cij[3,3] +cij[4,4] +cij[5,5])/3
cij[0,0] = cij[1,1] = cij[2,2] = c11
cij[0,1] = cij[0,2] = cij[1,2] = c12
cij[3,3] = cij[4,4] = cij[5,5] = c44
else:
raise ValueError('Invalid space group number, ',sgnum)
# Just symmetrize Cij
for i in range(6):
for j in range(i,6):
cij[j,i] = cij[i,j]
return cij
