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 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')
