def expand(self,n1,n2,n3):
#...expand unit vectors
self.a1= self.a1*n1
self.a2= self.a2*n2
self.a3= self.a3*n3
n123= n1*n2*n3
nsid= 0
for ai in self.atoms:
nsid= max(nsid,ai.sid)
natm_per_spcs= np.zeros((nsid,),dtype=int)
for ai in self.atoms:
sid= ai.sid -1
natm_per_spcs[sid] += 1
natm0= self.num_atoms()
atoms0= copy.copy(self.atoms)
self.atoms= []
aid= 0
for ai0 in atoms0:
ai0.pos[0] /= n1
ai0.pos[1] /= n2
ai0.pos[2] /= n3
for i1 in range(n1):
for i2 in range(n2):
for i3 in range(n3):
aid += 1
ai= Atom()
ai.sid= ai0.sid
x= ai0.pos[0]+1.0/n1*i1
y= ai0.pos[1]+1.0/n2*i2
z= ai0.pos[2]+1.0/n3*i3
ai.set_pos(x,y,z)
ai.set_auxd(ai0.auxd)
ai.set_id(aid)
self.atoms.append(ai)
def read_pmd(self,fname='pmd0000'):
f=open(fname,'r')
# 1st: lattice constant
self.alc= float(f.readline().split()[0])
# 2nd-4th: cell vectors
self.a1= np.array([float(x) for x in f.readline().split()])
self.a2= np.array([float(x) for x in f.readline().split()])
self.a3= np.array([float(x) for x in f.readline().split()])
# 5th-7th: velocity of cell vectors
tmp= f.readline().split()
tmp= f.readline().split()
tmp= f.readline().split()
# 8st: num of atoms
buff= f.readline().split()
natm= int(buff[0])
nauxd= 9
# 9th-: atom positions
self.atoms= []
for i in range(natm):
data= [float(x) for x in f.readline().split()]
ai= Atom()
ai.decode_tag(data[0])
ai.set_pos(data[1],data[2],data[3])
ai.set_auxd(data[4:4+nauxd])
self.atoms.append(ai)
f.close()
def read_POSCAR(self,fname='POSCAR'):
f=open(fname,'r')
# 1st: comment
self.c1= f.readline()
# 2nd: multiplying factor
self.alc= float(f.readline().split()[0])
# 3-5: lattice vectors
self.a1= np.array([float(x) for x in f.readline().split()])
self.a2= np.array([float(x) for x in f.readline().split()])
self.a3= np.array([float(x) for x in f.readline().split()])
# 6th: num of atoms par species
data= f.readline().split()
if( data[0].isdigit() ):
natm_per_spcs= np.array([int(d) for d in data])
else:
# skip one line and read next line
data= f.readline().split()
natm_per_spcs= np.array([int(d) for d in data])
# 7th: comment (in some cases, 8th line too)
self.c7= f.readline()
if self.c7[0] in ('s','S'):
self.c8= f.readline()
# hereafter: atom positions
sid= 0
self.atoms=[]
for ni in natm_per_spcs:
sid += 1
for j in range(ni):
line= f.readline().split()
data= [ float(line[i]) for i in range(3)]
ai= Atom()
ai.set_sid(sid)
ai.set_pos(data[0],data[1],data[2])
ai.set_auxd(line[3:])
ai.pbc()
self.atoms.append(ai)
f.close()
