def read_pmd(self, fname='pmd0000'):
f = open(fname, 'r')
# 1st: lattice constant
self.alc = float(f.readline().split()[0])
# 2nd-4th: cell vectors
for i in range(3):
data = f.readline().split()
self.a1[i] = float(data[0])
self.a2[i] = float(data[1])
self.a3[i] = float(data[2])
# 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
natm = int(f.readline().split()[0])
# 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_vel(data[4], data[5], data[6])
self.atoms.append(ai)
f.close()
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 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_akr(self,fname='akr0000'):
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: num of atoms
buff= f.readline().split()[0]
natm= int(buff[0])
nauxd= int(buff[1])
if nauxd < 3:
print '[Error] read_akr(): nauxd < 3 !!!'
sys.exit()
# 9th-: atom positions
self.atoms= []
for i in range(natm):
data= [float(x) for x in f.readline().split()]
ai= Atom()
ai.set_sid(data[0])
ai.set_pos(data[1],data[2],data[3])
# if there are less than 3 auxiliary data, there is not velocity
ai.set_vel(data[4],data[5],data[6])
self.atoms.append(ai)
f.close()
def fccBravaisCell():
s = AtomSystem()
#...lattice
alc = 1.0
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(alc, a1, a2, a3)
#...atom1
atom = Atom()
atom.set_pos(0.0, 0.0, 0.0)
atom.set_sid(1)
s.add_atom(atom)
#...atom2
atom = Atom()
atom.set_pos(0.5, 0.5, 0.0)
atom.set_sid(1)
s.add_atom(atom)
#...atom3
atom = Atom()
atom.set_pos(0.5, 0.0, 0.5)
atom.set_sid(1)
s.add_atom(atom)
#...atom4
atom = Atom()
atom.set_pos(0.0, 0.5, 0.5)
atom.set_sid(1)
s.add_atom(atom)
return s
def read_akr(self, fname='akr0000'):
f = open(fname, 'r')
# 1st: lattice constant
self.alc = float(f.readline().split()[0])
# 2nd-4th: cell vectors
for i in range(3):
data = f.readline().split()
self.a1[i] = float(data[0])
self.a2[i] = float(data[1])
self.a3[i] = float(data[2])
# 5th: num of atoms
natm = int(f.readline().split()[0])
# 9th-: atom positions
self.atoms = []
for i in range(natm):
data = [float(x) for x in f.readline().split()]
ai = Atom()
ai.set_sid(data[0])
ai.set_pos(data[1], data[2], data[3])
ai.set_vel(data[4], data[5], data[6])
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()
print ' amin = ', amin amax = options.amax print ' amax = ', amax distance = options.distance print ' distance = ', distance, ' Ang.' pmdexec = options.pmdexec asys = AtomSystem() 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
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
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
#...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)
for ixyz in range(3):
def make_polycrystal(grns,uc,n1,n2,n3):
u"""
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.
"""
sv= shift_vector()
system= AtomSystem()
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)
for ig in range(len(grns)):
grain= grns[ig]
rmat= grain.rmat
pi= grain.point
api= np.dot(hmat,pi)
for ix in range(-n1/2-1,n1/2+2):
print 'ix=',ix
for iy in range(-n2/2-1,n2/2+2):
for iz in range(-n3/2-1,n3/2+2):
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)
ari[0]= ari[0]+api[0]
ari[1]= ari[1]+api[1]
ari[2]= ari[2]+api[2]
# #...reduce into the supercell
# ri= np.dot(hmati,ari)
# ri[0]= pbc(ri[0])
# ri[1]= pbc(ri[1])
# ri[2]= pbc(ri[2])
# ari= np.dot(hmat,ri)
#...check distance from all the grain points
di= distance(ari,api)
isOutside= False
for jg in range(len(grns)):
gj= grns[jg]
for isv in range(27):
pj= gj.point
if jg == ig and isv == 13:
continue
svi= sv[isv]
pj= pj +svi
apj= np.dot(hmat,pj)
dj= distance(ari,apj)
if dj < di:
isOutside= True
break
if isOutside:
break
if isOutside:
break
#...here ri is inside this grain, register it
atom= Atom()
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_sid(uc.atoms[m].sid)
system.add_atom(atom)
#...remove too-close atoms at the grain boundaries
system.make_pair_list(rcut)
ls_remove= []
dmin2= dmin**2
xij= np.zeros((3,))
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]
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:
ls_remove.append(ia)
ls_remove.append(ja)
#...one of two will survive
#print ls_remove
count= [ ls_remove.count(ls_remove[i]) for i in range(len(ls_remove))]
#print count
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
return system
rcut = options.rcut
print ' rcut = ', rcut, ' Ang.'
rmin = options.rmin
print ' rmin = ', rmin, ' Ang.'
pmdexec = options.pmdexec
asys = AtomSystem()
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)
asys.add_atom(atom1)
atom2.set_pos(0.5, 0.0, 0.0)
atom2.set_id(2)
asys.add_atom(atom2)
hmin = rmin / (2 * rcut)
hd = (0.5 - hmin) / nsmpl
fout = open('out.2body', 'w')
for ip in range(nsmpl + 1):
print '.',
d = hmin + hd * ip
asys.atoms[1].pos[0] = d
asys.write_pmd('0000/pmd00000')
