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 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 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_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 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_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 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_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_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 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 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_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_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_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 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_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_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 doc_to_pos(doc, conf):
"""
Make a pos file, which has pmd format, from a document in MongoDB.
"""
psys = NAPSystem()
matrix = doc['calculations'][-1]['output']['crystal']['lattice']['matrix']
a1 = matrix[0]
a2 = matrix[1]
a3 = matrix[2]
psys.set_lattice(1.0, a1, a2, a3)
species_ids = conf['species_ids']
sites = doc['calculations'][-1]['output']['crystal']['sites']
for site in sites:
ra = site['abc']
ai = Atom()
ai.set_pos(ra[0], ra[1], ra[2])
ai.set_sid(species_ids[site['species'][0]['element']])
psys.add_atom(ai)
return psys
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 to_given_vector(infile,specorder,a1new,a2new,a3new):
psys = NAPSystem(fname=infile,specorder=specorder)
psys.assign_pbc()
psys.a1 = psys.a1 *psys.alc
psys.a2 = psys.a2 *psys.alc
psys.a3 = psys.a3 *psys.alc
psys.alc = 1.0
print('a1 = ',psys.a1)
print('a2 = ',psys.a2)
print('a3 = ',psys.a3)
pos = psys.get_real_positions()
spos = psys.get_scaled_positions()
for i in range(min(len(psys.atoms),10)):
a = psys.atoms[i]
print('{0:5d} {1:s}'.format(a.id,a.symbol)
+' {0:12.5f} {1:12.5f} {2:12.5f}'.format(spos[i,0],
spos[i,1],
spos[i,2])
+' {0:12.5f} {1:12.5f} {2:12.5f}'.format(pos[i,0],
pos[i,1],
pos[i,2]))
# print(psys.get_scaled_positions())
# print(psys.get_real_positions())
# sa1new = np.zeros(3,dtype=float)
# sa2new = np.zeros(3,dtype=float)
# sa3new = np.zeros(3,dtype=float)
#tmp = raw_input('Input new a1 vector: ')
#a1new[:] = [ float(x) for x in tmp.split(',') ]
# sa1new[:] = [ 0.5, 0.5, 0.0]
#tmp = raw_input('Input new a2 vector: ')
#a2new[:] = [ float(x) for x in tmp.split(',') ]
# sa2new[:] = [ 0.0, 1.0, 0.0 ]
#tmp = raw_input('Input new a3 vector: ')
#a3new[:] = [ float(x) for x in tmp.split(',') ]
# sa3new[:] = [ 0.5, 0.5, 1.0 ]
hmat = psys.get_hmat()
a1new = np.dot(hmat,sa1new)
a2new = np.dot(hmat,sa2new)
a3new = np.dot(hmat,sa3new)
print('new a1 in hmat_orig =',sa1new)
print('new a2 in hmat_orig =',sa2new)
print('new a3 in hmat_orig =',sa3new)
print('new a1 =',a1new)
print('new a2 =',a2new)
print('new a3 =',a3new)
psnew = NAPSystem(specorder=specorder)
psnew.set_lattice(psys.alc,a1new,a2new,a3new)
# Expand the original system for the search of atoms to be included
# in the new system.
# First, compute how much we have to expand the original system
hi = np.linalg.inv(hmat)
icsa1new = [0,0,0]
icsa2new = [0,0,0]
icsa3new = [0,0,0]
for i in range(3):
if sa1new[i] < 0.0:
icsa1new[i] = int(sa1new[i]-1.0)
else:
icsa1new[i] = int(sa1new[i]+1.0)
if sa2new[i] < 0.0:
icsa2new[i] = int(sa2new[i]-1.0)
else:
icsa2new[i] = int(sa2new[i]+1.0)
if sa3new[i] < 0.0:
icsa3new[i] = int(sa3new[i]-1.0)
else:
icsa3new[i] = int(sa3new[i]+1.0)
print(icsa1new)
print(icsa2new)
print(icsa3new)
for i in range(3):
if icsa1new[i] == 0:
raise RuntimeError('icsa1new[i] == 0')
if icsa2new[i] == 0:
raise RuntimeError('icsa2new[i] == 0')
if icsa3new[i] == 0:
raise RuntimeError('icsa3new[i] == 0')
irange1 = (min(icsa1new[0],icsa2new[0],icsa3new[0]),
max(icsa1new[0],icsa2new[0],icsa3new[0]))
irange2 = (min(icsa1new[1],icsa2new[1],icsa3new[1]),
max(icsa1new[1],icsa2new[1],icsa3new[1]))
irange3 = (min(icsa1new[2],icsa2new[2],icsa3new[2]),
max(icsa1new[2],icsa2new[2],icsa3new[2]))
print('irange1: ',irange1)
print('irange2: ',irange2)
print('irange3: ',irange3)
expos = []
symbols = psys.get_symbols()
print('symbols :',symbols)
exsymbols = []
print('Expanding the original system...')
for n3 in range(min(0,irange3[0]),irange3[1]):
for n2 in range(min(0,irange2[0]),irange2[1]):
for n1 in range(min(0,irange1[0]),irange1[1]):
for ia in range(len(spos)):
sposi = copy.deepcopy(spos[ia])
sposi[0] += n1
sposi[1] += n2
sposi[2] += n3
posi = np.dot(hmat,sposi)
symbol = symbols[ia]
# print(ia,n1,n2,n3,symbol,sposi)
expos.append(posi)
exsymbols.append(symbol)
print('Extracting the atoms inside the new unit vectors...')
hmat= psnew.get_hmat()
hi = np.linalg.inv(hmat)
for ia,posi in enumerate(expos):
sposi = np.dot(hi,posi)
if 0.0 <= sposi[0] < 1.0 and \
0.0 <= sposi[1] < 1.0 and \
0.0 <= sposi[2] < 1.0:
atom = Atom()
symbol = exsymbols[ia]
print('{0:5d} {1:s}'.format(ia,symbol)
+' {0:12.5f} {1:12.5f} {2:12.5f}'.format(sposi[0],
sposi[1],
sposi[2]))
atom.set_symbol(symbol)
atom.set_pos(sposi[0],sposi[1],sposi[2])
psnew.add_atom(atom)
tmp = None
#tmp = raw_input('Input periodic shift vector if you want: ')
tmp = ' 0.5, 0.0, 0.5'
if tmp:
shift = [ float(x) for x in tmp.split(',')]
for a in psnew.atoms:
a.pos[0] += shift[0]
a.pos[1] += shift[1]
a.pos[2] += shift[2]
psnew.assign_pbc()
psnew.write_POSCAR(infile+'.new')
print('Check '+infile+'.new')
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 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
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 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