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 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 make_bcc(latconst=1.0):
"""
Make a cell of bcc 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, 0.50)]
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 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 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
pmdexec = options.pmdexec
asys = NAPSystem()
# system size is bigger than 2*rcut
a1 = np.array([2.0, 0.0, 0.0])
a2 = np.array([0.0, 1.0, 0.0])
a3 = np.array([0.0, 0.0, 1.0])
alc = rcut
asys.set_lattice(alc, a1, a2, a3)
atom1 = Atom()
atom2 = Atom()
atom1.set_pos(0.0, 0.0, 0.0)
atom1.set_id(1)
atom1.set_sid(sid1)
asys.add_atom(atom1)
atom2.set_pos(0.5, 0.0, 0.0)
atom2.set_id(2)
atom2.set_sid(sid2)
asys.add_atom(atom2)
hmin = rmin / (2 * rcut)
hd = (0.5 - hmin) / nsmpl
os.system('cp pmdini pmdorig')
fout = open('out.2body', 'w')
for ip in range(nsmpl + 1):
print '.',
d = hmin + hd * ip
asys.atoms[1].pos[0] = d
hext[1] = sysext.a2 * sysext.alc
hext[2] = sysext.a3 * sysext.alc
#...make extended system corresponding to the phonopy definition
for ia in range(natm0):
ai0 = sys0.atoms[ia]
for i3 in range(r3):
for i2 in range(r2):
for i1 in range(r1):
ai = Atom()
ai.set_sid(ai0.sid)
p1 = (ai0.pos[0] + i1) / r1
p2 = (ai0.pos[1] + i2) / r2
p3 = (ai0.pos[2] + i3) / r3
ai.set_pos(p1, p2, p3)
sysext.add_atom(ai)
sysext.reset_ids()
natme = sysext.num_atoms()
print ' sysext.num_atoms()=', natme
# for ai in sysext.atoms:
# print ai.pos
os.system('cp pmdini pmdorig')
#...loop for all atoms in the extended system
fcmat = np.zeros((natme, natme, 3, 3))
for ia in range(natme):
print '.',
sys.stdout.flush()
ppos = np.array(sysext.atoms[ia].pos)
print(' amax = ',amax)
distance= options.distance
print(' distance = ',distance,' Ang.')
pmdexec= options.pmdexec
asys= NAPSystem()
a1= np.array([2.0, 0.0, 0.0])
a2= np.array([0.0, 2.0, 0.0])
a3= np.array([0.0, 0.0, 1.0])
alc= rcut
asys.set_lattice(alc,a1,a2,a3)
atom1= Atom()
atom1.set_pos(0.0,0.0,0.0)
atom1.set_id(1)
asys.add_atom(atom1)
hd= distance/(alc*2)
atom2= Atom()
atom2.set_pos(hd,0.0,0.0)
atom2.set_id(2)
asys.add_atom(atom2)
atom3= Atom()
atom3.set_pos(0.0,0.0,0.0)
atom3.set_id(3)
asys.add_atom(atom3)
da = (amax-amin)/nsmpl
fout= open('out.3body','w')
hext[1]= sysext.a2 *sysext.alc
hext[2]= sysext.a3 *sysext.alc
#...make extended system corresponding to the phonopy definition
for ia in range(natm0):
ai0= sys0.atoms[ia]
for i3 in range(r3):
for i2 in range(r2):
for i1 in range(r1):
ai= Atom()
ai.set_sid(ai0.sid)
p1= (ai0.pos[0]+i1)/r1
p2= (ai0.pos[1]+i2)/r2
p3= (ai0.pos[2]+i3)/r3
ai.set_pos(p1,p2,p3)
sysext.add_atom(ai)
sysext.reset_ids()
natme= sysext.num_atoms()
print ' sysext.num_atoms()=',natme
# for ai in sysext.atoms:
# print ai.pos
os.system('cp pmd0000 pmd0000.orig')
#...loop for all atoms in the extended system
fcmat= np.zeros((natme,natme,3,3))
for ia in range(natme):
print '.',
sys.stdout.flush()
ppos= np.array(sysext.atoms[ia].pos)
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')
