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
print ' rcut = ', rcut, ' Ang.' rmin = options.rmin print ' rmin = ', rmin, ' Ang.' sid1 = options.sid1 print ' sid1 = ', sid1 sid2 = options.sid2 print ' sid2 = ', sid2 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
natm0 = sys0.num_atoms()
h0 = np.zeros((3, 3))
h0[0] = sys0.a1 * sys0.alc
h0[1] = sys0.a2 * sys0.alc
h0[2] = sys0.a3 * sys0.alc
n1, n2, n3 = calc_extention_ratio(h0, rcut)
r1 = 2 * n1 + 1
r2 = 2 * n2 + 1
r3 = 2 * n3 + 1
print ' num of cells in each axis=', r1, r2, r3
print ' num of atoms in extended system=', natm0 * r1 * r2 * r3
sysext = NAPSystem()
sysext.set_lattice(sys0.alc, np.multiply(sys0.a1, r1),
np.multiply(sys0.a2, r2), np.multiply(sys0.a3, r3))
hext = np.zeros((3, 3))
hext[0] = sysext.a1 * sysext.alc
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
rcut= options.rcut
print(' rcut = ',rcut,' Ang.')
amin= options.amin
print(' amin = ',amin)
amax= options.amax
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)
h0=np.zeros((3,3))
h0[0]= sys0.a1 *sys0.alc
h0[1]= sys0.a2 *sys0.alc
h0[2]= sys0.a3 *sys0.alc
n1,n2,n3= calc_extention_ratio(h0,rcut)
r1= 2*n1+1
r2= 2*n2+1
r3= 2*n3+1
print ' num of cells in each axis=',r1,r2,r3
print ' num of atoms in extended system=',natm0*r1*r2*r3
sysext= NAPSystem()
sysext.set_lattice( sys0.alc
,np.multiply(sys0.a1,r1)
,np.multiply(sys0.a2,r2)
,np.multiply(sys0.a3,r3))
hext=np.zeros((3,3))
hext[0]= sysext.a1 *sysext.alc
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
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)
